A dynamic analysis of S&P 500, FTSE 100 and EURO STOXX 50 indices under different exchange rates

PubMed Central

Chen, Yanhua; Mantegna, Rosario N.; Zuev, Konstantin M.

2018-01-01

In this study, we assess the dynamic evolution of short-term correlation, long-term cointegration and Error Correction Model (hereafter referred to as ECM)-based long-term Granger causality between each pair of US, UK, and Eurozone stock markets from 1980 to 2015 using the rolling-window technique. A comparative analysis of pairwise dynamic integration and causality of stock markets, measured in common and domestic currency terms, is conducted to evaluate comprehensively how exchange rate fluctuations affect the time-varying integration among the S&P 500, FTSE 100 and EURO STOXX 50 indices. The results obtained show that the dynamic correlation, cointegration and ECM-based long-run Granger causality vary significantly over the whole sample period. The degree of dynamic correlation and cointegration between pairs of stock markets rises in periods of high volatility and uncertainty, especially under the influence of economic, financial and political shocks. Meanwhile, we observe the weaker and decreasing correlation and cointegration among the three developed stock markets during the recovery periods. Interestingly, the most persistent and significant cointegration among the three developed stock markets exists during the 2007–09 global financial crisis. Finally, the exchange rate fluctuations, also influence the dynamic integration and causality between all pairs of stock indices, with that influence increasing under the local currency terms. Our results suggest that the potential for diversifying risk by investing in the US, UK and Eurozone stock markets is limited during the periods of economic, financial and political shocks. PMID:29529092

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.

Actinide chemistry using singlet-paired coupled cluster and its combinations with density functionals

NASA Astrophysics Data System (ADS)

Garza, Alejandro J.; Sousa Alencar, Ana G.; Scuseria, Gustavo E.

2015-12-01

Singlet-paired coupled cluster doubles (CCD0) is a simplification of CCD that relinquishes a fraction of dynamic correlation in order to be able to describe static correlation. Combinations of CCD0 with density functionals that recover specifically the dynamic correlation missing in the former have also been developed recently. Here, we assess the accuracy of CCD0 and CCD0+DFT (and variants of these using Brueckner orbitals) as compared to well-established quantum chemical methods for describing ground-state properties of singlet actinide molecules. The f0 actinyl series (UO22+, NpO23+, PuO24+), the isoelectronic NUN, and thorium (ThO, ThO2+) and nobelium (NoO, NoO2) oxides are studied.

AB INITIO Molecular Dynamics Simulations on Local Structure and Electronic Properties in Liquid MgxBi1-x Alloys

NASA Astrophysics Data System (ADS)

Hao, Qing-Hai; You, Yu-Wei; Kong, Xiang-Shan; Liu, C. S.

2013-03-01

The microscopic structure and dynamics of liquid MgxBi1-x(x = 0.5, 0.6, 0.7) alloys together with pure liquid Mg and Bi metals were investigated by means of ab initio molecular dynamics simulations. We present results of structure properties including pair correlation function, structural factor, bond-angle distribution function and bond order parameter, and their composition dependence. The dynamical and electronic properties have also been studied. The structure factor and pair correlation function are in agreement with the available experimental data. The calculated bond-angle distribution function and bond order parameter suggest that the stoichiometric composition Mg3Bi2 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum electronic conductivity at this composition observed in previous experiments.

Temperature dependent structural and dynamical properties of liquid Cu80Si20 binary alloy

NASA Astrophysics Data System (ADS)

Suthar, P. H.; Shah, A. K.; Gajjar, P. N.

2018-05-01

Ashcroft and Langreth binary structure factor have been used to study for pair correlation function and the study of dynamical variable: velocity auto correlation functions, power spectrum and mean square displacement calculated based on the static harmonic well approximation in liquid Cu80Si20 binary alloy at wide temperature range (1140K, 1175K, 1210K, 1250K, 1373K, 1473K.). The effective interaction for the binary alloy is computed by our well established local pseudopotential along with the exchange and correction functions Sarkar et al(S). The negative dip in velocity auto correlation decreases as the various temperature is increases. For power spectrum as temperature increases, the peak of power spectrum shifts toward lower ω. Good agreement with the experiment is observed for the pair correlation functions. Velocity auto correlation showing the transferability of the local pseudopotential used for metallic liquid environment in the case of copper based binary alloys.

What Do They Have in Common? Physical Drivers of Streamflow Spatial Correlation and Prediction of Flow Regimes at Ungauged Locations in the Contiguous United States

NASA Astrophysics Data System (ADS)

Betterle, A.; Schirmer, M.; Botter, G.

2017-12-01

Streamflow dynamics strongly influence anthropogenic activities and the ecological functions of riverine and riparian habitats. However, the widespread lack of direct discharge measurements often challenges the set-up of conscious and effective decision-making processes, including droughts and floods protection, water resources management and river restoration practices. By characterizing the spatial correlation of daily streamflow timeseries at two arbitrary locations, this study provides a method to evaluate how spatially variable catchment-scale hydrological process affects the resulting streamflow dynamics along and across river systems. In particular, streamflow spatial correlation is described analytically as a function of morphological, climatic and vegetation properties in the contributing catchments, building on a joint probabilistic description of flow dynamics at pairs of outlets. The approach enables an explicit linkage between similarities of flow dynamics and spatial patterns of hydrologically relevant features of climate and landscape. Therefore, the method is suited to explore spatial patterns of streamflow dynamics across geomorphoclimatic gradients. In particular, we show how the streamflow correlation can be used at the continental scale to individuate catchment pairs with similar hydrological dynamics, thereby providing a useful tool for the estimate of flow duration curves in poorly gauged areas.

Molecular dynamics studies on troponin (TnI-TnT-TnC) complexes: insight into the regulation of muscle contraction.

PubMed

Varughese, Jayson F; Chalovich, Joseph M; Li, Yumin

2010-10-01

Mutations of any subunit of the troponin complex may lead to serious disorders. Rational approaches to managing these disorders require knowledge of the complex interactions among the three subunits that are required for proper function. Molecular dynamics (MD) simulations were performed for both skeletal (sTn) and cardiac (cTn) troponin. The interactions and correlated motions among the three components of the troponin complex were analyzed using both Molecular Mechanics-Generalized Born Surface Area (MMGBSA) and cross-correlation techniques. The TnTH2 helix was strongly positively correlated with the two long helices of TnI. The C domain of TnC was positively correlated with TnI and TnT. The N domain of TnC was negatively correlated with TnI and TnT in cTn, but not in sTn. The two C-domain calcium-binding sites of TnC were dynamically correlated. The two regulatory N-domain calcium-binding sites of TnC were dynamically correlated, even though the calcium-binding site I is dysfunctional. The strong interaction residue pairs and the strong dynamically correlated residues pairs among the three components of troponin complexes were identified. These correlated motions are consistent with the idea that there is a high degree of cooperativity among the components of the regulatory complex in response to Ca(2+) and other effectors. This approach may give insight into the mechanism by which mutations of troponin cause disease. It is interesting that some observed disease causing mutations fall within regions of troponin that are strongly correlated or interacted.

Dynamics analysis of SIR epidemic model with correlation coefficients and clustering coefficient in networks.

PubMed

Zhang, Juping; Yang, Chan; Jin, Zhen; Li, Jia

2018-07-14

In this paper, the correlation coefficients between nodes in states are used as dynamic variables, and we construct SIR epidemic dynamic models with correlation coefficients by using the pair approximation method in static networks and dynamic networks, respectively. Considering the clustering coefficient of the network, we analytically investigate the existence and the local asymptotic stability of each equilibrium of these models and derive threshold values for the prevalence of diseases. Additionally, we obtain two equivalent epidemic thresholds in dynamic networks, which are compared with the results of the mean field equations. Copyright © 2018 Elsevier Ltd. All rights reserved.

Maxwell-Stefan diffusion and dynamical correlation in molten LiF-KF: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Jain, Richa Naja; Chakraborty, Brahmananda; Ramaniah, Lavanya M.

2016-05-01

In this work our main objective is to compute Dynamical correlations, Onsager coefficients and Maxwell-Stefan (MS) diffusivities for molten salt LiF-KF mixture at various thermodynamic states through Green-Kubo formalism for the first time. The equilibrium molecular dynamics (MD) simulations were performed using BHM potential for LiF-KF mixture. The velocity autocorrelations functions involving Li ions reflect the endurance of cage dynamics or backscattering with temperature. The magnitude of Onsager coefficients for all pairs increases with increase in temperature. Interestingly most of the Onsager coefficients has almost maximum magnitude at the eutectic composition indicating the most dynamic character of the eutectic mixture. MS diffusivity hence diffusion for all ion pairs increases in the system with increasing temperature. Smooth variation of the diffusivity values denies any network formation in the mixture. Also, the striking feature is the noticeable concentration dependence of MS diffusivity between cation-cation pair, ĐLi-K which remains negative for most of the concentration range but changes sign to become positive for higher LiF concentration. The negative MS diffusivity is acceptable as it satisfies the non-negative entropy constraint governed by 2nd law of thermodynamics. This high diffusivity also vouches the candidature of molten salt as a coolant.

Dynamics and asymptotics of correlations in a many-body localized system

NASA Astrophysics Data System (ADS)

Campbell, Steve; Power, Matthew J. M.; De Chiara, Gabriele

2017-08-01

We examine the dynamics of nearest-neighbor bipartite concurrence and total correlations in the spin-1/2 XXZ model with random fields. We show, starting from factorized random initial states, that the concurrence can suffer entanglement sudden death in the long time limit and therefore may not be a useful indicator of the properties of the system. In contrast, we show that the total correlations capture the dynamics more succinctly, and further reveal a fundamental difference in the dynamics governed by the ergodic versus many-body localized phases, with the latter exhibiting dynamical oscillations. Finally, we consider an initial state composed of several singlet pairs and show that by fixing the correlation properties, while the dynamics do not reveal noticeable differences between the phases, the long-time values of the correlation measures appear to indicate the critical region.

Solving the two-dimensional Fokker-Planck equation for strongly correlated neurons

NASA Astrophysics Data System (ADS)

Deniz, Taşkın; Rotter, Stefan

2017-01-01

Pairs of neurons in brain networks often share much of the input they receive from other neurons. Due to essential nonlinearities of the neuronal dynamics, the consequences for the correlation of the output spike trains are generally not well understood. Here we analyze the case of two leaky integrate-and-fire neurons using an approach which is nonperturbative with respect to the degree of input correlation. Our treatment covers both weakly and strongly correlated dynamics, generalizing previous results based on linear response theory.

Transverse momentum and rapidity dependence of Hanbury-Brown Twiss correlations in Au+Au collisions at sNN= 62.4 and 200 GeV

NASA Astrophysics Data System (ADS)

Back, B. B.; Baker, M. D.; Ballintijn, M.; Barton, D. S.; Betts, R. R.; Bickley, A. A.; Bindel, R.; Budzanowski, A.; Busza, W.; Carroll, A.; Chai, Z.; Decowski, M. P.; García, E.; Gburek, T.; George, N.; Gulbrandsen, K.; Gushue, S.; Halliwell, C.; Hamblen, J.; Hauer, M.; Heintzelman, G. A.; Henderson, C.; Hofman, D. J.; Hollis, R. S.; Hołyński, R.; Holzman, B.; Iordanova, A.; Johnson, E.; Kane, J. L.; Katzy, J.; Khan, N.; Kucewicz, W.; Kulinich, P.; Kuo, C. M.; Lin, W. T.; Manly, S.; McLeod, D.; Mignerey, A. C.; Nouicer, R.; Olszewski, A.; Pak, R.; Park, I. C.; Pernegger, H.; Reed, C.; Remsberg, L. P.; Reuter, M.; Roland, C.; Roland, G.; Rosenberg, L.; Sagerer, J.; Sarin, P.; Sawicki, P.; Seals, H.; Sedykh, I.; Skulski, W.; Smith, C. E.; Stankiewicz, M. A.; Steinberg, P.; Stephans, G. S. F.; Sukhanov, A.; Tang, J.-L.; Tonjes, M. B.; Trzupek, A.; Vale, C.; Nieuwenhuizen, G. J. Van; Vaurynovich, S. S.; Verdier, R.; Veres, G. I.; Wenger, E.; Wolfs, F. L. H.; Wosiek, B.; Woźniak, K.; Wuosmaa, A. H.; Wysłouch, B.

2006-03-01

Two-particle correlations of identical charged pion pairs from Au+Au collisions at sNN=62.4 and 200 GeV were measured by the PHOBOS experiment at BNL Relativistic Heavy Ion Collider (RHIC). Data for the 15% most central events were analyzed with Bertsch-Pratt and Yano-Koonin-Podgoretskii parametrizations using pairs with rapidities of 0.4

Stabilization of Polar Nanoregions in Pb-free Ferroelectrics

DOE PAGES

Pramanick, A.; Dmowski, Wojciech; Egami, Takeshi; ...

2018-05-18

In this study, the formation of polar nanoregions through solid-solution additions is known to enhance significantly the functional properties of ferroelectric materials. Despite considerable progress in characterizing the microscopic behavior of polar nanoregions (PNR), understanding their real-space atomic structure and dynamics of their formation remains a considerable challenge. Here, using the method of dynamic pair distribution function, we provide direct insights into the role of solid-solution additions towards the stabilization of polar nanoregions in the Pb-free ferroelectric of Ba(Zr,Ti)O 3. It is shown that for an optimum level of substitution of Ti by larger Zr ions, the dynamics of atomicmore » displacements for ferroelectric polarization are slowed sufficiently below THz frequencies, which leads to increased local correlation among dipoles within PNRs. The dynamic pair distribution function technique demonstrates a unique capability to obtain insights into locally correlated atomic dynamics in disordered materials, including new Pb-free ferroelectrics, which is necessary to understand and control their functional properties.« less

Stabilization of Polar Nanoregions in Pb-free Ferroelectrics

NASA Astrophysics Data System (ADS)

Pramanick, A.; Dmowski, W.; Egami, T.; Budisuharto, A. Setiadi; Weyland, F.; Novak, N.; Christianson, A. D.; Borreguero, J. M.; Abernathy, D. L.; Jørgensen, M. R. V.

2018-05-01

The formation of polar nanoregions through solid-solution additions is known to enhance significantly the functional properties of ferroelectric materials. Despite considerable progress in characterizing the microscopic behavior of polar nanoregions (PNR), understanding their real-space atomic structure and dynamics of their formation remains a considerable challenge. Here, using the method of dynamic pair distribution function, we provide direct insights into the role of solid-solution additions towards the stabilization of polar nanoregions in the Pb-free ferroelectric of Ba (Zr ,Ti )O3 . It is shown that for an optimum level of substitution of Ti by larger Zr ions, the dynamics of atomic displacements for ferroelectric polarization are slowed sufficiently below THz frequencies, which leads to increased local correlation among dipoles within PNRs. The dynamic pair distribution function technique demonstrates a unique capability to obtain insights into locally correlated atomic dynamics in disordered materials, including new Pb-free ferroelectrics, which is necessary to understand and control their functional properties.

Stabilization of Polar Nanoregions in Pb-free Ferroelectrics

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

Pramanick, A.; Dmowski, Wojciech; Egami, Takeshi

In this study, the formation of polar nanoregions through solid-solution additions is known to enhance significantly the functional properties of ferroelectric materials. Despite considerable progress in characterizing the microscopic behavior of polar nanoregions (PNR), understanding their real-space atomic structure and dynamics of their formation remains a considerable challenge. Here, using the method of dynamic pair distribution function, we provide direct insights into the role of solid-solution additions towards the stabilization of polar nanoregions in the Pb-free ferroelectric of Ba(Zr,Ti)O 3. It is shown that for an optimum level of substitution of Ti by larger Zr ions, the dynamics of atomicmore » displacements for ferroelectric polarization are slowed sufficiently below THz frequencies, which leads to increased local correlation among dipoles within PNRs. The dynamic pair distribution function technique demonstrates a unique capability to obtain insights into locally correlated atomic dynamics in disordered materials, including new Pb-free ferroelectrics, which is necessary to understand and control their functional properties.« less

Heat flux and quantum correlations in dissipative cascaded systems

NASA Astrophysics Data System (ADS)

Lorenzo, Salvatore; Farace, Alessandro; Ciccarello, Francesco; Palma, G. Massimo; Giovannetti, Vittorio

2015-02-01

We study the dynamics of heat flux in the thermalization process of a pair of identical quantum systems that interact dissipatively with a reservoir in a cascaded fashion. Despite that the open dynamics of the bipartite system S is globally Lindbladian, one of the subsystems "sees" the reservoir in a state modified by the interaction with the other subsystem and hence it undergoes a non-Markovian dynamics. As a consequence, the heat flow exhibits a nonexponential time behavior which can greatly deviate from the case where each party is independently coupled to the reservoir. We investigate both thermal and correlated initial states of S and show that the presence of correlations at the beginning can considerably affect the heat-flux rate. We carry out our study in two paradigmatic cases—a pair of harmonic oscillators with a reservoir of bosonic modes and two qubits with a reservoir of fermionic modes—and compare the corresponding behaviors. In the case of qubits and for initial thermal states, we find that the trace distance discord is at any time interpretable as the correlated contribution to the total heat flux.

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

Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pair motions

NASA Astrophysics Data System (ADS)

Vatansever, Sezen; Gümüş, Zeynep H.; Erman, Burak

2016-11-01

K-Ras is the most frequently mutated oncogene in human cancers, but there are still no drugs that directly target it in the clinic. Recent studies utilizing dynamics information show promising results for selectively targeting mutant K-Ras. However, despite extensive characterization, the mechanisms by which K-Ras residue fluctuations transfer allosteric regulatory information remain unknown. Understanding the direction of information flow can provide new mechanistic insights for K-Ras targeting. Here, we present a novel approach -conditional time-delayed correlations (CTC) - using the motions of all residue pairs of a protein to predict directionality in the allosteric regulation of the protein fluctuations. Analyzing nucleotide-dependent intrinsic K-Ras motions with the new approach yields predictions that agree with the literature, showing that GTP-binding stabilizes K-Ras motions and leads to residue correlations with relatively long characteristic decay times. Furthermore, our study is the first to identify driver-follower relationships in correlated motions of K-Ras residue pairs, revealing the direction of information flow during allosteric modulation of its nucleotide-dependent intrinsic activity: active K-Ras Switch-II region motions drive Switch-I region motions, while α-helix-3L7 motions control both. Our results provide novel insights for strategies that directly target mutant K-Ras.

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.

Colloid-colloid hydrodynamic interaction around a bend in a quasi-one-dimensional channel.

PubMed

Liepold, Christopher; Zarcone, Ryan; Heumann, Tibor; Rice, Stuart A; Lin, Binhua

2017-07-01

We report a study of how a bend in a quasi-one-dimensional (q1D) channel containing a colloid suspension at equilibrium that exhibits single-file particle motion affects the hydrodynamic coupling between colloid particles. We observe both structural and dynamical responses as the bend angle becomes more acute. The structural response is an increasing depletion of particles in the vicinity of the bend and an increase in the nearest-neighbor separation in the pair correlation function for particles on opposite sides of the bend. The dynamical response monitored by the change in the self-diffusion [D_{11}(x)] and coupling [D_{12}(x)] terms of the pair diffusion tensor reveals that the pair separation dependence of D_{12} mimics that of the pair correlation function just as in a straight q1D channel. We show that the observed behavior is a consequence of the boundary conditions imposed on the q1D channel: both the single-file motion and the hydrodynamic flow must follow the channel around the bend.

Triplet correlation in sheared suspensions of Brownian particles

NASA Astrophysics Data System (ADS)

Yurkovetsky, Yevgeny; Morris, Jeffrey F.

2006-05-01

Triplet microstructure of sheared concentrated suspensions of Brownian monodisperse spherical particles is studied by sampling realizations of a three-dimensional unit cell subject to periodic boundary conditions obtained in accelerated Stokesian dynamics simulations. Triplets are regarded as a bridge between particle pairs and many-particle clusters thought responsible for shear thickening. Triplet-correlation data for weakly sheared near-equilibrium systems display an excluded volume effect of accumulated correlation for equilateral contacting triplets. As the Péclet number increases, there is a change in the preferred contacting isosceles triplet configuration, away from the "closed" triplet where the particles lie at the vertices of an equilateral triangle and toward the fully extended rod-like linear arrangement termed the "open" triplet. This transition is most pronounced for triplets lying in the plane of shear, where the open triplets' angular orientation with respect to the flow is very similar to that of a contacting pair. The correlation of suspension rheology to observed structure signals onset of larger clusters. An investigation of the predictive ability of Kirkwood's superposition approximation (KSA) provides valuable insights into the relationship between the pair and triplet probability distributions and helps achieve a better and more detailed understanding of the interplay of the pair and triplet dynamics. The KSA is seen more successfully to predict the shape of isosceles contacting triplet nonequilibrium distributions in the plane of shear than for similar configurations in equilibrium hard-sphere systems; in the sheared case, the discrepancies in magnitudes of distribution peaks are attributable to two interaction effects when pair average trajectories and locations of particles change in response to real, or "hard," and probabilistically favored ("soft") neighboring excluded volumes and, in the case of open triplets, due to changes in the correlation of the farthest separated pair caused by the fixed presence of the particle in the middle.

Construction and analysis of gene-gene dynamics influence networks based on a Boolean model.

PubMed

Mazaya, Maulida; Trinh, Hung-Cuong; Kwon, Yung-Keun

2017-12-21

Identification of novel gene-gene relations is a crucial issue to understand system-level biological phenomena. To this end, many methods based on a correlation analysis of gene expressions or structural analysis of molecular interaction networks have been proposed. They have a limitation in identifying more complicated gene-gene dynamical relations, though. To overcome this limitation, we proposed a measure to quantify a gene-gene dynamical influence (GDI) using a Boolean network model and constructed a GDI network to indicate existence of a dynamical influence for every ordered pair of genes. It represents how much a state trajectory of a target gene is changed by a knockout mutation subject to a source gene in a gene-gene molecular interaction (GMI) network. Through a topological comparison between GDI and GMI networks, we observed that the former network is denser than the latter network, which implies that there exist many gene pairs of dynamically influencing but molecularly non-interacting relations. In addition, a larger number of hub genes were generated in the GDI network. On the other hand, there was a correlation between these networks such that the degree value of a node was positively correlated to each other. We further investigated the relationships of the GDI value with structural properties and found that there are negative and positive correlations with the length of a shortest path and the number of paths, respectively. In addition, a GDI network could predict a set of genes whose steady-state expression is affected in E. coli gene-knockout experiments. More interestingly, we found that the drug-targets with side-effects have a larger number of outgoing links than the other genes in the GDI network, which implies that they are more likely to influence the dynamics of other genes. Finally, we found biological evidences showing that the gene pairs which are not molecularly interacting but dynamically influential can be considered for novel gene-gene relationships. Taken together, construction and analysis of the GDI network can be a useful approach to identify novel gene-gene relationships in terms of the dynamical influence.

Magnetoresistance in organic semiconductors: Including pair correlations in the kinetic equations for hopping transport

NASA Astrophysics Data System (ADS)

Shumilin, A. V.; Kabanov, V. V.; Dediu, V. I.

2018-03-01

We derive kinetic equations for polaron hopping in organic materials that explicitly take into account the double occupation possibility and pair intersite correlations. The equations include simplified phenomenological spin dynamics and provide a self-consistent framework for the description of the bipolaron mechanism of the organic magnetoresistance. At low applied voltages, the equations can be reduced to those for an effective resistor network that generalizes the Miller-Abrahams network and includes the effect of spin relaxation on the system resistivity. Our theory discloses the close relationship between the organic magnetoresistance and the intersite correlations. Moreover, in the absence of correlations, as in an ordered system with zero Hubbard energy, the magnetoresistance vanishes.

Multiscale synchrony behaviors of paired financial time series by 3D multi-continuum percolation

NASA Astrophysics Data System (ADS)

Wang, M.; Wang, J.; Wang, B. T.

2018-02-01

Multiscale synchrony behaviors and nonlinear dynamics of paired financial time series are investigated, in an attempt to study the cross correlation relationships between two stock markets. A random stock price model is developed by a new system called three-dimensional (3D) multi-continuum percolation system, which is utilized to imitate the formation mechanism of price dynamics and explain the nonlinear behaviors found in financial time series. We assume that the price fluctuations are caused by the spread of investment information. The cluster of 3D multi-continuum percolation represents the cluster of investors who share the same investment attitude. In this paper, we focus on the paired return series, the paired volatility series, and the paired intrinsic mode functions which are decomposed by empirical mode decomposition. A new cross recurrence quantification analysis is put forward, combining with multiscale cross-sample entropy, to investigate the multiscale synchrony of these paired series from the proposed model. The corresponding research is also carried out for two China stock markets as comparison.

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.

Homologous Chromosome Pairing in Drosophila melanogaster Proceeds through Multiple Independent Initiations

PubMed Central

Fung, Jennifer C.; Marshall, Wallace F.; Dernburg, Abby; Agard, David A.; Sedat, John W.

1998-01-01

The dynamics by which homologous chromosomes pair is currently unknown. Here, we use fluorescence in situ hybridization in combination with three-dimensional optical microscopy to show that homologous pairing of the somatic chromosome arm 2L in Drosophila occurs by independent initiation of pairing at discrete loci rather than by a processive zippering of sites along the length of chromosome. By evaluating the pairing frequencies of 11 loci on chromosome arm 2L over several timepoints during Drosophila embryonic development, we show that all 11 loci are paired very early in Drosophila development, within 13 h after egg deposition. To elucidate whether such pairing occurs by directed or undirected motion, we analyzed the pairing kinetics of histone loci during nuclear cycle 14. By measuring changes of nuclear length and correlating these changes with progression of time during cycle 14, we were able to express the pairing frequency and distance between homologous loci as a function of time. Comparing the experimentally determined dynamics of pairing to simulations based on previously proposed models of pairing motion, we show that the observed pairing kinetics are most consistent with a constrained random walk model and not consistent with a directed motion model. Thus, we conclude that simple random contacts through diffusion could suffice to allow pairing of homologous sites. PMID:9531544

Homologous chromosome pairing in Drosophila melanogaster proceeds through multiple independent initiations.

PubMed

Fung, J C; Marshall, W F; Dernburg, A; Agard, D A; Sedat, J W

1998-04-06

The dynamics by which homologous chromosomes pair is currently unknown. Here, we use fluorescence in situ hybridization in combination with three-dimensional optical microscopy to show that homologous pairing of the somatic chromosome arm 2L in Drosophila occurs by independent initiation of pairing at discrete loci rather than by a processive zippering of sites along the length of chromosome. By evaluating the pairing frequencies of 11 loci on chromosome arm 2L over several timepoints during Drosophila embryonic development, we show that all 11 loci are paired very early in Drosophila development, within 13 h after egg deposition. To elucidate whether such pairing occurs by directed or undirected motion, we analyzed the pairing kinetics of histone loci during nuclear cycle 14. By measuring changes of nuclear length and correlating these changes with progression of time during cycle 14, we were able to express the pairing frequency and distance between homologous loci as a function of time. Comparing the experimentally determined dynamics of pairing to simulations based on previously proposed models of pairing motion, we show that the observed pairing kinetics are most consistent with a constrained random walk model and not consistent with a directed motion model. Thus, we conclude that simple random contacts through diffusion could suffice to allow pairing of homologous sites.

The coupling between stability and ion pair formation in magnesium electrolytes from first-principles quantum mechanics and classical molecular dynamics

DOE PAGES

Rajput, Nav Nidhi; Qu, Xiaohuui; Sa, Niya; ...

2015-02-10

Here in this work we uncover a novel effect between concentration dependent ion pair formation and anion stability at reducing potentials, e.g., at the metal anode. Through comprehensive calculations using both first-principles as well as well-benchmarked classical molecular dynamics over a matrix of electrolytes, covering solvents and salt anions with a broad range in chemistry, we elucidate systematic correlations between molecular level interactions and composite electrolyte properties, such as electrochemical stability, solvation structure, and dynamics. We find that Mg electrolytes are highly prone to ion pair formation, even at modest concentrations, for a wide range of solvents with different dielectricmore » constants, which have implications for dynamics as well as charge transfer. Specifically, we observe that, at Mg metal potentials, the ion pair undergoes partial reduction at the Mg cation center (Mg 2+ -> Mg +), which competes with the charge transfer mechanism and can activate the anion to render it susceptible to decomposition. Specifically, TFSI exhibits a significant bond weakening while paired with the transient, partially reduced Mg +. In contrast, BH 4 $-$ and BF 4 $-$ are shown to be chemically stable in a reduced ion pair configuration. Furthermore, we observe that higher order glymes as well as DMSO improve the solubility of Mg salts, but only the longer glyme chains reduce the dynamics of the ions in solution. This information provides critical design metrics for future electrolytes as it elucidates a close connection between bulk solvation and cathodic stability as well as the dynamics of the salt.« less

Effects of Preferential Solvation Revealed by Time-Resolved Magnetic Field Effects

PubMed Central

2017-01-01

External magnetic fields can impact recombination yields of photoinduced electron transfer reactions by affecting the spin dynamics in transient, spin-correlated radical pair intermediates. For exciplex-forming donor–acceptor systems, this magnetic field effect (MFE) can be investigated sensitively by studying the delayed recombination fluorescence. Here, we investigate the effect of preferential solvation in microheterogeneous solvent mixtures on the radical pair dynamics of the system 9,10-dimethylanthracene (fluorophore)/N,N-dimethylaniline (quencher) by means of time-resolved magnetic field effect (TR-MFE) measurements, wherein the exciplex emission is recorded in the absence and the presence of an external magnetic field using time-correlated single photon counting (TCSPC). In microheterogeneous environments, the MFE of the exciplex emission occurs on a faster time scale than in iso-dielectric homogeneous solvents. In addition, the local polarity reported by the exciplex is enhanced compared to homogeneous solvent mixtures of the same macroscopic permittivity. Detailed analyses of the TR-MFE reveal that the quenching reaction directly yielding the radical ion pair is favored in microheterogeneous environments. This is in stark contrast to homogeneous media, for which the MFE predominantly involves direct formation of the exciplex, its subsequent dissociation to the magneto-sensitive radical pair, and re-encounters. These observations provide evidence for polar microdomains and enhanced caging, which are shown to have a significant impact on the reaction dynamics in microheterogeneous binary solvents. PMID:28263599

Effects of Preferential Solvation Revealed by Time-Resolved Magnetic Field Effects.

PubMed

Pham, Van Thi Bich; Hoang, Hao Minh; Grampp, Günter; Kattnig, Daniel R

2017-03-30

External magnetic fields can impact recombination yields of photoinduced electron transfer reactions by affecting the spin dynamics in transient, spin-correlated radical pair intermediates. For exciplex-forming donor-acceptor systems, this magnetic field effect (MFE) can be investigated sensitively by studying the delayed recombination fluorescence. Here, we investigate the effect of preferential solvation in microheterogeneous solvent mixtures on the radical pair dynamics of the system 9,10-dimethylanthracene (fluorophore)/N,N-dimethylaniline (quencher) by means of time-resolved magnetic field effect (TR-MFE) measurements, wherein the exciplex emission is recorded in the absence and the presence of an external magnetic field using time-correlated single photon counting (TCSPC). In microheterogeneous environments, the MFE of the exciplex emission occurs on a faster time scale than in iso-dielectric homogeneous solvents. In addition, the local polarity reported by the exciplex is enhanced compared to homogeneous solvent mixtures of the same macroscopic permittivity. Detailed analyses of the TR-MFE reveal that the quenching reaction directly yielding the radical ion pair is favored in microheterogeneous environments. This is in stark contrast to homogeneous media, for which the MFE predominantly involves direct formation of the exciplex, its subsequent dissociation to the magneto-sensitive radical pair, and re-encounters. These observations provide evidence for polar microdomains and enhanced caging, which are shown to have a significant impact on the reaction dynamics in microheterogeneous binary solvents.

Molecular dynamics study of thermodynamic scaling of the glass-transition dynamics in ionic liquids over wide temperature and pressure ranges.

PubMed

Habasaki, J; Casalini, R; Ngai, K L

2010-03-25

Experimentally, superpositioning of dynamic properties such as viscosity, relaxation times, or diffusion coefficients under different conditions of temperature T, pressure P, and volume V by the scaling variable TV(gamma) (where gamma is a material constant) has been reported as a general feature of many kinds of glass-forming materials. In the present work, molecular dynamics (MD) simulations have been performed to study the scaling of dynamics near the glass-transition regime of ionic liquids. Scaling in the simulated 1-ethyl-3-methylimidazolium nitrate (EMIM-NO(3)) system has been tested over wide ranges of temperatures and pressures. TV(gamma) scaling of the dynamics is well described by master curves with gamma = 4.0 +/- 0.2 and 3.8 +/- 0.2 for cation and anion, respectively. Structures and Coulombic terms of the corresponding states are found to be quite similar. The temperature and pressure dependence of the pair correlation function show similar trends and therefore can be superpositioned onto the master curve. Although the behaviors with gamma = 4 might be expected from the relation, gamma = n/3, for the dynamics with the soft-core-type potential U = epsilon(sigma/r)(n), with n = 12, pair potentials used in the MD simulation have a more complex form, and not all the repulsive terms can play their roles in the heterogeneous structures determined by ion-ion interactions. Scaling is related to the common part of effective potentials related to the pair correlation functions, including the many-body effect in real space.

Decomposition of Proteins into Dynamic Units from Atomic Cross-Correlation Functions.

PubMed

Calligari, Paolo; Gerolin, Marco; Abergel, Daniel; Polimeno, Antonino

2017-01-10

In this article, we present a clustering method of atoms in proteins based on the analysis of the correlation times of interatomic distance correlation functions computed from MD simulations. The goal is to provide a coarse-grained description of the protein in terms of fewer elements that can be treated as dynamically independent subunits. Importantly, this domain decomposition method does not take into account structural properties of the protein. Instead, the clustering of protein residues in terms of networks of dynamically correlated domains is defined on the basis of the effective correlation times of the pair distance correlation functions. For these properties, our method stands as a complementary analysis to the customary protein decomposition in terms of quasi-rigid, structure-based domains. Results obtained for a prototypal protein structure illustrate the approach proposed.

Enhancement of superexchange pairing in the periodically driven Hubbard model

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

Electron Correlation from the Adiabatic Connection for Multireference Wave Functions

NASA Astrophysics Data System (ADS)

Pernal, Katarzyna

2018-01-01

An adiabatic connection (AC) formula for the electron correlation energy is derived for a broad class of multireference wave functions. The AC expression recovers dynamic correlation energy and assures a balanced treatment of the correlation energy. Coupling the AC formalism with the extended random phase approximation allows one to find the correlation energy only from reference one- and two-electron reduced density matrices. If the generalized valence bond perfect pairing model is employed a simple closed-form expression for the approximate AC formula is obtained. This results in the overall M5 scaling of the computation cost making the method one of the most efficient multireference approaches accounting for dynamic electron correlation also for the strongly correlated systems.

A minimalistic approach to static and dynamic electron correlations: Amending generalized valence bond method with extended random phase approximation correlation correction

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

Chatterjee, Koushik; Jawulski, Konrad; Pastorczak, Ewa

A perfect-pairing generalized valence bond (GVB) approximation is known to be one of the simplest approximations, which allows one to capture the essence of static correlation in molecular systems. In spite of its attractive feature of being relatively computationally efficient, this approximation misses a large portion of dynamic correlation and does not offer sufficient accuracy to be generally useful for studying electronic structure of molecules. We propose to correct the GVB model and alleviate some of its deficiencies by amending it with the correlation energy correction derived from the recently formulated extended random phase approximation (ERPA). On the examples ofmore » systems of diverse electronic structures, we show that the resulting ERPA-GVB method greatly improves upon the GVB model. ERPA-GVB recovers most of the electron correlation and it yields energy barrier heights of excellent accuracy. Thanks to a balanced treatment of static and dynamic correlation, ERPA-GVB stays reliable when one moves from systems dominated by dynamic electron correlation to those for which the static correlation comes into play.« less

First-Principles Molecular Dynamics Simulations of NaCl in Water: Performance of Advanced Exchange-Correlation Approximations in Density Functional Theory

NASA Astrophysics Data System (ADS)

Yao, Yi; Kanai, Yosuke

Our ability to correctly model the association of oppositely charged ions in water is fundamental in physical chemistry and essential to various technological and biological applications of molecular dynamics (MD) simulations. MD simulations using classical force fields often show strong clustering of NaCl in the aqueous ionic solutions as a consequence of a deep contact pair minimum in the potential of mean force (PMF) curve. First-Principles Molecular Dynamics (FPMD) based on Density functional theory (DFT) with the popular PBE exchange-correlation approximation, on the other hand, show a different result with a shallow contact pair minimum in the PMF. We employed two of most promising exchange-correlation approximations, ωB97xv by Mardiorossian and Head-Gordon and SCAN by Sun, Ruzsinszky and Perdew, to examine the PMF using FPMD simulations. ωB97xv is highly empirically and optimized in the space of range-separated hybrid functional with a dispersion correction while SCAN is the most recent meta-GGA functional that is constructed by satisfying various known conditions in well-defined physical limits. We will discuss our findings for PMF, charge transfer, water dipoles, etc.

Frontal Cortex Activation Causes Rapid Plasticity of Auditory Cortical Processing

PubMed Central

Winkowski, Daniel E.; Bandyopadhyay, Sharba; Shamma, Shihab A.

2013-01-01

Neurons in the primary auditory cortex (A1) can show rapid changes in receptive fields when animals are engaged in sound detection and discrimination tasks. The source of a signal to A1 that triggers these changes is suspected to be in frontal cortical areas. How or whether activity in frontal areas can influence activity and sensory processing in A1 and the detailed changes occurring in A1 on the level of single neurons and in neuronal populations remain uncertain. Using electrophysiological techniques in mice, we found that pairing orbitofrontal cortex (OFC) stimulation with sound stimuli caused rapid changes in the sound-driven activity within A1 that are largely mediated by noncholinergic mechanisms. By integrating in vivo two-photon Ca2+ imaging of A1 with OFC stimulation, we found that pairing OFC activity with sounds caused dynamic and selective changes in sensory responses of neural populations in A1. Further, analysis of changes in signal and noise correlation after OFC pairing revealed improvement in neural population-based discrimination performance within A1. This improvement was frequency specific and dependent on correlation changes. These OFC-induced influences on auditory responses resemble behavior-induced influences on auditory responses and demonstrate that OFC activity could underlie the coordination of rapid, dynamic changes in A1 to dynamic sensory environments. PMID:24227723

Sign Crossover in All Maxwell-Stefan Diffusivities for Molten Salt LiF-BeF2: A Molecular Dynamics Study.

PubMed

Chakraborty, Brahmananda

2015-08-20

Applying Green-Kubo formalism and equilibrium molecular dynamics (MD) simulations, we have studied for the first time the dynamic correlation, Onsager coefficients, and Maxwell-Stefan (MS) diffusivities of molten salt LiF-BeF2, which is a potential candidate for a coolant in a high temperature reactor. We observe an unusual composition dependence and strikingly a crossover in sign for all the MS diffusivities at a composition of around 7% of LiF where the MS diffusivity between cation-anion pair (Đ(BeF) and Đ(LiF)) jumps from positive to negative value while the MS diffusivity between cation-cation pair (Đ(LiBe)) becomes positive from a negative value. Even though the negative MS diffusivities have been observed for electrolyte solutions between cation-cation pair, here we report negative MS diffusivity between cation-anion pair where Đ(BeF) shows a sharp rise around 66% of BeF2, reaches maximum value at 70% of BeF2, and then decreases almost exponentially with a sign change for BeF2 around 93%. For low mole fraction of LiF, Đ(BeF) follows the Debye-Huckel theory and rises with the square root of LiF mole fraction similar to the MS diffusivity between cation-anion pair in aqueous solution of electrolyte salt. Negative MS diffusivities while unusual are, however, shown to satisfy the non-negative entropy constraints at all thermodynamic states as required by the second law of thermodynamics. We have established a strong correlation between the structure and dynamics and predict that the formation of flouride polyanion network between Be and F ions and coulomb interaction is responsible for sharp variation of the MS diffusivities which controls the multicomponent diffusion phenomenon in LiF-BeF2 which has a strong impact on the performance of the reactor.

Evaluating Dynamic Bivariate Correlations in Resting-state fMRI: A comparison study and a new approach

PubMed Central

Lindquist, Martin A.; Xu, Yuting; Nebel, Mary Beth; Caffo, Brain S.

2014-01-01

To date, most functional Magnetic Resonance Imaging (fMRI) studies have assumed that the functional connectivity (FC) between time series from distinct brain regions is constant across time. However, recently, there has been increased interest in quantifying possible dynamic changes in FC during fMRI experiments, as it is thought this may provide insight into the fundamental workings of brain networks. In this work we focus on the specific problem of estimating the dynamic behavior of pair-wise correlations between time courses extracted from two different regions of the brain. We critique the commonly used sliding-windows technique, and discuss some alternative methods used to model volatility in the finance literature that could also prove useful in the neuroimaging setting. In particular, we focus on the Dynamic Conditional Correlation (DCC) model, which provides a model-based approach towards estimating dynamic correlations. We investigate the properties of several techniques in a series of simulation studies and find that DCC achieves the best overall balance between sensitivity and specificity in detecting dynamic changes in correlations. We also investigate its scalability beyond the bivariate case to demonstrate its utility for studying dynamic correlations between more than two brain regions. Finally, we illustrate its performance in an application to test-retest resting state fMRI data. PMID:24993894

Generalized-active-space pair-density functional theory: an efficient method to study large, strongly correlated, conjugated systems.

PubMed

Ghosh, Soumen; Cramer, Christopher J; Truhlar, Donald G; Gagliardi, Laura

2017-04-01

Predicting ground- and excited-state properties of open-shell organic molecules by electronic structure theory can be challenging because an accurate treatment has to correctly describe both static and dynamic electron correlation. Strongly correlated systems, i.e. , systems with near-degeneracy correlation effects, are particularly troublesome. Multiconfigurational wave function methods based on an active space are adequate in principle, but it is impractical to capture most of the dynamic correlation in these methods for systems characterized by many active electrons. We recently developed a new method called multiconfiguration pair-density functional theory (MC-PDFT), that combines the advantages of wave function theory and density functional theory to provide a more practical treatment of strongly correlated systems. Here we present calculations of the singlet-triplet gaps in oligoacenes ranging from naphthalene to dodecacene. Calculations were performed for unprecedently large orbitally optimized active spaces of 50 electrons in 50 orbitals, and we test a range of active spaces and active space partitions, including four kinds of frontier orbital partitions. We show that MC-PDFT can predict the singlet-triplet splittings for oligoacenes consistent with the best available and much more expensive methods, and indeed MC-PDFT may constitute the benchmark against which those other models should be compared, given the absence of experimental data.

Equilibrium properties and phase diagram of two-dimensional Yukawa systems

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

Hartmann, P.; Donko, Z.; Kutasi, K.

Properties of two-dimensional strongly coupled Yukawa systems are explored through molecular dynamics simulations. An effective coupling coefficient {gamma}{sup *} for the liquid phase is introduced on the basis of the constancy of the first peak amplitude of the pair-correlation functions. Thermodynamic quantities are calculated from the pair-correlation function. The solid-liquid transition of the system is investigated through the analysis of the bond-angular order parameter. The static structure function satisfies consistency relation, attesting to the reliability of the computational method. The response is shown to be governed by the correlational part of the inverse compressibility. An analysis of the velocity autocorrelationmore » demonstrates that this latter also exhibits a universal behavior.« less

Antiphase dual-color correlation in a reactant-product pair imparts ultrasensitivity in reaction-linked double-photoswitching fluorescence imaging.

PubMed

Wan, Wei; Zhu, Ming-Qiang; Tian, Zhiyuan; Li, Alexander D Q

2015-04-08

A pair of reversible photochemical reactions correlates their reactant and product specifically, and such a correlation uniquely distinguishes their correlated signal from others that are not linked by this reversible reaction. Here a nanoparticle-shielded fluorophore is photodriven to undergo structural dynamics, alternating between a green-fluorescence state and a red-fluorescence state. As time elapses, the fluorophore can be in either state but not both at the same time. Thus, the red fluorescence is maximized while the green fluorescence is minimized and vice versa. Such an antiphase dual-color (AD) corelationship between the red and green fluorescence maxima as well as between their minima can be exploited to greatly improve the signal-to-noise ratio, thus enhancing the ultimate detection limit. Potential benefits of this correlation include elimination of all interferences originating from single-color dyes and signal amplification of AD photoswitching molecules by orders of magnitude.

Frontiers in Fluctuation Spectroscopy: Measuring protein dynamics and protein spatio-temporal connectivity

NASA Astrophysics Data System (ADS)

Digman, Michelle

Fluorescence fluctuation spectroscopy has evolved from single point detection of molecular diffusion to a family of microscopy imaging correlation tools (i.e. ICS, RICS, STICS, and kICS) useful in deriving spatial-temporal dynamics of proteins in living cells The advantage of the imaging techniques is the simultaneous measurement of all points in an image with a frame rate that is increasingly becoming faster with better sensitivity cameras and new microscopy modalities such as the sheet illumination technique. A new frontier in this area is now emerging towards a high level of mapping diffusion rates and protein dynamics in the 2 and 3 dimensions. In this talk, I will discuss the evolution of fluctuation analysis from the single point source to mapping diffusion in whole cells and the technology behind this technique. In particular, new methods of analysis exploit correlation of molecular fluctuations originating from measurement of fluctuation correlations at distant points (pair correlation analysis) and methods that exploit spatial averaging of fluctuations in small regions (iMSD). For example the pair correlation fluctuation (pCF) analyses done between adjacent pixels in all possible radial directions provide a window into anisotropic molecular diffusion. Similar to the connectivity atlas of neuronal connections from the MRI diffusion tensor imaging these new tools will be used to map the connectome of protein diffusion in living cells. For biological reaction-diffusion systems, live single cell spatial-temporal analysis of protein dynamics provides a mean to observe stochastic biochemical signaling in the context of the intracellular environment which may lead to better understanding of cancer cell invasion, stem cell differentiation and other fundamental biological processes. National Institutes of Health Grant P41-RRO3155.

Transfer Ionization Studies for Proton on He - new Inside into the World of Correlation

NASA Astrophysics Data System (ADS)

Schmidt-Böcking, Horst

2005-04-01

Correlated many-particle dynamics in Coulombic systems, which is one of the unsolved fundamental problems in AMO-physics, can now be experimentally approached with so far unprecedented completeness and precision. The recent development of the COLTRIMS technique (COLd Target Recoil Ion Momentum Spectroscopy) provides a coincident multi-fragment imaging technique for eV and sub-eV fragment detection. In its completeness it is as powerful as the bubble chamber in high energy physics. In recent benchmark experiments quasi snapshots (duration as short an atto-sec) of the correlated dynamics between electrons and nuclei has been made for atomic and molecular objects. This new imaging technique has opened a powerful observation window into the hidden world of many-particle dynamics. Recent transfer ionization studies will be presented and the direct observation of correlated electron pairs will be discussed.

Davisson-Germer Prize in Atomic or Surface Physics: The COLTRIMS multi-particle imaging technique-new Insight into the World of Correlation

NASA Astrophysics Data System (ADS)

Schmidt-Bocking, Horst

2008-05-01

The correlated many-particle dynamics in Coulombic systems, which is one of the unsolved fundamental problems in AMO-physics, can now be experimentally approached with so far unprecedented completeness and precision. The recent development of the COLTRIMS technique (COLd Target Recoil Ion Momentum Spectroscopy) provides a coincident multi-fragment imaging technique for eV and sub-eV fragment detection. In its completeness it is as powerful as the bubble chamber in high energy physics. In recent benchmark experiments quasi snapshots (duration as short as an atto-sec) of the correlated dynamics between electrons and nuclei has been made for atomic and molecular objects. This new imaging technique has opened a powerful observation window into the hidden world of many-particle dynamics. Recent multiple-ionization studies will be presented and the observation of correlated electron pairs will be discussed.

Modeling meiotic chromosome pairing: nuclear envelope attachment, telomere-led active random motion, and anomalous diffusion

PubMed Central

Marshall, Wallace F.; Fung, Jennifer C.

2016-01-01

The recognition and pairing of homologous chromosomes during meiosis is a complex physical and molecular process involving a combination of polymer dynamics and molecular recognition events. Two highly conserved features of meiotic chromosome behavior are the attachment of telomeres to the nuclear envelope and the active random motion of telomeres driven by their interaction with cytoskeletal motor proteins. Both of these features have been proposed to facilitate the process of homolog pairing, but exactly what role these features play in meiosis remains poorly understood. Here we investigate the roles of active motion and nuclear envelope tethering using a Brownian dynamics simulation in which meiotic chromosomes are represented by a Rouse polymer model subjected to tethering and active forces at the telomeres. We find that tethering telomeres to the nuclear envelope slows down pairing relative to the rates achieved by un-attached chromosomes, but that randomly-directed active forces applied to the telomeres speeds up pairing dramatically in a manner that depends on the statistical properties of the telomere force fluctuations. The increased rate of initial pairing cannot be explained by stretching out of the chromosome conformation but instead seems to correlate with anomalous diffusion of sub-telomeric regions. PMID:27046097

Modeling meiotic chromosome pairing: nuclear envelope attachment, telomere-led active random motion, and anomalous diffusion

NASA Astrophysics Data System (ADS)

Marshall, Wallace F.; Fung, Jennifer C.

2016-04-01

The recognition and pairing of homologous chromosomes during meiosis is a complex physical and molecular process involving a combination of polymer dynamics and molecular recognition events. Two highly conserved features of meiotic chromosome behavior are the attachment of telomeres to the nuclear envelope and the active random motion of telomeres driven by their interaction with cytoskeletal motor proteins. Both of these features have been proposed to facilitate the process of homolog pairing, but exactly what role these features play in meiosis remains poorly understood. Here we investigate the roles of active motion and nuclear envelope tethering using a Brownian dynamics simulation in which meiotic chromosomes are represented by a Rouse polymer model subjected to tethering and active forces at the telomeres. We find that tethering telomeres to the nuclear envelope slows down pairing relative to the rates achieved by unattached chromosomes, but that randomly directed active forces applied to the telomeres speed up pairing dramatically in a manner that depends on the statistical properties of the telomere force fluctuations. The increased rate of initial pairing cannot be explained by stretching out of the chromosome conformation but instead seems to correlate with anomalous diffusion of sub-telomeric regions.

Evolution of correlation structure of industrial indices of U.S. equity markets.

PubMed

Buccheri, Giuseppe; Marmi, Stefano; Mantegna, Rosario N

2013-07-01

We investigate the dynamics of correlations present between pairs of industry indices of U.S. stocks traded in U.S. markets by studying correlation-based networks and spectral properties of the correlation matrix. The study is performed by using 49 industry index time series computed by K. French and E. Fama during the time period from July 1969 to December 2011, which spans more than 40 years. We show that the correlation between industry indices presents both a fast and a slow dynamics. The slow dynamics has a time scale longer than 5 years, showing that a different degree of diversification of the investment is possible in different periods of time. Moreover, we also detect a fast dynamics associated with exogenous or endogenous events. The fast time scale we use is a monthly time scale and the evaluation time period is a 3-month time period. By investigating the correlation dynamics monthly, we are able to detect two examples of fast variations in the first and second eigenvalue of the correlation matrix. The first occurs during the dot-com bubble (from March 1999 to April 2001) and the second occurs during the period of highest impact of the subprime crisis (from August 2008 to August 2009).

Evolution of correlation structure of industrial indices of U.S. equity markets

NASA Astrophysics Data System (ADS)

Buccheri, Giuseppe; Marmi, Stefano; Mantegna, Rosario N.

2013-07-01

We investigate the dynamics of correlations present between pairs of industry indices of U.S. stocks traded in U.S. markets by studying correlation-based networks and spectral properties of the correlation matrix. The study is performed by using 49 industry index time series computed by K. French and E. Fama during the time period from July 1969 to December 2011, which spans more than 40 years. We show that the correlation between industry indices presents both a fast and a slow dynamics. The slow dynamics has a time scale longer than 5 years, showing that a different degree of diversification of the investment is possible in different periods of time. Moreover, we also detect a fast dynamics associated with exogenous or endogenous events. The fast time scale we use is a monthly time scale and the evaluation time period is a 3-month time period. By investigating the correlation dynamics monthly, we are able to detect two examples of fast variations in the first and second eigenvalue of the correlation matrix. The first occurs during the dot-com bubble (from March 1999 to April 2001) and the second occurs during the period of highest impact of the subprime crisis (from August 2008 to August 2009).

Magnetic Fluctuations in Pair-Density-Wave Superconductors

NASA Astrophysics Data System (ADS)

Christensen, Morten H.; Jacobsen, Henrik; Maier, Thomas A.; Andersen, Brian M.

2016-04-01

Pair-density-wave superconductivity constitutes a novel electronic condensate proposed to be realized in certain unconventional superconductors. Establishing its potential existence is important for our fundamental understanding of superconductivity in correlated materials. Here we compute the dynamical magnetic susceptibility in the presence of a pair-density-wave ordered state and study its fingerprints on the spin-wave spectrum including the neutron resonance. In contrast to the standard case of d -wave superconductivity, we show that the pair-density-wave phase exhibits neither a spin gap nor a magnetic resonance peak, in agreement with a recent neutron scattering experiment on underdoped La1.905 Ba0.095 CuO4 [Z. Xu et al., Phys. Rev. Lett. 113, 177002 (2014)].

Preferential solvation, ion pairing, and dynamics of concentrated aqueous solutions of divalent metal nitrate salts

NASA Astrophysics Data System (ADS)

Yadav, Sushma; Chandra, Amalendu

2017-12-01

We have investigated the characteristics of preferential solvation of ions, structure of solvation shells, ion pairing, and dynamics of aqueous solutions of divalent alkaline-earth metal nitrate salts at varying concentration by means of molecular dynamics simulations. Hydration shell structures and the extent of preferential solvation of the metal and nitrate ions in the solutions are investigated through calculations of radial distribution functions, tetrahedral ordering, and also spatial distribution functions. The Mg2+ ions are found to form solvent separated ion-pairs while the Ca2+ and Sr2+ ions form contact ion pairs with the nitrate ions. These findings are further corroborated by excess coordination numbers calculated through Kirkwood-Buff G factors for different ion-ion and ion-water pairs. The ion-pairing propensity is found to be in the order of Mg(NO3) 2 < C a (NO3) 2 < S r (NO3) 2, and it follows the trend given by experimental activity coefficients. It is found that proper modeling of these solutions requires the inclusion of electronic polarization of the ions which is achieved in the current study through electronic continuum correction force fields. A detailed analysis of the effects of ion-pairs on the structure and dynamics of water around the hydrated ions is done through classification of water into different subspecies based on their locations around the cations or anions only or bridged between them. We have looked at the diffusion coefficients, relaxation of orientational correlation functions, and also the residence times of different subspecies of water to explore the dynamics of water in different structural environments in the solutions. The current results show that the water molecules are incorporated into fairly well-structured hydration shells of the ions, thus decreasing the single-particle diffusivities and increasing the orientational relaxation times of water with an increase in salt concentration. The different structural motifs also lead to the presence of substantial dynamical heterogeneity in these solutions of strongly interacting ions. The current study helps us to understand the molecular details of hydration structure, ion pairing, and dynamics of water in the solvation shells and also of ion diffusion in aqueous solutions of divalent metal nitrate salts.

Dynamics of Markets

NASA Astrophysics Data System (ADS)

McCauley, Joseph L.

2009-09-01

Preface; 1. Econophysics: why and what; 2. Neo-classical economic theory; 3. Probability and stochastic processes; 4. Introduction to financial economics; 5. Introduction to portfolio selection theory; 6. Scaling, pair correlations, and conditional densities; 7. Statistical ensembles: deducing dynamics from time series; 8. Martingale option pricing; 9. FX market globalization: evolution of the dollar to worldwide reserve currency; 10. Macroeconomics and econometrics: regression models vs. empirically based modeling; 11. Complexity; Index.

Dynamic leg length asymmetry during gait is not a valid method for estimating mild anatomic leg length discrepancy.

PubMed

Leporace, Gustavo; Batista, Luiz Alberto; Serra Cruz, Raphael; Zeitoune, Gabriel; Cavalin, Gabriel Armondi; Metsavaht, Leonardo

2018-03-01

The purpose of this study was to test the validity of dynamic leg length discrepancy (DLLD) during gait as a radiation-free screening method for measuring anatomic leg length discrepancy (ALLD). Thirty-three subjects with mild leg length discrepancy walked along a walkway and the dynamic leg length discrepancy (DLLD) was calculated using a motion analysis system. Pearson correlation and paired Student t -tests were applied to calculate the correlation and compare the differences between DLLD and ALLD (α = 0.05). The results of our study showed DLLD is not a valid method to predict ALLD in subjects with mild limb discrepancy.

Generalized-active-space pair-density functional theory: an efficient method to study large, strongly correlated, conjugated systems

DOE PAGES

Ghosh, Soumen; Cramer, Christopher J.; Truhlar, Donald G.; ...

2017-01-19

Predicting ground- and excited-state properties of open-shell organic molecules by electronic structure theory can be challenging because an accurate treatment has to correctly describe both static and dynamic electron correlation. Strongly correlated systems, i.e., systems with near-degeneracy correlation effects, are particularly troublesome. Multiconfigurational wave function methods based on an active space are adequate in principle, but it is impractical to capture most of the dynamic correlation in these methods for systems characterized by many active electrons. Here, we recently developed a new method called multiconfiguration pair-density functional theory (MC-PDFT), that combines the advantages of wave function theory and density functionalmore » theory to provide a more practical treatment of strongly correlated systems. Here we present calculations of the singlet–triplet gaps in oligoacenes ranging from naphthalene to dodecacene. Calculations were performed for unprecedently large orbitally optimized active spaces of 50 electrons in 50 orbitals, and we test a range of active spaces and active space partitions, including four kinds of frontier orbital partitions. We show that MC-PDFT can predict the singlet–triplet splittings for oligoacenes consistent with the best available and much more expensive methods, and indeed MC-PDFT may constitute the benchmark against which those other models should be compared, given the absence of experimental data.« less

Generalized-active-space pair-density functional theory: an efficient method to study large, strongly correlated, conjugated systems

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

Ghosh, Soumen; Cramer, Christopher J.; Truhlar, Donald G.

Predicting ground- and excited-state properties of open-shell organic molecules by electronic structure theory can be challenging because an accurate treatment has to correctly describe both static and dynamic electron correlation. Strongly correlated systems, i.e., systems with near-degeneracy correlation effects, are particularly troublesome. Multiconfigurational wave function methods based on an active space are adequate in principle, but it is impractical to capture most of the dynamic correlation in these methods for systems characterized by many active electrons. Here, we recently developed a new method called multiconfiguration pair-density functional theory (MC-PDFT), that combines the advantages of wave function theory and density functionalmore » theory to provide a more practical treatment of strongly correlated systems. Here we present calculations of the singlet–triplet gaps in oligoacenes ranging from naphthalene to dodecacene. Calculations were performed for unprecedently large orbitally optimized active spaces of 50 electrons in 50 orbitals, and we test a range of active spaces and active space partitions, including four kinds of frontier orbital partitions. We show that MC-PDFT can predict the singlet–triplet splittings for oligoacenes consistent with the best available and much more expensive methods, and indeed MC-PDFT may constitute the benchmark against which those other models should be compared, given the absence of experimental data.« less

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.

Ion Transport via Structural Relaxations in Polymerized Ionic Liquids

NASA Astrophysics Data System (ADS)

Ganesan, Venkat; Mogurampelly, Santosh

We study the mechanisms underlying ion transport in poly(1-butyl-3-vinylimidazolium-hexafluorophosphate) polymer electrolytes. We consider polymer electrolytes of varying polymerized ionic liquid to ionic liquid (polyIL:IL) ratios and use atomistic molecular dynamics (MD) simulations to probe the dynamical and structural characteristics of the electrolyte. Our results reveal that anion diffusion along polymer backbone occurs primarily viathe formation and breaking of ion-pairs involving threepolymerized cationic monomers of twodifferent polymer chains. Moreover, we observe that the ionic diffusivities exhibit a direct correlation with the structural relaxation times of the ion-pairs and hydrogen bonds (H-bonds). These results provide new insights into the mechanisms underlying ion transport in polymerized ionic liquid electrolytes.

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.

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

Spatial and polarization entanglement of lasing patterns and related dynamic behaviors in laser-diode-pumped solid-state lasers.

PubMed

Otsuka, K; Chu, S-C; Lin, C-C; Tokunaga, K; Ohtomo, T

2009-11-23

To provide the underlying physical mechanism for formations of spatial- and polarization-entangled lasing patterns (namely, SPEPs), we performed experiments using a c-cut Nd:GdVO(4) microchip laser with off-axis laser-diode pumping. This extends recent work on entangled lasing pattern generation from an isotropic laser, where such a pattern was explained only in terms of generalized coherent states (GCSs) formed by mathematical manipulation. Here, we show that polarization-resolved transverse patterns can be well explained by the transverse mode-locking of distinct orthogonal linearly polarized Ince-Gauss (IG) mode pairs rather than GCSs. Dynamic properties of SPEPs were experimentally examined in both free-running and modulated conditions to identify long-term correlations of IG mode pairs over time. The complete chaos synchronization among IG mode pairs subjected to external perturbation is also demonstrated.

Phase synchronization based minimum spanning trees for analysis of financial time series with nonlinear correlations

NASA Astrophysics Data System (ADS)

Radhakrishnan, Srinivasan; Duvvuru, Arjun; Sultornsanee, Sivarit; Kamarthi, Sagar

2016-02-01

The cross correlation coefficient has been widely applied in financial time series analysis, in specific, for understanding chaotic behaviour in terms of stock price and index movements during crisis periods. To better understand time series correlation dynamics, the cross correlation matrices are represented as networks, in which a node stands for an individual time series and a link indicates cross correlation between a pair of nodes. These networks are converted into simpler trees using different schemes. In this context, Minimum Spanning Trees (MST) are the most favoured tree structures because of their ability to preserve all the nodes and thereby retain essential information imbued in the network. Although cross correlations underlying MSTs capture essential information, they do not faithfully capture dynamic behaviour embedded in the time series data of financial systems because cross correlation is a reliable measure only if the relationship between the time series is linear. To address the issue, this work investigates a new measure called phase synchronization (PS) for establishing correlations among different time series which relate to one another, linearly or nonlinearly. In this approach the strength of a link between a pair of time series (nodes) is determined by the level of phase synchronization between them. We compare the performance of phase synchronization based MST with cross correlation based MST along selected network measures across temporal frame that includes economically good and crisis periods. We observe agreement in the directionality of the results across these two methods. They show similar trends, upward or downward, when comparing selected network measures. Though both the methods give similar trends, the phase synchronization based MST is a more reliable representation of the dynamic behaviour of financial systems than the cross correlation based MST because of the former's ability to quantify nonlinear relationships among time series or relations among phase shifted time series.

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

Jain, Richa Naja, E-mail: ltprichanaja@gmail.com; Chakraborty, Brahmananda; Ramaniah, Lavanya M.

In this work our main objective is to compute Dynamical correlations, Onsager coefficients and Maxwell-Stefan (MS) diffusivities for molten salt LiF-KF mixture at various thermodynamic states through Green–Kubo formalism for the first time. The equilibrium molecular dynamics (MD) simulations were performed using BHM potential for LiF–KF mixture. The velocity autocorrelations functions involving Li ions reflect the endurance of cage dynamics or backscattering with temperature. The magnitude of Onsager coefficients for all pairs increases with increase in temperature. Interestingly most of the Onsager coefficients has almost maximum magnitude at the eutectic composition indicating the most dynamic character of the eutectic mixture.more » MS diffusivity hence diffusion for all ion pairs increases in the system with increasing temperature. Smooth variation of the diffusivity values denies any network formation in the mixture. Also, the striking feature is the noticeable concentration dependence of MS diffusivity between cation-cation pair, Đ{sub Li-K} which remains negative for most of the concentration range but changes sign to become positive for higher LiF concentration. The negative MS diffusivity is acceptable as it satisfies the non-negative entropy constraint governed by 2{sup nd} law of thermodynamics. This high diffusivity also vouches the candidature of molten salt as a coolant.« less

Computational fluid dynamics endpoints to characterize obstructive sleep apnea syndrome in children

PubMed Central

Luo, Haiyan; Persak, Steven C.; Sin, Sanghun; McDonough, Joseph M.; Isasi, Carmen R.; Arens, Raanan

2013-01-01

Computational fluid dynamics (CFD) analysis may quantify the severity of anatomical airway restriction in obstructive sleep apnea syndrome (OSAS) better than anatomical measurements alone. However, optimal CFD model endpoints to characterize or assess OSAS have not been determined. To model upper airway fluid dynamics using CFD and investigate the strength of correlation between various CFD endpoints, anatomical endpoints, and OSAS severity, in obese children with OSAS and controls. CFD models derived from magnetic resonance images were solved at subject-specific peak tidal inspiratory flow; pressure at the choanae was set by nasal resistance. Model endpoints included airway wall minimum pressure (Pmin), flow resistance in the pharynx (Rpharynx), and pressure drop from choanae to a minimum cross section where tonsils and adenoids constrict the pharynx (dPTAmax). Significance of endpoints was analyzed using paired comparisons (t-test or Wilcoxon signed rank test) and Spearman correlation. Fifteen subject pairs were analyzed. Rpharynx and dPTAmax were higher in OSAS than control and most significantly correlated to obstructive apnea-hypopnea index (oAHI), r = 0.48 and r = 0.49, respectively (P < 0.01). Airway minimum cross-sectional correlation to oAHI was weaker (r = −0.39); Pmin was not significantly correlated. CFD model endpoints based on pressure drops in the pharynx were more closely associated with the presence and severity of OSAS than pressures including nasal resistance, or anatomical endpoints. This study supports the usefulness of CFD to characterize anatomical restriction of the pharynx and as an additional tool to evaluate subjects with OSAS. PMID:24265282

Extinction threshold for spatial forest dynamics with height structure.

PubMed

Garcia-Domingo, Josep L; Saldaña, Joan

2011-05-07

We present a pair-approximation model for spatial forest dynamics defined on a regular lattice. The model assumes three possible states for a lattice site: empty (gap site), occupied by an immature tree, and occupied by a mature tree, and considers three nonlinearities in the dynamics associated to the processes of light interference, gap expansion, and recruitment. We obtain an expression of the basic reproduction number R(0) which, in contrast to the one obtained under the mean-field approach, uses information about the spatial arrangement of individuals close to extinction. Moreover, we analyze the corresponding survival-extinction transition of the forest and the spatial correlations among gaps, immature and mature trees close to this critical point. Predictions of the pair-approximation model are compared with those of a cellular automaton. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

NMR studies on the structure and dynamics of lac operator DNA

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

Lee, S.C.

Nuclear Magnetic Resonance spectroscopy was used to elucidate the relationships between structure, dynamics and function of the gene regulatory sequence corresponding to the lactose operon operator of Escherichia coli. The length of the DNA fragments examined varied from 13 to 36 base pair, containing all or part of the operator sequence. These DNA fragments are either derived genetically or synthesized chemically. Resonances of the imino protons were assigned by one dimensional inter-base pair nuclear Overhauser enhancement (NOE) measurements. Imino proton exchange rates were measured by saturation recovery methods. Results from the kinetic measurements show an interesting dynamic heterogeneity with amore » maximum opening rate centered about a GTG/CAC sequence which correlates with the biological function of the operator DNA. This particular three base pair sequence occurs frequently and often symmetrically in prokaryotic nd eukaryotic DNA sites where one anticipates specific protein interaction for gene regulation. The observed sequence dependent imino proton exchange rate may be a reflection of variation of the local structure of regulatory DNA. The results also indicate that the observed imino proton exchange rates are length dependent.« less

The effect of movement and load on the dynamic coupling of abdominal electromyography.

PubMed

King, Adam C

2018-05-14

This study investigated the degree of neural coupling in abdominal muscle activity and whether the task constraints of movement and load altered the coupling within three muscle pairings. Nineteen young, physically-active individuals performed sit-up and reverse crunch movements in bodyweight (BW) and loaded (+4.54 kg) conditions. Surface electromyography (sEMG) was recorded from the rectus abdominus (RA), external oblique (EO), and transverse abdominus (TA) muscles. Linear (correlation coefficient) and non-linear (Cross-Approximate Entropy) measurements evaluated the degree of couplings across three muscle pairings. Compared to a resting coupling state, most conditions showed evidence of coupling. The linear coupling showed greater coupling compared to the resting state. Dynamic coupling showed lower degrees of coupling for the RA-EO and RA-TA pairings but stronger coupling for the EO-TA pairing with the sit-up movement exhibiting lower Cross-ApEn (higher dynamic coupling) than the reverse crunch. The results provide preliminary evidence of coupling in abdominal muscle activity that was influenced by movement, but not load. The functional roles of the RA (prime mover), EO and TA (stabilizers) muscles may have influenced the degree of coupling and future investigations are needed to better understand the coupling of abdominal muscle activity. Copyright © 2018 Elsevier B.V. All rights reserved.

Large-scale parent–child comparison confirms a strong paternal influence on telomere length

PubMed Central

Nordfjäll, Katarina; Svenson, Ulrika; Norrback, Karl-Fredrik; Adolfsson, Rolf; Roos, Göran

2010-01-01

Telomere length is documented to have a hereditary component, and both paternal and X-linked inheritance have been proposed. We investigated blood cell telomere length in 962 individuals with an age range between 0 and 102 years. Telomere length correlations were analyzed between parent–child pairs in different age groups and between grandparent–grandchild pairs. A highly significant correlation between the father's and the child's telomere length was observed (r=0.454, P<0.001), independent of the sex of the offspring (father–son: r=0.465, P<0.001; father–daughter: r=0.484, P<0.001). For mothers, the correlations were weaker (mother–child: r=0.148, P=0.098; mother–son: r=0.080, P=0.561; mother–daughter: r=0.297, P=0.013). A positive telomere length correlation was also observed for grandparent–grandchild pairs (r=0.272, P=0.013). Our findings indicate that fathers contribute significantly stronger to the telomere length of the offspring compared with mothers (P=0.012), but we cannot exclude a maternal influence on the daughter's telomeres. Interestingly, the father–child correlations diminished with increasing age (P=0.022), suggesting that nonheritable factors have an impact on telomere length dynamics during life. PMID:19826452

Role of ion-pair states in the predissociation dynamics of Rydberg states of molecular iodine.

PubMed

von Vangerow, J; Bogomolov, A S; Dozmorov, N V; Schomas, D; Stienkemeier, F; Baklanov, A V; Mudrich, M

2016-07-28

Using femtosecond pump-probe ion imaging spectroscopy, we establish the key role of I(+) + I(-) ion-pair (IP) states in the predissociation dynamics of molecular iodine I2 excited to Rydberg states. Two-photon excitation of Rydberg states lying above the lowest IP state dissociation threshold (1st tier) is found to be followed by direct parallel transitions into IP states of the 1st tier asymptotically correlating to a pair of I ions in their lowest states I(+)((3)P2) + I(-)((1)S0), of the 2nd tier correlating to I(+)((3)P0) + I(-)((1)S0), and of the 3rd tier correlating to I(+)((1)D2) + I(-)((1)S0). Predissociation via the 1st tier proceeds presumably with a delay of 1.6-1.7 ps which is close to the vibrational period in the 3rd tier state (3rd tier-mediated process). The 2nd tier IP state is concluded to be the main precursor for predissociation via lower lying Rydberg states proceeding with a characteristic time of 7-8 ps and giving rise to Rydberg atoms I(5s(2)5p(4)6s(1)). The channel generating I((2)P3/2) + I((2)P1/2) atoms with total kinetic energy corresponding to one-photon excitation is found to proceed via a pump - dump mechanism with dramatic change of angular anisotropy of this channel as compared with earlier nanosecond experiments.

Multicomponent diffusion in molten salt LiF-BeF2: Dynamical correlations and Maxwell-Stefan diffusivities

NASA Astrophysics Data System (ADS)

Chakraborty, Brahmananda; Ramaniah, Lavanya M.

2015-06-01

Applying Green-Kubo formalism and equilibrium molecular dynamics (MD) simulations, we have studied the dynamic correlation, Onsager coeeficients and Maxwell-Stefan (MS) Diffusivities of molten salt LiF-BeF2, which is used as coolant in high temperature reactor. All the diffusive flux correlations show back-scattering or cage dynamics which becomes pronouced at higher temperature. Although the MS diffusivities are expected to depend very lightly on the composition due to decoupling of thermodynamic factor, the diffusivity ĐLi-F and ĐBe-F decreases sharply for higher concentration of LiF and BeF2 respectively. Interestingly, all three MS diffusivities have highest magnitude for eutectic mixture at 1000K (except ĐBe-F at lower LiF mole fraction) which is desirable from coolant point of view. Although the diffusivity for positive-positive ion pair is negative it is not in violation of the second law of thermodynamics as it satisfies the non-negative entropic constraints.

Evidence of three-body correlation functions in Rb+ and Sr2+ acetonitrile solutions

NASA Astrophysics Data System (ADS)

D'Angelo, P.; Pavel, N. V.

1999-09-01

The local structure of Sr2+ and Rb+ ions in acetonitrile has been investigated by x-ray absorption spectroscopy (XAS) and molecular dynamics simulations. The extended x-ray absorption fine structure above the Sr and Rb K edges has been interpreted in the framework of multiple scattering (MS) formalism and, for the first time, clear evidence of MS contributions has been found in noncomplexing ion solutions. Molecular dynamics has been used to generate the partial pair and triangular distribution functions from which model χ(k) signals have been constructed. The Sr2+ and Rb+ acetonitrile pair distribution functions show very sharp and well-defined first peaks indicating the presence of a well organized first solvation shell. Most of the linear acetonitrile molecules have been found to be distributed like hedgehog spines around the Sr2+ and Rb+ ions. The presence of three-body correlations has been singled out by the existence of well-defined peaks in the triangular configurations. Excellent agreement has been found between the theoretical and experimental data enforcing the reliability of the interatomic potentials used in the simulations. These results demonstrate the ability of the XAS technique in probing the higher-order correlation functions in solution.

Revealing time bunching effect in single-molecule enzyme conformational dynamics.

PubMed

Lu, H Peter

2011-04-21

In this perspective, we focus our discussion on how the single-molecule spectroscopy and statistical analysis are able to reveal enzyme hidden properties, taking the study of T4 lysozyme as an example. Protein conformational fluctuations and dynamics play a crucial role in biomolecular functions, such as in enzymatic reactions. Single-molecule spectroscopy is a powerful approach to analyze protein conformational dynamics under physiological conditions, providing dynamic perspectives on a molecular-level understanding of protein structure-function mechanisms. Using single-molecule fluorescence spectroscopy, we have probed T4 lysozyme conformational motions under the hydrolysis reaction of a polysaccharide of E. coli B cell walls by monitoring the fluorescence resonant energy transfer (FRET) between a donor-acceptor probe pair tethered to T4 lysozyme domains involving open-close hinge-bending motions. Based on the single-molecule spectroscopic results, molecular dynamics simulation, a random walk model analysis, and a novel 2D statistical correlation analysis, we have revealed a time bunching effect in protein conformational motion dynamics that is critical to enzymatic functions. Bunching effect implies that conformational motion times tend to bunch in a finite and narrow time window. We show that convoluted multiple Poisson rate processes give rise to the bunching effect in the enzymatic reaction dynamics. Evidently, the bunching effect is likely common in protein conformational dynamics involving in conformation-gated protein functions. In this perspective, we will also discuss a new approach of 2D regional correlation analysis capable of analyzing fluctuation dynamics of complex multiple correlated and anti-correlated fluctuations under a non-correlated noise background. Using this new method, we are able to map out any defined segments along the fluctuation trajectories and determine whether they are correlated, anti-correlated, or non-correlated; after which, a cross correlation analysis can be applied for each specific segment to obtain a detailed fluctuation dynamics analysis.

Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics

PubMed Central

Dasgupta, Bhaskar; Kasahara, Kota; Kamiya, Narutoshi; Nakamura, Haruki; Kinjo, Akira R.

2014-01-01

The elastic network model (ENM) is a widely used method to study native protein dynamics by normal mode analysis (NMA). In ENM we need information about all pairwise distances, and the distance between contacting atoms is restrained to the native value. Therefore ENM requires O(N2) information to realize its dynamics for a protein consisting of N amino acid residues. To see if (or to what extent) such a large amount of specific structural information is required to realize native protein dynamics, here we introduce a novel model based on only O(N) restraints. This model, named the ‘contact number diffusion’ model (CND), includes specific distance restraints for only local (along the amino acid sequence) atom pairs, and semi-specific non-local restraints imposed on each atom, rather than atom pairs. The semi-specific non-local restraints are defined in terms of the non-local contact numbers of atoms. The CND model exhibits the dynamic characteristics comparable to ENM and more correlated with the explicit-solvent molecular dynamics simulation than ENM. Moreover, unrealistic surface fluctuations often observed in ENM were suppressed in CND. On the other hand, in some ligand-bound structures CND showed larger fluctuations of buried protein atoms interacting with the ligand compared to ENM. In addition, fluctuations from CND and ENM show comparable correlations with the experimental B-factor. Although there are some indications of the importance of some specific non-local interactions, the semi-specific non-local interactions are mostly sufficient for reproducing the native protein dynamics. PMID:24625758

Variety of Behavior of Equity Returns in Financial Markets

NASA Astrophysics Data System (ADS)

Bonanno, Giovanni; Lillo, Fabrizio; Mantegna, Rosario N.

2001-03-01

The price dynamics of a set of equities traded in an efficient market is pretty complex. It consists of almost not redundant time series which have (i) long-range correlated volatility and (ii) cross-correlation between each pair of equities. We perform a study of the statistical properties of an ensemble of equities returns which is fruitful to elucidate the nature and role of time and ensemble correlation. Specifically, we investigate a statistical ensemble of daily returns of n equities traded in United States financial markets. For each trading day of our database, we study the ensemble return distribution. We find that a typical ensemble return distribution exists in most of the trading days [1] with the exception of crash and rally days and of the days following to these extreme events [2]. We analyze each ensemble return distribution by extracting its first two central moments. We call the second moment of the ensemble return distribution the variety of the market. We choose this term because high variety implies a variated behavior of the equities returns in the considered day. We observe that the mean return and the variety are fluctuating in time and are stochastic processes themselves. The variety is a long-range correlated stochastic process. Customary time-averaged statistical properties of time series of stock returns are also considered. In general, time-averaged and portfolio-averaged returns have different statistical properties [1]. We infer from these differences information about the relative strength of correlation between equities and between different trading days. We also compare our empirical results with those predicted by the single-index model and we conclude that this simple model is unable to explain the statistical properties of the second moment of the ensemble return distribution. Correlation between pairs of equities are continuously present in the dynamics of a stock portfolio. Hence, it is relevant to investigate pair correlation in a efficient and original way. We propose to investigate these correlations at a daily and intra daily time horizon with a method based on concepts of random frustrated systems. Specifically, a hierarchical organization of the investigated equities is obtained by determining a metric distance between stocks and by investigating the properties of the subdominant ultrametric associated with it [3]. The high-frequency cross-correlation existing between pairs of equities are investigated in a set of 100 stocks traded in US equity markets. The decrease of the cross-correlation between the equity returns observed for diminishing time horizons progressively changes the nature of the hierarchical structure associated to each different time horizon [4]. The nature of the correlation present between pairs of time series of equity returns collected in a portfolio has a strong influence on the variety of the market. We finally discuss the relation between pair correlation and variety of an ensemble return distribution. References [1] Fabrizio Lillo and Rosario N. Mantegna, Variety and volatility in financial markets, Phys. Rev. E 62, 6126-6134 (2000). [2] Fabrizio Lillo and Rosario N. Mantegna, Symmetry alteration of ensemble return distribution in crash and rally days of financial market, Eur. Phys. J. B 15, 603-606 (2000). [3] Rosario N. Mantegna, Hierarchical structure in financial markets, Eur. Phys. J. B 11, 193-197 (1999). [4] Giovanni Bonanno, Fabrizio Lillo, and Rosario N. Mantegna, High-frequency cross-correlation in a set of stocks, Quantitative Finance (in press).

The happy marriage between electron-phonon superconductivity and Mott physics in Cs3C60: A first-principle phase diagram

NASA Astrophysics Data System (ADS)

Capone, Massimo; Nomura, Yusuke; Sakai, Shiro; Giovannetti, Gianluca; Arita, Ryotaro

The phase diagram of doped fullerides like Cs3C60 as a function of the spacing between fullerene molecules is characterized by a first-order transition between a Mott insulator and an s-wave superconductor with a dome-shaped behavior of the critical temperature. By means of an ab-initio modeling of the bandstructure, the electron-phonon interaction and the interaction parameter and a Dynamical Mean-Field Theory solution, we reproduce the phase diagram and demonstrate that phonon superconductivity benefits from strong correlations confirming earlier model predictions. The role of correlations is manifest also in infrared measurements carried out by L. Baldassarre. The superconducting phase shares many similarities with ''exotic'' superconductors with electronic pairing, suggesting that the anomalies in the ''normal'' state, rather than the pairing glue, can be the real common element unifying a wide family of strongly correlated superconductors including cuprates and iron superconductors

The relationship between 2D static features and 2D dynamic features used in gait recognition

NASA Astrophysics Data System (ADS)

Alawar, Hamad M.; Ugail, Hassan; Kamala, Mumtaz; Connah, David

2013-05-01

In most gait recognition techniques, both static and dynamic features are used to define a subject's gait signature. In this study, the existence of a relationship between static and dynamic features was investigated. The correlation coefficient was used to analyse the relationship between the features extracted from the "University of Bradford Multi-Modal Gait Database". This study includes two dimensional dynamic and static features from 19 subjects. The dynamic features were compromised of Phase-Weighted Magnitudes driven by a Fourier Transform of the temporal rotational data of a subject's joints (knee, thigh, shoulder, and elbow). The results concluded that there are eleven pairs of features that are considered significantly correlated with (p<0.05). This result indicates the existence of a statistical relationship between static and dynamics features, which challenges the results of several similar studies. These results bare great potential for further research into the area, and would potentially contribute to the creation of a gait signature using latent data.

Active Space Dependence in Multiconfiguration Pair-Density Functional Theory.

PubMed

Sharma, Prachi; Truhlar, Donald G; Gagliardi, Laura

2018-02-13

In multiconfiguration pair-density functional theory (MC-PDFT), multiconfiguration self-consistent-field calculations and on-top density functionals are combined to describe both static and dynamic correlation. Here, we investigate how the MC-PDFT total energy and its components depend on the active space choice in the case of the H 2 and N 2 molecules. The active space dependence of the on-top pair density, the total density, the ratio of on-top pair density to half the square of the electron density, and the satisfaction of the virial theorem are also explored. We find that the density and on-top pair density do not change significantly with changes in the active space. However, the on-top ratio does change significantly with respect to active space change, and this affects the on-top energy. This study provides a foundation for designing on-top density functionals and automatizing the active space choice in MC-PDFT.

Temporal evolution of oscillations and synchrony in GPi/muscle pairs in Parkinson's disease.

PubMed

Hurtado, José M; Rubchinsky, Leonid L; Sigvardt, Karen A; Wheelock, Vicki L; Pappas, Conrad T E

2005-03-01

Both standard spectral analysis and time-dependent phase correlation techniques were applied to 27 pairs of tremor-related single units in the globus pallidus internus (GPi) and EMG of patients with Parkinson's disease (PD) undergoing stereotactic neurosurgery. Over long time-scales (approximately 60 s), GPi tremor-related units were statistically coherent with restricted regions of the peripheral musculature displaying tremor. The distribution of pooled coherence across all pairs supports a classification of GPi cell/EMG oscillatory pairs into coherent or noncoherent. Analysis using approximately 2-s sliding windows shows that oscillatory activity in both GPi tremor units and muscles occurs intermittently over time. For brain/muscle pairs that are coherent, there is partial overlap in the times of oscillatory activity but, in most cases, no significant correlation between the times of oscillatory subepisodes in the two signals. Phase locking between coherent pairs occurs transiently; however, the phase delay is similar for different phase-locking subepisodes. Noncoherent pairs also show episodes of transient phase locking, but they occurred less frequently, and no preferred phase delay was seen across subepisodes. Tremor oscillations in pallidum and EMGs are punctuated by phase slips, which were classified as synchronizing or desynchronizing depending on their effect on phase locking. In coherent pairs, the incidence of synchronizing slips is higher than desynchronizing slips, whereas no significant difference was seen for noncoherent pairs. The results of this quantitative characterization of parkinsonian tremor provide a foundation for hypotheses about the structure and dynamical functioning of basal ganglia motor control networks involved in tremor generation.

Triplet correlation functions in liquid water

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

Dhabal, Debdas; Chakravarty, Charusita, E-mail: charus@chemistry.iitd.ac.in; Singh, Murari

Triplet correlations have been shown to play a crucial role in the transformation of simple liquids to anomalous tetrahedral fluids [M. Singh, D. Dhabal, A. H. Nguyen, V. Molinero, and C. Chakravarty, Phys. Rev. Lett. 112, 147801 (2014)]. Here we examine triplet correlation functions for water, arguably the most important tetrahedral liquid, under ambient conditions, using configurational ensembles derived from molecular dynamics (MD) simulations and reverse Monte Carlo (RMC) datasets fitted to experimental scattering data. Four different RMC data sets with widely varying hydrogen-bond topologies fitted to neutron and x-ray scattering data are considered [K. T. Wikfeldt, M. Leetmaa, M.more » P. Ljungberg, A. Nilsson, and L. G. M. Pettersson, J. Phys. Chem. B 113, 6246 (2009)]. Molecular dynamics simulations are performed for two rigid-body effective pair potentials (SPC/E and TIP4P/2005) and the monatomic water (mW) model. Triplet correlation functions are compared with other structural measures for tetrahedrality, such as the O–O–O angular distribution function and the local tetrahedral order distributions. In contrast to the pair correlation functions, which are identical for all the RMC ensembles, the O–O–O triplet correlation function can discriminate between ensembles with different degrees of tetrahedral network formation with the maximally symmetric, tetrahedral SYM dataset displaying distinct signatures of tetrahedrality similar to those obtained from atomistic simulations of the SPC/E model. Triplet correlations from the RMC datasets conform closely to the Kirkwood superposition approximation, while those from MD simulations show deviations within the first two neighbour shells. The possibilities for experimental estimation of triplet correlations of water and other tetrahedral liquids are discussed.« less

Local structure in anisotropic systems determined by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Komolkin, Andrei V.; Maliniak, Arnold

In the present communication we describe the investigation of local structure using a new visualization technique. The approach is based on two-dimensional pair correlation functions derived from a molecular dynamics computer simulation. We have used this method to analyse a trajectory produced in a simulation of a nematic liquid crystal of 4-n-pentyl-4'-cyanobiphenyl (5CB) (Komolkin et al., 1994, J. chem. Phys., 101, 4103). The molecule is assumed to have cylindrical symmetry, and the liquid crystalline phase is treated as uniaxial. The pair correlation functions or cylindrical distribution functions (CDFs) are calculated in the molecular (m) and laboratory (l) frames, gm2(z1 2, d1 2) and g12(Z1 2, D1 2). Anisotropic molecular organization in the liquid crystal is reflected in laboratory frame CDFs. The molecular excluded volume is determined and the effect of the fast motion in the alkyl chain is observed. The intramolecular distributions are included in the CDFs and indicate the size of the motional amplitude in the chain. Absence of long range order was confirmed, a feature typical for a nematic liquid crystal.

Side-to-side difference in dynamic unilateral balance ability and pitching performance in Japanese collegiate baseball pitchers.

PubMed

Yanagisawa, Osamu; Futatsubashi, Genki; Taniguchi, Hidenori

2018-01-01

[Purpose] To evaluate the side-to-side difference in dynamic unilateral balance ability and to determine the correlation of the balance ability with pitching performance in collegiate baseball pitchers. [Subjects and Methods] Twenty-five Japanese collegiate baseball pitchers participated in this study. Dynamic balance ability during a unilateral stance was bilaterally evaluated using the star excursion balance test (SEBT). The pitchers threw 20 fastballs at an official pitching distance; the maximal ball velocity and pitching accuracy (the number of strike/20 pitches × 100) were assessed. Side-to-side difference in scores of SEBT was assessed using a paired t-test. Correlations between SEBT scores and pitching performance were evaluated for both legs using a Pearson's correlation analysis. [Results] The pivot side showed significantly higher score of the SEBT in the anteromedial direction than the stride side. On the other hand, the SEBT scores in the pivot and stride legs did not have significant correlations with maximal ball velocity and pitching accuracy. [Conclusion] These findings suggest that marked side-to-side difference does not exist in the dynamic unilateral balance ability of collegiate baseball pitchers and that the dynamic unilateral balance ability of each leg is not directly related to maximal ball velocity and pitching accuracy.

Decorrelation of Neural-Network Activity by Inhibitory Feedback

PubMed Central

Einevoll, Gaute T.; Diesmann, Markus

2012-01-01

Correlations in spike-train ensembles can seriously impair the encoding of information by their spatio-temporal structure. An inevitable source of correlation in finite neural networks is common presynaptic input to pairs of neurons. Recent studies demonstrate that spike correlations in recurrent neural networks are considerably smaller than expected based on the amount of shared presynaptic input. Here, we explain this observation by means of a linear network model and simulations of networks of leaky integrate-and-fire neurons. We show that inhibitory feedback efficiently suppresses pairwise correlations and, hence, population-rate fluctuations, thereby assigning inhibitory neurons the new role of active decorrelation. We quantify this decorrelation by comparing the responses of the intact recurrent network (feedback system) and systems where the statistics of the feedback channel is perturbed (feedforward system). Manipulations of the feedback statistics can lead to a significant increase in the power and coherence of the population response. In particular, neglecting correlations within the ensemble of feedback channels or between the external stimulus and the feedback amplifies population-rate fluctuations by orders of magnitude. The fluctuation suppression in homogeneous inhibitory networks is explained by a negative feedback loop in the one-dimensional dynamics of the compound activity. Similarly, a change of coordinates exposes an effective negative feedback loop in the compound dynamics of stable excitatory-inhibitory networks. The suppression of input correlations in finite networks is explained by the population averaged correlations in the linear network model: In purely inhibitory networks, shared-input correlations are canceled by negative spike-train correlations. In excitatory-inhibitory networks, spike-train correlations are typically positive. Here, the suppression of input correlations is not a result of the mere existence of correlations between excitatory (E) and inhibitory (I) neurons, but a consequence of a particular structure of correlations among the three possible pairings (EE, EI, II). PMID:23133368

Could Relatedness Help Explain Why Individuals Lead in Bottlenose Dolphin Groups?

PubMed Central

Lewis, Jennifer S.; Wartzok, Douglas; Heithaus, Michael; Krützen, Michael

2013-01-01

In many species, particular individuals consistently lead group travel. While benefits to followers often are relatively obvious, including access to resources, benefits to leaders are often less obvious. This is especially true for species that feed on patchy mobile resources where all group members may locate prey simultaneously and food intake likely decreases with increasing group size. Leaders in highly complex habitats, however, could provide access to foraging resources for less informed relatives, thereby gaining indirect benefits by helping kin. Recently, leadership has been documented in a population of bottlenose dolphins (Tursiops truncatus) where direct benefits to leaders appear unlikely. To test whether leaders could benefit indirectly we examined relatedness between leader-follower pairs and compared these levels to pairs who associated but did not have leader-follower relationship (neither ever led the other). We found the average relatedness value for leader-follower pairs was greater than expected based on chance. The same was not found when examining non leader-follower pairs. Additionally, relatedness for leader-follower pairs was positively correlated with association index values, but no correlation was found for this measure in non leader-follower pairs. Interestingly, haplotypes were not frequently shared between leader-follower pairs (25%). Together, these results suggest that bottlenose dolphin leaders have the opportunity to gain indirect benefits by leading relatives. These findings provide a potential mechanism for the maintenance of leadership in a highly dynamic fission-fusion population with few obvious direct benefits to leaders. PMID:23516445

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

PubMed

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

2009-02-04

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

A homogeneous sample of binary galaxies: Basic observational properties

NASA Technical Reports Server (NTRS)

Karachentsev, I. D.

1990-01-01

A survey of optical characteristics for 585 binary systems, satisfying a condition of apparent isolation on the sky, is presented. Influences of various selection effects distorting the average parameters of the sample are noted. The pair components display mutual similarity over all the global properties: luminosity, diameter, morphological type, mass-to-luminosity ratio, angular momentum etc., which is not due only to selection effects. The observed correlations must be caused by common origin of pair members. Some features (nuclear activity, color index) could acquire similarity during synchronous evolution of double galaxies. Despite the observed isolation, the sample of double systems is seriously contaminated by accidental pairs, and also by members of groups and clusters. After removing false pairs estimates of orbital mass-to-luminosity ratio range from 0 to 30 f(solar), with the mean value (7.8 plus or minus 0.7) f(solar). Binary galaxies possess nearly circular orbits with a typical eccentrity e = 0.25, probably resulting from evolutionary selection driven by component mergers under dynamical friction. The double-galaxy population with space abundance 0.12 plus or minus 0.02 and characteristic merger timescale 0.2 H(exp -1) may significantly influence the rate of dynamical evolution of galaxies.

Multicomponent diffusion in molten salt LiF-BeF{sub 2}: Dynamical correlations and Maxwell–Stefan diffusivities

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

Chakraborty, Brahmananda, E-mail: brahma@barc.gov.in; Ramaniah, Lavanya M.

2015-06-24

Applying Green–Kubo formalism and equilibrium molecular dynamics (MD) simulations, we have studied the dynamic correlation, Onsager coeeficients and Maxwell–Stefan (MS) Diffusivities of molten salt LiF-BeF{sub 2}, which is used as coolant in high temperature reactor. All the diffusive flux correlations show back-scattering or cage dynamics which becomes pronouced at higher temperature. Although the MS diffusivities are expected to depend very lightly on the composition due to decoupling of thermodynamic factor, the diffusivity Đ{sub Li-F} and Đ{sub Be-F} decreases sharply for higher concentration of LiF and BeF{sub 2} respectively. Interestingly, all three MS diffusivities have highest magnitude for eutectic mixture atmore » 1000K (except Đ{sub Be-F} at lower LiF mole fraction) which is desirable from coolant point of view. Although the diffusivity for positive-positive ion pair is negative it is not in violation of the second law of thermodynamics as it satisfies the non-negative entropic constraints.« less

Vortex dynamics in two-dimensional Josephson junction arrays

NASA Astrophysics Data System (ADS)

Ashrafuzzaman, Md.; Capezzali, Massimiliano; Beck, Hans

2003-08-01

The dynamic response of two-dimensional Josephson junction arrays close to, but above the Berezinskii-Kosterlitz-Thouless (BKT) transition temperature is described in terms of the vortex dielectric function ɛ(ω) and the flux noise spectrum Sφ(ω). They are calculated by considering both the contributions of free vortices interacting through a screened Coulomb potential and the pair motion of vortices that are closer to each other than the BKT correlation length. This procedure allows us to understand various anomalous features in ɛ(ω) and in Sφ(ω) that have been observed both experimentally and in dynamic simulations.

Atomic Dynamics in Simple Liquid: de Gennes Narrowing Revisited

NASA Astrophysics Data System (ADS)

Wu, Bin; Iwashita, Takuya; Egami, Takeshi

2018-03-01

The de Gennes narrowing phenomenon is frequently observed by neutron or x -ray scattering measurements of the dynamics of complex systems, such as liquids, proteins, colloids, and polymers. The characteristic slowing down of dynamics in the vicinity of the maximum of the total scattering intensity is commonly attributed to enhanced cooperativity. In this Letter, we present an alternative view on its origin through the examination of the time-dependent pair correlation function, the van Hove correlation function, for a model liquid in two, three, and four dimensions. We find that the relaxation time increases monotonically with distance and the dependence on distance varies with dimension. We propose a heuristic explanation of this dependence based on a simple geometrical model. This finding sheds new light on the interpretation of the de Gennes narrowing phenomenon and the α -relaxation time.

Towards ab initio Calculations with the Dynamical Vertex Approximation

NASA Astrophysics Data System (ADS)

Galler, Anna; Kaufmann, Josef; Gunacker, Patrik; Pickem, Matthias; Thunström, Patrik; Tomczak, Jan M.; Held, Karsten

2018-04-01

While key effects of the many-body problem — such as Kondo and Mott physics — can be understood in terms of on-site correlations, non-local fluctuations of charge, spin, and pairing amplitudes are at the heart of the most fascinating and unresolved phenomena in condensed matter physics. Here, we review recent progress in diagrammatic extensions to dynamical mean-field theory for ab initio materials calculations. We first recapitulate the quantum field theoretical background behind the two-particle vertex. Next we discuss latest algorithmic advances in quantum Monte Carlo simulations for calculating such two-particle quantities using worm sampling and vertex asymptotics, before giving an introduction to the ab initio dynamical vertex approximation (AbinitioDΓA). Finally, we highlight the potential of AbinitioDΓA by detailing results for the prototypical correlated metal SrVO3.

Dynamics of Large-Scale Fluctuations in Native Proteins.

NASA Astrophysics Data System (ADS)

Erman, Burak; Erkip, Albert

2003-03-01

The fluctuations of residues of proteins about their equilibrium configurations are analyzed by Langevin dynamics. Residue pairs that are within a given cutoff distance of each other are assumed to be connected by linear springs. The action of the solvent and intramolecular interactions on each residue are treated as random noise. The correlations of fluctuations resulting from the solution of the Langevin equation are observed to be identical to those obtained by the Gaussian Network Model based on equilibrium statistical mechanics. The time delayed correlations of fluctuations, and the response of the protein to a given frequency and to a window of frequencies are determined. The fluctuations of the residues resulting from a given fixed externally applied frequency are evaluated for different modes of the system. Synchronous and asynchronous components of correlations for different modes are formulated. The results of the present study are applied to study the fluctuation dynamics of the 241 residue protein S. marcescens endonuclease (1QL0).

The Maximum Cross-Correlation approach to detecting translational motions from sequential remote-sensing images

NASA Astrophysics Data System (ADS)

Gao, J.; Lythe, M. B.

1996-06-01

This paper presents the principle of the Maximum Cross-Correlation (MCC) approach in detecting translational motions within dynamic fields from time-sequential remotely sensed images. A C program implementing the approach is presented and illustrated in a flowchart. The program is tested with a pair of sea-surface temperature images derived from Advanced Very High Resolution Radiometer (AVHRR) images near East Cape, New Zealand. Results show that the mean currents in the region have been detected satisfactorily with the approach.

Dependence of two-proton radioactivity on nuclear pairing models

NASA Astrophysics Data System (ADS)

Oishi, Tomohiro; Kortelainen, Markus; Pastore, Alessandro

2017-10-01

Sensitivity of two-proton emitting decay to nuclear pairing correlation is discussed within a time-dependent three-body model. We focus on the 6Be nucleus assuming α +p +p configuration, and its decay process is described as a time evolution of the three-body resonance state. For a proton-proton subsystem, a schematic density-dependent contact (SDDC) pairing model is employed. From the time-dependent calculation, we observed the exponential decay rule of a two-proton emission. It is shown that the density dependence does not play a major role in determining the decay width, which can be controlled only by the asymptotic strength of the pairing interaction. This asymptotic pairing sensitivity can be understood in terms of the dynamics of the wave function driven by the three-body Hamiltonian, by monitoring the time-dependent density distribution. With this simple SDDC pairing model, there remains an impossible trinity problem: it cannot simultaneously reproduce the empirical Q value, decay width, and the nucleon-nucleon scattering length. This problem suggests that a further sophistication of the theoretical pairing model is necessary, utilizing the two-proton radioactivity data as the reference quantities.

Probing the triplet correlation function in liquid water by experiments and molecular simulations.

PubMed

Dhabal, Debdas; Wikfeldt, Kjartan Thor; Skinner, Lawrie B; Chakravarty, Charusita; Kashyap, Hemant K

2017-01-25

Despite very significant developments in scattering experiments like X-ray and neutron diffraction, it has been challenging to elucidate the nature of tetrahedral molecular configurations in liquid water. A key question is whether the pair correlation functions, which can be obtained from scattering experiments, are sufficient to describe the tetrahedral ordering of water molecules. In our previous study (Dhabal et al., J. Chem. Phys., 2014, 141, 174504), using data-sets generated from reverse Monte Carlo and molecular dynamics simulations, we showed that the triplet correlation functions contain important information on the tetrahedrality of water in the liquid state. In the present study, X-ray scattering experiments and molecular dynamics (MD) simulations are used to link the isothermal pressure derivative of the structure factor with the triplet correlation functions for water. Triplet functions are determined for water up to 3.3 kbar at 298 K to display the effect of pressure on the water structure. The results suggest that triplet functions (H[combining tilde](q)) obtained using a rigid-body TIP4P/2005 water model are consistent with the experimental results. The triplet functions obtained in experiment as well as in simulations evince that in the case of tetrahedral liquids, exertion of higher pressure leads to a better agreement with the Kirkwood superposition approximation (KSA). We further validate this observation using the triplet correlation functions (g (3) (r,s,t)) calculated directly from simulation trajectory, revealing that both H[combining tilde](q) in q-space and g (3) (r,s,t) in real-space contain similar information on the tetrahedrality of liquids. This study demonstrates that the structure factor, even though it has only pair correlation information of the liquid structure, can shed light on three-body correlations in liquid water through its isothermal pressure derivative term.

Ion-ion dynamic structure factor, acoustic modes, and equation of state of two-temperature warm dense aluminum

NASA Astrophysics Data System (ADS)

Harbour, L.; Förster, G. D.; Dharma-wardana, M. W. C.; Lewis, Laurent J.

2018-04-01

The ion-ion dynamical structure factor and the equation of state of warm dense aluminum in a two-temperature quasiequilibrium state, with the electron temperature higher than the ion temperature, are investigated using molecular-dynamics simulations based on ion-ion pair potentials constructed from a neutral pseudoatom model. Such pair potentials based on density functional theory are parameter-free and depend directly on the electron temperature and indirectly on the ion temperature, enabling efficient computation of two-temperature properties. Comparison with ab initio simulations and with other average-atom calculations for equilibrium aluminum shows good agreement, justifying a study of quasiequilibrium situations. Analyzing the van Hove function, we find that ion-ion correlations vanish in a time significantly smaller than the electron-ion relaxation time so that dynamical properties have a physical meaning for the quasiequilibrium state. A significant increase in the speed of sound is predicted from the modification of the dispersion relation of the ion acoustic mode as the electron temperature is increased. The two-temperature equation of state including the free energy, internal energy, and pressure is also presented.

Dynamics of spontaneous flipping of a mismatched base in DNA duplex.

PubMed

Yin, Yandong; Yang, Lijiang; Zheng, Guanqun; Gu, Chan; Yi, Chengqi; He, Chuan; Gao, Yi Qin; Zhao, Xin Sheng

2014-06-03

DNA base flipping is a fundamental theme in DNA biophysics. The dynamics for a B-DNA base to spontaneously flip out of the double helix has significant implications in various DNA-protein interactions but are still poorly understood. The spontaneous base-flipping rate obtained previously via the imino proton exchange assay is most likely the rate of base wobbling instead of flipping. Using the diffusion-decelerated fluorescence correlation spectroscopy together with molecular dynamics simulations, we show that a base of a single mismatched base pair (T-G, T-T, or T-C) in a double-stranded DNA can spontaneously flip out of the DNA duplex. The extrahelical lifetimes are on the order of 10 ms, whereas the intrahelical lifetimes range from 0.3 to 20 s depending on the stability of the base pairs. These findings provide detailed understanding on the dynamics of DNA base flipping and lay down foundation to fully understand how exactly the repair proteins search and locate the target mismatched base among a vast excess of matched DNA bases.

Control of lasing from a highly photoexcited semiconductor microcavity

NASA Astrophysics Data System (ADS)

Hsu, Feng-Kuo

Technological advances in the fabrication of optical cavities and crystal growth have enabled the studies on macroscopic quantum states and emergent nonequilibrium phenomena of light-matter hybrids in condensed matter. Optical excitations in a semiconductor microcavity can result in a coupled electron-hole-photon (e-h-gamma) system, in which various many-body physics can be studied by varying particle densities and particle-particle interactions. Recently there have been reports of phenomena analogous to Bose-Einstein condensates or superfluids for exciton-polaritons in a microcavity. An exciton-polariton is a quasiparticle resulting from strong coupling between the cavity light field and the exciton (e-h pair) transition, and typically is only stable at a low density ( 10 11 to 1012 cm-2 or less). At a higher density, it has been theoretically predicted that pairing of electrons and holes can result in a BCS-like state at cryogenic temperatures, which can produce cooperative radiation known as superradiance. In this work, we explore cooperative phenomena caused by e-h correlation and many-body effect in a highly photoexcited microcavity at room temperature. High-density e-h plasmas in a photoexcited microcavity are studied under the following conditions: (1) the sample is photoexcited GaAs-based microcavity with large detuning between the band gap Eg of quantum well and cavity resonance to prevent carriers from radiative loss, (2) the density of e-h pairs is high enough to build long-range correlation with the assistance of cavity light field. The Fermi level of electron-hole pairs is about 80 meV above Eg, and (3) the e-h correlation is stabilized through thermal management, which includes modulating the excitation pulse laser temporally and spatially to reduce the heating and carrier diffusion effect. We have observed ultrafast (sub-10 picoseconds) spin-polarized lasing with sizable energy shifts and linewidth broadenings as pump flux is increased. With optically induced confinement, multiple-lasing modes were produced, with sequential lasing time depending on energies. These phenomena are attributed to the spin-dependent stimulated emission from correlated e-h pairs. We further performed a non-degenerate pump-probe spectroscopy to investigate dynamic carrier relaxation. We find transient resonances with significant changes in differential reflectivity that can last more than 1 ns. The resonance exhibits a polarization-dependent splitting in about 1 meV under circularly polarized pumping. All the aforementioned phenomena can be explained by the combination effect of carrier-induced refractive index change and the light-induced e-h correlation. Our research enriches the studies of coupled e-h-gamma systems at room temperature and a high-density regime; however, further experiments and theoretical works are required to claim and clarify the formation of such correlated e-h pairs in a highly photoexcited microcavity. Nonetheless, we have demonstrated that many-body effects can be harnessed to control lasing dynamics and energies in highly photoexcited semiconductor microcavities. We expect an improved understanding of the many-body effect resulted from e-h pairing to help the development of polarization-controlled and wavelength-tunable lasers.

Solute–solute correlations responsible for the prepeak in structure factors of undercooled Al-rich liquids: A molecular dynamics study

DOE PAGES

Zhang, Feng; Sun, Yang; Ye, Zhuo; ...

2015-05-06

In this study, we have performed molecular dynamics simulations on a typical Al-based alloy Al 90Sm 10. The short-range and medium-range correlations of the system are reliably produced by ab initio calculations, whereas the long-range correlations are obtained with the assistance of a semi-empirical potential well-fitted to ab initio data. Our calculations show that a prepeak in the structure factor of this system emerges well above the melting temperature, and the intensity of the prepeak increases with increasing undercooling of the liquid. These results are in agreement with x-ray diffraction experiments. The interplay between the short-range order of the systemmore » originating from the large affinity between Al and Sm atoms, and the intrinsic repulsion between Sm atoms gives rise to a stronger correlation in the second peak than the first peak in the Sm–Sm partial pair correlation function (PPCF), which in turn produces the prepeak in the structure factor.« less

Overcoming correlation fluctuations in two-photon interference experiments with differently bright and independently blinking remote quantum emitters

NASA Astrophysics Data System (ADS)

Weber, Jonas H.; Kettler, Jan; Vural, Hüseyin; Müller, Markus; Maisch, Julian; Jetter, Michael; Portalupi, Simone L.; Michler, Peter

2018-05-01

As a fundamental building block for quantum computation and communication protocols, the correct verification of the two-photon interference (TPI) contrast between two independent quantum light sources is of utmost importance. Here, we experimentally demonstrate how frequently present blinking dynamics and changes in emitter brightness critically affect the Hong-Ou-Mandel-type (HOM) correlation histograms of remote TPI experiments measured via the commonly utilized setup configuration. We further exploit this qualitative and quantitative explanation of the observed correlation dynamics to establish an alternative interferometer configuration, which is overcoming the discussed temporal fluctuations, giving rise to an error-free determination of the remote TPI visibility. We prove full knowledge of the obtained correlation by reproducing the measured correlation statistics via Monte Carlo simulations. As an exemplary system, we make use of two pairs of remote semiconductor quantum dots; however, the same conclusions apply for TPI experiments with flying qubits from any kind of remote solid-state quantum emitters.

State Anxiety and Nonlinear Dynamics of Heart Rate Variability in Students.

PubMed

Dimitriev, Dimitriy A; Saperova, Elena V; Dimitriev, Aleksey D

2016-01-01

Clinical and experimental research studies have demonstrated that the emotional experience of anxiety impairs heart rate variability (HRV) in humans. The present study investigated whether changes in state anxiety (SA) can also modulate nonlinear dynamics of heart rate. A group of 96 students volunteered to participate in the study. For each student, two 5-minute recordings of beat intervals (RR) were performed: one during a rest period and one just before a university examination, which was assumed to be a real-life stressor. Nonlinear analysis of HRV was performed. The Spielberger's State-Trait Anxiety Inventory was used to assess the level of SA. Before adjusting for heart rate, a Wilcoxon matched pairs test showed significant decreases in Poincaré plot measures, entropy, largest Lyapunov exponent (LLE), and pointwise correlation dimension (PD2), and an increase in the short-term fractal-like scaling exponent of detrended fluctuation analysis (α1) during the exam session, compared with the rest period. A Pearson analysis indicated significant negative correlations between the dynamics of SA and Poincaré plot axes ratio (SD1/SD2), and between changes in SA and changes in entropy measures. A strong negative correlation was found between the dynamics of SA and LLE. A significant positive correlation was found between the dynamics of SA and α1. The decreases in Poincaré plot measures (SD1, complex correlation measure), entropy measures, and LLE were still significant after adjusting for heart rate. Corrected α1 was increased during the exam session. As before, the dynamics of adjusted LLE was significantly correlated with the dynamics of SA. The qualitative increase in SA during academic examination was related to the decrease in the complexity and size of the Poincaré plot through a reduction of both the interbeat interval and its variation.

Role of temperature on static correlational properties in a spin-polarized electron gas

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

Arora, Priya; Moudgil, R. K., E-mail: rkmoudgil@kuk.ac.in; Kumar, Krishan

We have studied the effect of temperature on the static correlational properties of a spin-polarized three-dimensional electron gas (3DEG) over a wide coupling and temperature regime. This problem has been very recently studied by Brown et al. using the restricted path-integral Monte Carlo (RPIMC) technique in the warm-dense regime. To this endeavor, we have used the finite temperature version of the dynamical mean-field theory of Singwi et al, the so-called quantum STLS (qSTLS) approach. The static density structure factor and the static pair-correlation function are calculated, and compared with the RPIMC simulation data. We find an excellent agreement with themore » simulation at high temperature over a wide coupling range. However, the agreement is seen to somewhat deteriorate with decreasing temperature. The pair-correlation function is found to become small negative for small electron separation. This may be attributed to the inadequacy of the mean-field theory in dealing with the like spin electron correlations in the strong-coupling domain. A nice agreement with RPIMC data at high temperature seems to arise due to weakening of both the exchange and coulomb correlations with rising temperature.« less

Analysis of spatial correlations in a model two-dimensional liquid through eigenvalues and eigenvectors of atomic-level stress matrices.

PubMed

Levashov, V A; Stepanov, M G

2016-01-01

Considerations of local atomic-level stresses associated with each atom represent a particular approach to address structures of disordered materials at the atomic level. We studied structural correlations in a two-dimensional model liquid using molecular dynamics simulations in the following way. We diagonalized the atomic-level stress tensor of every atom and investigated correlations between the eigenvalues and orientations of the eigenvectors of different atoms as a function of distance between them. It is demonstrated that the suggested approach can be used to characterize structural correlations in disordered materials. In particular, we found that changes in the stress correlation functions on decrease of temperature are the most pronounced for the pairs of atoms with separation distance that corresponds to the first minimum in the pair density function. We also show that the angular dependencies of the stress correlation functions previously reported by Wu et al. [Phys. Rev. E 91, 032301 (2015)10.1103/PhysRevE.91.032301] do not represent the anisotropic Eshelby's stress fields, as it is suggested, but originate in the rotational properties of the stress tensors.

Benchmark of Dynamic Electron Correlation Models for Seniority-Zero Wave Functions and Their Application to Thermochemistry.

PubMed

Boguslawski, Katharina; Tecmer, Paweł

2017-12-12

Wave functions restricted to electron-pair states are promising models to describe static/nondynamic electron correlation effects encountered, for instance, in bond-dissociation processes and transition-metal and actinide chemistry. To reach spectroscopic accuracy, however, the missing dynamic electron correlation effects that cannot be described by electron-pair states need to be included a posteriori. In this Article, we extend the previously presented perturbation theory models with an Antisymmetric Product of 1-reference orbital Geminal (AP1roG) reference function that allows us to describe both static/nondynamic and dynamic electron correlation effects. Specifically, our perturbation theory models combine a diagonal and off-diagonal zero-order Hamiltonian, a single-reference and multireference dual state, and different excitation operators used to construct the projection manifold. We benchmark all proposed models as well as an a posteriori Linearized Coupled Cluster correction on top of AP1roG against CR-CC(2,3) reference data for reaction energies of several closed-shell molecules that are extrapolated to the basis set limit. Moreover, we test the performance of our new methods for multiple bond breaking processes in the homonuclear N 2 , C 2 , and F 2 dimers as well as the heteronuclear BN, CO, and CN + dimers against MRCI-SD, MRCI-SD+Q, and CR-CC(2,3) reference data. Our numerical results indicate that the best performance is obtained from a Linearized Coupled Cluster correction as well as second-order perturbation theory corrections employing a diagonal and off-diagonal zero-order Hamiltonian and a single-determinant dual state. These dynamic corrections on top of AP1roG provide substantial improvements for binding energies and spectroscopic properties obtained with the AP1roG approach, while allowing us to approach chemical accuracy for reaction energies involving closed-shell species.

Tracking quasi-stationary flow of weak fluorescent signals by adaptive multi-frame correlation.

PubMed

Ji, L; Danuser, G

2005-12-01

We have developed a novel cross-correlation technique to probe quasi-stationary flow of fluorescent signals in live cells at a spatial resolution that is close to single particle tracking. By correlating image blocks between pairs of consecutive frames and integrating their correlation scores over multiple frame pairs, uncertainty in identifying a globally significant maximum in the correlation score function has been greatly reduced as compared with conventional correlation-based tracking using the signal of only two consecutive frames. This approach proves robust and very effective in analysing images with a weak, noise-perturbed signal contrast where texture characteristics cannot be matched between only a pair of frames. It can also be applied to images that lack prominent features that could be utilized for particle tracking or feature-based template matching. Furthermore, owing to the integration of correlation scores over multiple frames, the method can handle signals with substantial frame-to-frame intensity variation where conventional correlation-based tracking fails. We tested the performance of the method by tracking polymer flow in actin and microtubule cytoskeleton structures labelled at various fluorophore densities providing imagery with a broad range of signal modulation and noise. In applications to fluorescent speckle microscopy (FSM), where the fluorophore density is sufficiently low to reveal patterns of discrete fluorescent marks referred to as speckles, we combined the multi-frame correlation approach proposed above with particle tracking. This hybrid approach allowed us to follow single speckles robustly in areas of high speckle density and fast flow, where previously published FSM analysis methods were unsuccessful. Thus, we can now probe cytoskeleton polymer dynamics in living cells at an entirely new level of complexity and with unprecedented detail.

Spatial patterns of close relationships across the lifespan

NASA Astrophysics Data System (ADS)

Jo, Hang-Hyun; Saramäki, Jari; Dunbar, Robin I. M.; Kaski, Kimmo

2014-11-01

The dynamics of close relationships is important for understanding the migration patterns of individual life-courses. The bottom-up approach to this subject by social scientists has been limited by sample size, while the more recent top-down approach using large-scale datasets suffers from a lack of detail about the human individuals. We incorporate the geographic and demographic information of millions of mobile phone users with their communication patterns to study the dynamics of close relationships and its effect in their life-course migration. We demonstrate how the close age- and sex-biased dyadic relationships are correlated with the geographic proximity of the pair of individuals, e.g., young couples tend to live further from each other than old couples. In addition, we find that emotionally closer pairs are living geographically closer to each other. These findings imply that the life-course framework is crucial for understanding the complex dynamics of close relationships and their effect on the migration patterns of human individuals.

Experiment design for pilot identification in compensatory tracking tasks

NASA Technical Reports Server (NTRS)

Wells, W. R.

1976-01-01

A design criterion for input functions in laboratory tracking tasks resulting in efficient parameter estimation is formulated. The criterion is that the statistical correlations between pairs of parameters be reduced in order to minimize the problem of nonuniqueness in the extraction process. The effectiveness of the method is demonstrated for a lower order dynamic system.

Implications of the effective one-component analysis of pair correlations in colloidal fluids with polydispersity

NASA Astrophysics Data System (ADS)

Pond, Mark J.; Errington, Jeffrey R.; Truskett, Thomas M.

2011-09-01

Partial pair-correlation functions of colloidal suspensions with continuous polydispersity can be challenging to characterize from optical microscopy or computer simulation data due to inadequate sampling. As a result, it is common to adopt an effective one-component description of the structure that ignores the differences between particle types. Unfortunately, whether this kind of simplified description preserves or averages out information important for understanding the behavior of the fluid depends on the degree of polydispersity and can be difficult to assess, especially when the corresponding multicomponent description of the pair correlations is unavailable for comparison. Here, we present a computer simulation study that examines the implications of adopting an effective one-component structural description of a polydisperse fluid. The square-well model that we investigate mimics key aspects of the experimental behavior of suspended colloids with short-range, polymer-mediated attractions. To characterize the partial pair-correlation functions and thermodynamic excess entropy of this system, we introduce a Monte Carlo sampling strategy appropriate for fluids with a large number of pseudo-components. The data from our simulations at high particle concentrations, as well as exact theoretical results for dilute systems, show how qualitatively different trends between structural order and particle attractions emerge from the multicomponent and effective one-component treatments, even with systems characterized by moderate polydispersity. We examine consequences of these differences for excess-entropy based scalings of shear viscosity, and we discuss how use of the multicomponent treatment reveals similarities between the corresponding dynamic scaling behaviors of attractive colloids and liquid water that the effective one-component analysis does not capture.

Correlation and Stacking of Relative Paleointensity and Oxygen Isotope Data

NASA Astrophysics Data System (ADS)

Lurcock, P. C.; Channell, J. E.; Lee, D.

2012-12-01

The transformation of a depth-series into a time-series is routinely implemented in the geological sciences. This transformation often involves correlation of a depth-series to an astronomically calibrated time-series. Eyeball tie-points with linear interpolation are still regularly used, although these have the disadvantages of being non-repeatable and not based on firm correlation criteria. Two automated correlation methods are compared: the simulated annealing algorithm (Huybers and Wunsch, 2004) and the Match protocol (Lisiecki and Lisiecki, 2002). Simulated annealing seeks to minimize energy (cross-correlation) as "temperature" is slowly decreased. The Match protocol divides records into intervals, applies penalty functions that constrain accumulation rates, and minimizes the sum of the squares of the differences between two series while maintaining the data sequence in each series. Paired relative paleointensity (RPI) and oxygen isotope records, such as those from IODP Site U1308 and/or reference stacks such as LR04 and PISO, are warped using known warping functions, and then the un-warped and warped time-series are correlated to evaluate the efficiency of the correlation methods. Correlations are performed in tandem to simultaneously optimize RPI and oxygen isotope data. Noise spectra are introduced at differing levels to determine correlation efficiency as noise levels change. A third potential method, known as dynamic time warping, involves minimizing the sum of distances between correlated point pairs across the whole series. A "cost matrix" between the two series is analyzed to find a least-cost path through the matrix. This least-cost path is used to nonlinearly map the time/depth of one record onto the depth/time of another. Dynamic time warping can be expanded to more than two dimensions and used to stack multiple time-series. This procedure can improve on arithmetic stacks, which often lose coherent high-frequency content during the stacking process.

Lightwave-driven quasiparticle collisions on a subcycle timescale

NASA Astrophysics Data System (ADS)

Langer, F.; Hohenleutner, M.; Schmid, C. P.; Poellmann, C.; Nagler, P.; Korn, T.; Schüller, C.; Sherwin, M. S.; Huttner, U.; Steiner, J. T.; Koch, S. W.; Kira, M.; Huber, R.

2016-05-01

Ever since Ernest Rutherford scattered α-particles from gold foils, collision experiments have revealed insights into atoms, nuclei and elementary particles. In solids, many-body correlations lead to characteristic resonances—called quasiparticles—such as excitons, dropletons, polarons and Cooper pairs. The structure and dynamics of quasiparticles are important because they define macroscopic phenomena such as Mott insulating states, spontaneous spin- and charge-order, and high-temperature superconductivity. However, the extremely short lifetimes of these entities make practical implementations of a suitable collider challenging. Here we exploit lightwave-driven charge transport, the foundation of attosecond science, to explore ultrafast quasiparticle collisions directly in the time domain: a femtosecond optical pulse creates excitonic electron-hole pairs in the layered dichalcogenide tungsten diselenide while a strong terahertz field accelerates and collides the electrons with the holes. The underlying dynamics of the wave packets, including collision, pair annihilation, quantum interference and dephasing, are detected as light emission in high-order spectral sidebands of the optical excitation. A full quantum theory explains our observations microscopically. This approach enables collision experiments with various complex quasiparticles and suggests a promising new way of generating sub-femtosecond pulses.

Lightwave-driven quasiparticle collisions on a subcycle timescale.

PubMed

Langer, F; Hohenleutner, M; Schmid, C P; Poellmann, C; Nagler, P; Korn, T; Schüller, C; Sherwin, M S; Huttner, U; Steiner, J T; Koch, S W; Kira, M; Huber, R

2016-05-12

Ever since Ernest Rutherford scattered α-particles from gold foils, collision experiments have revealed insights into atoms, nuclei and elementary particles. In solids, many-body correlations lead to characteristic resonances--called quasiparticles--such as excitons, dropletons, polarons and Cooper pairs. The structure and dynamics of quasiparticles are important because they define macroscopic phenomena such as Mott insulating states, spontaneous spin- and charge-order, and high-temperature superconductivity. However, the extremely short lifetimes of these entities make practical implementations of a suitable collider challenging. Here we exploit lightwave-driven charge transport, the foundation of attosecond science, to explore ultrafast quasiparticle collisions directly in the time domain: a femtosecond optical pulse creates excitonic electron-hole pairs in the layered dichalcogenide tungsten diselenide while a strong terahertz field accelerates and collides the electrons with the holes. The underlying dynamics of the wave packets, including collision, pair annihilation, quantum interference and dephasing, are detected as light emission in high-order spectral sidebands of the optical excitation. A full quantum theory explains our observations microscopically. This approach enables collision experiments with various complex quasiparticles and suggests a promising new way of generating sub-femtosecond pulses.

Caudal Regulates the Spatiotemporal Dynamics of Pair-Rule Waves in Tribolium

PubMed Central

El-Sherif, Ezzat; Zhu, Xin; Fu, Jinping; Brown, Susan J.

2014-01-01

In the short-germ beetle Tribolium castaneum, waves of pair-rule gene expression propagate from the posterior end of the embryo towards the anterior and eventually freeze into stable stripes, partitioning the anterior-posterior axis into segments. Similar waves in vertebrates are assumed to arise due to the modulation of a molecular clock by a posterior-to-anterior frequency gradient. However, neither a molecular candidate nor a functional role has been identified to date for such a frequency gradient, either in vertebrates or elsewhere. Here we provide evidence that the posterior gradient of Tc-caudal expression regulates the oscillation frequency of pair-rule gene expression in Tribolium. We show this by analyzing the spatiotemporal dynamics of Tc-even-skipped expression in strong and mild knockdown of Tc-caudal, and by correlating the extension, level and slope of the Tc-caudal expression gradient to the spatiotemporal dynamics of Tc-even-skipped expression in wild type as well as in different RNAi knockdowns of Tc-caudal regulators. Further, we show that besides its absolute importance for stripe generation in the static phase of the Tribolium blastoderm, a frequency gradient might serve as a buffer against noise during axis elongation phase in Tribolium as well as vertebrates. Our results highlight the role of frequency gradients in pattern formation. PMID:25329152

Atomic Dynamics in Simple Liquid: de Gennes Narrowing Revisited

DOE PAGES

Wu, Bin; Iwashita, Takuya; Egami, Takeshi

2018-03-27

The de Gennes narrowing phenomenon is frequently observed by neutron or x-ray scattering measurements of the dynamics of complex systems, such as liquids, proteins, colloids, and polymers. The characteristic slowing down of dynamics in the vicinity of the maximum of the total scattering intensity is commonly attributed to enhanced cooperativity. In this Letter, we present an alternative view on its origin through the examination of the time-dependent pair correlation function, the van Hove correlation function, for a model liquid in two, three, and four dimensions. We find that the relaxation time increases monotonically with distance and the dependence on distancemore » varies with dimension. We propose a heuristic explanation of this dependence based on a simple geometrical model. Furthermore, this finding sheds new light on the interpretation of the de Gennes narrowing phenomenon and the α-relaxation time.« less

Atomic Dynamics in Simple Liquid: de Gennes Narrowing Revisited

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

Wu, Bin; Iwashita, Takuya; Egami, Takeshi

The de Gennes narrowing phenomenon is frequently observed by neutron or x-ray scattering measurements of the dynamics of complex systems, such as liquids, proteins, colloids, and polymers. The characteristic slowing down of dynamics in the vicinity of the maximum of the total scattering intensity is commonly attributed to enhanced cooperativity. In this Letter, we present an alternative view on its origin through the examination of the time-dependent pair correlation function, the van Hove correlation function, for a model liquid in two, three, and four dimensions. We find that the relaxation time increases monotonically with distance and the dependence on distancemore » varies with dimension. We propose a heuristic explanation of this dependence based on a simple geometrical model. Furthermore, this finding sheds new light on the interpretation of the de Gennes narrowing phenomenon and the α-relaxation time.« less

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.

Microscopic Theory for the Role of Attractive Forces in the Dynamics of Supercooled Liquids.

PubMed

Dell, Zachary E; Schweizer, Kenneth S

2015-11-13

We formulate a microscopic, no adjustable parameter, theory of activated relaxation in supercooled liquids directly in terms of the repulsive and attractive forces within the framework of pair correlations. Under isochoric conditions, attractive forces can nonperturbatively modify slow dynamics, but at high enough density their influence vanishes. Under isobaric conditions, attractive forces play a minor role. High temperature apparent Arrhenius behavior and density-temperature scaling are predicted. Our results are consistent with recent isochoric simulations and isobaric experiments on a deeply supercooled molecular liquid. The approach can be generalized to treat colloidal gelation and glass melting, and other soft matter slow dynamics problems.

Constructing networks from a dynamical system perspective for multivariate nonlinear time series.

PubMed

Nakamura, Tomomichi; Tanizawa, Toshihiro; Small, Michael

2016-03-01

We describe a method for constructing networks for multivariate nonlinear time series. We approach the interaction between the various scalar time series from a deterministic dynamical system perspective and provide a generic and algorithmic test for whether the interaction between two measured time series is statistically significant. The method can be applied even when the data exhibit no obvious qualitative similarity: a situation in which the naive method utilizing the cross correlation function directly cannot correctly identify connectivity. To establish the connectivity between nodes we apply the previously proposed small-shuffle surrogate (SSS) method, which can investigate whether there are correlation structures in short-term variabilities (irregular fluctuations) between two data sets from the viewpoint of deterministic dynamical systems. The procedure to construct networks based on this idea is composed of three steps: (i) each time series is considered as a basic node of a network, (ii) the SSS method is applied to verify the connectivity between each pair of time series taken from the whole multivariate time series, and (iii) the pair of nodes is connected with an undirected edge when the null hypothesis cannot be rejected. The network constructed by the proposed method indicates the intrinsic (essential) connectivity of the elements included in the system or the underlying (assumed) system. The method is demonstrated for numerical data sets generated by known systems and applied to several experimental time series.

Molecular dynamics simulations of dense plasmas

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

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

1993-12-31

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

Diffusivity anomaly in modified Stillinger-Weber liquids

NASA Astrophysics Data System (ADS)

Sengupta, Shiladitya; Vasisht, Vishwas V.; Sastry, Srikanth

2014-01-01

By modifying the tetrahedrality (the strength of the three body interactions) in the well-known Stillinger-Weber model for silicon, we study the diffusivity of a series of model liquids as a function of tetrahedrality and temperature at fixed pressure. Previous work has shown that at constant temperature, the diffusivity exhibits a maximum as a function of tetrahedrality, which we refer to as the diffusivity anomaly, in analogy with the well-known anomaly in water upon variation of pressure at constant temperature. We explore to what extent the structural and thermodynamic changes accompanying changes in the interaction potential can help rationalize the diffusivity anomaly, by employing the Rosenfeld relation between diffusivity and the excess entropy (over the ideal gas reference value), and the pair correlation entropy, which provides an approximation to the excess entropy in terms of the pair correlation function. We find that in the modified Stillinger-Weber liquids, the Rosenfeld relation works well above the melting temperatures but exhibits deviations below, with the deviations becoming smaller for smaller tetrahedrality. Further we find that both the excess entropy and the pair correlation entropy at constant temperature go through maxima as a function of the tetrahedrality, thus demonstrating the close relationship between structural, thermodynamic, and dynamical anomalies in the modified Stillinger-Weber liquids.

Generalized rules for the optimization of elastic network models

NASA Astrophysics Data System (ADS)

Lezon, Timothy; Eyal, Eran; Bahar, Ivet

2009-03-01

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

Population Dynamics of Bulking and Foaming Bacteria in a Full-scale Wastewater Treatment Plant over Five Years.

PubMed

Jiang, Xiao-Tao; Guo, Feng; Zhang, Tong

2016-04-11

Bulking and foaming are two notorious problems in activated sludge wastewater treatment plants (WWTPs), which are mainly associated with the excessive growth of bulking and foaming bacteria (BFB). However, studies on affecting factors of BFB in full-scale WWTPs are still limited. In this study, data sets of high-throughput sequencing (HTS) of 16S V3-V4 amplicons of 58 monthly activated sludge samples from a municipal WWTP was re-analyzed to investigate the BFB dynamics and further to study the determinative factors. The population of BFB occupied 0.6~36% (averagely 8.5% ± 7.3%) of the total bacteria and showed seasonal variations with higher abundance in winter-spring than summer-autumn. Pair-wise correlation analysis and canonical correlation analysis (CCA) showed that Gordonia sp. was positively correlated with NO2-N and negatively correlated with NO3-N, and Nostocodia limicola II Tetraspharea sp. was negatively correlated with temperature and positively correlated with NH3-N in activated sludge. Bacteria species correlated with BFB could be clustered into two negatively related modules. Moreover, with intensive time series sampling, the dominant BFB could be accurately modeled with environmental interaction network, i.e. environmental parameters and biotic interactions between BFB and related bacteria, indicating that abiotic and biotic factors were both crucial to the dynamics of BFB.

Time-dependent vibrational spectral analysis of first principles trajectory of methylamine with wavelet transform.

PubMed

Biswas, Sohag; Mallik, Bhabani S

2017-04-12

The fluctuation dynamics of amine stretching frequencies, hydrogen bonds, dangling N-D bonds, and the orientation profile of the amine group of methylamine (MA) were investigated under ambient conditions by means of dispersion-corrected density functional theory-based first principles molecular dynamics (FPMD) simulations. Along with the dynamical properties, various equilibrium properties such as radial distribution function, spatial distribution function, combined radial and angular distribution functions and hydrogen bonding were also calculated. The instantaneous stretching frequencies of amine groups were obtained by wavelet transform of the trajectory obtained from FPMD simulations. The frequency-structure correlation reveals that the amine stretching frequency is weakly correlated with the nearest nitrogen-deuterium distance. The frequency-frequency correlation function has a short time scale of around 110 fs and a longer time scale of about 1.15 ps. It was found that the short time scale originates from the underdamped motion of intact hydrogen bonds of MA pairs. However, the long time scale of the vibrational spectral diffusion of N-D modes is determined by the overall dynamics of hydrogen bonds as well as the dangling ND groups and the inertial rotation of the amine group of the molecule.

Communication: a density functional with accurate fractional-charge and fractional-spin behaviour for s-electrons.

PubMed

Johnson, Erin R; Contreras-García, Julia

2011-08-28

We develop a new density-functional approach combining physical insight from chemical structure with treatment of multi-reference character by real-space modeling of the exchange-correlation hole. We are able to recover, for the first time, correct fractional-charge and fractional-spin behaviour for atoms of groups 1 and 2. Based on Becke's non-dynamical correlation functional [A. D. Becke, J. Chem. Phys. 119, 2972 (2003)] and explicitly accounting for core-valence separation and pairing effects, this method is able to accurately describe dissociation and strong correlation in s-shell many-electron systems. © 2011 American Institute of Physics

Condensed Matter Theories - Volume 22

NASA Astrophysics Data System (ADS)

Reinholz, Heidi; Röpke, Gerd; de Llano, Manuel

2007-09-01

pt. A. Fermi liquids. Pressure comparison between the spherical cellular model and the Thomas-Fermi model / G.A. Baker, Jr. Pair excitations and vertex corrections in Fermi fluids and the dynamic structure function of two-dimension 3He / H.M. Böhm, H. Godfrin, E. Krotscheck, H.J. Lauter, M. Meschke and M. Panholzer. Condensation of helium in wedges / E.S. Hernádez ... [et al.]. Non-Fermi liquid behavior from the Fermi-liquid approach / V.A. Khodel ... [et al.]. Theory of third sound and stability of thin 3He-4He superfluid films / E. Krotscheck and M.D. Miller. Pairing in asymmetrical Fermi systems / K.F. Quader and R. Liao. Ground-state properties of small 3He drops from quantum Monte Carlo simulations / E. Sola, J. Casulleras and J. Boronat. Ground-state energy and compressibility of a disordered two-dimensional electron gas / Tanatar ... [et al.]. Quasiexcitons in photoluminescence of incompressible quantum liquids / A. Wójs, A.G ladysiewicz and J.J. Quinn -- pt. B. Bose liquids. Quantum Boltzmann liquids / K.A. Gernoth, M L. Ristig and T. Lindenau. Condensate fraction in the dynamic structure function of Bose fluids / M. Saarela, F. Mazzanti and V. Apaja -- pt. C. Strongly-correlated electronic systems. Electron gas in high-field nanoscopic transport: metallic carbon nanotubes / F. Green and D. Neilson. Evolution and destruction of the Kondo effect in a capacitively coupled double dot system / D.E. Logan and M.R. Galpin. The method of increments-a wavefunction-based Ab-Initio correlation method for solids / B. Paulus. Fractionally charged excitations on frustrated lattices / E. Runge, F. Pollmann and P. Fulde. 5f Electrons in actinides: dual nature and photoemission spectra / G. Zwicknagl -- pt. D. Magnetism. Magnetism in disordered two-dimensional Kondo-Necklace / W. Brenig. On the de Haas-can Alphen oscillation in 2D / S. Fujita and D.L. Morabito. Dynamics in one-dimensional spin systems-density matrix reformalization group study / S. Nishimoto and M. Arikawa. Frustrated quantum antiferromagnets: application of high-order coupled cluster method / J. Richter ... [et al.]. Vorticity and antivorticity in submicron ferromagnetic films / H. Wang, M. Yan and C.E. Campbell -- pt. E. Conductivity. D-wave checkerboard bose condensate of mobile bipolarons / A.S. Alexandrov. Five possible reasons why high-Tc superconductivity is stalled / M. Grether and M. de Llano. Multistability and Multi 2[Pie symbol]-Kinks in the Frenkel-Kontorova model: an application to arrays of Josephson junctions / K.E. Kürten and C. Krattenthaler. Lowering of Boson-Fermion system energy with a gapped cooper resonant-pair dispersion relation / T.A. Mamedov and M. de Llano. The concept of correlated density and its application / K. Morawetz ... [et al.]. Competing local and non-local phase correlations in Fermionic systems with resonant pairing: the Boson-Fermion scenario / J. Ranninger. Superconducting order parameters in the extended Hubbard model: a simple mean-field study / J.S. Thakur and M.P. Das -- pt. F. Nuclear systems. Distribution of maxima of the antisymmetized wave function for the nucleons of a closed-shell and for the nucleons of all closed-shells in a nucleus / G.S. Anagnostatos. Pairing of strongly correlated nucleons / W.H. Dickhoff. Short range correlations in relativistic nuclear models / P.K. Panda, C. Providência and J. da Providência. Quartetting in attractive Fermi-systems and alpha particle condensation in nuclear systems / P. Schuck ... [et al.]. Alpha-alpha and Alpha-nucleus potentials: an energy-density fucntional approach / Z.F. Shehadeh ... [et al.]. -- pt. G. Density functional theory and MD simulations. Dynamics of metal clusters in rare gas clusters / M. Baer ... [et al.]. Reinhard and E. Suraud. Kohn-Sham calculations combined with an average pair-density functional theory / P. Gori-Giorgi and A. Savin. Correlations, collision frequency and optical properties in laser excited clusters / H. Reinholz, T. Raitza and G. Röpke -- pt. H. Biophysics. Condensed matter physics of biomolecule systems in a differential geometric framework / H. Bohr, J.I. Ipsen and S. Markvorsen. The brain's view of the natural world in motion: computing structure from function using directional Fourier transformations / B.K. Dellen, J.W. Clark and R. Wessel -- pt. I. Quantum information. Control and error prevention in condensed matter quantum computing devices / M.S. Byrd and L.A. Wu. Maxent approaches to qubits / C.M. Sarris, A.N. Proto and F B. Malik -- pt. J. New formalisms. Thermal coherent states, a broader class of mixed coherent states, and generalized thermo-field dynamics / R.F. Bishop and A. Vourdas. Ergodic condition and magnetic models / M. Howard Lee. From thermodynamics to Maxent / A. Plastino and E. M.F. Curado. Recent progress in the density-matrix renormalization group / U. Schollwöck.

Combinations of coupled cluster, density functionals, and the random phase approximation for describing static and dynamic correlation, and van der Waals interactions

NASA Astrophysics Data System (ADS)

Garza, Alejandro J.; Bulik, Ireneusz W.; Alencar, Ana G. Sousa; Sun, Jianwei; Perdew, John P.; Scuseria, Gustavo E.

2016-04-01

Contrary to standard coupled cluster doubles (CCD) and Brueckner doubles (BD), singlet-paired analogues of CCD and BD (denoted here as CCD0 and BD0) do not break down when static correlation is present, but neglect substantial amounts of dynamic correlation. In fact, CCD0 and BD0 do not account for any contributions from multielectron excitations involving only same-spin electrons at all. We exploit this feature to add - without introducing double counting, self-interaction, or increase in cost - the missing correlation to these methods via meta-GGA (generalised gradient approximation) density functionals (Tao-Perdew-Staroverov-Scuseria and strongly constrained and appropriately normed). Furthermore, we improve upon these CCD0+DFT blends by invoking range separation: the short- and long-range correlations absent in CCD0/BD0 are evaluated with density functional theory and the direct random phase approximation, respectively. This corrects the description of long-range van der Waals forces. Comprehensive benchmarking shows that the combinations presented here are very accurate for weakly correlated systems, while also providing a reasonable description of strongly correlated problems without resorting to symmetry breaking.

Amplitude envelope correlations measure synchronous cortical oscillations in performing musicians.

PubMed

Zamm, Anna; Debener, Stefan; Bauer, Anna-Katharina R; Bleichner, Martin G; Demos, Alexander P; Palmer, Caroline

2018-05-14

A major question facing cognitive neuroscience is measurement of interbrain synchrony between individuals performing joint actions. We describe the application of a novel method for measuring musicians' interbrain synchrony: amplitude envelope correlations (AECs). Amplitude envelopes (AEs) reflect energy fluctuations in cortical oscillations over time; AE correlations measure the degree to which two envelope fluctuations are temporally correlated, such as cortical oscillations arising from two individuals performing a joint action. Wireless electroencephalography was recorded from two pianists performing a musical duet; an analysis pipeline is described for computing AEs of cortical oscillations at the duet performance frequency (number of tones produced per second) to test whether these oscillations reflect the temporal dynamics of partners' performances. The pianists' AE correlations were compared with correlations based on a distribution of AEs simulated from white noise signals using the same methods. The AE method was also applied to the temporal characteristics of the pianists' performances, to show that the observed pair's AEs reflect the temporal dynamics of their performance. AE correlations offer a promising approach for assessing interbrain correspondences in cortical activity associated with performing joint tasks. © 2018 New York Academy of Sciences.

Quenched dynamics and spin-charge separation in an interacting topological lattice

NASA Astrophysics Data System (ADS)

Barbiero, L.; Santos, L.; Goldman, N.

2018-05-01

We analyze the static and dynamical properties of a one-dimensional topological lattice, the fermionic Su-Schrieffer-Heeger model, in the presence of on-site interactions. Based on a study of charge and spin correlation functions, we elucidate the nature of the topological edge modes, which, depending on the sign of the interactions, either display particles of opposite spin on opposite edges, or a pair and a holon. This study of correlation functions also highlights the strong entanglement that exists between the opposite edges of the system. This last feature has remarkable consequences upon subjecting the system to a quench, where an instantaneous edge-to-edge signal appears in the correlation functions characterizing the edge modes. Besides, other correlation functions are shown to propagate in the bulk according to the light cone imposed by the Lieb-Robinson bound. Our study reveals how one-dimensional lattices exhibiting entangled topological edge modes allow for a nontrivial correlation spreading, while providing an accessible platform to detect spin-charge separation using state-of-the-art experimental techniques.

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

PubMed

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

2008-04-26

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

Correlated phonons and the Tc-dependent dynamical phonon anomalies

NASA Astrophysics Data System (ADS)

Hakioğlu, T.; Türeci, H.

1997-11-01

Anomalously large low-temperature phonon anharmonicities can lead to static as well as dynamical changes in the low-temperature properties of the electron-phonon system. In this work, we focus our attention on the dynamically generated low-temperature correlations in an interacting electron-phonon system using a self-consistent dynamical approach in the intermediate coupling range. In the context of the model, the polaron correlations are produced by the charge-density fluctuations which are generated dynamically by the electron-phonon coupling. Conversely, the latter is influenced in the presence of the former. The purpose of this work is to examine the dynamics of this dual mechanism between the two using the illustrative Fröhlich model. In particular, the influence of the low-temperature phonon dynamics on the superconducting properties in the intermediate coupling range is investigated. The influence on the Holstein reduction factor as well as the enhancement in the zero-point fluctuations and in the electron-phonon coupling are calculated numerically. We also examine these effects in the presence of superconductivity. Within this model, the contribution of the electron-phonon interaction as one of the important elements in the mechanisms of superconductivity can reach values as high as 15-20% of the characteristic scale of the lattice vibrational energy. The second motivation of this work is to understand the nature of the Tc-dependent temperature anomalies observed in the Debye-Waller factor, dynamical pair correlations, and average atomic vibrational energies for a number of high-temperature superconductors. In our approach we do not claim nor believe that the electron-phonon interaction is the primary mechanism leading to high-temperature superconductivity. Nevertheless, our calculations suggest that the dynamically induced low-temperature phonon correlation model can account for these anomalies and illustrates their possible common origin. Finally, the relevance of incorporating these low-temperature effects into more realistic models of high-temperature superconductivity including both the charge and spin degrees and other similar ideas existing in the literature are discussed.

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

PubMed

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

2014-10-15

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

Determination of single-kidney glomerular filtration rate (GFR) with CT urography versus renal dynamic imaging Gates method.

PubMed

You, Shan; Ma, XianWu; Zhang, ChangZhu; Li, Qiang; Shi, WenWei; Zhang, Jing; Yuan, XiaoDong

2018-03-01

To present a single-kidney CT-GFR measurement and compare it with the renal dynamic imaging Gates-GFR. Thirty-six patients with hydronephrosis referred for CT urography and 99mTc-DTPA renal dynamic imaging were prospectively included. Informed consent was obtained from all patients. The CT urography protocol included non-contrast, nephrographic, and excretory phase imaging. The total CT-GFR was calculated by dividing the CT number increments of the total urinary system between the nephrographic and excretory phase by the products of iodine concentration in the aorta and the elapsed time, then multiplied by (1- Haematocrit). The total CT-GFR was then split into single-kidney CT-GFR by a left and right kidney proportionality factor. The results were compared with single-kidney Gates-GFR by using paired t-test, correlation analysis, and Bland-Altman plots. Paired difference between single-kidney CT-GFR (45.02 ± 13.91) and single-kidney Gates-GFR (51.21 ± 14.76) was 6.19 ± 5.63 ml/min, p<0.001, demonstrating 12.1% systematic underestimation with ±11.03 ml/min (±21.5%) measurement deviation. A good correlation was revealed between both measurements (r=0.87, p<0.001). The proposed single-kidney CT-GFR correlates and agrees well with the reference standard despite a systematic underestimation, therefore it could be a one-stop-shop for evaluating urinary tract morphology and split renal function. • A new CT method can assess split renal function • Only using images from CT urography and the value of haematocrit • A one-stop-shop CT technique without additional radiation dose.

State Anxiety and Nonlinear Dynamics of Heart Rate Variability in Students

PubMed Central

Dimitriev, Aleksey D.

2016-01-01

Objectives Clinical and experimental research studies have demonstrated that the emotional experience of anxiety impairs heart rate variability (HRV) in humans. The present study investigated whether changes in state anxiety (SA) can also modulate nonlinear dynamics of heart rate. Methods A group of 96 students volunteered to participate in the study. For each student, two 5-minute recordings of beat intervals (RR) were performed: one during a rest period and one just before a university examination, which was assumed to be a real-life stressor. Nonlinear analysis of HRV was performed. The Spielberger’s State-Trait Anxiety Inventory was used to assess the level of SA. Results Before adjusting for heart rate, a Wilcoxon matched pairs test showed significant decreases in Poincaré plot measures, entropy, largest Lyapunov exponent (LLE), and pointwise correlation dimension (PD2), and an increase in the short-term fractal-like scaling exponent of detrended fluctuation analysis (α1) during the exam session, compared with the rest period. A Pearson analysis indicated significant negative correlations between the dynamics of SA and Poincaré plot axes ratio (SD1/SD2), and between changes in SA and changes in entropy measures. A strong negative correlation was found between the dynamics of SA and LLE. A significant positive correlation was found between the dynamics of SA and α1. The decreases in Poincaré plot measures (SD1, complex correlation measure), entropy measures, and LLE were still significant after adjusting for heart rate. Corrected α1 was increased during the exam session. As before, the dynamics of adjusted LLE was significantly correlated with the dynamics of SA. Conclusions The qualitative increase in SA during academic examination was related to the decrease in the complexity and size of the Poincaré plot through a reduction of both the interbeat interval and its variation. PMID:26807793

Modeling cross-correlations and efficiency of Islamic and conventional banks from Saudi Arabia: Evidence from MF-DFA and MF-DXA approaches

NASA Astrophysics Data System (ADS)

Mensi, Walid; Hamdi, Atef; Shahzad, Syed Jawad Hussain; Shafiullah, Muhammad; Al-Yahyaee, Khamis Hamed

2018-07-01

This paper analyzes the dynamic efficiency and interdependence of Islamic and conventional banks of Saudi Arabia. This analysis applies the Multifractal Detrended Fluctuation Analysis (MF-DFA) and Multifractal Detrended Cross-Correlation Analysis (MF-DXA) approaches. The MF-DFA results show strong multifractality in the daily returns of Saudi banks. Moreover, all eight banks studied exhibit persistence correlation, which demonstrates inefficiency. The rolling window results show significant change in the inefficiency levels over the time. The cross-correlation analysis between bank-pairs exhibits long term interdependence between most of them. These findings indicate that the banking sector in Saudi Arabia suffers from inefficiency and exhibits long term memory.

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

Anion-Functionalized Task-Specific Ionic Liquids: Molecular Origin of Change in Viscosity upon CO2 Capture.

PubMed

Li, Ailin; Tian, Ziqi; Yan, Tianying; Jiang, De-en; Dai, Sheng

2014-12-26

The structure and dynamics of a task-specific ionic liquid (TSIL), trihexyl(tetradecyl)phosphonium imidazolate, before and after absorbing CO(2) were studied with a molecular dynamics (MD) simulation. This particular ionic liquid is one of several newly discovered azole-based TSILs for equimolar CO(2) capture. Unlike other TSILs whose viscosity increases drastically upon reaction with CO(2), its viscosity decreases after CO(2) absorption. This unique behavior was confirmed in our MD simulation. We find that after CO(2) absorption the translational dynamics of the whole system is accelerated, accompanied by an accelerated rotational dynamics of the cations. Radial distribution function and spatial distribution function analyses show that the anions become asymmetric after reaction with CO(2), and this causes the imbalance of the interaction between the positive and negative regions of the ions. The interaction between the phosphorus atom of the cation and oxygen atoms of the carboxyl group on the anion is enhanced, while that between the phosphorus atom and the naked nitrogen atom of the anion is weakened. The ion-pair correlation functions further support that the weakened interaction leads to faster dissociation of cation-anion pairs, thereby causing an accelerated dynamics. Hence, the asymmetry of anions influences the dynamics of the system and affects the viscosity. This insight may help design better TSILs with decreased viscosity for CO(2) capture.

Correlation range in a supercooled liquid via Green-Kubo expression for viscosity, local atomic stresses, and MD simulations

NASA Astrophysics Data System (ADS)

Levashov, Valentin A.; Egami, Takeshi; Morris, James R.

2009-03-01

We present a new approach to the issue of correlation range in supercooled liquids based on Green-Kubo expression for viscosity. The integrand of this expression is the average stress-stress autocorrelation function. This correlation function could be rewritten in terms of correlations among local atomic stresses at different times and distances. The features of the autocorrelation function decay with time depend on temperature and correlation range. Through this approach we can study the development of spatial correlation with time, thus directly addressing the question of dynamic heterogeneity. We performed MD simulations on a single component system of particles interacting through short range pair potential. Our results indicate that even above the crossover temperature correlations extend well beyond the nearest neighbors. Surprisingly we found that the system size effects exist even on relatively large systems. We also address the role of diffusion in decay of stress-stress correlation function.

Correlation Measurement of Lambda-anti-Lambda, Lambda-Lambda and anti-Lambda-anti-Lambda with the ATLAS detector at s=7 TeV

NASA Astrophysics Data System (ADS)

Cheng, Hok-Chuen

This thesis summaries the measurements of correlations between Lambda 0Lambda0, Lambda0Lambda 0, and Lambda0Lambda 0 hyperon pairs produced inclusively at the LHC, which are useful for a better understanding of the quark-antiquark pair production and jet fragmentation and hadronization processes. The analysis is based on hyperon pairs selected using the muon and minimum bias data samples collected at the ATLAS experiment from proton-proton collisions at a center-of-mass energy of 7 TeV in 2010. Excess Lambda0Lambda 0 are observed near the production threshold and are identified to be originated from the parton system in the string model in the MC sample, decaying either directly or through heavy strange resonances such as Sigma0 and Sigma*(1385). Dynamical correlations have been explored through a correlation function defined as the ratio of two-particle to single-particle densities. Positive correlation is observed for Lambda0Lambda0 and anticorrelation is observed for Lambda0Lambda 0 and Lambda0Lambda 0 for Q in [0,2] GeV. The structure replicates similar correlations in pp, pp, and pppp events in PYTHIA generator as predicted by the Lund string fragmentation model. Parameters of the "popcorn" mechanism implemented in the PYTHIA generator are tuned and are found to have little impact on the structure observed. The spin composition of the sample is extracted using a data-driven reference sample built by event mixing. Appropriate corrections have been made to the kinematic distributions in the reference sample by kinematic weighting to make sure that the detector effects are well modeled. A modified Pearson's chi2 test statistics is calculated for the costheta* distribution to determine the best-fitted A-value for data. The results are consistent with zero for both like-type and unlike-type hyperon pairs in Q ∈ [0,10] GeV and Q ∈ [1,10] GeV respectively. The data statistics in the range of Q ∈ [0, 1] GeV is currently too low for the estimation of the emitter size for Fermi-Dirac correlation.

Structural connectome topology relates to regional BOLD signal dynamics in the mouse brain

NASA Astrophysics Data System (ADS)

Sethi, Sarab S.; Zerbi, Valerio; Wenderoth, Nicole; Fornito, Alex; Fulcher, Ben D.

2017-04-01

Brain dynamics are thought to unfold on a network determined by the pattern of axonal connections linking pairs of neuronal elements; the so-called connectome. Prior work has indicated that structural brain connectivity constrains pairwise correlations of brain dynamics ("functional connectivity"), but it is not known whether inter-regional axonal connectivity is related to the intrinsic dynamics of individual brain areas. Here we investigate this relationship using a weighted, directed mesoscale mouse connectome from the Allen Mouse Brain Connectivity Atlas and resting state functional MRI (rs-fMRI) time-series data measured in 184 brain regions in eighteen anesthetized mice. For each brain region, we measured degree, betweenness, and clustering coefficient from weighted and unweighted, and directed and undirected versions of the connectome. We then characterized the univariate rs-fMRI dynamics in each brain region by computing 6930 time-series properties using the time-series analysis toolbox, hctsa. After correcting for regional volume variations, strong and robust correlations between structural connectivity properties and rs-fMRI dynamics were found only when edge weights were accounted for, and were associated with variations in the autocorrelation properties of the rs-fMRI signal. The strongest relationships were found for weighted in-degree, which was positively correlated to the autocorrelation of fMRI time series at time lag τ = 34 s (partial Spearman correlation ρ = 0.58 ), as well as a range of related measures such as relative high frequency power (f > 0.4 Hz: ρ = - 0.43 ). Our results indicate that the topology of inter-regional axonal connections of the mouse brain is closely related to intrinsic, spontaneous dynamics such that regions with a greater aggregate strength of incoming projections display longer timescales of activity fluctuations.

The role of virulence for in vivo superinfection fitness of a vertebrate RNA virus

USGS Publications Warehouse

Kell, Alison M.; Wargo, Andrew R.; Kurath, Gael

2013-01-01

We have developed a novel, in vivo superinfection fitness assay to examine superinfection dynamics and the role of virulence in superinfection fitness. This assay involves controlled, sequential infections of a natural, vertebrate host, Oncorhynchus mykiss (rainbow trout), with variants of a co-evolved viral pathogen, infectious hematopoietic necrosis virus (IHNV). Intervals between infections ranged from 12 hours to 7 days, and both frequency of superinfection and viral replication levels were examined. Using virus genotype pairs of equal and unequal virulence, we observed that superinfection generally occurred with decreasing frequency as the interval between exposures to each genotype increased. For both the equal virulence and unequal virulence genotype pairs, the frequency of superinfection was the same regardless of which genotype was used in the primary exposure. However, the ability to replicate in the context of superinfection did not differ between the genotypes of equal or unequal virulence tested here. For both genotype pairs, the mean viral load of the secondary virus was significantly reduced in superinfection, while primary virus replication was unaffected. Our results demonstrate, for the two genotype pairs examined, that superinfection restriction does occur for IHNV, and that higher virulence did not correlate with a significant difference in superinfection fitness. To our knowledge, this is the first assay to examine the role of virulence of an RNA virus in determining superinfection fitness dynamics within a natural, vertebrate host.

Evidence of quantum correlations in the H/D-transfer dynamics in the hydrogen bonds in partially deuterated benzoic acid crystals

NASA Astrophysics Data System (ADS)

Takeda, Sadamu; Tsuzumitani, Akihiko; Chatzidimitriou-Dreismann, C. A.

1992-10-01

A precise investigation of spin—lattice relaxation rates for protons and deuterons of partially deuterated benzoic acid crystals showed a remarkable quenching of the transfer rate of an HD pair in hydrogen-bonded dimeric units of carboxyl groups with increasing concentration of D in the surrounding hydrogen bonds. A similar effect was also observed for partially deuterated crystals of acetylenedicarboxylic acid. This finding supports recent theoretical predictions of thermally activated protonic quantum correlation in condensed matter and proposes a new mechanism for the proton transfer in hydrogen bonds in condensed matter.

Thermodynamic precursors, liquid-liquid transitions, dynamic and topological anomalies in densified liquid germania

NASA Astrophysics Data System (ADS)

Pacaud, F.; Micoulaut, M.

2015-08-01

The thermodynamic, dynamic, structural, and rigidity properties of densified liquid germania (GeO2) have been investigated using classical molecular dynamics simulation. We construct from a thermodynamic framework an analytical equation of state for the liquid allowing the possible detection of thermodynamic precursors (extrema of the derivatives of the free energy), which usually indicate the possibility of a liquid-liquid transition. It is found that for the present germania system, such precursors and the possible underlying liquid-liquid transition are hidden by the slowing down of the dynamics with decreasing temperature. In this respect, germania behaves quite differently when compared to parent tetrahedral systems such as silica or water. We then detect a diffusivity anomaly (a maximum of diffusion with changing density/volume) that is strongly correlated with changes in coordinated species, and the softening of bond-bending (BB) topological constraints that decrease the liquid rigidity and enhance transport. The diffusivity anomaly is finally substantiated from a Rosenfeld-type scaling law linked to the pair correlation entropy, and to structural relaxation.

Multiconfiguration Pair-Density Functional Theory and Complete Active Space Second Order Perturbation Theory. Bond Dissociation Energies of FeC, NiC, FeS, NiS, FeSe, and NiSe.

PubMed

Sharkas, Kamal; Gagliardi, Laura; Truhlar, Donald G

2017-12-07

We investigate the performance of multiconfiguration pair-density functional theory (MC-PDFT) and complete active space second-order perturbation theory for computing the bond dissociation energies of the diatomic molecules FeC, NiC, FeS, NiS, FeSe, and NiSe, for which accurate experimental data have become recently available [Matthew, D. J.; Tieu, E.; Morse, M. D. J. Chem. Phys. 2017, 146, 144310-144320]. We use three correlated participating orbital (CPO) schemes (nominal, moderate, and extended) to define the active spaces, and we consider both the complete active space (CAS) and the separated-pair (SP) schemes to specify the configurations included for a given active space. We found that the moderate SP-PDFT scheme with the tPBE on-top density functional has the smallest mean unsigned error (MUE) of the methods considered. This level of theory provides a balanced treatment of the static and dynamic correlation energies for the studied systems. This is encouraging because the method is low in cost even for much more complicated systems.

Spectral analysis of pair-correlation bandwidth: application to cell biology images.

PubMed

Binder, Benjamin J; Simpson, Matthew J

2015-02-01

Images from cell biology experiments often indicate the presence of cell clustering, which can provide insight into the mechanisms driving the collective cell behaviour. Pair-correlation functions provide quantitative information about the presence, or absence, of clustering in a spatial distribution of cells. This is because the pair-correlation function describes the ratio of the abundance of pairs of cells, separated by a particular distance, relative to a randomly distributed reference population. Pair-correlation functions are often presented as a kernel density estimate where the frequency of pairs of objects are grouped using a particular bandwidth (or bin width), Δ>0. The choice of bandwidth has a dramatic impact: choosing Δ too large produces a pair-correlation function that contains insufficient information, whereas choosing Δ too small produces a pair-correlation signal dominated by fluctuations. Presently, there is little guidance available regarding how to make an objective choice of Δ. We present a new technique to choose Δ by analysing the power spectrum of the discrete Fourier transform of the pair-correlation function. Using synthetic simulation data, we confirm that our approach allows us to objectively choose Δ such that the appropriately binned pair-correlation function captures known features in uniform and clustered synthetic images. We also apply our technique to images from two different cell biology assays. The first assay corresponds to an approximately uniform distribution of cells, while the second assay involves a time series of images of a cell population which forms aggregates over time. The appropriately binned pair-correlation function allows us to make quantitative inferences about the average aggregate size, as well as quantifying how the average aggregate size changes with time.

The modularity and dynamicity of miRNA-mRNA interactions in high-grade serous ovarian carcinomas and the prognostic implication.

PubMed

Zhang, Wensheng; Edwards, Andrea; Fan, Wei; Flemington, Erik K; Zhang, Kun

2016-08-01

Ovarian carcinoma is the fifth-leading cause of cancer death among women in the United States. Major reasons for this persistent mortality include the poor understanding of the underlying biology and a lack of reliable biomarkers. Previous studies have shown that aberrantly expressed MicroRNAs (miRNAs) are involved in carcinogenesis and tumor progression by post-transcriptionally regulating gene expression. However, the interference of miRNAs in tumorigenesis is quite complicated and far from being fully understood. In this work, by an integrative analysis of mRNA expression, miRNA expression and clinical data published by The Cancer Genome Atlas (TCGA), we studied the modularity and dynamicity of miRNA-mRNA interactions and the prognostic implications in high-grade serous ovarian carcinomas. With the top transcriptional correlations (Bonferroni-adjusted p-value<0.01) as inputs, we identified five miRNA-mRNA module pairs (MPs), each of which included one positive-connection (correlation) module and one negative-connection (correlation) module. The number of miRNAs or mRNAs in each module varied from 3 to 7 or from 2 to 873. Among the four major negative-connection modules, three fit well with the widely accepted miRNA-mediated post-transcriptional regulation theory. These modules were enriched with the genes relevant to cell cycle and immune response. Moreover, we proposed two novel algorithms to reveal the group or sample specific dynamic regulations between these two RNA classes. The obtained miRNA-mRNA dynamic network contains 3350 interactions captured across different cancer progression stages or tumor grades. We found that those dynamic interactions tended to concentrate on a few miRNAs (e.g. miRNA-936), and were more likely present on the miRNA-mRNA pairs outside the discovered modules. In addition, we also pinpointed a robust prognostic signature consisting of 56 modular protein-coding genes, whose co-expression patterns were predictive for the survival time of ovarian cancer patients in multiple independent cohorts. Copyright © 2016 Elsevier Ltd. All rights reserved.

The role of social attraction and its link with boldness in the collective movements of three-spined sticklebacks.

PubMed

Jolles, Jolle W; Fleetwood-Wilson, Adeline; Nakayama, Shinnosuke; Stumpe, Martin C; Johnstone, Rufus A; Manica, Andrea

2015-01-01

Social animals must time and coordinate their behaviour to ensure the benefits of grouping, resulting in collective movements and the potential emergence of leaders and followers. However, individuals often differ consistently from one another in how they cope with their environment, a phenomenon known as animal personality, which may affect how individuals use coordination rules and requiring them to compromise. Here we tracked the movements of pairs of three-spined sticklebacks, Gasterosteus aculeatus , separated by a transparent partition that allowed them to observe and interact with one another in a context containing cover. Individuals differed consistently in their tendency to approach their partner's compartment during collective movements. The strength of this social attraction was positively correlated with the behavioural coordination between members of a pair but was negatively correlated with an individual's tendency to lead. Social attraction may form part of a broader behavioural syndrome as it was predicted by the boldness of an individual, measured in isolation prior to the observation of pairs, and by the boldness of the partner. We found that bolder fish, and those paired with bolder partners, tended to approach their partner's compartment less closely. These findings provide important insights into the mechanisms that govern the dynamics and functioning of social groups and the emergence and maintenance of consistent behavioural differences.

The role of social attraction and its link with boldness in the collective movements of three-spined sticklebacks

PubMed Central

Jolles, Jolle W.; Fleetwood-Wilson, Adeline; Nakayama, Shinnosuke; Stumpe, Martin C.; Johnstone, Rufus A.; Manica, Andrea

2015-01-01

Social animals must time and coordinate their behaviour to ensure the benefits of grouping, resulting in collective movements and the potential emergence of leaders and followers. However, individuals often differ consistently from one another in how they cope with their environment, a phenomenon known as animal personality, which may affect how individuals use coordination rules and requiring them to compromise. Here we tracked the movements of pairs of three-spined sticklebacks, Gasterosteus aculeatus, separated by a transparent partition that allowed them to observe and interact with one another in a context containing cover. Individuals differed consistently in their tendency to approach their partner's compartment during collective movements. The strength of this social attraction was positively correlated with the behavioural coordination between members of a pair but was negatively correlated with an individual's tendency to lead. Social attraction may form part of a broader behavioural syndrome as it was predicted by the boldness of an individual, measured in isolation prior to the observation of pairs, and by the boldness of the partner. We found that bolder fish, and those paired with bolder partners, tended to approach their partner's compartment less closely. These findings provide important insights into the mechanisms that govern the dynamics and functioning of social groups and the emergence and maintenance of consistent behavioural differences. PMID:25598543

Dynamic pupillary exchange engages brain regions encoding social salience

PubMed Central

Harrison, Neil A.; Gray, Marcus A.; Critchley, Hugo D.

2008-01-01

Covert exchange of autonomic responses may shape social affective behavior, as observed in mirroring of pupillary responses during sadness processing. We examined how, independent of facial emotional expression, dynamic coherence between one's own and another's pupil size modulates regional brain activity. Fourteen subjects viewed pairs of eye stimuli while undergoing fMRI. Using continuous pupillometry biofeedback, the size of the observed pupils was varied, correlating positively or negatively with changes in participants’ own pupils. Viewing both static and dynamic stimuli activated right fusiform gyrus. Observing dynamically changing pupils activated STS and amygdala, regions engaged by non-static and salient facial features. Discordance between observed and observer's pupillary changes enhanced activity within bilateral anterior insula, left amygdala and anterior cingulate. In contrast, processing positively correlated pupils enhanced activity within left frontal operculum. Our findings suggest pupillary signals are monitored continuously during social interactions and that incongruent changes activate brain regions involved in tracking motivational salience and attentionally meaningful information. Naturalistically, dynamic coherence in pupillary change follows fluctuations in ambient light. Correspondingly, in social contexts discordant pupil response is likely to reflect divergence of dispositional state. Our data provide empirical evidence for an autonomically mediated extension of forward models of motor control into social interaction. PMID:19048432

Neural Correlates of Encoding within- and across-Domain Inter-Item Associations

ERIC Educational Resources Information Center

Park, Heekyeong; Rugg, Michael D.

2011-01-01

The neural correlates of the encoding of associations between pairs of words, pairs of pictures, and word-picture pairs were compared. The aims were to determine, first, whether the neural correlates of associative encoding vary according to study material and, second, whether encoding of across- versus within-material item pairs is associated…

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.

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

Molecular Dynamics Simulations of Grain Boundary and Bulk Diffusion in Metals.

NASA Astrophysics Data System (ADS)

Plimpton, Steven James

Diffusion is a microscopic mass transport mechanism that underlies many important macroscopic phenomena affecting the structural, electrical, and mechanical properties of metals. This thesis presents results from atomistic simulation studies of diffusion both in bulk and in the fast diffusion paths known as grain boundaries. Using the principles of molecular dynamics single boundaries are studied and their structure and dynamic properties characterized. In particular, tilt boundary bicrystal and bulk models of fcc Al and bcc alpha-Fe are simulated. Diffusion coefficients and activation energies for atomic motion are calculated for both models and compared to experimental data. The influence of the interatomic pair potential on the diffusion is studied in detail. A universal relation between the melting temperature that a pair potential induces in a simulated bulk model and the potential energy barrier height for atomic hopping is derived and used to correlate results for a wide variety of pair potentials. Using these techniques grain boundary and bulk diffusion coefficients for any fcc material can be estimated from simple static calculations without the need to perform more time-consuming dynamic simulations. The influences of two other factors on grain boundary diffusion are also studied because of the interest of the microelectronics industry in the diffusion related reliability problem known as electromigration. The first factor, known to affect the self diffusion rate of Al, is the presence of Cu impurity atoms in Al tilt boundaries. The bicrystal model for Al is seeded randomly with Cu atoms and a simple hybrid Morse potential used to model the Al-Cu interaction. While some effect due to the Cu is noted, it is concluded that pair potentials are likely an inadequate approximation for the alloy system. The second factor studied is the effect of the boundary orientation angle on the diffusion rate. Symmetric bcc Fe boundaries are relaxed to find optimal structures and their diffusion coefficients calculated. Good agreement is found with the dislocation pipe model for tilt boundary diffusion.

Approximate degeneracy of J =1 spatial correlators in high temperature QCD

NASA Astrophysics Data System (ADS)

Rohrhofer, C.; Aoki, Y.; Cossu, G.; Fukaya, H.; Glozman, L. Ya.; Hashimoto, S.; Lang, C. B.; Prelovsek, S.

2017-11-01

We study spatial isovector meson correlators in Nf=2 QCD with dynamical domain-wall fermions on 3 23×8 lattices at temperatures T =220 - 380 MeV . We measure the correlators of spin-one (J =1 ) operators including vector, axial-vector, tensor and axial-tensor. Restoration of chiral U (1 )A and S U (2 )L×S U (2 )R symmetries of QCD implies degeneracies in vector-axial-vector (S U (2 )L×S U (2 )R) and tensor-axial-tensor (U (1 )A) pairs, which are indeed observed at temperatures above Tc. Moreover, we observe an approximate degeneracy of all J =1 correlators with increasing temperature. This approximate degeneracy suggests emergent S U (2 )CS and S U (4 ) symmetries at high temperatures, that mix left- and right-handed quarks.

Quantum correlation of fiber-based telecom-band photon pairs through standard loss and random media.

PubMed

Sua, Yong Meng; Malowicki, John; Lee, Kim Fook

2014-08-15

We study quantum correlation and interference of fiber-based telecom-band photon pairs with one photon of the pair experiencing multiple scattering in a random medium. We measure joint probability of two-photon detection for signal photon in a normal channel and idler photon in a channel, which is subjected to two independent conditions: standard loss (neutral density filter) and random media. We observe that both conditions degrade the correlation of signal and idler photons, and depolarization of the idler photon in random medium can enhance two-photon interference at certain relative polarization angles. Our theoretical calculation on two-photon polarization correlation and interference as a function of mean free path is in agreement with our experiment data. We conclude that quantum correlation of a polarization-entangled photon pair is better preserved than a polarization-correlated photon pair as one photon of the pair scatters through a random medium.

Balanced Synaptic Input Shapes the Correlation between Neural Spike Trains

PubMed Central

Litwin-Kumar, Ashok; Oswald, Anne-Marie M.; Urban, Nathaniel N.; Doiron, Brent

2011-01-01

Stimulus properties, attention, and behavioral context influence correlations between the spike times produced by a pair of neurons. However, the biophysical mechanisms that modulate these correlations are poorly understood. With a combined theoretical and experimental approach, we show that the rate of balanced excitatory and inhibitory synaptic input modulates the magnitude and timescale of pairwise spike train correlation. High rate synaptic inputs promote spike time synchrony rather than long timescale spike rate correlations, while low rate synaptic inputs produce opposite results. This correlation shaping is due to a combination of enhanced high frequency input transfer and reduced firing rate gain in the high input rate state compared to the low state. Our study extends neural modulation from single neuron responses to population activity, a necessary step in understanding how the dynamics and processing of neural activity change across distinct brain states. PMID:22215995

Dynamic cross-correlations between entangled biofilaments as they diffuse

PubMed Central

Tsang, Boyce; Dell, Zachary E.; Jiang, Lingxiang; Schweizer, Kenneth S.; Granick, Steve

2017-01-01

Entanglement in polymer and biological physics involves a state in which linear interthreaded macromolecules in isotropic liquids diffuse in a spatially anisotropic manner beyond a characteristic mesoscopic time and length scale (tube diameter). The physical reason is that linear macromolecules become transiently localized in directions transverse to their backbone but diffuse with relative ease parallel to it. Within the resulting broad spectrum of relaxation times there is an extended period before the longest relaxation time when filaments occupy a time-averaged cylindrical space of near-constant density. Here we show its implication with experiments based on fluorescence tracking of dilutely labeled macromolecules. The entangled pairs of aqueous F-actin biofilaments diffuse with separation-dependent dynamic cross-correlations that exceed those expected from continuum hydrodynamics up to strikingly large spatial distances of ≈15 µm, which is more than 104 times the size of the solvent water molecules in which they are dissolved, and is more than 50 times the dynamic tube diameter, but is almost equal to the filament length. Modeling this entangled system as a collection of rigid rods, we present a statistical mechanical theory that predicts these long-range dynamic correlations as an emergent consequence of an effective long-range interpolymer repulsion due to the de Gennes correlation hole, which is a combined consequence of chain connectivity and uncrossability. The key physical assumption needed to make theory and experiment agree is that solutions of entangled biofilaments localized in tubes that are effectively dynamically incompressible over the relevant intermediate time and length scales. PMID:28283664

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

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

Berrada, K., E-mail: kberrada@ictp.it; The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, Miramare-Trieste; Ooi, C. H. Raymond

Robustness of the geometric phase (GP) with respect to different noise effects is a basic condition for an effective quantum computation. Here, we propose a useful quantum system with real physical parameters by studying the GP of a pair of Stokes and anti-Stokes photons, involving Raman emission processes with and without photonic band gap (PBG) effect. We show that the properties of GP are very sensitive to the change of the Rabi frequency and time, exhibiting collapse phenomenon as the time becomes significantly large. The system allows us to obtain a state which remains with zero GP for longer times.more » This result plays a significant role to enhance the stabilization and control of the system dynamics. Finally, we investigate the nonlocal correlation (entanglement) between the pair photons by taking into account the effect of different parameters. An interesting correlation between the GP and entanglement is observed showing that the PBG stabilizes the fluctuations in the system and makes the entanglement more robust against the change of time and frequency.« less

The entangled accelerating universe

NASA Astrophysics Data System (ADS)

González-Díaz, Pedro F.; Robles-Pérez, Salvador

2009-08-01

Using the known result that the nucleation of baby universes in correlated pairs is equivalent to spacetime squeezing, we show in this Letter that there exists a T-duality symmetry between two-dimensional warp drives, which are physically expressible as localized de Sitter little universes, and two-dimensional Tolman-Hawking and Gidding-Strominger baby universes respectively correlated in pairs, so that the creation of warp drives is also equivalent to spacetime squeezing. Perhaps more importantly, it has been also seen that the nucleation of warp drives entails a violation of the Bell's inequalities, and hence the phenomena of quantum entanglement, complementarity and wave function collapse. These results are generalized to the case of any dynamically accelerating universe filled with dark or phantom energy whose creation is also physically equivalent to spacetime squeezing and to the violation of the Bell's inequalities, so that the universe we are living in should be governed by essential sharp quantum theory laws and must be a quantum entangled system.

Long-Lived Correlated Triplet Pairs in a π-Stacked Crystalline Pentacene Derivative.

PubMed

Folie, Brendan D; Haber, Jonah B; Refaely-Abramson, Sivan; Neaton, Jeffrey B; Ginsberg, Naomi S

2018-02-14

Singlet fission is the spin-conserving process by which a singlet exciton splits into two triplet excitons. Singlet fission occurs via a correlated triplet pair intermediate, but direct evidence of this state has been scant, and in films of TIPS-pentacene, a small molecule organic semiconductor, even the rate of fission has been unclear. We use polarization-resolved transient absorption microscopy on individual crystalline domains of TIPS-pentacene to establish the fission rate and demonstrate that the initially created triplets remain bound for a surprisingly long time, hundreds of picoseconds, before separating. Furthermore, using a broadband probe, we show that it is possible to determine absorbance spectra of individual excited species in a crystalline solid. We find that triplet interactions perturb the absorbance, and provide evidence that triplet interaction and binding could be caused by the π-stacked geometry. Elucidating the relationship between the lattice structure and the electronic structure and dynamics has important implications for the creation of photovoltaic devices that aim to boost efficiency via singlet fission.

Two-dimensional fluorescence lifetime correlation spectroscopy. 2. Application.

PubMed

Ishii, Kunihiko; Tahara, Tahei

2013-10-03

In the preceding article, we introduced the theoretical framework of two-dimensional fluorescence lifetime correlation spectroscopy (2D FLCS). In this article, we report the experimental implementation of 2D FLCS. In this method, two-dimensional emission-delay correlation maps are constructed from the photon data obtained with the time-correlated single photon counting (TCSPC), and then they are converted to 2D lifetime correlation maps by the inverse Laplace transform. We develop a numerical method to realize reliable transformation, employing the maximum entropy method (MEM). We apply the developed actual 2D FLCS to two real systems, a dye mixture and a DNA hairpin. For the dye mixture, we show that 2D FLCS is experimentally feasible and that it can identify different species in an inhomogeneous sample without any prior knowledge. The application to the DNA hairpin demonstrates that 2D FLCS can disclose microsecond spontaneous dynamics of biological molecules in a visually comprehensible manner, through identifying species as unique lifetime distributions. A FRET pair is attached to the both ends of the DNA hairpin, and the different structures of the DNA hairpin are distinguished as different fluorescence lifetimes in 2D FLCS. By constructing the 2D correlation maps of the fluorescence lifetime of the FRET donor, the equilibrium dynamics between the open and the closed forms of the DNA hairpin is clearly observed as the appearance of the cross peaks between the corresponding fluorescence lifetimes. This equilibrium dynamics of the DNA hairpin is clearly separated from the acceptor-missing DNA that appears as an isolated diagonal peak in the 2D maps. The present study clearly shows that newly developed 2D FLCS can disclose spontaneous structural dynamics of biological molecules with microsecond time resolution.

Mutation Pattern of Paired Immunoglobulin Heavy and Light Variable Domains in Chronic Lymphocytic Leukemia B Cells

PubMed Central

Ghiotto, Fabio; Marcatili, Paolo; Tenca, Claudya; Calevo, Maria Grazia; Yan, Xiao-Jie; Albesiano, Emilia; Bagnara, Davide; Colombo, Monica; Cutrona, Giovanna; Chu, Charles C; Morabito, Fortunato; Bruno, Silvia; Ferrarini, Manlio; Tramontano, Anna; Fais, Franco; Chiorazzi, Nicholas

2011-01-01

B-cell chronic lymphocytic leukemia (CLL) patients display leukemic clones bearing either germline or somatically mutated immunoglobulin heavy variable (IGHV ) genes. Most information on CLL immunoglobulins (Igs), such as the definition of stereotyped B-cell receptors (BCRs), was derived from germline unmutated Igs. In particular, detailed studies on the distribution and nature of mutations in paired heavy- and light-chain domains of CLL clones bearing mutated Igs are lacking. To address the somatic hyper-mutation dynamics of CLL Igs, we analyzed the mutation pattern of paired IGHV–diversity-joining (IGHV-D-J ) and immunoglobulin kappa/lambda variable-joining (IGK/LV-J ) rearrangements of 193 leukemic clones that displayed ≥2% mutations in at least one of the two immunoglobulin variable (IGV ) genes (IGHV and/or IGK/LV ). The relationship between the mutation frequency in IGHV and IGK/LV complementarity determining regions (CDRs) and framework regions (FRs) was evaluated by correlation analysis. Replacement (R) mutation frequency within IGK/LV chain CDRs correlated significantly with mutation frequency of paired IGHV CDRs in λ but not κ isotype CLL clones. CDRs of IGKV-J rearrangements displayed a lower percentage of R mutations than IGHVs. The frequency/pattern of mutations in kappa CLL Igs differed also from that in κ-expressing normal B cells described in the literature. Instead, the mutation frequency within the FRs of IGHV and either IGKV or IGLV was correlated. Notably, the amount of diversity introduced by replaced amino acids was comparable between IGHVs and IGKVs. The data indicate a different mutation pattern between κ and λ isotype CLL clones and suggest an antigenic selection that, in κ samples, operates against CDR variation. PMID:21785810

CL-20/DNB co-crystal based PBX with PEG: molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Zhang, Jiang; Gao, Pei; Xiao, Ji Jun; Zhao, Feng; Xiao, He Ming

2016-12-01

Molecular dynamics simulation was carried out for CL-20/DNB co-crystal based PBX (polymer-bonded explosive) blended with polymer PEG (polyethylene glycol). In this paper, the miscibility of the PBX models is investigated through the calculated binding energy. Pair correlation function (PCF) analysis is applied to study the interaction of the interface structures in the PBX models. The mechanical properties of PBXs are also discussed to understand the change of the mechanical properties after adding the polymer. Moreover, the calculated diffusion coefficients of the interfacial explosive molecules are used to discuss the dispersal ability of CL-20 and DNB molecules in the interface layer.

Greed, fear and stock market dynamics

NASA Astrophysics Data System (ADS)

Westerhoff, Frank H.

2004-11-01

We present a behavioral stock market model in which traders are driven by greed and fear. In general, the agents optimistically believe in rising markets and thus buy stocks. But if stock prices change too abruptly, they panic and sell stocks. Our model mimics some stylized facts of stock market dynamics: (1) stock prices increase over time, (2) stock markets sometimes crash, (3) stock prices show little pair correlation between successive daily changes, and (4) periods of low volatility alternate with periods of high volatility. A strong feature of the model is that stock prices completely evolve according to a deterministic low-dimensional nonlinear law of motion.

Rigidity and soft percolation in the glass transition of an atomistic model of ionic liquid, 1-ethyl-3-methyl imidazolium nitrate, from molecular dynamics simulations—Existence of infinite overlapping networks in a fragile ionic liquid

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

Habasaki, Junko, E-mail: habasaki.j.aa@m.titech.ac.jp; Ngai, K. L.

The typical ionic liquid, 1-ethyl-3-methyl imidazolium nitrate (EMIM-NO{sub 3}), was examined by molecular dynamics simulations of an all-atomistic model to show the characteristics of networks of cages and/or bonds in the course of vitrification of this fragile glass-former. The system shows changes of dynamics at two characteristic temperatures, T{sub B} (or T{sub c}) and the glass transition temperature T{sub g}, found in other fragile glass forming liquids [K. L. Ngai and J. Habasaki, J. Chem. Phys. 141, 114502 (2014)]. On decreasing temperature, the number of neighboring cation-anion pairs, N{sub B}, within the first minimum of the pair correlation function, g(r){submore » min}, increases. On crossing T{sub B} (>T{sub g}), the system volume and diffusion coefficient both show changes in temperature dependence, and as usual at T{sub g}. The glass transition temperature, T{sub g}, is characterized by the saturation of the total number of “bonds,” N{sub B} and the corresponding decrease in degree of freedom, F = [(3N − 6) − N{sub B}], of the system consisting of N particles. Similar behavior holds for the other ion-ion pairs. Therefore, as an alternative, the dynamics of glass transition can be interpreted conceptually by rigidity percolation. Before saturation occurring at T{sub g}, the number of bonds shows a remarkable change at around T{sub B}. This temperature is associated with the disappearance of the loosely packed coordination polyhedra of anions around cation (or vice versa), related to the loss of geometrical freedom of the polyhedra, f{sub g}, of each coordination polyhedron, which can be defined by f{sub g} = [(3N{sub V} − 6) − N{sub b}]. Here, 3N{sub v} is the degree of freedom of N{sub V} vertices of the polyhedron, and N{sub b} is number of fictive bonds. The packing of polyhedra is characterized by the soft percolation of cages, which allows further changes with decreasing temperature. The power spectrum of displacement of the central ion in the cage is found to be correlated with the fluctuation of N{sub b} of cation-cation (or anion-anion) pairs in the polyhedron, although the effect from the coordination shells beyond the neighboring ions is not negligible.« less

Network Characteristics of Collective Chemosensing

NASA Astrophysics Data System (ADS)

Sun, Bo; Duclos, Guillaume; Stone, Howard A.

2013-04-01

The collective chemosensing of nonexcitable mammalian cells involves a biochemical network that features gap junction communications and heterogeneous single cell activities. To understand the integrated multicellular chemosensing, we study the calcium dynamics of micropatterned fibroblast cell colonies in response to adenosine triphosphate (ATP) stimulation. We find that the cross-correlation function between the responses of individual cells decays with topological distance as a power law for large colonies and much faster for smaller colonies. Furthermore, the strongly correlated cell pairs tend to form clusters and are more likely to exceed the percolation threshold. At a given topological distance, the cross-correlations exhibit characteristics of Poisson distributions, which allows us to estimate the unitary conductance of a single gap junction which is in good agreement with direct experimental measurements.

Superconductivity from a non-Fermi-liquid metal: Kondo fluctuation mechanism in slave-fermion theory

NASA Astrophysics Data System (ADS)

Kim, Ki-Seok

2010-03-01

We propose Kondo fluctuation mechanism of superconductivity, differentiated from the spin-fluctuation theory as the standard model for unconventional superconductivity in the weak-coupling approach. Based on the U(1) slave-fermion representation of an effective Anderson lattice model, where localized spins are described by the Schwinger boson theory and hybridization or Kondo fluctuations weaken antiferromagnetic correlations of localized spins, we found an antiferromagnetic quantum critical point from an antiferromagnetic metal to a heavy-fermion metal in our recent study. The Kondo-induced antiferromagnetic quantum critical point was shown to be described by both conduction electrons and fermionic holons interacting with critical spin fluctuations given by deconfined bosonic spinons with a spin quantum number 1/2. Surprisingly, such critical modes turned out to be described by the dynamical exponent z=3 , giving rise to the well-known non-Fermi-liquid physics such as the divergent Grüneisen ratio with an exponent 2/3 and temperature-linear resistivity in three dimensions. We find that the z=3 antiferromagnetic quantum critical point becomes unstable against superconductivity, where critical spinon excitations give rise to pairing correlations between conduction electrons and between fermionic holons, respectively, via hybridization fluctuations. Such two kinds of pairing correlations result in multigap unconventional superconductivity around the antiferromagnetic quantum critical point of the slave-fermion theory, where s -wave pairing is not favored generically due to strong correlations. We show that the ratio between each superconducting gap for conduction electrons Δc and holons Δf and the transition temperature Tc is 2Δc/Tc˜9 and 2Δf/Tc˜O(10-1) , remarkably consistent with CeCoIn5 . A fingerprint of the Kondo mechanism is emergence of two kinds of resonance modes in not only spin but also charge fluctuations, where the charge resonance mode at an antiferromagnetic wave vector originates from d -wave pairing of spinless holons. We discuss how the Kondo fluctuation theory differs from the spin-fluctuation approach.

Amorphization driven by defect-induced mechanical instability.

PubMed

Jiang, Chao; Zheng, Ming-Jie; Morgan, Dane; Szlufarska, Izabela

2013-10-11

Using ab initio molecular dynamics simulations, we perform a comparative study of the defect accumulation process in silicon carbide (SiC) and zirconium carbide (ZrC). Interestingly, we find that the fcc Si sublattice in SiC spontaneously and gradually collapses following the continuous introduction of C Frenkel pairs (FPs). Above a critical amorphization dose of ~0.33 displacements per atom (dpa), the pair correlation function exhibits no long-range order. In contrast, the fcc Zr sublattice in ZrC remains structurally stable against C sublattice displacements up to the highest dose of 1.0 dpa considered. Consequently, ZrC cannot be amorphized by the accumulation of C FPs. We propose defect-induced mechanical instability as the key mechanism driving the amorphization of SiC under electron irradiation.

Nonlinear two-dimensional terahertz photon echo and rotational spectroscopy in the gas phase.

PubMed

Lu, Jian; Zhang, Yaqing; Hwang, Harold Y; Ofori-Okai, Benjamin K; Fleischer, Sharly; Nelson, Keith A

2016-10-18

Ultrafast 2D spectroscopy uses correlated multiple light-matter interactions for retrieving dynamic features that may otherwise be hidden under the linear spectrum; its extension to the terahertz regime of the electromagnetic spectrum, where a rich variety of material degrees of freedom reside, remains an experimental challenge. We report a demonstration of ultrafast 2D terahertz spectroscopy of gas-phase molecular rotors at room temperature. Using time-delayed terahertz pulse pairs, we observe photon echoes and other nonlinear signals resulting from molecular dipole orientation induced by multiple terahertz field-dipole interactions. The nonlinear time domain orientation signals are mapped into the frequency domain in 2D rotational spectra that reveal J-state-resolved nonlinear rotational dynamics. The approach enables direct observation of correlated rotational transitions and may reveal rotational coupling and relaxation pathways in the ground electronic and vibrational state.

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.

Failure mode and bending moment of canine pancarpal arthrodesis constructs stabilized with two different implant systems.

PubMed

Wininger, Fred A; Kapatkin, Amy S; Radin, Alex; Shofer, Frances S; Smith, Gail K

2007-12-01

To compare failure mode and bending moment of a canine pancarpal arthrodesis construct using either a 2.7 mm/3.5 mm hybrid dynamic compression plate (HDCP) or a 3.5 mm dynamic compression plate (DCP). Paired in vitro biomechanical testing of canine pancarpal arthrodesis constructs stabilized with either a 2.7/3.5 HDCP or 3.5 DCP. Paired cadaveric canine antebrachii (n=5). Pancarpal arthrodesis constructs were loaded to failure (point of maximum load) in 4-point bending using a materials-testing machine. Using this point of failure, bending moments were calculated from system variables for each construct and the 2 plating systems compared using a paired t-test. To examine the relationship between metacarpal diameter and screw diameter failure loads, linear regression was used and Pearson' correlation coefficient was calculated. Significance was set at P<.05. HDCP failed at higher loads than DCP for 9 of 10 constructs. The absolute difference in failure rates between the 2 plates was 0.552+/-0.182 N m, P=.0144 (95% confidence interval: -0.58 to 1.68). This is an 8.1% mean difference in bending strength. There was a significant linear correlation r=0.74 (P-slope=.014) and 0.8 (P-slope=.006) between metacarpal diameter and failure loads for the HDCP and 3.5 DCP, respectively. There was a small but significant difference between bending moment at failure between 2.7/3.5 HDCP and 3.5 DCP constructs; however, the difference may not be clinically evident in all patients. The 2.7/3.5 HDCP has physical and mechanical properties making it a more desirable plate for pancarpal arthrodesis.

A dynamical system perspective to understanding badminton singles game play.

PubMed

Chow, Jia Yi; Seifert, Ludovic; Hérault, Romain; Chia, Shannon Jing Yi; Lee, Miriam Chang Yi

2014-02-01

By altering the task constraints of cooperative and competitive game contexts in badminton, insights can be obtained from a dynamical systems perspective to investigate the underlying processes that results in either a gradual shift or transition of playing patterns. Positional data of three pairs of skilled female badminton players (average age 20.5±1.38years) were captured and analyzed. Local correlation coefficient, which provides information on the relationship of players' displacement data, between each pair of players was computed for angle and distance from base position. Speed scalar product was in turn established from speed vectors of the players. The results revealed two patterns of playing behaviors (i.e., in-phase and anti-phase patterns) for movement displacement. Anti-phase relation was the dominant coupling pattern for speed scalar relationships among the pairs of players. Speed scalar product, as a collective variable, was different between cooperative and competitive plays with a greater variability in amplitude seen in competitive plays leading to a winning point. The findings from this study provide evidence for increasing stroke variability to perturb existing stable patterns of play and highlights the potential for speed scalar product to be a collective variable to distinguish different patterns of play (e.g., cooperative and competitive). Copyright © 2013 Elsevier B.V. All rights reserved.

Lightwave-driven quasiparticle collisions on a sub-cycle timescale

PubMed Central

Langer, F.; Hohenleutner, M.; Schmid, C.; Poellmann, C.; Nagler, P.; Korn, T.; Schüller, C.; Sherwin, M. S.; Huttner, U.; Steiner, J. T.; Koch, S. W.; Kira, M.; Huber, R.

2016-01-01

Ever since Ernest Rutherford first scattered α-particles from gold foils1, collision experiments have revealed unique insights into atoms, nuclei, and elementary particles2. In solids, many-body correlations also lead to characteristic resonances3, called quasiparticles, such as excitons, dropletons4, polarons, or Cooper pairs. Their structure and dynamics define spectacular macroscopic phenomena, ranging from Mott insulating states via spontaneous spin and charge order to high-temperature superconductivity5. Fundamental research would immensely benefit from quasiparticle colliders, but the notoriously short lifetimes of quasiparticles6 have challenged practical solutions. Here we exploit lightwave-driven charge transport7–24, the backbone of attosecond science9–13, to explore ultrafast quasiparticle collisions directly in the time domain: A femtosecond optical pulse creates excitonic electron–hole pairs in the layered dichalcogenide tungsten diselenide while a strong terahertz field accelerates and collides the electrons with the holes. The underlying wave packet dynamics, including collision, pair annihilation, quantum interference and dephasing, are detected as light emission in high-order spectral sidebands17–19 of the optical excitation. A full quantum theory explains our observations microscopically. This approach opens the door to collision experiments with a broad variety of complex quasiparticles and suggests a promising new way of sub-femtosecond pulse generation. PMID:27172045

Two-mode thermal-noise squeezing in an electromechanical resonator.

PubMed

Mahboob, I; Okamoto, H; Onomitsu, K; Yamaguchi, H

2014-10-17

An electromechanical resonator is developed in which mechanical nonlinearities can be dynamically engineered to emulate the nondegenerate parametric down-conversion interaction. In this configuration, phonons are simultaneously generated in pairs in two macroscopic vibration modes, resulting in the amplification of their motion. In parallel, two-mode thermal squeezed states are also created, which exhibit fluctuations below the thermal motion of their constituent modes as well as harboring correlations between the modes that become almost perfect as their amplification is increased. The existence of correlations between two massive phonon ensembles paves the way towards an entangled macroscopic mechanical system at the single phonon level.

Precollisional velocity correlations in a hard-disk fluid with dissipative collisions.

PubMed

Soto, R; Piasecki, J; Mareschal, M

2001-09-01

Velocity correlations are studied in granular fluids, modeled by the inelastic hard sphere gas. Making a density expansion of the Bogoliubov-Born-Green-Kirkwood-Yvon hierarchy for the evolution of the reduced distributions, we predict the presence of precollisional velocity correlations. They are created by the propagation through correlated sequences of collisions (ring events) of the velocity correlations generated after dissipative collisions. The correlations have their origin in the dissipative character of collisions, being always present in granular fluids. The correlations, that manifest microscopically as an alignment of the velocities of a colliding pair produce modifications of collisional averages, in particular, the virial pressure. The pressure shows a reduction with respect to the elastic case as a consequence of the velocity alignment. Good qualitative agreement is obtained for the comparison of the numerical evaluations of the obtained analytical expressions and molecular dynamics results that showed evidence of precollisional velocity correlations [R. Soto and M. Mareschal, Phys. Rev. E 63, 041303 (2001)].

Microscopic analysis of shape transition in neutron-deficient Yb isotopes

NASA Astrophysics Data System (ADS)

Fu, Y.; Tong, H.; Wang, X. F.; Wang, H.; Wang, D. Q.; Wang, X. Y.; Yao, J. M.

2018-01-01

The development of nuclear collectivity in even-even Yb-170152 is studied with three types of mean-field calculations: the nonrelativistic Hartree-Fock plus BCS calculation using the Skyrme SLy4 force plus a density-dependent δ pairing force and the relativistic mean-field calculation using a point-coupling energy functional supplemented with either a density-independent δ pairing force or a separable pairing force. The low-lying states are obtained by solving a five-dimensional collective Hamiltonian with parameters determined from the three mean-field solutions. The energy surfaces, excitation energies, electric multiple transition strengths, and differential isotope shifts are presented in comparison with available data. Our results show that different treatments of pairing correlations have a significant influence on the speed of developing collectivity as the increase of neutron number. All the calculations demonstrate the important role of dynamic shape-mixing effects in resolving the puzzle in the dramatic increase of charge radius from 152Yb to 154Yb and the role of triaxiality in Yb 160 ,162 ,164 .

Excess entropy and crystallization in Stillinger-Weber and Lennard-Jones fluids

NASA Astrophysics Data System (ADS)

Dhabal, Debdas; Nguyen, Andrew Huy; Singh, Murari; Khatua, Prabir; Molinero, Valeria; Bandyopadhyay, Sanjoy; Chakravarty, Charusita

2015-10-01

Molecular dynamics simulations are used to contrast the supercooling and crystallization behaviour of monatomic liquids that exemplify the transition from simple to anomalous, tetrahedral liquids. As examples of simple fluids, we use the Lennard-Jones (LJ) liquid and a pair-dominated Stillinger-Weber liquid (SW16). As examples of tetrahedral, water-like fluids, we use the Stillinger-Weber model with variable tetrahedrality parameterized for germanium (SW20), silicon (SW21), and water (SW23.15 or mW model). The thermodynamic response functions show clear qualitative differences between simple and water-like liquids. For simple liquids, the compressibility and the heat capacity remain small on isobaric cooling. The tetrahedral liquids in contrast show a very sharp rise in these two response functions as the lower limit of liquid-phase stability is reached. While the thermal expansivity decreases with temperature but never crosses zero in simple liquids, in all three tetrahedral liquids at the studied pressure, there is a temperature of maximum density below which thermal expansivity is negative. In contrast to the thermodynamic response functions, the excess entropy on isobaric cooling does not show qualitatively different features for simple and water-like liquids; however, the slope and curvature of the entropy-temperature plots reflect the heat capacity trends. Two trajectory-based computational estimation methods for the entropy and the heat capacity are compared for possible structural insights into supercooling, with the entropy obtained from thermodynamic integration. The two-phase thermodynamic estimator for the excess entropy proves to be fairly accurate in comparison to the excess entropy values obtained by thermodynamic integration, for all five Lennard-Jones and Stillinger-Weber liquids. The entropy estimator based on the multiparticle correlation expansion that accounts for both pair and triplet correlations, denoted by Strip, is also studied. Strip is a good entropy estimator for liquids where pair and triplet correlations are important such as Ge and Si, but loses accuracy for purely pair-dominated liquids, like LJ fluid, or near the crystallization temperature (Tthr). Since local tetrahedral order is compatible with both liquid and crystalline states, the reorganisation of tetrahedral liquids is accompanied by a clear rise in the pair, triplet, and thermodynamic contributions to the heat capacity, resulting in the heat capacity anomaly. In contrast, the pair-dominated liquids show increasing dominance of triplet correlations on approaching crystallization but no sharp rise in either the pair or thermodynamic heat capacities.

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

Dhabal, Debdas; Chakravarty, Charusita, E-mail: charus@chemistry.iitd.ac.in; Nguyen, Andrew Huy

Molecular dynamics simulations are used to contrast the supercooling and crystallization behaviour of monatomic liquids that exemplify the transition from simple to anomalous, tetrahedral liquids. As examples of simple fluids, we use the Lennard-Jones (LJ) liquid and a pair-dominated Stillinger-Weber liquid (SW{sub 16}). As examples of tetrahedral, water-like fluids, we use the Stillinger-Weber model with variable tetrahedrality parameterized for germanium (SW{sub 20}), silicon (SW{sub 21}), and water (SW{sub 23.15} or mW model). The thermodynamic response functions show clear qualitative differences between simple and water-like liquids. For simple liquids, the compressibility and the heat capacity remain small on isobaric cooling. Themore » tetrahedral liquids in contrast show a very sharp rise in these two response functions as the lower limit of liquid-phase stability is reached. While the thermal expansivity decreases with temperature but never crosses zero in simple liquids, in all three tetrahedral liquids at the studied pressure, there is a temperature of maximum density below which thermal expansivity is negative. In contrast to the thermodynamic response functions, the excess entropy on isobaric cooling does not show qualitatively different features for simple and water-like liquids; however, the slope and curvature of the entropy-temperature plots reflect the heat capacity trends. Two trajectory-based computational estimation methods for the entropy and the heat capacity are compared for possible structural insights into supercooling, with the entropy obtained from thermodynamic integration. The two-phase thermodynamic estimator for the excess entropy proves to be fairly accurate in comparison to the excess entropy values obtained by thermodynamic integration, for all five Lennard-Jones and Stillinger-Weber liquids. The entropy estimator based on the multiparticle correlation expansion that accounts for both pair and triplet correlations, denoted by S{sub trip}, is also studied. S{sub trip} is a good entropy estimator for liquids where pair and triplet correlations are important such as Ge and Si, but loses accuracy for purely pair-dominated liquids, like LJ fluid, or near the crystallization temperature (T{sub thr}). Since local tetrahedral order is compatible with both liquid and crystalline states, the reorganisation of tetrahedral liquids is accompanied by a clear rise in the pair, triplet, and thermodynamic contributions to the heat capacity, resulting in the heat capacity anomaly. In contrast, the pair-dominated liquids show increasing dominance of triplet correlations on approaching crystallization but no sharp rise in either the pair or thermodynamic heat capacities.« less

Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.

PubMed

Hacisuleyman, Aysima; Erman, Burak

2017-01-01

It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others. We apply the model to Ubiquitin, whose allosteric activity has not been emphasized until recently, and show that there are indeed systematic pathways of entropy and information transfer between residues that correlate well with the activities of the protein. We use 600 nanosecond molecular dynamics trajectories for Ubiquitin and its complex with human polymerase iota and evaluate entropy transfer between all pairs of residues of Ubiquitin and quantify the binding susceptibility changes upon complex formation. We explain the complex formation propensities of Ubiquitin in terms of entropy transfer. Important residues taking part in allosteric communication in Ubiquitin predicted by our approach are in agreement with results of NMR relaxation dispersion experiments. Finally, we show that time delayed correlation of fluctuations of two interacting residues possesses an intrinsic causality that tells which residue controls the interaction and which one is controlled. Our work shows that time delayed correlations, entropy transfer and causality are the required new concepts for explaining allosteric communication in proteins.

Exciton Correlations in Intramolecular Singlet Fission

DOE PAGES

Sanders, Samuel N.; Kumarasamy, Elango; Pun, Andrew B.; ...

2016-05-16

We have synthesized a series of asymmetric pentacene-tetracene heterodimers with a variable-length conjugated bridge that undergo fast and efficient intramolecular singlet fission (iSF). These compounds have distinct singlet and triplet energies, which allow us to study the spatial dynamics of excitons during the iSF process, including the significant role of exciton correlations in promoting triplet pair generation and recombination. We demonstrate that the primary photoexcitations in conjugated dimers are delocalized singlets that enable fast and efficient iSF. However, in these asymmetric dimers, the singlet becomes more localized on the lower energy unit as the length of the bridge is increased,more » slowing down iSF relative to analogous symmetric dimers. We resolve the recombination kinetics of the inequivalent triplets produced via iSF, and find that they primarily decay via concerted processes. By identifying different decay channels, including delayed fluorescence via triplet-triplet annihilation, we can separate transient species corresponding to both correlated triplet pairs and uncorrelated triplets. Recombination of the triplet pair proceeds rapidly despite our experimental and theoretical demonstration that individual triplets are highly localized and unable to be transported across the conjugated linker. In this class of compounds, the rate of formation and yield of uncorrelated triplets increases with bridge length. Overall, these constrained, asymmetric systems provide a unique platform to isolate and study transient species essential for singlet fission, which are otherwise difficult to observe in symmetric dimers or condensed phases.« less

Tree-level correlations in the strong field regime

NASA Astrophysics Data System (ADS)

Gelis, François

2017-09-01

We consider the correlation function of an arbitrary number of local observables in quantum field theory, in situations where the field amplitude is large. Using a quasi-classical approximation (valid for a highly occupied initial mixed state, or for a coherent initial state if the classical dynamics has instabilities), we show that at tree level these correlations are dominated by fluctuations at the initial time. We obtain a general expression of the correlation functions in terms of the classical solution of the field equation of motion and its derivatives with respect to its initial conditions, that can be arranged graphically as the sum of labeled trees where the nodes are the individual observables, and the links are pairs of derivatives acting on them. For 3-point (and higher) correlation functions, there are additional tree-level terms beyond the quasi-classical approximation, generated by fluctuations in the bulk.

Demonstration of spectral correlation control in a source of polarization-entangled photon pairs at telecom wavelength.

PubMed

Lutz, Thomas; Kolenderski, Piotr; Jennewein, Thomas

2014-03-15

Spectrally correlated photon pairs can be used to improve the performance of long-range fiber-based quantum communication protocols. We present a source based on spontaneous parametric downconversion, which allows one to control spectral correlations within the entangled photon pair without spectral filtering by changing the pump-pulse duration or the characteristics of the coupled spatial modes. The spectral correlations and polarization entanglement are characterized. We find that the generated photon pairs can feature both positive spectral correlations, decorrelation, or negative correlations at the same time as polarization entanglement with a high fidelity of 0.97 (no background subtraction) with the expected Bell state.

Universal Long Ranged Correlations in Driven Binary Mixtures

NASA Astrophysics Data System (ADS)

Poncet, Alexis; Bénichou, Olivier; Démery, Vincent; Oshanin, Gleb

2017-03-01

When two populations of "particles" move in opposite directions, like oppositely charged colloids under an electric field or intersecting flows of pedestrians, they can move collectively, forming lanes along their direction of motion. The nature of this "laning transition" is still being debated and, in particular, the pair correlation functions, which are the key observables to quantify this phenomenon, have not been characterized yet. Here, we determine the correlations using an analytical approach based on a linearization of the stochastic equations for the density fields, which is valid for dense systems of soft particles. We find that the correlations decay algebraically along the direction of motion, and have a self-similar exponential profile in the transverse direction. Brownian dynamics simulations confirm our theoretical predictions and show that they also hold beyond the validity range of our analytical approach, pointing to a universal behavior.

Sporadic and thermospheric enhanced sodium layers observed by a lidar chain over China

NASA Astrophysics Data System (ADS)

Dou, X. K.; Qiu, S. C.; Xue, X. H.; Chen, T. D.; Ning, B. Q.

2013-10-01

We report the statistical features of sporadic sodium layers (SSLs) and the thermospheric enhanced sodium layers (TeSLs) observed by a lidar chain located at Beijing (40.2°N, 116.2°E), Hefei (31.8°N, 117.3°E), Wuhan (30.5°N, 114.4°E), and Haikou (19.5°N, 109.1°E). The average SSL occurrence rate was approximately 46.0, 12.3, 13.8, and 15.0 h per SSL at Beijing, Hefei, Wuhan, and Haikou, respectively. However, the TeSLs occurred relatively infrequently and were more likely to appear at low and high latitudinal sites. Both the SSLs and TeSLs at four lidar sites showed evident summer enhancements and correlated well with Es (foEs>4 MHz). The coobservations of SSLs at three lidar site pairs, i.e., Hefei-Beijing, Hefei-Wuhan, and Hefei-Beijing, indicated that a large-scale SSL extended horizontally for at least a few hundred kilometers and exhibited a tidal-induced modulation. Moreover, the SSLs were better correlated for the Hefei-Wuhan and Hefei-Haikou pairs than the Hefei-Beijing pair, which suggested a difference in the dynamical/chemical process in mesosphere and lower thermosphere (MLT) between the Beijing site and the other sites.

Sporadic and Thermospheric Enhanced Sodium Layers Observed by a Lidar Chain over China

NASA Astrophysics Data System (ADS)

Xue, X.

2013-12-01

We report the statistical features of sporadic sodium layers (SSLs) and the thermospheric enhanced sodium layers (TeSLs) observed by a lidar chain located at Beijing (40.2N,116.2E), Hefei (31.8N, 117.3E), Wuhan (30.5N, 114.4E), and Haikou (19.5N, 109.1E). The average SSL occurrence rate was approximately 46.0, 12.3, 13.8, and 15.0 hr per SSL at Beijing, Hefei, Wuhan, and Haikou, respectively. However, the TeSLs occurred relatively infrequently and were more likely to appear at low and high latitudinal sites. Both the SSLs and TeSLs at four lidar sites showed evident summer enhancements and correlated well with Es (foEs>4MHz). The co-observations of SSLs at three lidar site pairs, i.e., Hefei -- Beijing, Hefei -- Wuhan and Hefei -- Beijing, indicated that a large-scale SSL extended horizontally for at least a few hundred kilometers and exhibited a tidal-induced modulation. Moreover, the SSLs were better correlated for the Hefei -- Wuhan and Hefei -- Haikou pairs than the Hefei -- Beijing pair, which suggested a difference in the dynamical/chemical process in mesosphere and lower thermosphere (MLT) between the Beijing site and the other sites.

A Review of Digital Image Correlation Applied to Structura Dynamics

NASA Astrophysics Data System (ADS)

Niezrecki, Christopher; Avitabile, Peter; Warren, Christopher; Pingle, Pawan; Helfrick, Mark

2010-05-01

A significant amount of interest exists in performing non-contacting, full-field surface velocity measurement. For many years traditional non-contacting surface velocity measurements have been made by using scanning Doppler laser vibrometry, shearography, pulsed laser interferometry, pulsed holography, or an electronic speckle pattern interferometer (ESPI). Three dimensional (3D) digital image correlation (DIC) methods utilize the alignment of a stereo pair of images to obtain full-field geometry data, in three dimensions. Information about the change in geometry of an object over time can be found by comparing a sequence of images and virtual strain gages (or position sensors) can be created over the entire visible surface of the object of interest. Digital imaging techniques were first developed in the 1980s but the technology has only recently been exploited in industry and research due to the advances of digital cameras and personal computers. The use of DIC for structural dynamic measurement has only very recently been investigated. Within this paper, the advantages and limits of using DIC for dynamic measurement are reviewed. Several examples of using DIC for dynamic measurement are presented on several vibrating and rotating structures.

Quantum measurement-induced dynamics of many-body ultracold bosonic and fermionic systems in optical lattices

NASA Astrophysics Data System (ADS)

Mazzucchi, Gabriel; Kozlowski, Wojciech; Caballero-Benitez, Santiago F.; Elliott, Thomas J.; Mekhov, Igor B.

2016-02-01

Trapping ultracold atoms in optical lattices enabled numerous breakthroughs uniting several disciplines. Coupling these systems to quantized light leads to a plethora of new phenomena and has opened up a new field of study. Here we introduce an unusual additional source of competition in a many-body strongly correlated system: We prove that quantum backaction of global measurement is able to efficiently compete with intrinsic short-range dynamics of an atomic system. The competition becomes possible due to the ability to change the spatial profile of a global measurement at a microscopic scale comparable to the lattice period without the need of single site addressing. In coherence with a general physical concept, where new competitions typically lead to new phenomena, we demonstrate nontrivial dynamical effects such as large-scale multimode oscillations, long-range entanglement, and correlated tunneling, as well as selective suppression and enhancement of dynamical processes beyond the projective limit of the quantum Zeno effect. We demonstrate both the breakup and protection of strongly interacting fermion pairs by measurement. Such a quantum optical approach introduces into many-body physics novel processes, objects, and methods of quantum engineering, including the design of many-body entangled environments for open systems.

Perception of differences in naturalistic dynamic scenes, and a V1-based model.

PubMed

To, Michelle P S; Gilchrist, Iain D; Tolhurst, David J

2015-01-16

We investigate whether a computational model of V1 can predict how observers rate perceptual differences between paired movie clips of natural scenes. Observers viewed 198 pairs of movies clips, rating how different the two clips appeared to them on a magnitude scale. Sixty-six of the movie pairs were naturalistic and those remaining were low-pass or high-pass spatially filtered versions of those originals. We examined three ways of comparing a movie pair. The Spatial Model compared corresponding frames between each movie pairwise, combining those differences using Minkowski summation. The Temporal Model compared successive frames within each movie, summed those differences for each movie, and then compared the overall differences between the paired movies. The Ordered-Temporal Model combined elements from both models, and yielded the single strongest predictions of observers' ratings. We modeled naturalistic sustained and transient impulse functions and compared frames directly with no temporal filtering. Overall, modeling naturalistic temporal filtering improved the models' performance; in particular, the predictions of the ratings for low-pass spatially filtered movies were much improved by employing a transient impulse function. The correlations between model predictions and observers' ratings rose from 0.507 without temporal filtering to 0.759 (p = 0.01%) when realistic impulses were included. The sustained impulse function and the Spatial Model carried more weight in ratings for normal and high-pass movies, whereas the transient impulse function with the Ordered-Temporal Model was most important for spatially low-pass movies. This is consistent with models in which high spatial frequency channels with sustained responses primarily code for spatial details in movies, while low spatial frequency channels with transient responses code for dynamic events. © 2015 ARVO.

Quantifying Intracranial Aneurysm Wall Permeability for Risk Assessment Using Dynamic Contrast-Enhanced MRI: A Pilot Study.

PubMed

Vakil, P; Ansari, S A; Cantrell, C G; Eddleman, C S; Dehkordi, F H; Vranic, J; Hurley, M C; Batjer, H H; Bendok, B R; Carroll, T J

2015-05-01

Pathological changes in the intracranial aneurysm wall may lead to increases in its permeability; however the clinical significance of such changes has not been explored. The purpose of this pilot study was to quantify intracranial aneurysm wall permeability (K(trans), VL) to contrast agent as a measure of aneurysm rupture risk and compare these parameters against other established measures of rupture risk. We hypothesized K(trans) would be associated with intracranial aneurysm rupture risk as defined by various anatomic, imaging, and clinical risk factors. Twenty-seven unruptured intracranial aneurysms in 23 patients were imaged with dynamic contrast-enhanced MR imaging, and wall permeability parameters (K(trans), VL) were measured in regions adjacent to the aneurysm wall and along the paired control MCA by 2 blinded observers. K(trans) and VL were evaluated as markers of rupture risk by comparing them against established clinical (symptomatic lesions) and anatomic (size, location, morphology, multiplicity) risk metrics. Interobserver agreement was strong as shown in regression analysis (R(2) > 0.84) and intraclass correlation (intraclass correlation coefficient >0.92), indicating that the K(trans) can be reliably assessed clinically. All intracranial aneurysms had a pronounced increase in wall permeability compared with the paired healthy MCA (P < .001). Regression analysis demonstrated a significant trend toward an increased K(trans) with increasing aneurysm size (P < .001). Logistic regression showed that K(trans) also predicted risk in anatomic (P = .02) and combined anatomic/clinical (P = .03) groups independent of size. We report the first evidence of dynamic contrast-enhanced MR imaging-modeled contrast permeability in intracranial aneurysms. We found that contrast agent permeability across the aneurysm wall correlated significantly with both aneurysm size and size-independent anatomic risk factors. In addition, K(trans) was a significant and size-independent predictor of morphologically and clinically defined high-risk aneurysms. © 2015 by American Journal of Neuroradiology.

Single-camera displacement field correlation method for centrosymmetric 3D dynamic deformation measurement

NASA Astrophysics Data System (ADS)

Zhao, Jiaye; Wen, Huihui; Liu, Zhanwei; Rong, Jili; Xie, Huimin

2018-05-01

Three-dimensional (3D) deformation measurements are a key issue in experimental mechanics. In this paper, a displacement field correlation (DFC) method to measure centrosymmetric 3D dynamic deformation using a single camera is proposed for the first time. When 3D deformation information is collected by a camera at a tilted angle, the measured displacement fields are coupling fields of both the in-plane and out-of-plane displacements. The features of the coupling field are analysed in detail, and a decoupling algorithm based on DFC is proposed. The 3D deformation to be measured can be inverted and reconstructed using only one coupling field. The accuracy of this method was validated by a high-speed impact experiment that simulated an underwater explosion. The experimental results show that the approach proposed in this paper can be used in 3D deformation measurements with higher sensitivity and accuracy, and is especially suitable for high-speed centrosymmetric deformation. In addition, this method avoids the non-synchronisation problem associated with using a pair of high-speed cameras, as is common in 3D dynamic measurements.

Quantum correlations of lights in macroscopic environments

NASA Astrophysics Data System (ADS)

Sua, Yong Meng

This dissertation presents a detailed study in exploring quantum correlations of lights in macroscopic environments. We have explored quantum correlations of single photons, weak coherent states, and polarization-correlated/polarization-entangled photons in macroscopic environments. These included macroscopic mirrors, macroscopic photon number, spatially separated observers, noisy photons source and propagation medium with loss or disturbances. We proposed a measurement scheme for observing quantum correlations and entanglement in the spatial properties of two macroscopic mirrors using single photons spatial compass state. We explored the phase space distribution features of spatial compass states, such as chessboard pattern by using the Wigner function. The displacement and tilt correlations of the two mirrors were manifested through the propensities of the compass states. This technique can be used to extract Einstein-Podolsky-Rosen correlations (EPR) of the two mirrors. We then formulated the discrete-like property of the propensity P b(m,n), which can be used to explore environmental perturbed quantum jumps of the EPR correlations in phase space. With single photons spatial compass state, the variances in position and momentum are much smaller than standard quantum limit when using a Gaussian TEM 00 beam. We observed intrinsic quantum correlations of weak coherent states between two parties through balanced homodyne detection. Our scheme can be used as a supplement to decoy-state BB84 protocol and differential phase-shift QKD protocol. We prepared four types of bipartite correlations +/- cos2(theta1 +/- theta 2) that shared between two parties. We also demonstrated bits correlations between two parties separated by 10 km optical fiber. The bits information will be protected by the large quantum phase fluctuation of weak coherent states, adding another physical layer of security to these protocols for quantum key distribution. Using 10 m of highly nonlinear fiber (HNLF) at 77 K, we observed coincidence to accidental-coincidence ratio of 130+/-5 for correlated photon-pair and Two-Photon Interference visibility >98% entangled photon-pair. We also verified the non-local behavior of polarization-entangled photon pair by violating Clauser-Horne-Shimony-Holt Bell's inequality by more than 12 standard deviations. With the HNLF at 300 K (77 K), photon-pair production rate about factor 3(2) higher than a 300 m dispersion-shifted fiber is observed. Then, we studied quantum correlation and interference of photon-pairs; with one photon of the photon-pair experiencing multiple scattering in a random medium. We observed that depolarization noise photon in multiple scattering degrading the purity of photon-pair, and the existence of Raman noise photon in a photon-pair source will contribute to the depolarization affect. We found that quantum correlation of polarization-entangled photon-pair is better preserved than polarization-correlated photon-pair as one photon of the photon-pair scattered through a random medium. Our findings showed that high purity polarization-entangled photon-pair is better candidate for long distance quantum key distribution.

Lindemann histograms as a new method to analyse nano-patterns and phases

NASA Astrophysics Data System (ADS)

Makey, Ghaith; Ilday, Serim; Tokel, Onur; Ibrahim, Muhamet; Yavuz, Ozgun; Pavlov, Ihor; Gulseren, Oguz; Ilday, Omer

The detection, observation, and analysis of material phases and atomistic patterns are of great importance for understanding systems exhibiting both equilibrium and far-from-equilibrium dynamics. As such, there is intense research on phase transitions and pattern dynamics in soft matter, statistical and nonlinear physics, and polymer physics. In order to identify phases and nano-patterns, the pair correlation function is commonly used. However, this approach is limited in terms of recognizing competing patterns in dynamic systems, and lacks visualisation capabilities. In order to solve these limitations, we introduce Lindemann histogram quantification as an alternative method to analyse solid, liquid, and gas phases, along with hexagonal, square, and amorphous nano-pattern symmetries. We show that the proposed approach based on Lindemann parameter calculated per particle maps local number densities to material phase or particles pattern. We apply the Lindemann histogram method on dynamical colloidal self-assembly experimental data and identify competing patterns.

Noise switching at a dynamical critical point in a cavity-conductor hybrid

NASA Astrophysics Data System (ADS)

Armour, Andrew D.; Kubala, Björn; Ankerhold, Joachim

2017-12-01

Coupling a mesoscopic conductor to a microwave cavity can lead to fascinating feedback effects which generate strong correlations between the dynamics of photons and charges. We explore the connection between cavity dynamics and charge transport in a model system consisting of a voltage-biased Josephson junction embedded in a high-Q cavity, focusing on the behavior as the system is tuned through a dynamical critical point. On one side of the critical point the noise is strongly suppressed, signaling the existence of a regime of highly coherent transport, but on the other side it switches abruptly to a much larger value. Using a semiclassical approach we show that this behavior arises because of the strongly nonlinear cavity drive generated by the Cooper pairs. We also uncover an equivalence between charge and photonic current noise in the system which opens up a route to detecting the critical behavior through straightforward microwave measurements.

Electron Pairing, Repulsion, and Correlation: A Simplistic Approach

ERIC Educational Resources Information Center

Olsson, Lars-Fride; Kloo, Lars

2004-01-01

The interplay between a nucleus and an electron pair is explained through a basic application of an electrostatic and balanced model to determine the correlated and repulsive movements of the electron pair. The stable correlation depends on the positive charge produced by the combined force, which in turn establishes a negative potential energy.

On the pair correlations of neutral K, D, B and BS mesons with close momenta produced in inclusive multiparticle processes

NASA Astrophysics Data System (ADS)

Lyuboshitz, Valery V.; Lyuboshitz, Vladimir L.

2016-04-01

The phenomenological structure of inclusive cross-sections of the production of two neutral K mesons in collisions of hadrons and nuclei is investigated taking into account the strangeness conservation in strong and electromagnetic interactions. Relations describing the dependenceof the correlations of two short-lived and two long-lived neutral kaons KS∘ KS∘, KL∘ KL∘ and the correlations of ;mixed; pairs KS∘ KL∘ at small relative momenta upon the space-time parameters of the generation region of K∘ and Kbar∘ mesons have been obtained. It is shown that under the strangeness conservation the correlation functions of the pairs KS∘ KS∘ and KL∘ KL∘, produced in the same inclusive process, coincide, and the difference between the correlation functions of the pairs KS∘ KS∘ and KS∘ KL∘ is conditioned exclusively by the production of the pairs of non-identical neutral kaons K∘Kbar∘. Analogous correlations for the pairs of neutral heavy mesons D∘ ,B∘ and BS∘, generated in multiple processes with the charm (beauty) conservation, are analyzed, and differences from the case of neutral K mesons are discussed.

Marcus Theory of Ion-Pairing

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

Roy, Santanu; Baer, Marcel D.; Mundy, Christopher J.

We present a theory for ion pair dissociation and association, motivated by the concepts of the Marcus theory of electron transfer. Despite the extensive research on ion-pairing in many chemical and biological processes, much can be learned from the exploration of collective reaction coordinates. To this end, we explore two reaction coordinates, ion pair distance and coordination number. The study of the correlation between these reaction coordinates provides a new insight into the mechanism and kinetics of ion pair dissociation and association in water. The potential of mean force on these 2D-surfaces computed from molecular dynamics simulations of different monovalentmore » ion pairs reveal a Marcus-like mechanism for ion-pairing: Water molecules rearrange forming an activated coordination state prior to ion pair dissociation or association, followed by relaxation of the coordination state due to further water rearrangement. Like Marcus theory, we find the existence of an inverted region where the transition rates are slower with increasing exergonicity. This study provides a new perspective for the future investigations of ion-pairing and transport. SR, CJM, and GKS were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative, a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL). The research was performed using PNNL Institutional Computing. PNNL is a multi-program national laboratory operated by Battelle for the U.S. Department of Energy.« less

Packing of poly(tetrafluoroethylene) in the liquid state: Molecular dynamics simulation and theory

NASA Astrophysics Data System (ADS)

Tsige, Mesfin; Curro, John G.; Grest, Gary S.

2008-12-01

Molecular dynamics simulations and polymer reference interaction site model theory calculations were carried out on the C48F98 oligomer of poly(tetrafluoroethylene) (PTFE) at 500 and 600 K. The exp-6 force field of Borodin, Smith, and Bedrov, was used in both the simulation and theory. The agreement between theory and simulation was equivalent to earlier studies on polyolefin melts. The intermolecular pair correlation functions of PTFE were shifted to larger distances relative to polyethylene (PE) due to the difference in the van der Waals radii of F and H atoms. A similar shift to lower wave vectors was found in the structure factor of PTFE relative to PE.

Delay-correlation landscape reveals characteristic time delays of brain rhythms and heart interactions

PubMed Central

Lin, Aijing; Liu, Kang K. L.; Bartsch, Ronny P.; Ivanov, Plamen Ch.

2016-01-01

Within the framework of ‘Network Physiology’, we ask a fundamental question of how modulations in cardiac dynamics emerge from networked brain–heart interactions. We propose a generalized time-delay approach to identify and quantify dynamical interactions between physiologically relevant brain rhythms and the heart rate. We perform empirical analysis of synchronized continuous EEG and ECG recordings from 34 healthy subjects during night-time sleep. For each pair of brain rhythm and heart interaction, we construct a delay-correlation landscape (DCL) that characterizes how individual brain rhythms are coupled to the heart rate, and how modulations in brain and cardiac dynamics are coordinated in time. We uncover characteristic time delays and an ensemble of specific profiles for the probability distribution of time delays that underly brain–heart interactions. These profiles are consistently observed in all subjects, indicating a universal pattern. Tracking the evolution of DCL across different sleep stages, we find that the ensemble of time-delay profiles changes from one physiologic state to another, indicating a strong association with physiologic state and function. The reported observations provide new insights on neurophysiological regulation of cardiac dynamics, with potential for broad clinical applications. The presented approach allows one to simultaneously capture key elements of dynamic interactions, including characteristic time delays and their time evolution, and can be applied to a range of coupled dynamical systems. PMID:27044991

Delay-correlation landscape reveals characteristic time delays of brain rhythms and heart interactions

NASA Astrophysics Data System (ADS)

Lin, Aijing; Liu, Kang K. L.; Bartsch, Ronny P.; Ivanov, Plamen Ch.

2016-05-01

Within the framework of `Network Physiology', we ask a fundamental question of how modulations in cardiac dynamics emerge from networked brain-heart interactions. We propose a generalized time-delay approach to identify and quantify dynamical interactions between physiologically relevant brain rhythms and the heart rate. We perform empirical analysis of synchronized continuous EEG and ECG recordings from 34 healthy subjects during night-time sleep. For each pair of brain rhythm and heart interaction, we construct a delay-correlation landscape (DCL) that characterizes how individual brain rhythms are coupled to the heart rate, and how modulations in brain and cardiac dynamics are coordinated in time. We uncover characteristic time delays and an ensemble of specific profiles for the probability distribution of time delays that underly brain-heart interactions. These profiles are consistently observed in all subjects, indicating a universal pattern. Tracking the evolution of DCL across different sleep stages, we find that the ensemble of time-delay profiles changes from one physiologic state to another, indicating a strong association with physiologic state and function. The reported observations provide new insights on neurophysiological regulation of cardiac dynamics, with potential for broad clinical applications. The presented approach allows one to simultaneously capture key elements of dynamic interactions, including characteristic time delays and their time evolution, and can be applied to a range of coupled dynamical systems.

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.

Dynamics of Cancer Cell near Collagen Fiber Chain

NASA Astrophysics Data System (ADS)

Kim, Jihan; Sun, Bo

Cell migration is an integrated process that is important in life. Migration is essential for embryonic development as well as homeostatic processes such as wound healing and immune responses. When cell migrates through connective extracellular matrix (ECM), it applies cellular traction force to ECM and senses the rigidity of their local environment. We used human breast cancer cell (MDA-MB-231) which is highly invasive and applies strong traction force to ECM. As cancer cell applies traction force to type I collage-based ECM, it deforms collagen fibers near the surface. Patterns of deforming collagen fibers are significantly different with pairs of cancer cells compared to a single cancer cell. While a pair of cancer cells within 60 um creates aligned collagen fiber chains between them permanently, a single cancer cell does not form any fiber chains. In this experiment we measured a cellular response and an interaction between a pair of cells through the chain. Finally, we analyzed correlation of directions between cancer cell migration and the collagen chain alignment.

Fluctuation scaling of quotation activities in the foreign exchange market

NASA Astrophysics Data System (ADS)

Sato, Aki-Hiro; Nishimura, Maiko; Hołyst, Janusz A.

2010-07-01

We study the scaling behavior of quotation activities for various currency pairs in the foreign exchange market. The components’ centrality is estimated from multiple time series and visualized as a currency pair network. The power-law relationship between a mean of quotation activity and its standard deviation for each currency pair is found. The scaling exponent α and the ratio between common and specific fluctuations η increase with the length of the observation time window Δt. The result means that although for Δt=1 (min), the market dynamics are governed by specific processes, and at a longer time scale Δt>100 (min) the common information flow becomes more important. We point out that quotation activities are not independently Poissonian for Δt=1 (min), and temporally or mutually correlated activities of quotations can happen even at this time scale. A stochastic model for the foreign exchange market based on a bipartite graph representation is proposed.

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.

Variational Monte Carlo study of pentaquark states

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

Mark W. Paris

2005-07-01

Accurate numerical solution of the five-body Schrodinger equation is effected via variational Monte Carlo. The spectrum is assumed to exhibit a narrow resonance with strangeness S=+1. A fully antisymmetrized and pair-correlated five-quark wave function is obtained for the assumed non-relativistic Hamiltonian which has spin, isospin, and color dependent pair interactions and many-body confining terms which are fixed by the non-exotic spectra. Gauge field dynamics are modeled via flux tube exchange factors. The energy determined for the ground states with J=1/2 and negative (positive) parity is 2.22 GeV (2.50 GeV). A lower energy negative parity state is consistent with recent latticemore » results. The short-range structure of the state is analyzed via its diquark content.« less

Coupling of a high-energy excitation to superconducting quasiparticles in a cuprate from coherent charge fluctuation spectroscopy

PubMed Central

Mansart, Barbara; Lorenzana, José; Mann, Andreas; Odeh, Ahmad; Scarongella, Mariateresa; Chergui, Majed; Carbone, Fabrizio

2013-01-01

Dynamical information on spin degrees of freedom of proteins or solids can be obtained by NMR and electron spin resonance. A technique with similar versatility for charge degrees of freedom and their ultrafast correlations could move the understanding of systems like unconventional superconductors forward. By perturbing the superconducting state in a high-Tc cuprate, using a femtosecond laser pulse, we generate coherent oscillations of the Cooper pair condensate that can be described by an NMR/electron spin resonance formalism. The oscillations are detected by transient broad-band reflectivity and are found to resonate at the typical scale of Mott physics (2.6 eV), suggesting the existence of a nonretarded contribution to the pairing interaction, as in unconventional (non-Migdal–Eliashberg) theories.

Molecular dynamics of the water liquid-vapor interface

NASA Technical Reports Server (NTRS)

Wilson, M. A.; Pohorille, A.; Pratt, L. R.; MacElroy, R. D. (Principal Investigator)

1987-01-01

The results of molecular dynamics calculations on the equilibrium interface between liquid water and its vapor at 325 K are presented. For the TIP4P model of water intermolecular pair potentials, the average surface dipole density points from the vapor to the liquid. The most common orientations of water molecules have the C2 nu molecular axis roughly parallel to the interface. The distributions are quite broad and therefore compatible with the intermolecular correlations characteristic of bulk liquid water. All near-neighbor pairs in the outermost interfacial layers are hydrogen bonded according to the common definition adopted here. The orientational preferences of water molecules near a free surface differ from those near rigidly planar walls which can be interpreted in terms of patterns found in hexagonal ice 1. The mean electric field in the interfacial region is parallel to the mean polarization which indicates that attention cannot be limited to dipolar charge distributions in macroscopic descriptions of the electrical properties of this interface. The value of the surface tension obtained is 132 +/- 46 dyn/cm, significantly different from the value for experimental water of 68 dyn/cm at 325 K.

Correlation between discharge timings of pairs of motor units reveals the presence but not the proportion of common synaptic input to motor neurons

PubMed Central

Negro, Francesco; Farina, Dario

2017-01-01

We investigated whether correlation measures derived from pairs of motor unit (MU) spike trains are reliable indicators of the degree of common synaptic input to motor neurons. Several 50-s isometric contractions of the biceps brachii muscle were performed at different target forces ranging from 10 to 30% of the maximal voluntary contraction relying on force feedback. Forty-eight pairs of MUs were examined at various force levels. Motor unit synchrony was assessed by cross-correlation analysis using three indexes: the output correlation as the peak of the cross-histogram (ρ) and the number of synchronous spikes per second (CIS) and per trigger (E). Individual analysis of MU pairs revealed that ρ, CIS, and E were most often positively associated with discharge rate (87, 85, and 76% of the MU pairs, respectively) and negatively with interspike interval variability (69, 65, and 62% of the MU pairs, respectively). Moreover, the behavior of synchronization indexes with discharge rate (and interspike interval variability) varied greatly among the MU pairs. These results were consistent with theoretical predictions, which showed that the output correlation between pairs of spike trains depends on the statistics of the input current and motor neuron intrinsic properties that differ for different motor neuron pairs. In conclusion, the synchronization between MU firing trains is necessarily caused by the (functional) common input to motor neurons, but it is not possible to infer the degree of shared common input to a pair of motor neurons on the basis of correlation measures of their output spike trains. NEW & NOTEWORTHY The strength of correlation between output spike trains is only poorly associated with the degree of common input to the population of motor neurons. The synchronization between motor unit firing trains is necessarily caused by the (functional) common input to motor neurons, but it is not possible to infer the degree of shared common input to a pair of motor neurons on the basis of correlation measures of their output spike trains. PMID:28100652

Correlated Debye model for atomic motions in metal nanocrystals

NASA Astrophysics Data System (ADS)

Scardi, P.; Flor, A.

2018-05-01

The Correlated Debye model for the mean square relative displacement of atoms in near-neighbour coordination shells has been extended to include the effect of finite crystal size. This correctly explains the increase in Debye-Waller coefficient observed for metal nanocrystals. A good match with Molecular Dynamics simulations of Pd nanocrystals is obtained if, in addition to the phonon confinement effect of the finite domain size, proper consideration is also given to the static disorder component caused by the undercoordination of surface atoms. The new model, which addresses the analysis of the Pair Distribution Function and powder diffraction data collected at different temperatures, was preliminarily tested on recently published experimental data on nanocrystalline Pt powders.

Does the Atmosphere Precess?

NASA Astrophysics Data System (ADS)

Hester, R. E., Jr.

2015-12-01

The study considers a north-south pair of mid-latitude rings of atmospheric mass, symmetric with respect to the equator, and rotating with respect to the distant stars. The mass and angular velocity are assigned similar to the annual and zonal mean upper level westerlies. Their relatively rapid rotation is assumed to allow a rigid body approximation on long time and space scales. The rings are constrained to move as if rigidly connected to a common axis of rotation. The pair thus constitutes a symmetric top with a fixed pivot point at the center of mass. Analysis of the dynamics follows the classical mechanics approach used for precession of the equinoxes. The theoretical rate of precession for this highly idealized system yields a period on the order of decades. The predicted dynamics appears consistent with three prior studies of observational data: latitudinal movements of atmospheric circulation above far Southern Australia, latitudinal movements of ocean circulation in the Kuroshio Extension, and changes in global Atmospheric Angular Momentum before and after 1976. Each of these observational records indicates correlation with the Pacific Decadal Oscillation. The theoretical dynamics in combination with the observations suggests the axis of rotation of the atmospheric westerlies is offset from the Earth axis by a few degrees, and further, that this axis precesses around a mean axis on a time scale of a few decades.

A Molecular Dynamics-Quantum Mechanics Theoretical Study of DNA-Mediated Charge Transport in Hydrated Ionic Liquids.

PubMed

Meng, Zhenyu; Kubar, Tomas; Mu, Yuguang; Shao, Fangwei

2018-05-08

Charge transport (CT) through biomolecules is of high significance in the research fields of biology, nanotechnology, and molecular devices. Inspired by our previous work that showed the binding of ionic liquid (IL) facilitated charge transport in duplex DNA, in silico simulation is a useful means to understand the microscopic mechanism of the facilitation phenomenon. Here molecular dynamics simulations (MD) of duplex DNA in water and hydrated ionic liquids were employed to explore the helical parameters. Principal component analysis was further applied to capture the subtle conformational changes of helical DNA upon different environmental impacts. Sequentially, CT rates were calculated by a QM/MM simulation of the flickering resonance model based upon MD trajectories. Herein, MD simulation illustrated that the binding of ionic liquids can restrain dynamic conformation and lower the on-site energy of the DNA base. Confined movement among the adjacent base pairs was highly related to the increase of electronic coupling among base pairs, which may lead DNA to a CT facilitated state. Sequentially combining MD and QM/MM analysis, the rational correlations among the binding modes, the conformational changes, and CT rates illustrated the facilitation effects from hydrated IL on DNA CT and supported a conformational-gating mechanism.

Combination of Wavefunction and Density Functional Approximations for Describing Electronic Correlation

NASA Astrophysics Data System (ADS)

Garza, Alejandro J.

Perhaps the most important approximations to the electronic structure problem in quantum chemistry are those based on coupled cluster and density functional theories. Coupled cluster theory has been called the ``gold standard'' of quantum chemistry due to the high accuracy that it achieves for weakly correlated systems. Kohn-Sham density functionals based on semilocal approximations are, without a doubt, the most widely used methods in chemistry and material science because of their high accuracy/cost ratio. The root of the success of coupled cluster and density functionals is their ability to efficiently describe the dynamic part of the electron correlation. However, both traditional coupled cluster and density functional approximations may fail catastrophically when substantial static correlation is present. This severely limits the applicability of these methods to a plethora of important chemical and physical problems such as, e.g., the description of bond breaking, transition states, transition metal-, lanthanide- and actinide-containing compounds, and superconductivity. In an attempt to tackle this problem, nonstandard (single-reference) coupled cluster-based techniques that aim to describe static correlation have been recently developed: pair coupled cluster doubles (pCCD) and singlet-paired coupled cluster doubles (CCD0). The ability to describe static correlation in pCCD and CCD0 comes, however, at the expense of important amounts of dynamic correlation so that the high accuracy of standard coupled cluster becomes unattainable. Thus, the reliable and efficient description of static and dynamic correlation in a simultaneous manner remains an open problem for quantum chemistry and many-body theory in general. In this thesis, different ways to combine pCCD and CCD0 with density functionals in order to describe static and dynamic correlation simultaneously (and efficiently) are explored. The combination of wavefunction and density functional methods has a long history in quantum chemistry (practical implementations have appeared in the literature since the 1970s). However, this kind of techniques have not achieved widespread use due to problems such as double counting of correlation and the symmetry dilemma--the fact that wavefunction methods respect the symmetries of Hamiltonian, while modern functionals are designed to work with broken symmetry densities. Here, particular mathematical features of pCCD and CCD0 are exploited to avoid these problems in an efficient manner. The two resulting families of approximations, denoted as pCCD+DFT and CCD0+DFT, are shown to be able to describe static and dynamic correlation in standard benchmark calculations. Furthermore, it is also shown that CCD0+DFT lends itself to combination with correlation from the direct random phase approximation (dRPA). Inclusion of dRPA in the long-range via the technique of range-separation allows for the description of dispersion correlation, the remaining part of the correlation. Thus, when combined with the dRPA, CCD0+DFT can account for all three-types of electron correlation that are necessary to accurately describe molecular systems. Lastly, applications of CCD0+DFT to actinide chemistry are considered in this work. The accuracy of CCD0+DFT for predicting equilibrium geometries and vibrational frequencies of actinide molecules and ions is assessed and compared to that of well-established quantum chemical methods. For this purpose, the f0 actinyl series (UO2 2+, NpO 23+, PuO24+, the isoelectronic NUN, and Thorium (ThO, ThO2+) and Nobelium (NoO, NoO2) oxides are studied. It is shown that the CCD0+DFT description of these species agrees with available experimental data and is comparable with the results given by the highest-level calculations that are possible for such heavy compounds while being, at least, an order of magnitude lower in computational cost.

Experimental Investigation of Triplet Correlation Approximations for Fluid Water.

PubMed

Pallewela, Gayani N; Ploetz, Elizabeth A; Smith, Paul E

2018-08-25

Triplet correlations play a central role in our understanding of fluids and their properties. Of particular interest is the relationship between the pair and triplet correlations. Here we use a combination of Fluctuation Solution Theory and experimental pair radial distribution functions to investigate the accuracy of the Kirkwood Superposition Approximation (KSA), as given by integrals over the relevant pair and triplet correlation functions, at a series of state points for pure water using only experimental quantities. The KSA performs poorly, in agreement with a variety of other studies. Several additional approximate relationships between the pair and triplet correlations in fluids are also investigated and generally provide good agreement for the fluid thermodynamics for regions of the phase diagram where the compressibility is small. A simple power law relationship between the pair and triplet fluctuations is particularly successful for state points displaying low to moderately high compressibilities.

MicroRNA networks in mouse lung organogenesis.

PubMed

Dong, Jie; Jiang, Guoqian; Asmann, Yan W; Tomaszek, Sandra; Jen, Jin; Kislinger, Thomas; Wigle, Dennis A

2010-05-26

MicroRNAs (miRNAs) are known to be important regulators of both organ development and tumorigenesis. MiRNA networks and their regulation of messenger RNA (mRNA) translation and protein expression in specific biological processes are poorly understood. We explored the dynamic regulation of miRNAs in mouse lung organogenesis. Comprehensive miRNA and mRNA profiling was performed encompassing all recognized stages of lung development beginning at embryonic day 12 and continuing to adulthood. We analyzed the expression patterns of dynamically regulated miRNAs and mRNAs using a number of statistical and computational approaches, and in an integrated manner with protein levels from an existing mass-spectrometry derived protein database for lung development. In total, 117 statistically significant miRNAs were dynamically regulated during mouse lung organogenesis and clustered into distinct temporal expression patterns. 11,220 mRNA probes were also shown to be dynamically regulated and clustered into distinct temporal expression patterns, with 3 major patterns accounting for 75% of all probes. 3,067 direct miRNA-mRNA correlation pairs were identified involving 37 miRNAs. Two defined correlation patterns were observed upon integration with protein data: 1) increased levels of specific miRNAs directly correlating with downregulation of predicted mRNA targets; and 2) increased levels of specific miRNAs directly correlating with downregulation of translated target proteins without detectable changes in mRNA levels. Of 1345 proteins analyzed, 55% appeared to be regulated in this manner with a direct correlation between miRNA and protein level, but without detectable change in mRNA levels. Systematic analysis of microRNA, mRNA, and protein levels over the time course of lung organogenesis demonstrates dynamic regulation and reveals 2 distinct patterns of miRNA-mRNA interaction. The translation of target proteins affected by miRNAs independent of changes in mRNA level appears to be a prominent mechanism of developmental regulation in lung organogenesis.

Rotational and translational dynamics and their relation to hydrogen bond lifetimes in an ionic liquid by means of NMR relaxation time experiments and molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Strate, Anne; Neumann, Jan; Overbeck, Viviane; Bonsa, Anne-Marie; Michalik, Dirk; Paschek, Dietmar; Ludwig, Ralf

2018-05-01

We report a concerted theoretical and experimental effort to determine the reorientational dynamics as well as hydrogen bond lifetimes for the doubly ionic hydrogen bond +OH⋯O- in the ionic liquid (2-hydroxyethyl)trimethylammonium bis(trifluoromethylsulfonyl)imide [Ch][NTf2] by using a combination of NMR relaxation time experiments, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. Due to fast proton exchange, the determination of rotational correlation times is challenging. For molecular liquids, 17O-enhanced proton relaxation time experiments have been used to determine the rotational correlation times for the OH vectors in water or alcohols. As an alternative to those expensive isotopic substitution experiments, we employed a recently introduced approach which is providing access to the rotational dynamics from a single NMR deuteron quadrupolar relaxation time experiment. Here, the deuteron quadrupole coupling constants (DQCCs) are obtained from a relation between the DQCC and the δ1H proton chemical shifts determined from a set of DFT calculated clusters in combination with experimentally determined proton chemical shifts. The NMR-obtained rotational correlation times were compared to those obtained from MD simulations and then related to viscosities for testing the applicability of popular hydrodynamic models. In addition, hydrogen bond lifetimes were derived, using hydrogen bond population correlation functions computed from MD simulations. Here, two different time domains were observed: The short-time contributions to the hydrogen lifetimes and the reorientational correlation times have roughly the same size and are located in the picosecond range, whereas the long-time contributions decay with relaxation times in the nanosecond regime and are related to rather slow diffusion processes. The computed average hydrogen bond lifetime is dominated by the long-time process, highlighting the importance and longevity of hydrogen-bonded ion pairs in these ionic liquids.

Networks as Renormalized Models for Emergent Behavior in Physical Systems

NASA Astrophysics Data System (ADS)

Paczuski, Maya

2005-09-01

Networks are paradigms for describing complex biological, social and technological systems. Here I argue that networks provide a coherent framework to construct coarsegrained models for many different physical systems. To elucidate these ideas, I discuss two long-standing problems. The first concerns the structure and dynamics of magnetic fields in the solar corona, as exemplified by sunspots that startled Galileo almost 400 years ago. We discovered that the magnetic structure of the corona embodies a scale free network, with spots at all scales. A network model representing the three-dimensional geometry of magnetic fields, where links rewire and nodes merge when they collide in space, gives quantitative agreement with available data, and suggests new measurements. Seismicity is addressed in terms of relations between events without imposing space-time windows. A metric estimates the correlation between any two earthquakes. Linking strongly correlated pairs, and ignoring pairs with weak correlation organizes the spatio-temporal process into a sparse, directed, weighted network. New scaling laws for seismicity are found. For instance, the aftershock decay rate decreases as ~ 1/t in time up to a correlation time, tomori. An estimate from the data gives tomori to be about one year for small magnitude 3 earthquakes, about 1400 years for the Landers event, and roughly 26,000 years for the earthquake causing the 2004 Asian tsunami. Our results confirm Kagan's conjecture that aftershocks can rumble on for centuries.

Dynamic Evolution of Financial Network and its Relation to Economic Crises

NASA Astrophysics Data System (ADS)

Gao, Ya-Chun; Wei, Zong-Wen; Wang, Bing-Hong

2013-02-01

The static topology properties of financial networks have been widely investigated since the work done by Mantegna, yet their dynamic evolution with time is little considered. In this paper, we comprehensively study the dynamic evolution of financial network by a sliding window technique. The vertices and edges of financial network are represented by the stocks from S&P500 components and correlations between pairs of daily returns of price fluctuation, respectively. Furthermore, the duration of stock price fluctuation, spanning from January 4, 1985 to September 14, 2009, makes us to carefully observe the relation between the dynamic topological properties and big financial crashes. The empirical results suggest that the financial network has the robust small-world property when the time evolves, and the topological structure drastically changes when the big financial crashes occur. This correspondence between the dynamic evolution of financial network and big financial crashes may provide a novel view to understand the origin of economic crisis.

A high-order time-accurate interrogation method for time-resolved PIV

NASA Astrophysics Data System (ADS)

Lynch, Kyle; Scarano, Fulvio

2013-03-01

A novel method is introduced for increasing the accuracy and extending the dynamic range of time-resolved particle image velocimetry (PIV). The approach extends the concept of particle tracking velocimetry by multiple frames to the pattern tracking by cross-correlation analysis as employed in PIV. The working principle is based on tracking the patterned fluid element, within a chosen interrogation window, along its individual trajectory throughout an image sequence. In contrast to image-pair interrogation methods, the fluid trajectory correlation concept deals with variable velocity along curved trajectories and non-zero tangential acceleration during the observed time interval. As a result, the velocity magnitude and its direction are allowed to evolve in a nonlinear fashion along the fluid element trajectory. The continuum deformation (namely spatial derivatives of the velocity vector) is accounted for by adopting local image deformation. The principle offers important reductions of the measurement error based on three main points: by enlarging the temporal measurement interval, the relative error becomes reduced; secondly, the random and peak-locking errors are reduced by the use of least-squares polynomial fits to individual trajectories; finally, the introduction of high-order (nonlinear) fitting functions provides the basis for reducing the truncation error. Lastly, the instantaneous velocity is evaluated as the temporal derivative of the polynomial representation of the fluid parcel position in time. The principal features of this algorithm are compared with a single-pair iterative image deformation method. Synthetic image sequences are considered with steady flow (translation, shear and rotation) illustrating the increase of measurement precision. An experimental data set obtained by time-resolved PIV measurements of a circular jet is used to verify the robustness of the method on image sequences affected by camera noise and three-dimensional motions. In both cases, it is demonstrated that the measurement time interval can be significantly extended without compromising the correlation signal-to-noise ratio and with no increase of the truncation error. The increase of velocity dynamic range scales more than linearly with the number of frames included for the analysis, which supersedes by one order of magnitude the pair correlation by window deformation. The main factors influencing the performance of the method are discussed, namely the number of images composing the sequence and the polynomial order chosen to represent the motion throughout the trajectory.

Local structure order in Pd 78Cu 6Si 16 liquid

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

Yue, G. Q.; Zhang, Y.; Sun, Y.

2015-02-05

The short-range order (SRO) in Pd 78Cu 6Si 16 liquid was studied by high energy x-ray diffraction and ab initio molecular dynamics (MD) simulations. The calculated pair correlation functions at different temperatures agree well with the experimental results. The partial pair correlation functions from ab intio MD simulations indicate that Si atoms prefer to be uniformly distributed while Cu atoms tend to aggregate. By performing structure analysis using Honeycutt-Andersen index, Voronoi tessellation, and atomic cluster alignment method, we show that the icosahedron and face-centered cubic SRO increase upon cooling. The dominant SRO is the Pd-centered Pd 9Si 2 motif, namelymore » the structure of which motif is similar to the structure of Pd-centered clusters in the Pd 9Si 2 crystal. The study further confirms the existence of trigonal prism capped with three half-octahedra that is reported as a structural unit in Pd-based amorphous alloys. The majority of Cu-centered clusters are icosahedra, suggesting that the presence of Cu is benefit to promote the glass forming ability.« less

Topological Characteristics of the Hong Kong Stock Market: A Test-based P-threshold Approach to Understanding Network Complexity

NASA Astrophysics Data System (ADS)

Xu, Ronghua; Wong, Wing-Keung; Chen, Guanrong; Huang, Shuo

2017-02-01

In this paper, we analyze the relationship among stock networks by focusing on the statistically reliable connectivity between financial time series, which accurately reflects the underlying pure stock structure. To do so, we firstly filter out the effect of market index on the correlations between paired stocks, and then take a t-test based P-threshold approach to lessening the complexity of the stock network based on the P values. We demonstrate the superiority of its performance in understanding network complexity by examining the Hong Kong stock market. By comparing with other filtering methods, we find that the P-threshold approach extracts purely and significantly correlated stock pairs, which reflect the well-defined hierarchical structure of the market. In analyzing the dynamic stock networks with fixed-size moving windows, our results show that three global financial crises, covered by the long-range time series, can be distinguishingly indicated from the network topological and evolutionary perspectives. In addition, we find that the assortativity coefficient can manifest the financial crises and therefore can serve as a good indicator of the financial market development.

Proton configurations and pairing correlations at the N=80 superdeformed shell closure: Study of 145Tb

NASA Astrophysics Data System (ADS)

Mullins, S. M.; Schmeing, N. C.; Flibotte, S.; Hackman, G.; Rodriguez, J. L.; Waddington, J. C.; Yao, L.; Andrews, H. R.; Galindo-Uribarri, A.; Janzen, V. P.; Radford, D. C.; Ward, D.; Degraaf, J.; Drake, T. E.; Pilotte, S.; Paul, E. S.

1994-11-01

A superdeformed band has been observed in the N=80 nucleus 145Tb which was produced with the reactions 112Sn(37Cl,2p2n) and 118Sn(31P,4n) at bombarding energies of 187 and 160 MeV, respectively. Since superdeformed bands also exist in the three lighter N=80 isotones 142Sm, 143Eu, and 144Gd, it is now possible to understand the valence-proton configurations of these bands in a systematic way. The T(2) dynamic moment of inertia in 145Tb shows no evidence for the N = 6 quasiproton crossing that is observed in 144Gd. Comparison with cranked Woods-Saxon and total Routhian surface calculations suggests that the proton configuration in 145Tb is 61⊗[404]29/2+ in which the quasiproton crossing is blocked. Furthermore, like 143Eu and 142Sm, there is no evidence in the T (2) for the N=6 quasineutron crossing predicted by the calculations. This may indicate that static neutron pairing correlations are quenched at the N=80 superdeformed shell closure.

Ionic structures and transport properties of hot dense W and U plasmas

NASA Astrophysics Data System (ADS)

Hou, Yong; Yuan, Jianmin

2016-10-01

We have combined the average-atom model with the hyper-netted chain approximation (AAHNC) to describe the electronic and ionic structure of uranium and tungsten in the hot dense matter regime. When the electronic structure is described within the average-atom model, the effects of others ions on the electronic structure are considered by the correlation functions. And the ionic structure is calculated though using the hyper-netted chain (HNC) approximation. The ion-ion pair potential is calculated using the modified Gordon-Kim model based on the electronic density distribution in the temperature-depended density functional theory. And electronic and ionic structures are determined self-consistently. On the basis of the ion-ion pair potential, we perform the classical (CMD) and Langevin (LMD) molecular dynamics to simulate the ionic transport properties, such as ionic self-diffusion and shear viscosity coefficients, through the ionic velocity correlation functions. Due that the free electrons become more and more with increasing the plasma temperature, the influence of the electron-ion collisions on the transport properties become more and more important.

Multiconfiguration Pair-Density Functional Theory.

PubMed

Li Manni, Giovanni; Carlson, Rebecca K; Luo, Sijie; Ma, Dongxia; Olsen, Jeppe; Truhlar, Donald G; Gagliardi, Laura

2014-09-09

We present a new theoretical framework, called Multiconfiguration Pair-Density Functional Theory (MC-PDFT), which combines multiconfigurational wave functions with a generalization of density functional theory (DFT). A multiconfigurational self-consistent-field (MCSCF) wave function with correct spin and space symmetry is used to compute the total electronic density, its gradient, the on-top pair density, and the kinetic and Coulomb contributions to the total electronic energy. We then use a functional of the total density, its gradient, and the on-top pair density to calculate the remaining part of the energy, which we call the on-top-density-functional energy in contrast to the exchange-correlation energy of Kohn-Sham DFT. Because the on-top pair density is an element of the two-particle density matrix, this goes beyond the Hohenberg-Kohn theorem that refers only to the one-particle density. To illustrate the theory, we obtain first approximations to the required new type of density functionals by translating conventional density functionals of the spin densities using a simple prescription, and we perform post-SCF density functional calculations using the total density, density gradient, and on-top pair density from the MCSCF calculations. Double counting of dynamic correlation or exchange does not occur because the MCSCF energy is not used. The theory is illustrated by applications to the bond energies and potential energy curves of H2, N2, F2, CaO, Cr2, and NiCl and the electronic excitation energies of Be, C, N, N(+), O, O(+), Sc(+), Mn, Co, Mo, Ru, N2, HCHO, C4H6, c-C5H6, and pyrazine. The method presented has a computational cost and scaling similar to MCSCF, but a quantitative accuracy, even with the present first approximations to the new types of density functionals, that is comparable to much more expensive multireference perturbation theory methods.

Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin

PubMed Central

2017-01-01

It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others. We apply the model to Ubiquitin, whose allosteric activity has not been emphasized until recently, and show that there are indeed systematic pathways of entropy and information transfer between residues that correlate well with the activities of the protein. We use 600 nanosecond molecular dynamics trajectories for Ubiquitin and its complex with human polymerase iota and evaluate entropy transfer between all pairs of residues of Ubiquitin and quantify the binding susceptibility changes upon complex formation. We explain the complex formation propensities of Ubiquitin in terms of entropy transfer. Important residues taking part in allosteric communication in Ubiquitin predicted by our approach are in agreement with results of NMR relaxation dispersion experiments. Finally, we show that time delayed correlation of fluctuations of two interacting residues possesses an intrinsic causality that tells which residue controls the interaction and which one is controlled. Our work shows that time delayed correlations, entropy transfer and causality are the required new concepts for explaining allosteric communication in proteins. PMID:28095404

Open charm and dileptons from relativistic heavy-ion collisions

NASA Astrophysics Data System (ADS)

Song, Taesoo; Cassing, Wolfgang; Moreau, Pierre; Bratkovskaya, Elena

2018-06-01

Dileptons are considered as one of the cleanest signals of the quark-gluon plasma (QGP); however, the QGP radiation is masked by many background sources from either hadronic decays or semileptonic decays from correlated charm pairs. In this study, we investigate the relative contribution of these channels in heavy-ion collisions from √{sNN}=8 GeV to 5 TeV with a focus on the competition between the thermal QGP radiation and the semileptonic decays from correlated D -meson pairs. As a tool, we employ the parton-hadron-string dynamics (PHSD) transport approach to study dilepton spectra in Pb + Pb (Au + Au) collisions in a wide energy range, incorporating for the first time a fully microscopic treatment of the charm dynamics and their semileptonic decays. We find that the dileptons from correlated D -meson decays dominate the thermal radiation from the QGP in central Pb + Pb collisions at the intermediate masses (1.2 GeV 40 GeV, while for √{sNN}=8 to 20 GeV the contribution from D ,D ¯ decays to the intermediate mass dilepton spectra is subleading such that one should observe a rather clear signal from the QGP radiation. We furthermore study the pT spectra and the RA A(pT) of single electrons at different energies as well as the excitation function of the inverse slope of the mT spectra for intermediate-mass dileptons from the QGP and from charm decays. We find moderate but characteristic changes in the inverse slope parameter for √{sNN}> 20 GeV which can be observed experimentally in high statistics data. Additionally, we provide detailed predictions for dilepton spectra from Pb + Pb collisions at √{sNN}= 5.02 TeV.

Diffusion Tensor Analysis by Two-Dimensional Pair Correlation of Fluorescence Fluctuations in Cells.

PubMed

Di Rienzo, Carmine; Cardarelli, Francesco; Di Luca, Mariagrazia; Beltram, Fabio; Gratton, Enrico

2016-08-23

In a living cell, the movement of biomolecules is highly regulated by the cellular organization into subcompartments that impose barriers to diffusion, can locally break the spatial isotropy, and ultimately guide these molecules to their targets. Despite the pivotal role of these processes, experimental tools to fully probe the complex connectivity (and accessibility) of the cell interior with adequate spatiotemporal resolution are still lacking. Here, we show how the heterogeneity of molecular dynamics and the location of barriers to molecular motion can be mapped in live cells by exploiting a two-dimensional (2D) extension of the pair correlation function (pCF) analysis. Starting from a time series of images collected for the same field of view, the resulting 2D pCF is calculated in the proximity of each point for each time delay and allows us to probe the spatial distribution of the molecules that started from a given pixel. This 2D pCF yields an accurate description of the preferential diffusive routes. Furthermore, we combine this analysis with the image-derived mean-square displacement approach and gain information on the average nanoscopic molecular displacements in different directions. Through these quantities, we build a fluorescence-fluctuation-based diffusion tensor that contains information on speed and directionality of the local dynamical processes. Contrary to classical fluorescence correlation spectroscopy and related methods, this combined approach can distinguish between isotropic and anisotropic local diffusion. We argue that the measurement of this iMSD tensor will contribute to advance our understanding of the role played by the intracellular environment in the regulation of molecular diffusion at the nanoscale. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

The dynamics of reproductive rate, offspring survivorship and growth in the lined seahorse, Hippocampus erectus Perry, 1810

PubMed Central

Lin, Qiang; Li, Gang; Qin, Geng; Lin, Junda; Huang, Liangmin; Sun, Hushan; Feng, Peiyong

2012-01-01

Summary Seahorses are the vertebrate group with the embryonic development occurring within a special pouch in males. To understand the reproductive efficiency of the lined seahorse, Hippocampus erectus Perry, 1810 under controlled breeding experiments, we investigated the dynamics of reproductive rate, offspring survivorship and growth over births by the same male seahorses. The mean brood size of the 1-year old pairs in the 1st birth was 85.4±56.9 per brood, which was significantly smaller than that in the 6th birth (465.9±136.4 per brood) (P<0.001). The offspring survivorship and growth rate increased with the births. The fecundity was positively correlated with the length of brood pouches of males and trunk of females. The fecundity of 1-year old male and 2-year old female pairs was significantly higher than that from 1-year old couples (P<0.001). The brood size (552.7±150.4) of the males who mated with females that were isolated for the gamete-preparation, was larger than those (467.8±141.2) from the long-term pairs (P<0.05). Moreover, the offspring from the isolated females had higher survival and growth rates. Our results showed that the potential reproductive rate of seahorses H. erectus increased with the brood pouch development. PMID:23213429

Analysis of the Electronic Structure of the Special Pair of a Bacterial Photosynthetic Reaction Center by 13 C Photochemically Induced Dynamic Nuclear Polarization Magic-Angle Spinning NMR Using a Double-Quantum Axis.

PubMed

Najdanova, Marija; Gräsing, Daniel; Alia, A; Matysik, Jörg

2018-01-01

The origin of the functional symmetry break in bacterial photosynthesis challenges since several decades. Although structurally very similar, the two branches of cofactors in the reaction center (RC) protein complex act very differently. Upon photochemical excitation, an electron is transported along one branch, while the other remains inactive. Photochemically induced dynamic nuclear polarization (photo-CIDNP) magic-angle spinning (MAS) 13 C NMR revealed that the two bacteriochlorophyll cofactors forming the "Special Pair" donor dimer are already well distinguished in the electronic ground state. These previous studies are relying solely on 13 C- 13 C correlation experiments as radio-frequency-driven recoupling (RFDR) and dipolar-assisted rotational resonance (DARR). Obviously, the chemical-shift assignment is difficult in a dimer of tetrapyrrole macrocycles, having eight pyrrole rings of similar chemical shifts. To overcome this problem, an INADEQUATE type of experiment using a POST C7 symmetry-based approach is applied to selectively isotope-labeled bacterial RC of Rhodobacter (R.) sphaeroides wild type (WT). We, therefore, were able to distinguish unresolved sites of the macromolecular dimer. The obtained chemical-shift pattern is in-line with a concentric assembly of negative charge within the common center of the Special Pair supermolecule in the electronic ground state. © 2017 The American Society of Photobiology.

Colloid-Colloid Hydrodynamic Interaction Around a Bend in a Quasi-One-Dimensional Channel

NASA Astrophysics Data System (ADS)

Liepold, Christopher; Zarcone, Ryan; Heumann, Tibor; Lin, Binhua; Rice, Stuart

We report a study of the correlation between a pair of particles in a colloid suspension in a bent quasi-one-dimensional (q1d) channel as a function of bend angle. As the bend angle becomes more acute, we observe an increasing depletion of particles in the vicinity of the bend and an increase in the nearest-neighbor separation in the pair correlation function for particles on opposite sides of the bend. Further, we observe that the peak value of D12, the coupling term in the pair diffusion tensor that characterizes the effect of the motion of particle 1 on particle 2, coincides with the first peak in the pair correlation function, and that the pair separation dependence of D12 mimics that of the pair correlation function. We show that the observed behavior is a consequence of the geometric constraints imposed by the single-file requirement that the particle centers lie on the centerline of the channel and the requirement that the hydrodynamic flow must follow the channel around the bend. We find that the correlation between a pair of particles in a colloidal suspension in a bent q1D channel has the same functional dependence on the pair correlation function as in a straight q1D channel when measured in a coordinate system that follows the centerline of the bent channel. NSF MRSEC (DMR-1420709), Dreyfus Foundation (SI-14-014).

Deposition-temperature dependence of structural anisotropy in amorphous Tb-Fe films

NASA Astrophysics Data System (ADS)

Harris, V. G.; Elam, W. T.; Koon, N. C.; Hellman, F.

1994-02-01

The anisotropic local structure in a series of amorphous Tb26Fe74 films deposited at different deposition temperatures and having different magnetic anisotropy energies have been investigated using polarization-dependent extended x-ray-absorption fine-structure measurements. Samples deposited at temperatures >=300 K exhibit anisotropic pair correlations where like atomic pairs are favored in plane and unlike pairs are favored out of plane. Both the anisotropic pair correlations and the perpendicular magnetic anisotropy increase with increasing deposition temperature. In contrast, a sample deposited at 77 K was found to have isotropic pair correlations, low perpendicular magnetic anisotropy, and a large (~=1%) in-plane compression.

Functional network connectivity analysis based on partial correlation in Alzheimer's disease

NASA Astrophysics Data System (ADS)

Zhang, Nan; Guan, Xiaoting; Zhang, Yumei; Li, Jingjing; Chen, Hongyan; Chen, Kewei; Fleisher, Adam; Yao, Li; Wu, Xia

2009-02-01

Functional network connectivity (FNC) measures the temporal dependency among the time courses of functional networks. However, the marginal correlation between two networks used in the classic FNC analysis approach doesn't separate the FNC from the direct/indirect effects of other networks. In this study, we proposed an alternative approach based on partial correlation to evaluate the FNC, since partial correlation based FNC can reveal the direct interaction between a pair of networks, removing dependencies or influences from others. Previous studies have demonstrated less task-specific activation and less rest-state activity in Alzheimer's disease (AD). We applied present approach to contrast FNC differences of resting state network (RSN) between AD and normal controls (NC). The fMRI data under resting condition were collected from 15 AD and 16 NC. FNC was calculated for each pair of six RSNs identified using Group ICA, thus resulting in 15 (2 out of 6) pairs for each subject. Partial correlation based FNC analysis indicated 6 pairs significant differences between groups, while marginal correlation only revealed 2 pairs (involved in the partial correlation results). Additionally, patients showed lower correlation than controls among most of the FNC differences. Our results provide new evidences for the disconnection hypothesis in AD.

Thermophysical properties of krypton-helium gas mixtures from ab initio pair potentials

PubMed Central

2017-01-01

A new potential energy curve for the krypton-helium atom pair was developed using supermolecular ab initio computations for 34 interatomic distances. Values for the interaction energies at the complete basis set limit were obtained from calculations with the coupled-cluster method with single, double, and perturbative triple excitations and correlation consistent basis sets up to sextuple-zeta quality augmented with mid-bond functions. Higher-order coupled-cluster excitations up to the full quadruple level were accounted for in a scheme of successive correction terms. Core-core and core-valence correlation effects were included. Relativistic corrections were considered not only at the scalar relativistic level but also using full four-component Dirac–Coulomb and Dirac–Coulomb–Gaunt calculations. The fitted analytical pair potential function is characterized by a well depth of 31.42 K with an estimated standard uncertainty of 0.08 K. Statistical thermodynamics was applied to compute the krypton-helium cross second virial coefficients. The results show a very good agreement with the best experimental data. Kinetic theory calculations based on classical and quantum-mechanical approaches for the underlying collision dynamics were utilized to compute the transport properties of krypton-helium mixtures in the dilute-gas limit for a large temperature range. The results were analyzed with respect to the orders of approximation of kinetic theory and compared with experimental data. Especially the data for the binary diffusion coefficient confirm the predictive quality of the new potential. Furthermore, inconsistencies between two empirical pair potential functions for the krypton-helium system from the literature could be resolved. PMID:28595411

Thermophysical properties of krypton-helium gas mixtures from ab initio pair potentials

NASA Astrophysics Data System (ADS)

Jäger, Benjamin; Bich, Eckard

2017-06-01

A new potential energy curve for the krypton-helium atom pair was developed using supermolecular ab initio computations for 34 interatomic distances. Values for the interaction energies at the complete basis set limit were obtained from calculations with the coupled-cluster method with single, double, and perturbative triple excitations and correlation consistent basis sets up to sextuple-zeta quality augmented with mid-bond functions. Higher-order coupled-cluster excitations up to the full quadruple level were accounted for in a scheme of successive correction terms. Core-core and core-valence correlation effects were included. Relativistic corrections were considered not only at the scalar relativistic level but also using full four-component Dirac-Coulomb and Dirac-Coulomb-Gaunt calculations. The fitted analytical pair potential function is characterized by a well depth of 31.42 K with an estimated standard uncertainty of 0.08 K. Statistical thermodynamics was applied to compute the krypton-helium cross second virial coefficients. The results show a very good agreement with the best experimental data. Kinetic theory calculations based on classical and quantum-mechanical approaches for the underlying collision dynamics were utilized to compute the transport properties of krypton-helium mixtures in the dilute-gas limit for a large temperature range. The results were analyzed with respect to the orders of approximation of kinetic theory and compared with experimental data. Especially the data for the binary diffusion coefficient confirm the predictive quality of the new potential. Furthermore, inconsistencies between two empirical pair potential functions for the krypton-helium system from the literature could be resolved.

Dependence of the atomic level Green-Kubo stress correlation function on wavevector and frequency: molecular dynamics results from a model liquid.

PubMed

Levashov, V A

2014-09-28

We report on a further investigation of a new method that can be used to address vibrational dynamics and propagation of stress waves in liquids. The method is based on the decomposition of the macroscopic Green-Kubo stress correlation function into the atomic level stress correlation functions. This decomposition, as was demonstrated previously for a model liquid studied in molecular dynamics simulations, reveals the presence of stress waves propagating over large distances and a structure that resembles the pair density function. In this paper, by performing the Fourier transforms of the atomic level stress correlation functions, we elucidate how the lifetimes of the stress waves and the ranges of their propagation depend on their frequency, wavevector, and temperature. These results relate frequency and wavevector dependence of the generalized viscosity to the character of propagation of the shear stress waves. In particular, the results suggest that an increase in the value of the frequency dependent viscosity at low frequencies with decrease of temperature is related to the increase in the ranges of propagation of the stress waves of the corresponding low frequencies. We found that the ranges of propagation of the shear stress waves of frequencies less than half of the Einstein frequency extend well beyond the nearest neighbor shell even above the melting temperature. The results also show that the crossover from quasilocalized to propagating behavior occurs at frequencies usually associated with the Boson peak.

A Molecular Dynamics Simulation of the Molten Ternary System (Li, K, Cs)Cl

NASA Astrophysics Data System (ADS)

Matsumiya, Masahiko; Takagi, Ryuzo

2000-12-01

The self-exchange velocity (SEV) of neighboring unlike ions, has been evaluated by molecular dynamics simulations of molten CsCl, (Li, K)C1 and (Li, K, Cs)Cl at 673 K. From the increase of the SEV's in the same order as the internal mobilities it is conjectured that there is a strong correlation between these two properties. The pair correlation functions, and the self-diffusion coefficients and the SEV's of Li+, K+, and Cs+ with reference to Cl- have also been calculated. The results allow to conclude that the self-exchange velocity of the cations become vCs < vK < vLi at xCs =0.1 and vLi < vK < vCs at xCs > 0.4. The sequence of the self-diffusion coefficients agrees with that of the SEV's. The results enable to conclude that it is possible to enrich Cs at up to xCs ~ 0.3 - 0.4 in the molten LiCl-KCl eutectic system.

Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis.

PubMed

Hurst, Travis; Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

2018-05-10

The selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) method probes RNA local structural and dynamic information at single nucleotide resolution. To gain quantitative insights into the relationship between nucleotide flexibility, RNA 3D structure, and SHAPE reactivity, we develop a 3D Structure-SHAPE Relationship model (3DSSR) to rebuild SHAPE profiles from 3D structures. The model starts from RNA structures and combines nucleotide interaction strength and conformational propensity, ligand (SHAPE reagent) accessibility, and base-pairing pattern through a composite function to quantify the correlation between SHAPE reactivity and nucleotide conformational stability. The 3DSSR model shows the relationship between SHAPE reactivity and RNA structure and energetics. Comparisons between the 3DSSR-predicted SHAPE profile and the experimental SHAPE data show correlation, suggesting that the extracted analytical function may have captured the key factors that determine the SHAPE reactivity profile. Furthermore, the theory offers an effective method to sieve RNA 3D models and exclude models that are incompatible with experimental SHAPE data.

Interplay between proton-neutron pairing and deformation in self-conjugated medium mass nuclei

NASA Astrophysics Data System (ADS)

Gambacurta, Danilo; Lacroix, Denis

2016-05-01

We employ a model combining self-consistent mean-field and shell model techniques to study the competition between particle-like and proton-neutron pairing correlations in fp-shell even-even self-conjugate nuclei. Deformation effects are realistically and microscopically described. The resulting approach can give a precise description of pairing correlations and eventually treat the coexistence of different condensate formed of pairs with different total spin/ isospin. The standard BCS calculations are systematically compared with approaches including correlation effects beyond the independent quasi-particle picture. The competition between proton-neutron correlations in the isoscalar and isovector channels is also analyzed, as well as their dependence on the deformation properties.

Surprising loss of three-dimensionality in low-energy spin correlations on approaching superconductivity in Fe 1 + y Te 1 - x Se x

DOE PAGES

Xu, Zhijun; Schneeloch, J. A.; Wen, Jinsheng; ...

2017-10-06

We report inelastic neutron scattering measurements of low-energy ( ℏ ω ≲ 10 meV) magnetic excitations in the “11” system Fe 1+y Te 1-x Se x. The spin correlations are two-dimensional (2D) in the superconducting samples at low temperature, but appear much more three-dimensional (3D) when the temperature rises well above T c ~ 15 K, with a clear increase of the (dynamic) spin correlation length perpendicular to the Fe planes. This behavior is extremely unusual; typically, the suppression of thermal fluctuations at low temperature would favor the enhancement of 3D correlations, or even ordering, and the reversion to 2Dmore » cannot be naturally explained when only the spin degree of freedom is considered. Our results suggest that the low temperature physics in the 11 system, in particular the evolution of low-energy spin excitations towards superconducting pairing, intrinsically involves changes in orbital correlations.« less

Surprising loss of three-dimensionality in low-energy spin correlations on approaching superconductivity in Fe1 +yTe1 -xSex

NASA Astrophysics Data System (ADS)

Xu, Zhijun; Schneeloch, J. A.; Wen, Jinsheng; Winn, B. L.; Granroth, G. E.; Zhao, Yang; Gu, Genda; Zaliznyak, Igor; Tranquada, J. M.; Birgeneau, R. J.; Xu, Guangyong

2017-10-01

We report inelastic neutron scattering measurements of low-energy (ℏ ω ≲10 meV) magnetic excitations in the "11" system Fe1 +yTe1 -xSex . The spin correlations are two-dimensional (2D) in the superconducting samples at low temperature, but appear much more three-dimensional (3D) when the temperature rises well above Tc˜15 K, with a clear increase of the (dynamic) spin correlation length perpendicular to the Fe planes. This behavior is extremely unusual; typically, the suppression of thermal fluctuations at low temperature would favor the enhancement of 3D correlations, or even ordering, and the reversion to 2D cannot be naturally explained when only the spin degree of freedom is considered. Our results suggest that the low temperature physics in the 11 system, in particular the evolution of low-energy spin excitations towards superconducting pairing, intrinsically involves changes in orbital correlations.

Surprising loss of three-dimensionality in low-energy spin correlations on approaching superconductivity in Fe 1 + y Te 1 - x Se x

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

Xu, Zhijun; Schneeloch, J. A.; Wen, Jinsheng

We report inelastic neutron scattering measurements of low-energy ( ℏ ω ≲ 10 meV) magnetic excitations in the “11” system Fe 1+y Te 1-x Se x. The spin correlations are two-dimensional (2D) in the superconducting samples at low temperature, but appear much more three-dimensional (3D) when the temperature rises well above T c ~ 15 K, with a clear increase of the (dynamic) spin correlation length perpendicular to the Fe planes. This behavior is extremely unusual; typically, the suppression of thermal fluctuations at low temperature would favor the enhancement of 3D correlations, or even ordering, and the reversion to 2Dmore » cannot be naturally explained when only the spin degree of freedom is considered. Our results suggest that the low temperature physics in the 11 system, in particular the evolution of low-energy spin excitations towards superconducting pairing, intrinsically involves changes in orbital correlations.« less

Low-noise current amplifier based on mesoscopic Josephson junction.

PubMed

Delahaye, J; Hassel, J; Lindell, R; Sillanpää, M; Paalanen, M; Seppä, H; Hakonen, P

2003-02-14

We used the band structure of a mesoscopic Josephson junction to construct low-noise amplifiers. By taking advantage of the quantum dynamics of a Josephson junction, i.e., the interplay of interlevel transitions and the Coulomb blockade of Cooper pairs, we created transistor-like devices, Bloch oscillating transistors, with considerable current gain and high-input impedance. In these transistors, the correlated supercurrent of Cooper pairs is controlled by a small base current made up of single electrons. Our devices reached current and power gains on the order of 30 and 5, respectively. The noise temperature was estimated to be around 1 kelvin, but noise temperatures of less than 0.1 kelvin can be realistically achieved. These devices provide quantum-electronic building blocks that will be useful at low temperatures in low-noise circuit applications with an intermediate impedance level.

Cooperative Search of Autonomous Vehicles for Unknown Targets

NASA Astrophysics Data System (ADS)

Yang, Sheng Qing; Yu, Jian Qiao; Zhang, Si Yu

2013-01-01

We study the orbital-dependent superconducting pairing in a five-orbital t-J1-J2 model for iron pnictides. Depending on the orbital selectivity of electron correlations and the orbital characters along the Fermi surface, the superconducting gap in an A_{1g} pairing state may exhibit anisotropy. This anisotropy varies with the degree of J1-J2 magnetic frustration. We have also calculated the dynamical spin susceptibility in the superconducting state. The frequency dependence of the susceptibility at the antiferromagnetic wavevector (\\pi,0) shows a resonance, whose width is enhanced by the orbital dependence of the superconducting gap; when the latter is sufficiently strong, the resonance peak may be split into two. We discuss the implications of our results on the recent angle-resolved photoemission and neutron-scattering measurements in several superconducting iron pnictides.

A new look at the near-wall turbulence structure

NASA Astrophysics Data System (ADS)

Choi, Kwing-So

An experiment was carried out in the BMT environmental wind tunnel (4.8 m x 2.4 m x 15 m) in order to study the near-wall structure of the turbulent boundary layer, particular attention being given to the dynamics of the 'near-wall bursts'. Conditional sampling of the wall-shear stress fluctuations was extensively used along with a simultaneous application of flow visualization using a streak-smoke wire and a sheet of laser light. The results suggested that a 'near-wall burst' was taking place between a pair of smoke tubes, which was interpreted as a pair of stretched legs of neighboring hairpin loops. The spanwise spacing of the 'near-wall bursts' determined from a conditional space correlation of skin-friction signals was found to be a function of the threshold value used in burst detection.

Molecular dynamics simulation of polymer electrolytes based on poly(ethylene oxide) and ionic liquids. II. Dynamical properties.

PubMed

Costa, Luciano T; Ribeiro, Mauro C C

2007-10-28

Dynamical properties of polymer electrolytes based on poly(ethylene oxide) (PEO) and ionic liquids of 1-alkyl-3-methylimidazolium cations were calculated by molecular dynamics simulations with previously proposed models [L. T. Costa and M. C. Ribeiro, J. Chem. Phys. 124, 184902 (2006)]. The effect of changing the ionic liquid concentration, temperature, and the 1-alkyl-chain lengths, [1,3-dimethylimidazolium]PF(6) and [1-butyl-3-methylimidazolium]PF(6) ([dmim]PF(6) and [bmim]PF(6)), was investigated. Cation diffusion coefficient is higher than those of anion and oxygen atoms of PEO chains. Ionic mobility in PEO[bmim]PF(6) is higher than in PEO[dmim]PF(6), so that the ionic conductivity kappa of the former is approximately ten times larger than the latter. The ratio between kappa and its estimate from the Nernst-Einstein equation kappa/kappa(NE), which is inversely proportional to the strength of ion pairs, is higher in ionic liquid polymer electrolytes than in polymer electrolytes based on inorganic salts with Li(+) cations. Calculated time correlation functions corroborate previous evidence from the analysis of equilibrium structure that the ion pairs in ionic liquid polymer electrolytes are relatively weak. Structural relaxation at distinct spatial scales is revealed by the calculation of the intermediate scattering function at different wavevectors. These data are reproduced with stretched exponential functions, so that temperature and wavevector dependences of best fit parameters can be compared with corresponding results for polymer electrolytes containing simpler ions.

Structural analysis of graphene and h-BN: A molecular dynamics approach

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

Thomas, Siby; Ajith, K. M., E-mail: ajith@nitk.ac.in; Valsakumar, M. C.

2016-05-06

Classical molecular dynamics simulation is employed to analyze pair correlations in graphene and h-BN at various temperatures to explore the integrity of their respective structures. As the temperature increases, the height fluctuations in the out-of-plane direction of both graphene and h-BN are found to increase. The positional spread of atoms also increases with temperature. Thus the amplitude of the peak positions in the radial distribution function (RDF) decreases with temperature. It is found that FWHM of peaks in the RDF of h-BN is smaller as compared to those of graphene which implies that the structure of h-BN is more robustmore » as compared to that of graphene with respect to their respective empirical potential.« less

Convergence of third order correlation energy in atoms and molecules.

PubMed

Kahn, Kalju; Granovsky, Alex A; Noga, Jozef

2007-01-30

We have investigated the convergence of third order correlation energy within the hierarchies of correlation consistent basis sets for helium, neon, and water, and for three stationary points of hydrogen peroxide. This analysis confirms that singlet pair energies converge much slower than triplet pair energies. In addition, singlet pair energies with (aug)-cc-pVDZ and (aug)-cc-pVTZ basis sets do not follow a converging trend and energies with three basis sets larger than aug-cc-pVTZ are generally required for reliable extrapolations of third order correlation energies, making so the explicitly correlated R12 calculations preferable.

Synchronization, non-linear dynamics and low-frequency fluctuations: Analogy between spontaneous brain activity and networked single-transistor chaotic oscillators

PubMed Central

Minati, Ludovico; Chiesa, Pietro; Tabarelli, Davide; D'Incerti, Ludovico

2015-01-01

In this paper, the topographical relationship between functional connectivity (intended as inter-regional synchronization), spectral and non-linear dynamical properties across cortical areas of the healthy human brain is considered. Based upon functional MRI acquisitions of spontaneous activity during wakeful idleness, node degree maps are determined by thresholding the temporal correlation coefficient among all voxel pairs. In addition, for individual voxel time-series, the relative amplitude of low-frequency fluctuations and the correlation dimension (D2), determined with respect to Fourier amplitude and value distribution matched surrogate data, are measured. Across cortical areas, high node degree is associated with a shift towards lower frequency activity and, compared to surrogate data, clearer saturation to a lower correlation dimension, suggesting presence of non-linear structure. An attempt to recapitulate this relationship in a network of single-transistor oscillators is made, based on a diffusive ring (n = 90) with added long-distance links defining four extended hub regions. Similarly to the brain data, it is found that oscillators in the hub regions generate signals with larger low-frequency cycle amplitude fluctuations and clearer saturation to a lower correlation dimension compared to surrogates. The effect emerges more markedly close to criticality. The homology observed between the two systems despite profound differences in scale, coupling mechanism and dynamics appears noteworthy. These experimental results motivate further investigation into the heterogeneity of cortical non-linear dynamics in relation to connectivity and underline the ability for small networks of single-transistor oscillators to recreate collective phenomena arising in much more complex biological systems, potentially representing a future platform for modelling disease-related changes. PMID:25833429

Synchronization, non-linear dynamics and low-frequency fluctuations: Analogy between spontaneous brain activity and networked single-transistor chaotic oscillators

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

Minati, Ludovico, E-mail: lminati@ieee.org, E-mail: ludovico.minati@unitn.it, E-mail: lminati@istituto-besta.it; Center for Mind/Brain Sciences, University of Trento, Trento; Chiesa, Pietro

In this paper, the topographical relationship between functional connectivity (intended as inter-regional synchronization), spectral and non-linear dynamical properties across cortical areas of the healthy human brain is considered. Based upon functional MRI acquisitions of spontaneous activity during wakeful idleness, node degree maps are determined by thresholding the temporal correlation coefficient among all voxel pairs. In addition, for individual voxel time-series, the relative amplitude of low-frequency fluctuations and the correlation dimension (D{sub 2}), determined with respect to Fourier amplitude and value distribution matched surrogate data, are measured. Across cortical areas, high node degree is associated with a shift towards lower frequencymore » activity and, compared to surrogate data, clearer saturation to a lower correlation dimension, suggesting presence of non-linear structure. An attempt to recapitulate this relationship in a network of single-transistor oscillators is made, based on a diffusive ring (n = 90) with added long-distance links defining four extended hub regions. Similarly to the brain data, it is found that oscillators in the hub regions generate signals with larger low-frequency cycle amplitude fluctuations and clearer saturation to a lower correlation dimension compared to surrogates. The effect emerges more markedly close to criticality. The homology observed between the two systems despite profound differences in scale, coupling mechanism and dynamics appears noteworthy. These experimental results motivate further investigation into the heterogeneity of cortical non-linear dynamics in relation to connectivity and underline the ability for small networks of single-transistor oscillators to recreate collective phenomena arising in much more complex biological systems, potentially representing a future platform for modelling disease-related changes.« less

Electrocortical correlations between pairs of isolated people: A reanalysis

PubMed Central

Radin, Dean

2017-01-01

A previously reported experiment collected electrocortical data recorded simultaneously in pairs of people separated by distance. Reanalysis of those data confirmed the presence of a time-synchronous, statistically significant correlation in brain electrical activity of these distant “sender-receiver” pairs. Given the sensory shielding employed in the original experiment to avoid mundane explanations for such a correlation, this outcome is suggestive of an anomalous intersubjective connection. PMID:28713556

Spin-correlated doublet pairs as intermediate states in charge separation processes

NASA Astrophysics Data System (ADS)

Kraffert, Felix; Behrends, Jan

2017-10-01

Spin-correlated charge-carrier pairs play a crucial role as intermediate states in charge separation both in natural photosynthesis as well as in solar cells. Using transient electron paramagnetic resonance (trEPR) spectroscopy in combination with spectral simulations, we study spin-correlated polaron pairs in polymer:fullerene blends as organic solar cells materials. The semi-analytical simulations presented here are based on the well-established theoretical description of spin-correlated radical pairs in biological systems, however, explicitly considering the disordered nature of polymer:fullerene blends. The large degree of disorder leads to the fact that many different relative orientations between both polarons forming the spin-correlated pairs have to be taken into account. This has important implications for the spectra, which differ significantly from those of spin-correlated radical pairs with a fixed relative orientation. We systematically study the influence of exchange and dipolar couplings on the trEPR spectra and compare the simulation results to measured X- and Q-band trEPR spectra. Our results demonstrate that assuming dipolar couplings alone does not allow us to reproduce the experimental spectra. Due to the rather delocalised nature of polarons in conjugated organic semiconductors, a significant isotropic exchange coupling needs to be included to achieve good agreement between experiments and simulations.

Individual Differences in Dynamic Measures of Verbal Learning Abilities in Young Twin Pairs and Their Older Siblings

ERIC Educational Resources Information Center

van Soelen, Inge L. C.; van den Berg, Stephanie M.; Dekker, Peter H.; van Leeuwen, Marieke; Peper, Jiska S.; Hulshoff Pol, Hilleke E.; Boomsma, Dorret I.

2009-01-01

We explored the genetic background of individual differences in dynamic measures of verbal learning ability in children, using a Dutch version of the Auditory Verbal Learning Test (AVLT). Nine-year-old twin pairs (N = 112 pairs) were recruited from the Netherlands Twin Register. When possible, an older sibling between 10 and 14 years old…

Many-body quantum dynamics in the decay of bent dark solitons of Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Katsimiga, G. C.; Mistakidis, S. I.; Koutentakis, G. M.; Kevrekidis, P. G.; Schmelcher, P.

2017-12-01

The beyond mean-field (MF) dynamics of a bent dark soliton (BDS) embedded in a two-dimensional repulsively interacting Bose-Einstein condensate is explored. We examine the case of a single BDS comparing the MF dynamics to a correlated approach, the multi-configuration time-dependent Hartree method for bosons. Dynamical snaking of this bent structure is observed, signaling the onset of fragmentation which becomes significant during the vortex nucleation. In contrast to the MF approximation ‘filling’ of the vortex core is observed, leading in turn to the formation of filled-core vortices, instead of the MF vortex-antivortex pairs. The resulting smearing effect in the density is a rather generic feature, occurring when solitonic structures are exposed to quantum fluctuations. Here, we show that this filling owes its existence to the dynamical building of an antidark structure developed in the next-to-leading order orbital. We further demonstrate that the aforementioned beyond MF dynamics can be experimentally detected using the variance of single shot measurements. Additionally, a variety of excitations including vortices, oblique dark solitons, and open ring dark soliton-like structures building upon higher-lying orbitals is observed. We demonstrate that signatures of the higher-lying orbital excitations emerge in the total density, and can be clearly captured by inspecting the one-body coherence. In the latter context, the localization of one-body correlations exposes the existence of the multi-orbital vortex-antidark structure.

What Is a Simple Liquid?

NASA Astrophysics Data System (ADS)

Ingebrigtsen, Trond S.; Schrøder, Thomas B.; Dyre, Jeppe C.

2012-01-01

This paper is an attempt to identify the real essence of simplicity of liquids in John Locke’s understanding of the term. Simple liquids are traditionally defined as many-body systems of classical particles interacting via radially symmetric pair potentials. We suggest that a simple liquid should be defined instead by the property of having strong correlations between virial and potential-energy equilibrium fluctuations in the NVT ensemble. There is considerable overlap between the two definitions, but also some notable differences. For instance, in the new definition simplicity is not a direct property of the intermolecular potential because a liquid is usually only strongly correlating in part of its phase diagram. Moreover, not all simple liquids are atomic (i.e., with radially symmetric pair potentials) and not all atomic liquids are simple. The main part of the paper motivates the new definition of liquid simplicity by presenting evidence that a liquid is strongly correlating if and only if its intermolecular interactions may be ignored beyond the first coordination shell (FCS). This is demonstrated by NVT simulations of the structure and dynamics of several atomic and three molecular model liquids with a shifted-forces cutoff placed at the first minimum of the radial distribution function. The liquids studied are inverse power-law systems (r-n pair potentials with n=18,6,4), Lennard-Jones (LJ) models (the standard LJ model, two generalized Kob-Andersen binary LJ mixtures, and the Wahnstrom binary LJ mixture), the Buckingham model, the Dzugutov model, the LJ Gaussian model, the Gaussian core model, the Hansen-McDonald molten salt model, the Lewis-Wahnstrom ortho-terphenyl model, the asymmetric dumbbell model, and the single-point charge water model. The final part of the paper summarizes properties of strongly correlating liquids, emphasizing that these are simpler than liquids in general. Simple liquids, as defined here, may be characterized in three quite different ways: (1) chemically by the fact that the liquid’s properties are fully determined by interactions from the molecules within the FCS, (2) physically by the fact that there are isomorphs in the phase diagram, i.e., curves along which several properties like excess entropy, structure, and dynamics, are invariant in reduced units, and (3) mathematically by the fact that throughout the phase diagram the reduced-coordinate constant-potential-energy hypersurfaces define a one-parameter family of compact Riemannian manifolds. No proof is given that the chemical characterization follows from the strong correlation property, but we show that this FCS characterization is consistent with the existence of isomorphs in strongly correlating liquids’ phase diagram. Finally, we note that the FCS characterization of simple liquids calls into question the physical basis of standard perturbation theory, according to which the repulsive and attractive forces play fundamentally different roles for the physics of liquids.

SO(8) fermion dynamical symmetry and strongly correlated quantum Hall states in monolayer graphene

NASA Astrophysics Data System (ADS)

Wu, Lian-Ao; Murphy, Matthew; Guidry, Mike

2017-03-01

A formalism is presented for treating strongly correlated graphene quantum Hall states in terms of an SO(8) fermion dynamical symmetry that includes pairing as well as particle-hole generators. The graphene SO(8) algebra is isomorphic to an SO(8) algebra that has found broad application in nuclear physics, albeit with physically very different generators, and exhibits a strong formal similarity to SU(4) symmetries that have been proposed to describe high-temperature superconductors. The well-known SU(4) symmetry of quantum Hall ferromagnetism for single-layer graphene is recovered as one subgroup of SO(8), but the dynamical symmetry structure associated with the full set of SO(8) subgroup chains extends quantum Hall ferromagnetism and allows analytical many-body solutions for a rich set of collective states exhibiting spontaneously broken symmetry that may be important for the low-energy physics of graphene in strong magnetic fields. The SO(8) symmetry permits a natural definition of generalized coherent states that correspond to symmetry-constrained Hartree-Fock-Bogoliubov solutions, or equivalently a microscopically derived Ginzburg-Landau formalism, exhibiting the interplay between competing spontaneously broken symmetries in determining the ground state.

Injury incidence and balance in rugby players.

PubMed

M, Jaco Ras; Puckree, Threethambal

2014-01-01

Objective : This study determined and correlated injury incidence and balance in rugby players. A prospective survey with balance testing was conducted on first year rugby academy players (N= 114). Injury incidence, static and dynamic balance were tested pre and post-season using a Biosway portable balance system. The data was analysed using paired and independent samples t-tests at p<0.05, Odds ratios, and Spearman's correlation coefficients. 75.50% participated, 71.40% were 18 years old, and 71.40% were White. Injury was sustained by 83% of players with the knee (25%) most commonly injured. Injury incidence was 1.52 per player with an injury rate of 5.95 injuries per 1000 match playing hours. The Stability Index increased significantly (p=0.03) by 15% in the medial/lateral direction post-season compared to pre-season. Significant differences in post-test anterior posterior and overall static and front and front right dynamic stability between injured and uninjured players were noted. Risk factors for injury included the scrum-half (14.80%) playing position, injuries in the 2nd half of the match (57%), and during contact (67%). Conclusion : Injury incidence was related to static and dynamic balance in forward right direction only.

Injury incidence and balance in rugby players

PubMed Central

M, Jaco Ras; Puckree, Threethambal

2014-01-01

Objective : This study determined and correlated injury incidence and balance in rugby players. Methods: A prospective survey with balance testing was conducted on first year rugby academy players (N= 114). Injury incidence, static and dynamic balance were tested pre and post-season using a Biosway portable balance system. The data was analysed using paired and independent samples t-tests at p<0.05, Odds ratios, and Spearman’s correlation coefficients. Results: 75.50% participated, 71.40% were 18 years old, and 71.40% were White. Injury was sustained by 83% of players with the knee (25%) most commonly injured. Injury incidence was 1.52 per player with an injury rate of 5.95 injuries per 1000 match playing hours. The Stability Index increased significantly (p=0.03) by 15% in the medial/lateral direction post-season compared to pre-season. Significant differences in post-test anterior posterior and overall static and front and front right dynamic stability between injured and uninjured players were noted. Risk factors for injury included the scrum-half (14.80%) playing position, injuries in the 2nd half of the match (57%), and during contact (67%). Conclusion : Injury incidence was related to static and dynamic balance in forward right direction only. PMID:25674136

Thermodynamics and Kinetics of Na+/K+-Formate Ion Pairs Association in Polarizable Water: A Molecular Dynamics Study

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

Nguyen, Phuong T.; Nguyen, Van T.; Annapureddy, Harsha V.

2012-12-03

To elevate our understanding of ion specific activity in biological systems, the potential of mean force approach was utilized to study solvent effects on 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, stronger binding between the Na+-formate pair was found in comparison to the K+-formate pair in water, a finding that agrees with experimental and theoretical studies of these systems. The kinetics of ion-pair interconversions were studied using transition rate theory, along with a variety of theoretical approachesmore » such as the Kramers and Grote Hynes theories. These rate results were used to predict solvent effects on dynamical features of contact ion-pair association, in which faster dynamics were found for K+-formate pairs than for Na+-formate pairs. This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences (BES), Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory is a multiprogram national laboratory operated for DOE by Battelle.« less

Correlations of daily flows at streamgages in and near West Virginia, 1930-2011, and streamflow characteristics relevant to the use of index streamgages

USGS Publications Warehouse

Messinger, Terence; Paybins, Katherine S.

2014-01-01

Correlation of flows at pairs of streamgages were evaluated using a Spearman’s rho correlation coefficient to better identify gages that can be used as index gages to estimate daily flow at ungaged stream sites in West Virginia. Much of West Virginia (77 percent) is within areas where Spearman’s rho for daily streamflow between streamgages on unregulated streams (unregulated streamgages) is greater than 0.9; most withdrawals from ungaged streams for shale gas well hydraulic fracturing are being made in these areas. Most of West Virginia (>99 percent) is within zones where Spearman’s rho between streamgages on unregulated streams is greater than 0.85. Withdrawals for hydraulic fracturing are made from ungaged streams in areas where Spearman’s rho between streamgages on unregulated streams is less than 0.9, but because spatial correlation is partly a function of the density of the streamgaging network, adding or reactivating several streamgages would be likely to result in correlations of 0.90 or higher in these areas. Seasonal differences in the strength and spatial extent of correlations of daily streamflows are great. The strongest correlations among streamgages are for fall, followed by spring, then winter. One possible explanation for the weak correlations for summer may be that precipitation and runoff associated with convective storms affect one basin and miss nearby basins. A comparison of correlation patterns during previously identified climatic periods shows that the strongest correlations occurred during 1963–69, a period of drought, and the weakest during 1970–79, a wet period. The apparent effect of frequent rain during 1970–79 overshadowed streamgage-network density, which was at its historic maximum in West Virginia at that time, so that the extent of areas with high correlation to at least one streamgage was smaller during 1970–79 than during 1963–69. Correlations for 1992 to 2011 were slightly weaker than those for 1963 to 1969. The relation between correlation and distance between basin centroids was determined to be stronger for streamgage pairs in the Ohio River Basin than for pairs in the Atlantic Slope River Basins, which in turn was stronger than the relation between pairs of streamgages split between the two major basins. Quantile regression equations were developed for these three comparisons to estimate the Spearman’s rho correlation coefficient for streamgage pairs using distance between basin centroids as a predictor variable. The equations can be used for streamgage network planning. For the Ohio River Basin, the distance between basin centroids at which 50 percent of streamgage pairs would exceed a Spearman’s rho of 0.95 is 9 miles. The distance between basin centroids at which 50 percent of streamgage pairs would exceed a Spearman’s rho of 0.90 is 25 miles, and the distance at which 50 percent of streamgage pairs would exceed a Spearman’s rho of 0.85 is 48 miles. For the Atlantic Slope River Basins, the distance between basin centroids at which 50 percent of streamgage pairs would exceed a Spearman’s rho of 0.95 is 1 mile. The distance between basin centroids at which 50 percent of streamgage pairs would exceed a Spearman’s rho of 0.90 is 13 miles, and the distance at which 50 percent of streamgage pairs would exceed a Spearman’s rho of 0.85 is 41 miles. For pairs of streamgages split between the two major basins, the regression equation gives a value of 0.84 for the correlation coefficient at zero miles. On maps of correlations, the shape of strongly correlated areas for streamgages in the Ohio River Basin is generally round. In the Valley and Ridge Physiographic Province, which generally coincides with the Atlantic Slope River Basins within the study area, areas strongly correlated with streamgages generally coincide with major valleys.

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

PubMed Central

He, Feng; Zeng, An-Ping

2006-01-01

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

Enhanced sampling simulations of DNA step parameters.

PubMed

Karolak, Aleksandra; van der Vaart, Arjan

2014-12-15

A novel approach for the selection of step parameters as reaction coordinates in enhanced sampling simulations of DNA is presented. The method uses three atoms per base and does not require coordinate overlays or idealized base pairs. This allowed for a highly efficient implementation of the calculation of all step parameters and their Cartesian derivatives in molecular dynamics simulations. Good correlation between the calculated and actual twist, roll, tilt, shift, and slide parameters is obtained, while the correlation with rise is modest. The method is illustrated by its application to the methylated and unmethylated 5'-CATGTGACGTCACATG-3' double stranded DNA sequence. One-dimensional umbrella simulations indicate that the flexibility of the central CG step is only marginally affected by methylation. © 2014 Wiley Periodicals, Inc.

Too Much Matching: A Social Relations Model Enhancement of the Pairing Game

ERIC Educational Resources Information Center

Eastwick, Paul W.; Buck, April A.

2014-01-01

The Pairing Game is a popular classroom demonstration that illustrates how people select romantic partners who approximate their own desirability. However, this game produces matching correlations that greatly exceed the correlations that characterize actual romantic pairings, perhaps because the game does not incorporate the social relations…

Two-Point Microrheology of Phase-Separated Domains in Lipid Bilayers

PubMed Central

Hormel, Tristan T.; Reyer, Matthew A.; Parthasarathy, Raghuveer

2015-01-01

Though the importance of membrane fluidity for cellular function has been well established for decades, methods for measuring lipid bilayer viscosity remain challenging to devise and implement. Recently, approaches based on characterizing the Brownian dynamics of individual tracers such as colloidal particles or lipid domains have provided insights into bilayer viscosity. For fluids in general, however, methods based on single-particle trajectories provide a limited view of hydrodynamic response. The technique of two-point microrheology, in which correlations between the Brownian dynamics of pairs of tracers report on the properties of the intervening medium, characterizes viscosity at length-scales that are larger than that of individual tracers and has less sensitivity to tracer-induced distortions, but has never been applied to lipid membranes. We present, to our knowledge, the first two-point microrheological study of lipid bilayers, examining the correlated motion of domains in phase-separated lipid vesicles and comparing one- and two-point results. We measure two-point correlation functions in excellent agreement with the forms predicted by two-dimensional hydrodynamic models, analysis of which reveals a viscosity intermediate between those of the two lipid phases, indicative of global fluid properties rather than the viscosity of the local neighborhood of the tracer. PMID:26287625

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

Costigliola, Lorenzo; Schrøder, Thomas B.; Dyre, Jeppe C.

The recent theoretical prediction by Maimbourg and Kurchan [e-print http://arxiv.org/abs/1603.05023 (2016)] that for regular pair-potential systems the virial potential-energy correlation coefficient increases towards unity as the dimension d goes to infinity is investigated for the standard 12-6 Lennard-Jones fluid. This is done by computer simulations for d = 2, 3, 4 going from the critical point along the critical isotherm/isochore to higher density/temperature. In both cases the virial potential-energy correlation coefficient increases significantly. For a given density and temperature relative to the critical point, with increasing number of dimension the Lennard-Jones system conforms better to the hidden-scale-invariance property characterized bymore » high virial potential-energy correlations (a property that leads to the existence of isomorphs in the thermodynamic phase diagram, implying that it becomes effectively one-dimensional in regard to structure and dynamics). The present paper also gives the first numerical demonstration of isomorph invariance of structure and dynamics in four dimensions. Our findings emphasize the need for a universally applicable 1/d expansion in liquid-state theory; we conjecture that the systems known to obey hidden scale invariance in three dimensions are those for which the yet-to-be-developed 1/d expansion converges rapidly.« less

Accurate van der Waals coefficients from density functional theory

PubMed Central

Tao, Jianmin; Perdew, John P.; Ruzsinszky, Adrienn

2012-01-01

The van der Waals interaction is a weak, long-range correlation, arising from quantum electronic charge fluctuations. This interaction affects many properties of materials. A simple and yet accurate estimate of this effect will facilitate computer simulation of complex molecular materials and drug design. Here we develop a fast approach for accurate evaluation of dynamic multipole polarizabilities and van der Waals (vdW) coefficients of all orders from the electron density and static multipole polarizabilities of each atom or other spherical object, without empirical fitting. Our dynamic polarizabilities (dipole, quadrupole, octupole, etc.) are exact in the zero- and high-frequency limits, and exact at all frequencies for a metallic sphere of uniform density. Our theory predicts dynamic multipole polarizabilities in excellent agreement with more expensive many-body methods, and yields therefrom vdW coefficients C6, C8, C10 for atom pairs with a mean absolute relative error of only 3%. PMID:22205765

Anisotropy of stress correlation in two-dimensional liquids and a pseudospin model

DOE PAGES

Wu, Bin; Iwashita, Takuya; Egami, Takeshi

2015-11-04

Liquids are condensed matter in which atoms are strongly correlated in position and momentum. The atomic pair density function (PDF) is used often in describing such correlation. However, elucidation of many properties requires higher degrees of correlation than the pair correlation. For instance, viscosity depends upon the stress correlations in space and time. We examine the cross correlation between the stress correlation at the atomic level and the PDF for two-dimensional liquids. We introduce the concept of the stress-resolved pair distribution function (SRPDF) that uses the sign of atomic-level stress as a selection rule to include particles from density correlations.more » The connection between SRPDFs and stress correlation function is explained through an approximation in which the shear stress is replaced by a pseudospin. Lastly, we further assess the possibility of interpreting the long-range stress correlation as a consequence of short-range Ising-like pseudospin interactions.« less

Hepatopulmonary shunting on Tc99m-MAA liver mapping: correlation with dynamic cross-sectional imaging and description of different shunting patterns.

PubMed

Bermo, Mohammed; Matesan, Manuela C; Itani, Malak; Behnia, Fatemeh; Vesselle, Hubert J

2018-04-09

The purpose of the study was to correlate lung shunt fraction (LSF) calculated by intra-arterial injection of Technetium-99m (Tc-99m)-labeled macroaggregated albumin (MAA) in a hepatic artery branch with the presence of certain patterns of vascular shunts on dynamic CT or MRI of the liver. This retrospective study was approved by the institutional review board and informed consent was waived. We reviewed 523 MAA scans in 453 patients (301 men, 152 women) performed from July 2007 to June 2015 and their correlative cross-sectional imaging. Patterns of vascular shunts on dynamic CT or MRI performed within 3 months of the MAA study and that potentially divert hepatic arterial inflow to the systemic venous return were defined as "target shunts." Dynamic CT or MRI was classified into three groups with target shunt present, absent, or indeterminate. The mean LSF was compared across the first and second groups using paired t test. 342 CT and MRI studies met inclusion criteria: target shunts were present in 63 studies, absent in 271 studies, and 8 studies were indeterminate. When target shunts were visualized, the mean LSF on corresponding MAA scans was 12.9 ± 10.36% (95% CI 10.29-15.15%) compared to 4.3 ± 3.17% (95% CI 3.93-4.68%) when no target shunt was visualized. The difference was statistically significant (p value < 0.001). Identified target shunts were either direct (arteriohepatic venous shunt) or indirect (arterioportal shunt combined with a portosystemic shunt). Visualizing certain patterns of vascular shunting on a dynamic CT or MRI scan is associated with high LSF.

NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1†

PubMed Central

Parkesh, Raman; Fountain, Matthew; Disney, Matthew D.

2011-01-01

The NMR structure of an RNA with a copy of the 5′CUG/3′GUC motif found in the triplet repeating disorder myotonic dystrophy type 1 (DM1) is disclosed. The lowest energy conformation of the UU pair is a single hydrogen bonded structure; however, the UU protons undergo exchange indicating structural dynamics. Molecular dynamics simulations show that the single hydrogen bonded structure is the most populated one but the UU pair interconverts between 0, 1, and 2 hydrogen bonded pairs. These studies have implications for the recognition of the DM1 RNA by small molecules and proteins. PMID:21204525

The California-Kepler Survey. V. Peas in a Pod: Planets in a Kepler Multi-planet System Are Similar in Size and Regularly Spaced

NASA Astrophysics Data System (ADS)

Weiss, Lauren M.; Marcy, Geoffrey W.; Petigura, Erik A.; Fulton, Benjamin J.; Howard, Andrew W.; Winn, Joshua N.; Isaacson, Howard T.; Morton, Timothy D.; Hirsch, Lea A.; Sinukoff, Evan J.; Cumming, Andrew; Hebb, Leslie; Cargile, Phillip A.

2018-01-01

We have established precise planet radii, semimajor axes, incident stellar fluxes, and stellar masses for 909 planets in 355 multi-planet systems discovered by Kepler. In this sample, we find that planets within a single multi-planet system have correlated sizes: each planet is more likely to be the size of its neighbor than a size drawn at random from the distribution of observed planet sizes. In systems with three or more planets, the planets tend to have a regular spacing: the orbital period ratios of adjacent pairs of planets are correlated. Furthermore, the orbital period ratios are smaller in systems with smaller planets, suggesting that the patterns in planet sizes and spacing are linked through formation and/or subsequent orbital dynamics. Yet, we find that essentially no planets have orbital period ratios smaller than 1.2, regardless of planet size. Using empirical mass–radius relationships, we estimate the mutual Hill separations of planet pairs. We find that 93% of the planet pairs are at least 10 mutual Hill radii apart, and that a spacing of ∼20 mutual Hill radii is most common. We also find that when comparing planet sizes, the outer planet is larger in 65% ± 0.4% of cases, and the typical ratio of the outer to inner planet size is positively correlated with the temperature difference between the planets. This could be the result of photo-evaporation. Based on observations obtained at the W. M. Keck Observatory, which is operated jointly by the University of California and the California Institute of Technology. Keck time has been granted by the University of California, and California Institute of Technology, and the University of Hawaii.

Efficient algorithm for multiconfiguration pair-density functional theory with application to the heterolytic dissociation energy of ferrocene

NASA Astrophysics Data System (ADS)

Sand, Andrew M.; Truhlar, Donald G.; Gagliardi, Laura

2017-01-01

The recently developed multiconfiguration pair-density functional theory (MC-PDFT) combines multiconfiguration wave function theory with a density functional that depends on the on-top pair density of an electronic system. In an MC-PDFT calculation, there are two steps: a conventional multiconfiguration self-consistent-field (MCSCF) calculation and a post-MCSCF evaluation of the energy with an on-top density functional. In this work, we present the details of the MC-PDFT algorithm that avoids steeply scaling steps that are present in other post-self-consistent-field multireference calculations of dynamic correlation energy. We demonstrate the favorable scaling by considering systems of H2 molecules with active spaces of several different sizes. We then apply the MC-PDFT method to calculate the heterolytic dissociation enthalpy of ferrocene. We find that MC-PDFT yields results that are at least as accurate as complete active space second-order perturbation theory and are more stable with respect to basis set, but at a fraction of the cost in both time and memory.

Efficient algorithm for multiconfiguration pair-density functional theory with application to the heterolytic dissociation energy of ferrocene.

PubMed

Sand, Andrew M; Truhlar, Donald G; Gagliardi, Laura

2017-01-21

The recently developed multiconfiguration pair-density functional theory (MC-PDFT) combines multiconfiguration wave function theory with a density functional that depends on the on-top pair density of an electronic system. In an MC-PDFT calculation, there are two steps: a conventional multiconfiguration self-consistent-field (MCSCF) calculation and a post-MCSCF evaluation of the energy with an on-top density functional. In this work, we present the details of the MC-PDFT algorithm that avoids steeply scaling steps that are present in other post-self-consistent-field multireference calculations of dynamic correlation energy. We demonstrate the favorable scaling by considering systems of H 2 molecules with active spaces of several different sizes. We then apply the MC-PDFT method to calculate the heterolytic dissociation enthalpy of ferrocene. We find that MC-PDFT yields results that are at least as accurate as complete active space second-order perturbation theory and are more stable with respect to basis set, but at a fraction of the cost in both time and memory.

Electrocortical Dynamics in Children with a Language-Learning Impairment Before and After Audiovisual Training.

PubMed

Heim, Sabine; Choudhury, Naseem; Benasich, April A

2016-05-01

Detecting and discriminating subtle and rapid sound changes in the speech environment is a fundamental prerequisite of language processing, and deficits in this ability have frequently been observed in individuals with language-learning impairments (LLI). One approach to studying associations between dysfunctional auditory dynamics and LLI, is to implement a training protocol tapping into this potential while quantifying pre- and post-intervention status. Event-related potentials (ERPs) are highly sensitive to the brain correlates of these dynamic changes and are therefore ideally suited for examining hypotheses regarding dysfunctional auditory processes. In this study, ERP measurements to rapid tone sequences (standard and deviant tone pairs) along with behavioral language testing were performed in 6- to 9-year-old LLI children (n = 21) before and after audiovisual training. A non-treatment group of children with typical language development (n = 12) was also assessed twice at a comparable time interval. The results indicated that the LLI group exhibited considerable gains on standardized measures of language. In terms of ERPs, we found evidence of changes in the LLI group specifically at the level of the P2 component, later than 250 ms after the onset of the second stimulus in the deviant tone pair. These changes suggested enhanced discrimination of deviant from standard tone sequences in widespread cortices, in LLI children after training.

Molecular simulation study of dynamical properties of room temperature ionic liquids with carbon pieces

DOE PAGES

Feng, Guang; Zhao, Wei; Cummings, Peter T.; ...

2016-03-29

Room temperature ionic liquids (RTILs) with dispersed carbon pieces exhibit distinctive physiochemical properties. In order to explore the molecular mechanism, RTILs/carbon pieces mixture we investigated it by molecular dynamics (MD) simulation in this work. Rigid and flexible carbon pieces in the form of graphene with different thicknesses and carbon nanotubes in different sizes were dispersed in a representative RTIL 1-butyl-3-methyl-imidazolium dicyanamide ([Bmim][DCA]). Our study demonstrated that the diffusion coefficients of RTILs in the presence of flexible carbons are similar to those of bulk RTILs at varying temperatures, which is in contrast to the decreased diffusion of RTILs in the presencemore » of rigid carbons. In addition, interfacial ion number density at rigid carbon surfaces was higher than that at flexible ones, which is correlated with the accessible external surface area of carbon pieces. The life time of cation-anion pair in the presence of carbon pieces also exhibited a dependence on carbon flexibility. RTILs with dispersed rigid carbon pieces showed longer ion pair life time than those with flexible ones, in consistence with the observation in diffusion coefficients. Furthermore, this work highlights the necessity of including the carbon flexibility when performing MD simulation of RTILs in the presence of dispersed carbon pieces in order to obtain the reliable dynamical and interfacial structural properties.« less

A pair of new moisture-dynamic diagnostic parameters for heavy rain location

NASA Astrophysics Data System (ADS)

Yuan, Kai; Zhu, Zhiwei; Li, Ming

2018-06-01

In this study, the regional persistent heavy rain process occurred in the middle and lower reaches of the Yangtze River valley from 30 June 2016 to 7 July 2016 is analyzed. We find that the pure dynamic parameters [e.g., vorticity ( V) and divergence ( D)] and two-dimensional moisture-dynamic parameters [e.g., moist vorticity ( MV), moist divergence ( MD)] have difficulty in capturing the rainfall location during such a critical process. Given the poor performance of these traditional parameters, a pair of new parameters [namely, one-dimensional moist vorticity ( ODMV) and one-dimensional moist divergence ( ODMD)] based on low-level jet is proposed for diagnosing heavy rain location. The results show that (1) ODMV and ODMD have better relations with rain belt in terms of spatial distribution. Precipitation occurs in positive (negative) region of ODMV ( ODMD), and heavy rainfall accurately locates in the positive (negative) center of ODMV ( ODMD); (2) ODMV and ODMD also have good correlation with the precipitation in terms of temporal variation (significant at the 99% confidence level). When ODMV ( ODMD) is in strong positive (negative) phase, precipitation is large, and vice versa; (3) the threat score of ODMV and ODMD for the areal-mean rainfall is improved by 119% and 16%, respectively, compared to V/ D and MV/ MD. It is anticipated that the proposed new parameters would facilitate the skills of diagnosing and forecasting the heavy rainfall.

A molecular dynamic investigation for shock induced phase transition of water

NASA Astrophysics Data System (ADS)

Mitra, Nilanjan; Neogi, Anupam

2015-06-01

Atomistic equilibrium molecular dynamics (EMD) was carried out to investigate shock induced phase transition of bulk liquid water. Multi-scale shock technique (MSST) was utilized to investigate low (US = 2 . 5km /s) to strong (US = 6 . 5km /s) intensity shock response on an extended flexible three point model up to 100 ns. The thermodynamic pathway of phase transition from liquid water to ice VII was investigated using temporal variation of thermodynamic state variables, power spectrum analyses of O-H bond vibration along with temporal evolution of pair correlation function between O-O, O-H and H-H atoms. Static structure factor along with pair-distribution function extended up to 20 Å was calculated and compared against the ideal ice VII to get information regarding long range ordering. Bragg reflection at different crystal planes were evaluated to investigate percentage of crystallinity of the shocked sample. Specific questions answered in this work involves: What is the exact time frame after the passage of shock at certain intensity in which nucleation of solid phase can be observed? Is it a complete or partial phase transition? Are external nucleators essential for this transformation? What is the percentage of crystallinity of the nucleated phase?

Leptotene/Zygotene Chromosome Movement Via the SUN/KASH Protein Bridge in Caenorhabditis elegans

PubMed Central

Baudrimont, Antoine; Penkner, Alexandra; Woglar, Alexander; Machacek, Thomas; Wegrostek, Christina; Gloggnitzer, Jiradet; Fridkin, Alexandra; Klein, Franz; Gruenbaum, Yosef; Pasierbek, Pawel; Jantsch, Verena

2010-01-01

The Caenorhabditis elegans inner nuclear envelope protein matefin/SUN-1 plays a conserved, pivotal role in the process of genome haploidization. CHK-2–dependent phosphorylation of SUN-1 regulates homologous chromosome pairing and interhomolog recombination in Caenorhabditis elegans. Using time-lapse microscopy, we characterized the movement of matefin/SUN-1::GFP aggregates (the equivalent of chromosomal attachment plaques) and showed that the dynamics of matefin/SUN-1 aggregates remained unchanged throughout leptonene/zygotene, despite the progression of pairing. Movement of SUN-1 aggregates correlated with chromatin polarization. We also analyzed the requirements for the formation of movement-competent matefin/SUN-1 aggregates in the context of chromosome structure and found that chromosome axes were required to produce wild-type numbers of attachment plaques. Abrogation of synapsis led to a deceleration of SUN-1 aggregate movement. Analysis of matefin/SUN-1 in a double-strand break deficient mutant revealed that repair intermediates influenced matefin/SUN-1 aggregate dynamics. Investigation of movement in meiotic regulator mutants substantiated that proper orchestration of the meiotic program and effective repair of DNA double-strand breaks were necessary for the wild-type behavior of matefin/SUN-1 aggregates. PMID:21124819

Multi-epoch observations with high spatial resolution of multiple T Tauri systems

NASA Astrophysics Data System (ADS)

Csépány, Gergely; van den Ancker, Mario; Ábrahám, Péter; Köhler, Rainer; Brandner, Wolfgang; Hormuth, Felix; Hiss, Hector

2017-07-01

Context. In multiple pre-main-sequence systems the lifetime of circumstellar discs appears to be shorter than around single stars, and the actual dissipation process may depend on the binary parameters of the systems. Aims: We report high spatial resolution observations of multiple T Tauri systems at optical and infrared wavelengths. We determine whether the components are gravitationally bound and orbital motion is visible, derive orbital parameters, and investigate possible correlations between the binary parameters and disc states. Methods: We selected 18 T Tau multiple systems (16 binary and two triple systems, yielding 16 + 2 × 2 = 20 binary pairs) in the Taurus-Auriga star-forming region from a previous survey, with spectral types from K1 to M5 and separations from 0.22″ (31 AU) to 5.8″ (814 AU). We analysed data acquired in 2006-07 at Calar Alto using the AstraLux lucky imaging system, along with data from SPHERE and NACO at the VLT, and from the literature. Results: We found ten pairs to orbit each other, five pairs that may show orbital motion, and five likely common proper motion pairs. We found no obvious correlation between the stellar parameters and binary configuration. The 10 μm infra-red excess varies between 0.1 and 7.2 mag (similar to the distribution in single stars, where it is between 1.7 and 9.1), implying that the presence of the binary star does not greatly influence the emission from the inner disc. Conclusions: We have detected orbital motion in young T Tauri systems over a timescale of ≈ 20 yr. Further observations with even longer temporal baseline will provide crucial information on the dynamics of these young stellar systems.

Understanding the atomic-level Green-Kubo stress correlation function for a liquid through phonons in a model crystal

NASA Astrophysics Data System (ADS)

Levashov, V. A.

2014-11-01

In order to gain insight into the connection between the vibrational dynamics and the atomic-level Green-Kubo stress correlation function in liquids, we consider this connection in a model crystal instead. Of course, vibrational dynamics in liquids and crystals are quite different and it is not expected that the results obtained on a model crystal should be valid for liquids. However, these considerations provide a benchmark to which the results of the previous molecular dynamics simulations can be compared. Thus, assuming that vibrations are plane waves, we derive analytical expressions for the atomic-level stress correlation functions in the classical limit and analyze them. These results provide, in particular, a recipe for analysis of the atomic-level stress correlation functions in Fourier space and extraction of the wave-vector and frequency-dependent information. We also evaluate the energies of the atomic-level stresses. The energies obtained are significantly smaller than the energies previously determined in molecular dynamics simulations of several model liquids. This result suggests that the average energies of the atomic-level stresses in liquids and glasses are largely determined by the structural disorder. We discuss this result in the context of equipartition of the atomic-level stress energies. Analysis of the previously published data suggests that it is possible to speak about configurational and vibrational contributions to the average energies of the atomic-level stresses in a glass state. However, this separation in a liquid state is problematic. We also introduce and briefly consider the atomic-level transverse current correlation function. Finally, we address the broadening of the peaks in the pair distribution function with increase of distance. We find that the peaks' broadening (by ≈40 % ) occurs due to the transverse vibrational modes, while contribution from the longitudinal modes does not change with distance.

Effects of stressor characteristics on early warning signs of critical transitions and "critical coupling" in complex dynamical systems.

PubMed

Blume, Steffen O P; Sansavini, Giovanni

2017-12-01

Complex dynamical systems face abrupt transitions into unstable and catastrophic regimes. These critical transitions are triggered by gradual modifications in stressors, which push the dynamical system towards unstable regimes. Bifurcation analysis can characterize such critical thresholds, beyond which systems become unstable. Moreover, the stochasticity of the external stressors causes small-scale fluctuations in the system response. In some systems, the decomposition of these signal fluctuations into precursor signals can reveal early warning signs prior to the critical transition. Here, we present a dynamical analysis of a power system subjected to an increasing load level and small-scale stochastic load perturbations. We show that the auto- and cross-correlations of bus voltage magnitudes increase, leading up to a Hopf bifurcation point, and further grow until the system collapses. This evidences a gradual transition into a state of "critical coupling," which is complementary to the established concept of "critical slowing down." Furthermore, we analyze the effects of the type of load perturbation and load characteristics on early warning signs and find that gradient changes in the autocorrelation provide early warning signs of the imminent critical transition under white-noise but not for auto-correlated load perturbations. Furthermore, the cross-correlation between all voltage magnitude pairs generally increases prior to and beyond the Hopf bifurcation point, indicating "critical coupling," but cannot provide early warning indications. Finally, we show that the established early warning indicators are oblivious to limit-induced bifurcations and, in the case of the power system model considered here, only react to an approaching Hopf bifurcation.

Collision dynamics of two-dimensional non-Abelian vortices

NASA Astrophysics Data System (ADS)

Mawson, Thomas; Petersen, Timothy C.; Simula, Tapio

2017-09-01

We study computationally the collision dynamics of vortices in a two-dimensional spin-2 Bose-Einstein condensate. In contrast to Abelian vortex pairs, which annihilate or pass through each other, we observe non-Abelian vortex pairs to undergo rungihilation—an event that converts the colliding vortices into a rung vortex. The resulting rung defect subsequently decays to another pair of non-Abelian vortices of different type, accompanied by a magnetization reversal.

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.

Energy correlations of photon pairs generated by a silicon microring resonator probed by Stimulated Four Wave Mixing.

PubMed

Grassani, Davide; Simbula, Angelica; Pirotta, Stefano; Galli, Matteo; Menotti, Matteo; Harris, Nicholas C; Baehr-Jones, Tom; Hochberg, Michael; Galland, Christophe; Liscidini, Marco; Bajoni, Daniele

2016-04-01

Compact silicon integrated devices, such as micro-ring resonators, have recently been demonstrated as efficient sources of quantum correlated photon pairs. The mass production of integrated devices demands the implementation of fast and reliable techniques to monitor the device performances. In the case of time-energy correlations, this is particularly challenging, as it requires high spectral resolution that is not currently achievable in coincidence measurements. Here we reconstruct the joint spectral density of photons pairs generated by spontaneous four-wave mixing in a silicon ring resonator by studying the corresponding stimulated process, namely stimulated four wave mixing. We show that this approach, featuring high spectral resolution and short measurement times, allows one to discriminate between nearly-uncorrelated and highly-correlated photon pairs.

Neural Correlates of Encoding Within- and Across-Domain Inter-Item Associations

PubMed Central

Park, Heekyeong; Rugg, Michael D.

2012-01-01

The neural correlates of the encoding of associations between pairs of words, pairs of pictures, and word-picture pairs were compared. The aims were to determine first, whether the neural correlates of associative encoding vary according to study material and second, whether encoding of across- versus within-material item pairs is associated with dissociable patterns of hippocampal and perirhinal activity, as predicted by the ‘domain dichotomy’ hypothesis of medial temporal lobe (MTL) function. While undergoing fMRI scanning, subjects (n = 24) were presented with the three classes of study pairs, judging which of the denoted objects fit into the other. Outside of the scanner, subjects then undertook an associative recognition task, discriminating between intact study pairs, rearranged pairs comprising items that had been presented on different study trials, and unstudied item pairs. The neural correlates of successful associative encoding – subsequent associative memory effects – were operationalized as the difference in activity between study pairs correctly judged intact versus pairs incorrectly judged rearranged on the subsequent memory test. Pair type-independent subsequent memory effects were evident in the left inferior frontal gyrus (IFG) and the hippocampus. Picture-picture pairs elicited material-selective effects in regions of fusiform cortex that were also activated to a greater extent on picture trials than word trials, while word-word pairs elicited material-selective subsequent memory effects in left lateral temporal cortex. Contrary to the domain-dichotomy hypothesis, neither hippocampal nor perirhinal subsequent memory effects differed depending on whether they were elicited by within- versus across-material study pairs. It is proposed that the left IFG plays a domain-general role in associative encoding, that associative encoding can also be facilitated by enhanced processing in material-selective cortical regions, and that the hippocampus and perirhinal cortex contribute equally to the formation of inter-item associations regardless of whether the items belong to the same or to different processing domains. PMID:21254802

Dependence of the rate of LiF ion pairing on the description of molecular interaction

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

Pluharova, Eva; Baer, Marcel D.; Schenter, Gregory K.

2016-03-03

We present an analysis of the dynamics of ion-pairing of Lithium Fluoride (LiF) in aqueous solvent using both detailed molecular simulation as well as reduced models within a Gener- alized Langevin Equation (GLE) framework. We explored the sensitivity of the ion-pairing phenomena to the details of descriptions of molecular interaction, comparing two empirical potentials to explicit quantum based density functional theory. We find quantitative differences in the potentials of mean force for ion-pairing as well as time dependent frictions that lead to variations in the rate constant and reactive flux correlation functions. These details reflect differences in solvent response tomore » ion-pairing between different representations of molecular interaction and influence anharmonicity of the dynamic response. We find that the short time anharmonic response is recovered with a GLE parameterization. Recovery of the details of long time response may require extensions to the reduced model. We show that the utility of using a reduced model leads to a straight forward application of variational transition state the- ory concepts to the condensed phase system. The significance of this is reflected in the analysis of committor distributions and the variation of planar hypersurfaces, leading to an improved understanding of factors that determine the rate of LiF ion-pairing. CJM and GKS are supported by the U.S. Department of Energy‘s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest Na- tional Laboratory (PNNL) is operated for the Department of Energy by Battelle. MDB is grateful for the support of Laboratory Directed Research and Development funding under the auspices of PNNL’s Laboratory Initiative Materials Synthesis and Simulation across Scales (MS3). Additional computing resources were generously allocated by PNNL’s Institutional Computing program. EP acknowledges support from PNNL’s Alternate Sponsored Fellowship program and IMPRS Dres- den.Support to P.J. from the Czech Science Foundation (grant P208/12/G016) and the Academy of Sciences (Praemium Academie award) is gratefully acknowledged.« less

Observation of sea-ice dynamics using synthetic aperture radar images: Automated analysis

NASA Technical Reports Server (NTRS)

Vesecky, John F.; Samadani, Ramin; Smith, Martha P.; Daida, Jason M.; Bracewell, Ronald N.

1988-01-01

The European Space Agency's ERS-1 satellite, as well as others planned to follow, is expected to carry synthetic-aperture radars (SARs) over the polar regions beginning in 1989. A key component in utilization of these SAR data is an automated scheme for extracting the sea-ice velocity field from a time sequence of SAR images of the same geographical region. Two techniques for automated sea-ice tracking, image pyramid area correlation (hierarchical correlation) and feature tracking, are described. Each technique is applied to a pair of Seasat SAR sea-ice images. The results compare well with each other and with manually tracked estimates of the ice velocity. The advantages and disadvantages of these automated methods are pointed out. Using these ice velocity field estimates it is possible to construct one sea-ice image from the other member of the pair. Comparing the reconstructed image with the observed image, errors in the estimated velocity field can be recognized and a useful probable error display created automatically to accompany ice velocity estimates. It is suggested that this error display may be useful in segmenting the sea ice observed into regions that move as rigid plates of significant ice velocity shear and distortion.

Topological Characteristics of the Hong Kong Stock Market: A Test-based P-threshold Approach to Understanding Network Complexity

PubMed Central

Xu, Ronghua; Wong, Wing-Keung; Chen, Guanrong; Huang, Shuo

2017-01-01

In this paper, we analyze the relationship among stock networks by focusing on the statistically reliable connectivity between financial time series, which accurately reflects the underlying pure stock structure. To do so, we firstly filter out the effect of market index on the correlations between paired stocks, and then take a t-test based P-threshold approach to lessening the complexity of the stock network based on the P values. We demonstrate the superiority of its performance in understanding network complexity by examining the Hong Kong stock market. By comparing with other filtering methods, we find that the P-threshold approach extracts purely and significantly correlated stock pairs, which reflect the well-defined hierarchical structure of the market. In analyzing the dynamic stock networks with fixed-size moving windows, our results show that three global financial crises, covered by the long-range time series, can be distinguishingly indicated from the network topological and evolutionary perspectives. In addition, we find that the assortativity coefficient can manifest the financial crises and therefore can serve as a good indicator of the financial market development. PMID:28145494

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.

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

Magnetic field effects in hybrid perovskite devices

NASA Astrophysics Data System (ADS)

Zhang, C.; Sun, D.; Sheng, C.-X.; Zhai, Y. X.; Mielczarek, K.; Zakhidov, A.; Vardeny, Z. V.

2015-05-01

Magnetic field effects have been a successful tool for studying carrier dynamics in organic semiconductors as the weak spin-orbit coupling in these materials gives rise to long spin relaxation times. As the spin-orbit coupling is strong in organic-inorganic hybrid perovskites, which are promising materials for photovoltaic and light-emitting applications, magnetic field effects are expected to be negligible in these optoelectronic devices. We measured significant magneto-photocurrent, magneto-electroluminescence and magneto-photoluminescence responses in hybrid perovskite devices and thin films, where the amplitude and shape are correlated to each other through the electron-hole lifetime, which depends on the perovskite film morphology. We attribute these responses to magnetic-field-induced spin-mixing of the photogenerated electron-hole pairs with different g-factors--the Δg model. We validate this model by measuring large Δg (~ 0.65) using field-induced circularly polarized photoluminescence, and electron-hole pair lifetime using picosecond pump-probe spectroscopy.

Observation of Transverse Spin-Dependent Azimuthal Correlations of Charged Pion Pairs in p↑+p at √{s }=200 GeV

NASA Astrophysics Data System (ADS)

Adamczyk, L.; Adkins, J. K.; Agakishiev, G.; Aggarwal, M. M.; Ahammed, Z.; Alekseev, I.; Alford, J.; Aparin, A.; Arkhipkin, D.; Aschenauer, E. C.; Averichev, G. S.; Banerjee, A.; Bellwied, R.; Bhasin, A.; Bhati, A. K.; Bhattarai, P.; Bielcik, J.; Bielcikova, J.; Bland, L. C.; Bordyuzhin, I. G.; Bouchet, J.; Brandin, A. V.; Bunzarov, I.; Burton, T. P.; Butterworth, J.; Caines, H.; Calderón de la Barca Sánchez, M.; Campbell, J. M.; Cebra, D.; Cervantes, M. C.; Chakaberia, I.; Chaloupka, P.; Chang, Z.; Chattopadhyay, S.; Chen, J. H.; Chen, X.; Cheng, J.; Cherney, M.; Christie, W.; Contin, G.; Crawford, H. J.; Das, S.; De Silva, L. C.; Debbe, R. R.; Dedovich, T. G.; Deng, J.; Derevschikov, A. A.; di Ruzza, B.; Didenko, L.; Dilks, C.; Dong, X.; Drachenberg, J. L.; Draper, J. E.; Du, C. M.; Dunkelberger, L. E.; Dunlop, J. C.; Efimov, L. G.; Engelage, J.; Eppley, G.; Esha, R.; Evdokimov, O.; Eyser, O.; Fatemi, R.; Fazio, S.; Federic, P.; Fedorisin, J.; Feng, Z.; Filip, P.; Fisyak, Y.; Flores, C. E.; Fulek, L.; Gagliardi, C. A.; Garand, D.; Geurts, F.; Gibson, A.; Girard, M.; Greiner, L.; Grosnick, D.; Gunarathne, D. S.; Guo, Y.; Gupta, S.; Gupta, A.; Guryn, W.; Hamad, A.; Hamed, A.; Haque, R.; Harris, J. W.; He, L.; Heppelmann, S.; Heppelmann, S.; Hirsch, A.; Hoffmann, G. W.; Hofman, D. J.; Horvat, S.; Huang, B.; Huang, X.; Huang, H. Z.; Huck, P.; Humanic, T. J.; Igo, G.; Jacobs, W. W.; Jang, H.; Jiang, K.; Judd, E. G.; Kabana, S.; Kalinkin, D.; Kang, K.; Kauder, K.; Ke, H. W.; Keane, D.; Kechechyan, A.; Khan, Z. H.; Kikola, D. P.; Kisel, I.; Kisiel, A.; Kochenda, L.; Koetke, D. D.; Kollegger, T.; Kosarzewski, L. K.; Kraishan, A. F.; Kravtsov, P.; Krueger, K.; Kulakov, I.; Kumar, L.; Kycia, R. A.; Lamont, M. A. C.; Landgraf, J. M.; Landry, K. D.; Lauret, J.; Lebedev, A.; Lednicky, R.; Lee, J. H.; Li, X.; Li, C.; Li, W.; Li, Z. M.; Li, Y.; Li, X.; Lisa, M. A.; Liu, F.; Ljubicic, T.; Llope, W. J.; Lomnitz, M.; Longacre, R. S.; Luo, X.; Ma, Y. G.; Ma, G. L.; Ma, L.; Ma, R.; Magdy, N.; Majka, R.; Manion, A.; Margetis, S.; Markert, C.; Masui, H.; Matis, H. S.; McDonald, D.; Meehan, K.; Minaev, N. G.; Mioduszewski, S.; Mohanty, B.; Mondal, M. M.; Morozov, D.; Mustafa, M. K.; Nandi, B. K.; Nasim, Md.; Nayak, T. K.; Nigmatkulov, G.; Nogach, L. V.; Noh, S. Y.; Novak, J.; Nurushev, S. B.; Odyniec, G.; Ogawa, A.; Oh, K.; Okorokov, V.; Olvitt, D.; Page, B. S.; Pak, R.; Pan, Y. X.; Pandit, Y.; Panebratsev, Y.; Pawlik, B.; Pei, H.; Perkins, C.; Peterson, A.; Pile, P.; Planinic, M.; Pluta, J.; Poljak, N.; Poniatowska, K.; Porter, J.; Posik, M.; Poskanzer, A. M.; Pruthi, N. K.; Putschke, J.; Qiu, H.; Quintero, A.; Ramachandran, S.; Raniwala, R.; Raniwala, S.; Ray, R. L.; Ritter, H. G.; Roberts, J. B.; Rogachevskiy, O. V.; Romero, J. L.; Roy, A.; Ruan, L.; Rusnak, J.; Rusnakova, O.; Sahoo, N. R.; Sahu, P. K.; Sakrejda, I.; Salur, S.; Sandweiss, J.; Sarkar, A.; Schambach, J.; Scharenberg, R. P.; Schmah, A. M.; Schmidke, W. B.; Schmitz, N.; Seger, J.; Seyboth, P.; Shah, N.; Shahaliev, E.; Shanmuganathan, P. V.; Shao, M.; Sharma, M. K.; Sharma, B.; Shen, W. Q.; Shi, S. S.; Shou, Q. Y.; Sichtermann, E. P.; Sikora, R.; Simko, M.; Skoby, M. J.; Smirnov, D.; Smirnov, N.; Song, L.; Sorensen, P.; Spinka, H. M.; Srivastava, B.; Stanislaus, T. D. S.; Stepanov, M.; Stock, R.; Strikhanov, M.; Stringfellow, B.; Sumbera, M.; Summa, B.; Sun, X.; Sun, Z.; Sun, X. M.; Sun, Y.; Surrow, B.; Svirida, N.; Szelezniak, M. A.; Tang, A. H.; Tang, Z.; Tarnowsky, T.; Tawfik, A. N.; Thomas, J. H.; Timmins, A. R.; Tlusty, D.; Tokarev, M.; Trentalange, S.; Tribble, R. E.; Tribedy, P.; Tripathy, S. K.; Trzeciak, B. A.; Tsai, O. D.; Ullrich, T.; Underwood, D. G.; Upsal, I.; Van Buren, G.; van Nieuwenhuizen, G.; Vandenbroucke, M.; Varma, R.; Vasiliev, A. N.; Vertesi, R.; Videbæk, F.; Viyogi, Y. P.; Vokal, S.; Voloshin, S. A.; Vossen, A.; Wang, G.; Wang, Y.; Wang, F.; Wang, Y.; Wang, H.; Wang, J. S.; Webb, J. C.; Webb, G.; Wen, L.; Westfall, G. D.; Wieman, H.; Wissink, S. W.; Witt, R.; Wu, Y. F.; Xiao, Z. G.; Xie, W.; Xin, K.; Xu, Q. H.; Xu, Z.; Xu, H.; Xu, N.; Xu, Y. F.; Yang, Q.; Yang, Y.; Yang, S.; Yang, Y.; Yang, C.; Ye, Z.; Yepes, P.; Yi, L.; Yip, K.; Yoo, I.-K.; Yu, N.; Zbroszczyk, H.; Zha, W.; Zhang, X. P.; Zhang, J.; Zhang, Y.; Zhang, J.; Zhang, J. B.; Zhang, S.; Zhang, Z.; Zhao, J.; Zhong, C.; Zhou, L.; Zhu, X.; Zoulkarneeva, Y.; Zyzak, M.; STAR Collaboration

2015-12-01

We report the observation of transverse polarization-dependent azimuthal correlations in charged pion pair production with the STAR experiment in p↑+p collisions at RHIC. These correlations directly probe quark transversity distributions. We measure signals in excess of 5 standard deviations at high transverse momenta, at high pseudorapidities η >0.5 , and for pair masses around the mass of the ρ meson. This is the first direct transversity measurement in p +p collisions.

Risperidone Effects on Brain Dynamic Connectivity-A Prospective Resting-State fMRI Study in Schizophrenia.

PubMed

Lottman, Kristin K; Kraguljac, Nina V; White, David M; Morgan, Charity J; Calhoun, Vince D; Butt, Allison; Lahti, Adrienne C

2017-01-01

Resting-state functional connectivity studies in schizophrenia evaluating average connectivity over the entire experiment have reported aberrant network integration, but findings are variable. Examining time-varying (dynamic) functional connectivity may help explain some inconsistencies. We assessed dynamic network connectivity using resting-state functional MRI in patients with schizophrenia, while unmedicated ( n  = 34), after 1 week ( n  = 29) and 6 weeks of treatment with risperidone ( n  = 24), as well as matched controls at baseline ( n  = 35) and after 6 weeks ( n  = 19). After identifying 41 independent components (ICs) comprising resting-state networks, sliding window analysis was performed on IC timecourses using an optimal window size validated with linear support vector machines. Windowed correlation matrices were then clustered into three discrete connectivity states (a relatively sparsely connected state, a relatively abundantly connected state, and an intermediately connected state). In unmedicated patients, static connectivity was increased between five pairs of ICs and decreased between two pairs of ICs when compared to controls, dynamic connectivity showed increased connectivity between the thalamus and somatomotor network in one of the three states. State statistics indicated that, in comparison to controls, unmedicated patients had shorter mean dwell times and fraction of time spent in the sparsely connected state, and longer dwell times and fraction of time spent in the intermediately connected state. Risperidone appeared to normalize mean dwell times after 6 weeks, but not fraction of time. Results suggest that static connectivity abnormalities in schizophrenia may partly be related to altered brain network temporal dynamics rather than consistent dysconnectivity within and between functional networks and demonstrate the importance of implementing complementary data analysis techniques.

Femtosecond-laser induced dynamics of CO on Ru(0001): Deep insights from a hot-electron friction model including surface motion

NASA Astrophysics Data System (ADS)

Scholz, Robert; Floß, Gereon; Saalfrank, Peter; Füchsel, Gernot; Lončarić, Ivor; Juaristi, J. I.

2016-10-01

A Langevin model accounting for all six molecular degrees of freedom is applied to femtosecond-laser induced, hot-electron driven dynamics of Ru(0001)(2 ×2 ):CO. In our molecular dynamics with electronic friction approach, a recently developed potential energy surface based on gradient-corrected density functional theory accounting for van der Waals interactions is adopted. Electronic friction due to the coupling of molecular degrees of freedom to electron-hole pairs in the metal are included via a local density friction approximation, and surface phonons by a generalized Langevin oscillator model. The action of ultrashort laser pulses enters through a substrate-mediated, hot-electron mechanism via a time-dependent electronic temperature (derived from a two-temperature model), causing random forces acting on the molecule. The model is applied to laser induced lateral diffusion of CO on the surface, "hot adsorbate" formation, and laser induced desorption. Reaction probabilities are strongly enhanced compared to purely thermal processes, both for diffusion and desorption. Reaction yields depend in a characteristic (nonlinear) fashion on the applied laser fluence, as well as branching ratios for various reaction channels. Computed two-pulse correlation traces for desorption and other indicators suggest that aside from electron-hole pairs, phonons play a non-negligible role for laser induced dynamics in this system, acting on a surprisingly short time scale. Our simulations on precomputed potentials allow for good statistics and the treatment of long-time dynamics (300 ps), giving insight into this system which hitherto has not been reached. We find generally good agreement with experimental data where available and make predictions in addition. A recently proposed laser induced population of physisorbed precursor states could not be observed with the present low-coverage model.

Molecular dynamics study of thermodynamic stability and dynamics of [Li(glyme)]+ complex in lithium-glyme solvate ionic liquids

NASA Astrophysics Data System (ADS)

Shinoda, Wataru; Hatanaka, Yuta; Hirakawa, Masashi; Okazaki, Susumu; Tsuzuki, Seiji; Ueno, Kazuhide; Watanabe, Masayoshi

2018-05-01

Equimolar mixtures of glymes and organic lithium salts are known to produce solvate ionic liquids, in which the stability of the [Li(glyme)]+ complex plays an important role in determining the ionic dynamics. Since these mixtures have attractive physicochemical properties for application as electrolytes, it is important to understand the dependence of the stability of the [Li(glyme)]+ complex on the ion dynamics. A series of microsecond molecular dynamics simulations has been conducted to investigate the dynamic properties of these solvate ionic liquids. Successful solvate ionic liquids with high stability of the [Li(glyme)]+ complex have been shown to have enhanced ion dynamics. Li-glyme pair exchange rarely occurs: its characteristic time is longer than that of ion diffusion by one or two orders of magnitude. Li-glyme pair exchange most likely occurs through cluster formation involving multiple [Li(glyme)]+ pairs. In this process, multiple exchanges likely take place in a concerted manner without the production of energetically unfavorable free glyme or free Li+ ions.

Positive Noise Cross Correlation in a Copper Pair Splitter.

NASA Astrophysics Data System (ADS)

Das, Anindya; Ronen, Yuval; Heiblum, Moty; Shtrikman, Hadas; Mahalu, Diana

2012-02-01

Entanglement is in heart of the Einstein-Podolsky-Rosen (EPR) paradox, in which non-locality is a fundamental property. Up to date spin entanglement of electrons had not been demonstrated. Here, we provide direct evidence of such entanglement by measuring: non-local positive current correlation and positive cross correlation among current fluctuations, both of separated electrons born by a Cooper-pair-beam-splitter. The realization of the splitter is provided by injecting current from an Al superconductor contact into two, single channel, pure InAs nanowires - each intercepted by a Coulomb blockaded quantum dot (QD). The QDs impedes strongly the flow of Cooper pairs allowing easy single electron transport. The passage of electron in one wire enables the simultaneous passage of the other in the neighboring wire. The splitting efficiency of the Cooper pairs (relative to Cooper pairs actual current) was found to be ˜ 40%. The positive cross-correlations in the currents and their fluctuations (shot noise) are fully consistent with entangled electrons produced by the beam splitter.

Molecular dynamics simulations on the local order of liquid and amorphous ZnTe

NASA Astrophysics Data System (ADS)

Rino, José Pedro; Borges, Denilson; Mota, Rita C.; Silva, Maurício A. P.

2008-05-01

Molecular dynamics studies of structural and dynamical correlations of molten and vitreous states under several conditions of density and temperature were performed. We use an effective recently proposed interatomic potential, consisting of two- and three-body covalent interactions which has successfully described the structural, dynamical, and structural phase transformation induced by pressure in ZnTe [D. S. Borges and J. P. Rino, Phys. Rev. B 72, 014107 (2005)]. The two-body term of the interaction potential consists of Coulomb interaction resulting from charge transfer, steric repulsion due to atomic sizes, charge-dipole interaction to include the effect of electronic polarizability of anions, and dipole-dipole (van der Waals) interactions. The three-body covalent term is a modification of the Stillinger-Weber potential. Molecular dynamics simulations in isobaric-isenthalpic ensemble have been performed for systems amounting to 4096 and 64 000 particles. Starting from a crystalline zinc-blende (ZB) structure, the system is initially heated until a very homogeneous liquid is obtained. The vitreous zinc telluride phase is attained by cooling the liquid at sufficiently fast cooling rates, while slower cooling rates lead to a disordered ZB crystalline structure. Two- and three-body correlations for the liquid and vitreous phases are analyzed through pair distribution functions, static structure factors, and bond angle distributions. In particular, the neutron static structure factor for the liquid phase is in very good agreement with both the reported experimental data and first-principles simulations.

Continuity of Genetic and Environmental Influences on Cognition across the Life Span: A Meta-Analysis of Longitudinal Twin and Adoption Studies

PubMed Central

Tucker-Drob, Elliot M.; Briley, Daniel A.

2014-01-01

The longitudinal rank-order stability of cognitive ability increases dramatically over the lifespan. Multiple theoretical perspectives have proposed that genetic and/or environmental mechanisms underlie the longitudinal stability of cognition, and developmental trends therein. However, the patterns of stability of genetic and environmental influences on cognition over the lifespan largely remain poorly understood. We searched for longitudinal studies of cognition that reported raw genetically-informative longitudinal correlations or parameter estimates from longitudinal behavior genetic models. We identified 150 combinations of time points and measures from 15 independent longitudinal samples. In total, longitudinal data came from 4,538 monozygotic twin pairs raised together, 7,777 dizygotic twin pairs raised together, 34 monozygotic twin pairs raised apart, 78 dizygotic twin pairs raised apart, 141 adoptive sibling pairs, and 143 non-adoptive sibling pairs, ranging in age from infancy through late adulthood. At all ages, cross-time genetic correlations and shared environmental correlations were substantially larger than cross-time nonshared environmental correlations. Cross-time correlations for genetic and shared environmental components were low during early childhood, increased sharply over child development, and remained relatively high from adolescence through late adulthood. Cross-time correlations for nonshared environmental components were low across childhood and increased gradually to moderate magnitudes in adulthood. Increasing phenotypic stability over child development was almost entirely mediated by genetic factors. Time-based decay of genetic and shared environmental stability was more pronounced earlier in child development. Results are interpreted in reference to theories of gene-environment interaction and correlation. PMID:24611582

Correlation of WAIS IQ in 10 Pairs of Brothers.

ERIC Educational Resources Information Center

Matarazzo, Joseph D.; And Others

1978-01-01

Pairs of brothers were individually examined with Wechsler Adult Intelligence Scale some 10 months apart by an experienced clinical psychologist unaware of the consanguineous relationship. Correlation of .42 for Full Scale IQ is consistent with median correlation reported by Erlenmeyer-Kimling and Jarvik in their 1963 literature review.…

Nucleon Isovector Pairing in Nuclei: Microscopic Approach, Boson Representation, and Collective Model

NASA Astrophysics Data System (ADS)

Jolos, R. V.; Kartavenko, V. G.; Kolganova, E. A.

2018-03-01

Nucleon pair correlations in atomic nuclei are analyzed within a nuclear microscopic model with residual isovector pairing forces. These are formulated in the boson representation of fermion operators whereby the collective mode of pair excitations can be isolated without restricting the size of the one-particle basis. This method allows one to analyze the fluctuations in the nonsuperfluid phase of nuclear matter, its phase transition to the superfluid phase, and strong pair correlations. The performance of the method is exemplified by numerical results for the nuclei in the vicinity of the doubly magic 56Ni nucleus.

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

Odd-frequency triplet pairing in mixed-parity superconductors

NASA Astrophysics Data System (ADS)

Cuoco, Mario; Gentile, Paola; Noce, Canio; Romano, Alfonso; Annunziata, Gaetano; Linder, Jacob

2012-02-01

We show that mixed-parity superconductors may exhibit equal-spin pair correlations that are odd-in-time and can be tuned by means of an applied field. The direction and the amplitude of the pair correlator in the spin space turn out to be strongly dependent on the symmetry of the order parameter, and thus provide a tool to identify different types of singlet-triplet mixed configurations. We suggest that odd-in-time spin-polarized pair correlations can be generated without magnetic inhomogeneities in superconducting/ferromagnetic hybrids with non-centrosymmetric superconductor or when parity mixing is induced at the interface. Paola Gentile, Canio Noce, Alfonso Romano, Gaetano Annunziata, Jacob Linder, Mario Cuoco, arXiv:1109.4885

Temporal Quantum Correlations in Inelastic Light Scattering from Water.

PubMed

Kasperczyk, Mark; de Aguiar Júnior, Filomeno S; Rabelo, Cassiano; Saraiva, Andre; Santos, Marcelo F; Novotny, Lukas; Jorio, Ado

2016-12-09

Water is one of the most prevalent chemicals on our planet, an integral part of both our environment and our existence as a species. Yet it is also rich in anomalous behaviors. Here we reveal that water is a novel-yet ubiquitous-source for quantum correlated photon pairs at ambient conditions. The photon pairs are produced through Raman scattering, and the correlations arise from the shared quantum of a vibrational mode between the Stokes and anti-Stokes scattering events. We confirm the nonclassical nature of the produced photon pairs by showing that the cross-correlation and autocorrelations of the signals violate a Cauchy-Schwarz inequality by over 5 orders of magnitude. The unprecedented degree of violating the inequality in pure water, as well as the well-defined polarization properties of the photon pairs, points to its usefulness in quantum information.

Bell pair creation in current of Kondo-correlated dot

NASA Astrophysics Data System (ADS)

Sakano, Rui; Oguri, Akira; Nishikawa, Yunori; Abe, Eisuke

Recently, local-Fermi-liquid properties in non-linear currents and shot noises through the Kondo dot have been investigated both theoretically and experimentally. We suggest a new entangled-electron-pair generator utilizing mechanism of quasiparticle-pair creation which has been observed as enhancement of shot noise in the quantum dot. Using the renormalized perturbation theory for an orbital-degenerate impurity Anderson model and the full counting statistics, we calculate the Clauser-Horne-Shimony-Holt type Bell's correlator for currents through correlated two different channels of a Kondo correlated dot. It is shown that residual exchange-interactions of the local-Fermi-liquid create spin-entangled quasiparticle-pairs in nonlinear current and this results in violation of the Bell's inequality. This work was partially supported by JSPS KAKENHI Grant Numbers JP26220711, JP26400319, JP15K05181 and JP16K17723.

Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics.

PubMed

Tanzi, Luana; Ramondo, Fabio; Caminiti, Ruggero; Campetella, Marco; Di Luca, Andrea; Gontrani, Lorenzo

2015-09-21

We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.

Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics

NASA Astrophysics Data System (ADS)

Tanzi, Luana; Ramondo, Fabio; Caminiti, Ruggero; Campetella, Marco; Di Luca, Andrea; Gontrani, Lorenzo

2015-09-01

We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.

Neural noise and movement-related codes in the macaque supplementary motor area.

PubMed

Averbeck, Bruno B; Lee, Daeyeol

2003-08-20

We analyzed the variability of spike counts and the coding capacity of simultaneously recorded pairs of neurons in the macaque supplementary motor area (SMA). We analyzed the mean-variance functions for single neurons, as well as signal and noise correlations between pairs of neurons. All three statistics showed a strong dependence on the bin width chosen for analysis. Changes in the correlation structure of single neuron spike trains over different bin sizes affected the mean-variance function, and signal and noise correlations between pairs of neurons were much smaller at small bin widths, increasing monotonically with the width of the bin. Analyses in the frequency domain showed that the noise between pairs of neurons, on average, was most strongly correlated at low frequencies, which explained the increase in noise correlation with increasing bin width. The coding performance was analyzed to determine whether the temporal precision of spike arrival times and the interactions within and between neurons could improve the prediction of the upcoming movement. We found that in approximately 62% of neuron pairs, the arrival times of spikes at a resolution between 66 and 40 msec carried more information than spike counts in a 200 msec bin. In addition, in 19% of neuron pairs, inclusion of within (11%)- or between-neuron (8%) correlations in spike trains improved decoding accuracy. These results suggest that in some SMA neurons elements of the spatiotemporal pattern of activity may be relevant for neural coding.

Fired Cartridge Case Identification Using Optical Images and the Congruent Matching Cells (CMC) Method

PubMed Central

Tong, Mingsi; Song, John; Chu, Wei; Thompson, Robert M

2014-01-01

The Congruent Matching Cells (CMC) method for ballistics identification was invented at the National Institute of Standards and Technology (NIST). The CMC method is based on the correlation of pairs of small correlation cells instead of the correlation of entire images. Four identification parameters – TCCF, Tθ, Tx and Ty are proposed for identifying correlated cell pairs originating from the same firearm. The correlation conclusion (matching or non-matching) is determined by whether the number of CMC is ≥ 6. This method has been previously validated using a set of 780 pair-wise 3D topography images. However, most ballistic images stored in current local and national databases are in an optical intensity (grayscale) format. As a result, the reliability of applying the CMC method on optical intensity images is an important issue. In this paper, optical intensity images of breech face impressions captured on the same set of 40 cartridge cases are correlated and analyzed for the validation test of CMC method using optical images. This includes correlations of 63 pairs of matching images and 717 pairs of non-matching images under top ring lighting. Tests of the method do not produce any false identification (false positive) or false exclusion (false negative) results, which support the CMC method and the proposed identification criterion, C = 6, for firearm breech face identifications using optical intensity images. PMID:26601045

Fired Cartridge Case Identification Using Optical Images and the Congruent Matching Cells (CMC) Method.

PubMed

Tong, Mingsi; Song, John; Chu, Wei; Thompson, Robert M

2014-01-01

The Congruent Matching Cells (CMC) method for ballistics identification was invented at the National Institute of Standards and Technology (NIST). The CMC method is based on the correlation of pairs of small correlation cells instead of the correlation of entire images. Four identification parameters - T CCF, T θ, T x and T y are proposed for identifying correlated cell pairs originating from the same firearm. The correlation conclusion (matching or non-matching) is determined by whether the number of CMC is ≥ 6. This method has been previously validated using a set of 780 pair-wise 3D topography images. However, most ballistic images stored in current local and national databases are in an optical intensity (grayscale) format. As a result, the reliability of applying the CMC method on optical intensity images is an important issue. In this paper, optical intensity images of breech face impressions captured on the same set of 40 cartridge cases are correlated and analyzed for the validation test of CMC method using optical images. This includes correlations of 63 pairs of matching images and 717 pairs of non-matching images under top ring lighting. Tests of the method do not produce any false identification (false positive) or false exclusion (false negative) results, which support the CMC method and the proposed identification criterion, C = 6, for firearm breech face identifications using optical intensity images.

Brueckner G -matrix approach for neutron-proton pairing correlations in the deformed BCS approach

NASA Astrophysics Data System (ADS)

Ha, Eunja; Cheoun, Myung-Ki; Šimkovic, F.

2015-10-01

Ground states of even-even Ge isotopes with mass number A =64 -76 have been studied in the deformed Bardeen-Cooper-Schrieffer (BCS) theory by taking neutron-proton (n p ) pairing correlations as well as neutron-neutron (n n ) and proton-proton (p p ) pairing correlations. The n p pairing has two different modes J =0 ,T =1 (isotriplet) and J =1 ,T =0 (isosinglet). In this work, the Brueckner G matrix, based on the CD-Bonn potential, has been exploited to reduce the ambiguity regarding nucleon-nucleon interactions inside nuclei compared to the results by a simple schematic phenomenological force. We found that the G matrix plays important roles to obtain reasonable descriptions of even-even nuclei compared to the schematic force. The n p pairing strength has been shown to have a clear correlation with quadrupole deformation parameter β2 for the isotopes, and affects the smearing of the Fermi surfaces of not only N =Z nuclei but also N ≠Z nuclei. In particular, the coexistence of the like particle (n n and p p ) and the n p pairing modes was found to become more salient by the G -matrix approach than by the schematic force approach.

Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for -1 ribosomal frameshifting stimulation

NASA Astrophysics Data System (ADS)

Zhong, Zhensheng; Yang, Lixia; Zhang, Haiping; Shi, Jiahao; Vandana, J. Jeya; Lam, Do Thuy Uyen Ha; Olsthoorn, René C. L.; Lu, Lanyuan; Chen, Gang

2016-12-01

Minus-one ribosomal frameshifting is a translational recoding mechanism widely utilized by many RNA viruses to generate accurate ratios of structural and catalytic proteins. An RNA pseudoknot structure located in the overlapping region of the gag and pro genes of Simian Retrovirus type 1 (SRV-1) stimulates frameshifting. However, the experimental characterization of SRV-1 pseudoknot (un)folding dynamics and the effect of the base triple formation is lacking. Here, we report the results of our single-molecule nanomanipulation using optical tweezers and theoretical simulation by steered molecular dynamics. Our results directly reveal that the energetic coupling between loop 2 and stem 1 via minor-groove base triple formation enhances the mechanical stability. The terminal base pair in stem 1 (directly in contact with a translating ribosome at the slippery site) also affects the mechanical stability of the pseudoknot. The -1 frameshifting efficiency is positively correlated with the cooperative one-step unfolding force and inversely correlated with the one-step mechanical unfolding rate at zero force. A significantly improved correlation was observed between -1 frameshifting efficiency and unfolding rate at forces of 15-35 pN, consistent with the fact that the ribosome is a force-generating molecular motor with helicase activity. No correlation was observed between thermal stability and -1 frameshifting efficiency.

Attention-related changes in correlated neuronal activity arise from normalization mechanisms

PubMed Central

Verhoef, Bram-Ernst; Maunsell, John H.R.

2017-01-01

Attention is believed to enhance perception by altering the correlations between pairs of neurons. How attention changes neuronal correlations is unknown. Using multi-electrodes in primate visual cortex, we measured spike-count correlations when single or multiple stimuli were presented, and stimuli were attended or unattended. When stimuli were unattended, adding a suppressive, non-preferred, stimulus beside a preferred stimulus increased spike-count correlations between pairs of similarly-tuned neurons, but decreased spike-count correlations between pairs of oppositely-tuned neurons. These changes are explained by a stochastic normalization model containing populations of oppositely-tuned, mutually-suppressive neurons. Importantly, this model also explains why attention decreased (attend preferred stimulus) or increased (attend non-preferred stimulus) correlations: as an indirect consequence of attention-related changes in the inputs to normalization mechanisms. Our findings link normalization mechanisms to correlated neuronal activity and attention, showing that normalization mechanisms shape response correlations and that these correlations change when attention biases normalization mechanisms. PMID:28553943

Stochastic Evolution of Augmented Born-Infeld Equations

NASA Astrophysics Data System (ADS)

Holm, Darryl D.

2018-06-01

This paper compares the results of applying a recently developed method of stochastic uncertainty quantification designed for fluid dynamics to the Born-Infeld model of nonlinear electromagnetism. The similarities in the results are striking. Namely, the introduction of Stratonovich cylindrical noise into each of their Hamiltonian formulations introduces stochastic Lie transport into their dynamics in the same form for both theories. Moreover, the resulting stochastic partial differential equations retain their unperturbed form, except for an additional term representing induced Lie transport by the set of divergence-free vector fields associated with the spatial correlations of the cylindrical noise. The explanation for this remarkable similarity lies in the method of construction of the Hamiltonian for the Stratonovich stochastic contribution to the motion in both cases, which is done via pairing spatial correlation eigenvectors for cylindrical noise with the momentum map for the deterministic motion. This momentum map is responsible for the well-known analogy between hydrodynamics and electromagnetism. The momentum map for the Maxwell and Born-Infeld theories of electromagnetism treated here is the 1-form density known as the Poynting vector. Two appendices treat the Hamiltonian structures underlying these results.

The role of telomere dynamics in aging and cancer

NASA Astrophysics Data System (ADS)

Blagoev, Krastan; Goodwin, Edwin

2006-03-01

Telomere length changes are far more dynamic than previously thought. In addition to a gradual loss of ˜100 base pairs per telomere in each cell division, losses as well as gains may occur within a single cell cycle. We are investigating how telomere exchange, extension, and deletion affect the proliferative potential of telomerase-negative somatic cells. Experimental techniques are being devised to detect dynamic telomere processes and quantify both the frequency and length changes of each. In parallel, a ``dynamic telomere model'' is being used that incorporates telomere dynamics to study how the telomere size distribution evolves with time. This is an essential step towards understanding the role that telomere dynamics play in the normal aging of tissues and organisms. The model casts light on relationships not otherwise easily explained by a deterministic ``mitotic clock,'' or to what extent the shortest initial telomere determines the onset of senescence. We also expect to identify biomarkers that will correlate with aging better than average telomere length and to shed light on the transition to unlimited growth found in telomerase-negative tumor cells having the ALT (alternative lengthening of telomeres) phenotype, and to evaluate strategies to suppress the growth of these tumors.

Entropic uncertainty for spin-1/2 XXX chains in the presence of inhomogeneous magnetic fields and its steering via weak measurement reversals

NASA Astrophysics Data System (ADS)

Wang, Dong; Ming, Fei; Huang, Ai-Jun; Sun, Wen-Yang; Ye, Liu

2017-09-01

The uncertainty principle configures a low bound to the measuring precision for a pair of non-commuting observables, and hence is considerably nontrivial to quantum precision measurement in the field of quantum information theory. In this letter, we consider the entropic uncertainty relation (EUR) in the context of quantum memory in a two-qubit isotropic Heisenberg spin chain. Specifically, we explore the dynamics of EUR in a practical scenario, where two associated nodes of a one-dimensional XXX-spin chain, under an inhomogeneous magnetic field, are connected to a thermal entanglement. We show that the temperature and magnetic field effect can lead to the inflation of the measuring uncertainty, stemming from the reduction of systematic quantum correlation. Notably, we reveal that, firstly, the uncertainty is not fully dependent on the observed quantum correlation of the system; secondly, the dynamical behaviors of the measuring uncertainty are relatively distinct with respect to ferromagnetism and antiferromagnetism chains. Meanwhile, we deduce that the measuring uncertainty is dramatically correlated with the mixedness of the system, implying that smaller mixedness tends to reduce the uncertainty. Furthermore, we propose an effective strategy to control the uncertainty of interest by means of quantum weak measurement reversal. Therefore, our work may shed light on the dynamics of the measuring uncertainty in the Heisenberg spin chain, and thus be important to quantum precision measurement in various solid-state systems.

Effect of structural mount dynamics on a pair of operating Stirling Convertors

NASA Astrophysics Data System (ADS)

Goodnight, Thomas W.; Suárez, Vicente J.; Hughes, William O.; Samorezov, Sergey

2002-01-01

The U.S. Department of Energy (DOE), in conjunction with NASA John H. Glenn Research Center and Stirling Technology Company, are currently developing a Stirling convertor for a Stirling Radioisotope Generator (SRG). NASA Headquarters and DOE have identified the SRG for potential use as an advanced spacecraft power system for future NASA deep-space and Mars surface missions. Low-level dynamic base-shake tests were conducted on a dynamic simulation of the structural mount for a pair of Operating Stirling Convertors. These tests were conducted at NASA Glenn Research Center's Structural Dynamics Laboratory as part of the development of this technology. The purpose of these tests was to identify the changes in transmissibility and the effect on structural dynamic response on a pair of operating Stirling Technology Demonstration Convertors (TDCs). This paper addresses the base-shake test, setup, procedure and results conducted on the Stirling TDC mount simulator in April 2001. .

Singlet-paired coupled cluster theory for open shells

NASA Astrophysics Data System (ADS)

Gomez, John A.; Henderson, Thomas M.; Scuseria, Gustavo E.

2016-06-01

Restricted single-reference coupled cluster theory truncated to single and double excitations accurately describes weakly correlated systems, but often breaks down in the presence of static or strong correlation. Good coupled cluster energies in the presence of degeneracies can be obtained by using a symmetry-broken reference, such as unrestricted Hartree-Fock, but at the cost of good quantum numbers. A large body of work has shown that modifying the coupled cluster ansatz allows for the treatment of strong correlation within a single-reference, symmetry-adapted framework. The recently introduced singlet-paired coupled cluster doubles (CCD0) method is one such model, which recovers correct behavior for strong correlation without requiring symmetry breaking in the reference. Here, we extend singlet-paired coupled cluster for application to open shells via restricted open-shell singlet-paired coupled cluster singles and doubles (ROCCSD0). The ROCCSD0 approach retains the benefits of standard coupled cluster theory and recovers correct behavior for strongly correlated, open-shell systems using a spin-preserving ROHF reference.

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.

Comparative study of the requantization of the time-dependent mean field for the dynamics of nuclear pairing

NASA Astrophysics Data System (ADS)

Ni, Fang; Nakatsukasa, Takashi

2018-04-01

To describe quantal collective phenomena, it is useful to requantize the time-dependent mean-field dynamics. We study the time-dependent Hartree-Fock-Bogoliubov (TDHFB) theory for the two-level pairing Hamiltonian, and compare results of different quantization methods. The one constructing microscopic wave functions, using the TDHFB trajectories fulfilling the Einstein-Brillouin-Keller quantization condition, turns out to be the most accurate. The method is based on the stationary-phase approximation to the path integral. We also examine the performance of the collective model which assumes that the pairing gap parameter is the collective coordinate. The applicability of the collective model is limited for the nuclear pairing with a small number of single-particle levels, because the pairing gap parameter represents only a half of the pairing collective space.

The Evolution and Expression Pattern of Human Overlapping lncRNA and Protein-coding Gene Pairs.

PubMed

Ning, Qianqian; Li, Yixue; Wang, Zhen; Zhou, Songwen; Sun, Hong; Yu, Guangjun

2017-03-27

Long non-coding RNA overlapping with protein-coding gene (lncRNA-coding pair) is a special type of overlapping genes. Protein-coding overlapping genes have been well studied and increasing attention has been paid to lncRNAs. By studying lncRNA-coding pairs in human genome, we showed that lncRNA-coding pairs were more likely to be generated by overprinting and retaining genes in lncRNA-coding pairs were given higher priority than non-overlapping genes. Besides, the preference of overlapping configurations preserved during evolution was based on the origin of lncRNA-coding pairs. Further investigations showed that lncRNAs promoting the splicing of their embedded protein-coding partners was a unilateral interaction, but the existence of overlapping partners improving the gene expression was bidirectional and the effect was decreased with the increased evolutionary age of genes. Additionally, the expression of lncRNA-coding pairs showed an overall positive correlation and the expression correlation was associated with their overlapping configurations, local genomic environment and evolutionary age of genes. Comparison of the expression correlation of lncRNA-coding pairs between normal and cancer samples found that the lineage-specific pairs including old protein-coding genes may play an important role in tumorigenesis. This work presents a systematically comprehensive understanding of the evolution and the expression pattern of human lncRNA-coding pairs.

Dynamics in entangled polyethylene melts using coarse-grained models

NASA Astrophysics Data System (ADS)

Peters, Brandon L.; Grest, Gary S.; Salerno, K. Michael; Agrawal, Anupriya; Perahia, Dvora

Polymer dynamics creates distinctive viscoelastic behavior as a result of a coupled interplay of motion on multiple length scales. Capturing the broad time and length scales of polymeric motion however, remains a challenge. Using polyethylene (PE) as a model system, we probe the effects of the degree of coarse graining on polymer dynamics. Coarse-grained (CG) potentials are derived using iterative Boltzmann inversion (iBi) with 2-6 methyl groups per CG bead from all fully atomistic melt simulations for short chains. While the iBi methods produces non-bonded potentials which give excellent agreement for the atomistic and CG pair correlation functions, the pressure P = 100-500MPa for the CG model. Correcting for potential so P 0 leads to non-bonded models with slightly smaller effective diameter and much deeper minimum. However, both the pressure and non-pressure corrected CG models give similar results for mean squared displacement (MSD) and the stress auto correlation function G(t) for PE melts above the melting point. The time rescaling factor between CG and atomistic models is found to be nearly the same for both CG models. Transferability of potential for different temperatures was tested by comparing the MSD and G(t) for potentials generated at different temperatures.

Structure and dynamics of single hydrophobic/ionic heteropolymers at the vapor-liquid interface of water.

PubMed

Vembanur, Srivathsan; Venkateshwaran, Vasudevan; Garde, Shekhar

2014-04-29

We focus on the conformational stability, structure, and dynamics of hydrophobic/charged homopolymers and heteropolymers at the vapor-liquid interface of water using extensive molecular dynamics simulations. Hydrophobic polymers collapse into globular structures in bulk water but unfold and sample a broad range of conformations at the vapor-liquid interface of water. We show that adding a pair of charges to a hydrophobic polymer at the interface can dramatically change its conformations, stabilizing hairpinlike structures, with molecular details depending on the location of the charged pair in the sequence. The translational dynamics of homopolymers and heteropolymers are also different, whereas the homopolymers skate on the interface with low drag, the tendency of charged groups to remain hydrated pulls the heteropolymers toward the liquid side of the interface, thus pinning them, increasing drag, and slowing the translational dynamics. The conformational dynamics of heteropolymers are also slower than that of the homopolymer and depend on the location of the charged groups in the sequence. Conformational dynamics are most restricted for the end-charged heteropolymer and speed up as the charge pair is moved toward the center of the sequence. We rationalize these trends using the fundamental understanding of the effects of the interface on primitive pair-level interactions between two hydrophobic groups and between oppositely charged ions in its vicinity.

Characterization of microscopic deformation through two-point spatial correlation functions

NASA Astrophysics Data System (ADS)

Huang, Guan-Rong; Wu, Bin; Wang, Yangyang; Chen, Wei-Ren

2018-01-01

The molecular rearrangements of most fluids under flow and deformation do not directly follow the macroscopic strain field. In this work, we describe a phenomenological method for characterizing such nonaffine deformation via the anisotropic pair distribution function (PDF). We demonstrate how the microscopic strain can be calculated in both simple shear and uniaxial extension, by perturbation expansion of anisotropic PDF in terms of real spherical harmonics. Our results, given in the real as well as the reciprocal space, can be applied in spectrum analysis of small-angle scattering experiments and nonequilibrium molecular dynamics simulations of soft matter under flow.

Inorganic proton conducting electrolyte coupled oxide-based dendritic transistors for synaptic electronics.

PubMed

Wan, Chang Jin; Zhu, Li Qiang; Zhou, Ju Mei; Shi, Yi; Wan, Qing

2014-05-07

Ionic/electronic hybrid devices with synaptic functions are considered to be the essential building blocks for neuromorphic systems and brain-inspired computing. Here, artificial synapses based on indium-zinc-oxide (IZO) transistors gated by nanogranular SiO2 proton-conducting electrolyte films are fabricated on glass substrates. Spike-timing dependent plasticity and paired-pulse facilitation are successfully mimicked in an individual bottom-gate transistor. Most importantly, dynamic logic and dendritic integration established by spatiotemporally correlated spikes are also mimicked in dendritic transistors with two in-plane gates as the presynaptic input terminals.

Organic/inorganic hybrid synaptic transistors gated by proton conducting methylcellulose films

NASA Astrophysics Data System (ADS)

Wan, Chang Jin; Zhu, Li Qiang; Wan, Xiang; Shi, Yi; Wan, Qing

2016-01-01

The idea of building a brain-inspired cognitive system has been around for several decades. Recently, electric-double-layer transistors gated by ion conducting electrolytes were reported as the promising candidates for synaptic electronics and neuromorphic system. In this letter, indium-zinc-oxide transistors gated by proton conducting methylcellulose electrolyte films were experimentally demonstrated with synaptic plasticity including paired-pulse facilitation and spatiotemporal-correlated dynamic logic. More importantly, a model based on proton-related electric-double-layer modulation and stretched-exponential decay function was proposed, and the theoretical results are in good agreement with the experimentally measured synaptic behaviors.

Mapping the nanoscale energetic landscape in conductive polymer films with spatially super-resolved exciton dynamics

NASA Astrophysics Data System (ADS)

Ginsberg, Naomi

2015-03-01

The migration of Frenkel excitons, tightly-bound electron-hole pairs, in polymeric organic semiconducting films is critical to the efficiency of bulk heterojunction solar cells. While these materials exhibit a high degree of structural heterogeneity on the nanoscale, traditional measurements of exciton diffusion lengths are performed on bulk samples. Since both the characteristic length scales of structural heterogeneity and the reported bulk diffusion lengths are smaller than the optical diffraction limit, we adapt far-field super-resolution fluorescence imaging to uncover the correlations between the structural and energetic landscapes that the excitons explore.

Characterization of microscopic deformation through two-point spatial correlation functions.

PubMed

Huang, Guan-Rong; Wu, Bin; Wang, Yangyang; Chen, Wei-Ren

2018-01-01

The molecular rearrangements of most fluids under flow and deformation do not directly follow the macroscopic strain field. In this work, we describe a phenomenological method for characterizing such nonaffine deformation via the anisotropic pair distribution function (PDF). We demonstrate how the microscopic strain can be calculated in both simple shear and uniaxial extension, by perturbation expansion of anisotropic PDF in terms of real spherical harmonics. Our results, given in the real as well as the reciprocal space, can be applied in spectrum analysis of small-angle scattering experiments and nonequilibrium molecular dynamics simulations of soft matter under flow.

Cosmological BCS mechanism and the big bang singularity

NASA Astrophysics Data System (ADS)

Alexander, Stephon; Biswas, Tirthabir

2009-07-01

We provide a novel mechanism that resolves the big bang singularity present in Friedman-Lemaitre-Robertson-Walker space-times without the need for ghost fields. Building on the fact that a four-fermion interaction arises in general relativity when fermions are covariantly coupled, we show that at early times the decrease in scale factor enhances the correlation between pairs of fermions. This enhancement leads to a BCS-like condensation of the fermions and opens a gap dynamically driving the Hubble parameter H to zero and results in a nonsingular bounce, at least in some special cases.

Viscosity of particulate soap films: approaching the jamming of 2D capillary suspensions.

PubMed

Timounay, Yousra; Rouyer, Florence

2017-05-14

We compute the effective viscosity of particulate soap films thanks to local velocity fields obtained by Particle Image Velocimetry (PIV) during film retraction experiments. We identify the jamming of these 2D capillary suspensions at a critical particle surface fraction (≃0.84) where effective viscosity diverges. Pair correlation function and number of neighbors in contact or close to contact reveal the cohesive nature of this 2D capillary granular media. The experimental 2D dynamic viscosities can be predicted by a model considering viscous dissipation at the liquid interfaces induced by the motion of individual particles.

Organic/inorganic hybrid synaptic transistors gated by proton conducting methylcellulose films

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

Wan, Chang Jin; Wan, Qing, E-mail: wanqing@nju.edu.cn, E-mail: yshi@nju.edu.cn; Ningbo Institute of Material Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201

The idea of building a brain-inspired cognitive system has been around for several decades. Recently, electric-double-layer transistors gated by ion conducting electrolytes were reported as the promising candidates for synaptic electronics and neuromorphic system. In this letter, indium-zinc-oxide transistors gated by proton conducting methylcellulose electrolyte films were experimentally demonstrated with synaptic plasticity including paired-pulse facilitation and spatiotemporal-correlated dynamic logic. More importantly, a model based on proton-related electric-double-layer modulation and stretched-exponential decay function was proposed, and the theoretical results are in good agreement with the experimentally measured synaptic behaviors.

Strong Neutron Pairing in core+4 n Nuclei

NASA Astrophysics Data System (ADS)

Revel, A.; Marqués, F. M.; Sorlin, O.; Aumann, T.; Caesar, C.; Holl, M.; Panin, V.; Vandebrouck, M.; Wamers, F.; Alvarez-Pol, H.; Atar, L.; Avdeichikov, V.; Beceiro-Novo, S.; Bemmerer, D.; Benlliure, J.; Bertulani, C. A.; Boillos, J. M.; Boretzky, K.; Borge, M. J. G.; Caamaño, M.; Casarejos, E.; Catford, W. N.; Cederkäll, J.; Chartier, M.; Chulkov, L.; Cortina-Gil, D.; Cravo, E.; Crespo, R.; Datta Pramanik, U.; Díaz Fernández, P.; Dillmann, I.; Elekes, Z.; Enders, J.; Ershova, O.; Estradé, A.; Farinon, F.; Fraile, L. M.; Freer, M.; Galaviz, D.; Geissel, H.; Gernhäuser, R.; Golubev, P.; Göbel, K.; Hagdahl, J.; Heftrich, T.; Heil, M.; Heine, M.; Heinz, A.; Henriques, A.; Ignatov, A.; Johansson, H. T.; Jonson, B.; Kahlbow, J.; Kalantar-Nayestanaki, N.; Kanungo, R.; Kelic-Heil, A.; Knyazev, A.; Kröll, T.; Kurz, N.; Labiche, M.; Langer, C.; Le Bleis, T.; Lemmon, R.; Lindberg, S.; Machado, J.; Marganiec, J.; Movsesyan, A.; Nacher, E.; Najafi, M.; Nilsson, T.; Nociforo, C.; Paschalis, S.; Perea, A.; Petri, M.; Pietri, S.; Plag, R.; Reifarth, R.; Ribeiro, G.; Rigollet, C.; Röder, M.; Rossi, D.; Savran, D.; Scheit, H.; Simon, H.; Syndikus, I.; Taylor, J. T.; Tengblad, O.; Thies, R.; Togano, Y.; Velho, P.; Volkov, V.; Wagner, A.; Weick, H.; Wheldon, C.; Wilson, G.; Winfield, J. S.; Woods, P.; Yakorev, D.; Zhukov, M.; Zilges, A.; Zuber, K.; R³B Collaboration

2018-04-01

The emission of neutron pairs from the neutron-rich N =12 isotones 18C and 20O has been studied by high-energy nucleon knockout from 19N and 21O secondary beams, populating unbound states of the two isotones up to 15 MeV above their two-neutron emission thresholds. The analysis of triple fragment-n -n correlations shows that the decay 19N (-1 p ) 18C* → 16C +n +n is clearly dominated by direct pair emission. The two-neutron correlation strength, the largest ever observed, suggests the predominance of a 14C core surrounded by four valence neutrons arranged in strongly correlated pairs. On the other hand, a significant competition of a sequential branch is found in the decay 21O (-1 n )20O*→18O +n +n , attributed to its formation through the knockout of a deeply bound neutron that breaks the 16O core and reduces the number of pairs.

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.

Communication: Studies of the Lennard-Jones fluid in 2, 3, and 4 dimensions highlight the need for a liquid-state 1/d expansion.

PubMed

Costigliola, Lorenzo; Schrøder, Thomas B; Dyre, Jeppe C

2016-06-21

The recent theoretical prediction by Maimbourg and Kurchan [e-print arXiv:1603.05023 (2016)] that for regular pair-potential systems the virial potential-energy correlation coefficient increases towards unity as the dimension d goes to infinity is investigated for the standard 12-6 Lennard-Jones fluid. This is done by computer simulations for d = 2, 3, 4 going from the critical point along the critical isotherm/isochore to higher density/temperature. In both cases the virial potential-energy correlation coefficient increases significantly. For a given density and temperature relative to the critical point, with increasing number of dimension the Lennard-Jones system conforms better to the hidden-scale-invariance property characterized by high virial potential-energy correlations (a property that leads to the existence of isomorphs in the thermodynamic phase diagram, implying that it becomes effectively one-dimensional in regard to structure and dynamics). The present paper also gives the first numerical demonstration of isomorph invariance of structure and dynamics in four dimensions. Our findings emphasize the need for a universally applicable 1/d expansion in liquid-state theory; we conjecture that the systems known to obey hidden scale invariance in three dimensions are those for which the yet-to-be-developed 1/d expansion converges rapidly.

Accurate potential energy surface for the 1(2)A' state of NH(2): scaling of external correlation versus extrapolation to the complete basis set limit.

PubMed

Li, Y Q; Varandas, A J C

2010-09-16

An accurate single-sheeted double many-body expansion potential energy surface is reported for the title system which is suitable for dynamics and kinetics studies of the reactions of N(2D) + H2(X1Sigmag+) NH(a1Delta) + H(2S) and their isotopomeric variants. It is obtained by fitting ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pVQZ basis set, after slightly correcting semiempirically the dynamical correlation using the double many-body expansion-scaled external correlation method. The function so obtained is compared in detail with a potential energy surface of the same family obtained by extrapolating the calculated raw energies to the complete basis set limit. The topographical features of the novel global potential energy surface are examined in detail and found to be in general good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. The novel function has been built so as to become degenerate at linear geometries with the ground-state potential energy surface of A'' symmetry reported by our group, where both form a Renner-Teller pair.

Resting state networks in empirical and simulated dynamic functional connectivity.

PubMed

Glomb, Katharina; Ponce-Alvarez, Adrián; Gilson, Matthieu; Ritter, Petra; Deco, Gustavo

2017-10-01

It is well-established that patterns of functional connectivity (FC) - measures of correlated activity between pairs of voxels or regions observed in the human brain using neuroimaging - are robustly expressed in spontaneous activity during rest. These patterns are not static, but exhibit complex spatio-temporal dynamics. Over the last years, a multitude of methods have been proposed to reveal these dynamics on the level of the whole brain. One finding is that the brain transitions through different FC configurations over time, and substantial effort has been put into characterizing these configurations. However, the dynamics governing these transitions are more elusive, specifically, the contribution of stationary vs. non-stationary dynamics is an active field of inquiry. In this study, we use a whole-brain approach, considering FC dynamics between 66 ROIs covering the entire cortex. We combine an innovative dimensionality reduction technique, tensor decomposition, with a mean field model which possesses stationary dynamics. It has been shown to explain resting state FC averaged over time and multiple subjects, however, this average FC summarizes the spatial distribution of correlations while hiding their temporal dynamics. First, we apply tensor decomposition to resting state scans from 24 healthy controls in order to characterize spatio-temporal dynamics present in the data. We simultaneously utilize temporal and spatial information by creating tensors that are subsequently decomposed into sets of brain regions ("communities") that share similar temporal dynamics, and their associated time courses. The tensors contain pairwise FC computed inside of overlapping sliding windows. Communities are discovered by clustering features pooled from all subjects, thereby ensuring that they generalize. We find that, on the group level, the data give rise to four distinct communities that resemble known resting state networks (RSNs): default mode network, visual network, control networks, and somatomotor network. Second, we simulate data with our stationary mean field model whose nodes are connected according to results from DTI and fiber tracking. In this model, all spatio-temporal structure is due to noisy fluctuations around the average FC. We analyze the simulated data in the same way as the empirical data in order to determine whether stationary dynamics can explain the emergence of distinct FC patterns (RSNs) which have their own time courses. We find that this is the case for all four networks using the spatio-temporal information revealed by tensor decomposition if nodes in the simulation are connected according to model-based effective connectivity. Furthermore, we find that these results require only a small part of the FC values, namely the highest values that occur across time and ROI pair. Our findings show that stationary dynamics can account for the emergence of RSNs. We provide an innovative method that does not make strong assumptions about the underlying data and is generally applicable to resting state or task data from different subject populations. Copyright © 2017 Elsevier Inc. All rights reserved.

Dynamical Networks Characterization of Space Weather Events

NASA Astrophysics Data System (ADS)

Orr, L.; Chapman, S. C.; Dods, J.; Gjerloev, J. W.

2017-12-01

Space weather can cause disturbances to satellite systems, impacting navigation technology and telecommunications; it can cause power loss and aviation disruption. A central aspect of the earth's magnetospheric response to space weather events are large scale and rapid changes in ionospheric current patterns. Space weather is highly dynamic and there are still many controversies about how the current system evolves in time. The recent SuperMAG initiative, collates ground-based vector magnetic field time series from over 200 magnetometers with 1-minute temporal resolution. In principle this combined dataset is an ideal candidate for quantification using dynamical networks. Network properties and parameters allow us to characterize the time dynamics of the full spatiotemporal pattern of the ionospheric current system. However, applying network methodologies to physical data presents new challenges. We establish whether a given pair of magnetometers are connected in the network by calculating their canonical cross correlation. The magnetometers are connected if their cross correlation exceeds a threshold. In our physical time series this threshold needs to be both station specific, as it varies with (non-linear) individual station sensitivity and location, and able to vary with season, which affects ground conductivity. Additionally, the earth rotates and therefore the ground stations move significantly on the timescales of geomagnetic disturbances. The magnetometers are non-uniformly spatially distributed. We will present new methodology which addresses these problems and in particular achieves dynamic normalization of the physical time series in order to form the network. Correlated disturbances across the magnetometers capture transient currents. Once the dynamical network has been obtained [1][2] from the full magnetometer data set it can be used to directly identify detailed inferred transient ionospheric current patterns and track their dynamics. We will show our first results that use network properties such as cliques and clustering coefficients to map these highly dynamic changes in ionospheric current patterns.[l] Dods et al, J. Geophys. Res 120, doi:10.1002/2015JA02 (2015). [2] Dods et al, J. Geophys. Res. 122, doi:10.1002/2016JA02 (2017).

Irreducible correlation functions of the S matrix in the coordinate representation: application in calculating Lorentzian half-widths and shifts.

PubMed

Ma, Q; Tipping, R H; Boulet, C

2006-01-07

By introducing the coordinate representation, the derivation of the perturbation expansion of the Liouville S matrix is formulated in terms of classically behaved autocorrelation functions. Because these functions are characterized by a pair of irreducible tensors, their number is limited to a few. They represent how the overlaps of the potential components change with a time displacement, and under normal conditions, their magnitudes decrease by several orders of magnitude when the displacement reaches several picoseconds. The correlation functions contain all dynamical information of the collision processes necessary in calculating half-widths and shifts and can be easily derived with high accuracy. Their well-behaved profiles, especially the rapid decrease of the magnitude, enables one to transform easily the dynamical information contained in them from the time domain to the frequency domain. More specifically, because these correlation functions are well time limited, their continuous Fourier transforms should be band limited. Then, the latter can be accurately replaced by discrete Fourier transforms and calculated with a standard fast Fourier transform method. Besides, one can easily calculate their Cauchy principal integrations and derive all functions necessary in calculating half-widths and shifts. A great advantage resulting from introducing the coordinate representation and choosing the correlation functions as the starting point is that one is able to calculate the half-widths and shifts with high accuracy, no matter how complicated the potential models are and no matter what kind of trajectories are chosen. In any case, the convergence of the calculated results is always guaranteed. As a result, with this new method, one can remove some uncertainties incorporated in the current width and shift studies. As a test, we present calculated Raman Q linewidths for the N2-N2 pair based on several trajectories, including the more accurate "exact" ones. Finally, by using this new method as a benchmark, we have carried out convergence checks for calculated values based on usual methods and have found that some results in the literature are not converged.

The similiarity of facial expressions in response to emotion-inducing films in reared-apart twins.

PubMed

Kendler, K S; Halberstadt, L J; Butera, F; Myers, J; Bouchard, T; Ekman, P

2008-10-01

While the role of genetic factors in self-report measures of emotion has been frequently studied, we know little about the degree to which genetic factors influence emotional facial expressions. Twenty-eight pairs of monozygotic (MZ) and dizygotic (DZ) twins from the Minnesota Study of Twins Reared Apart were shown three emotion-inducing films and their facial responses recorded. These recordings were blindly scored by trained raters. Ranked correlations between twins were calculated controlling for age and sex. Twin pairs were significantly correlated for facial expressions of general positive emotions, happiness, surprise and anger, but not for general negative emotions, sadness, or disgust or average emotional intensity. MZ pairs (n=18) were more correlated than DZ pairs (n=10) for most but not all emotional expressions. Since these twin pairs had minimal contact with each other prior to testing, these results support significant genetic effects on the facial display of at least some human emotions in response to standardized stimuli. The small sample size resulted in estimated twin correlations with very wide confidence intervals.

Dynamic patterning by the Drosophila pair-rule network reconciles long-germ and short-germ segmentation

PubMed Central

2017-01-01

Drosophila segmentation is a well-established paradigm for developmental pattern formation. However, the later stages of segment patterning, regulated by the “pair-rule” genes, are still not well understood at the system level. Building on established genetic interactions, I construct a logical model of the Drosophila pair-rule system that takes into account the demonstrated stage-specific architecture of the pair-rule gene network. Simulation of this model can accurately recapitulate the observed spatiotemporal expression of the pair-rule genes, but only when the system is provided with dynamic “gap” inputs. This result suggests that dynamic shifts of pair-rule stripes are essential for segment patterning in the trunk and provides a functional role for observed posterior-to-anterior gap domain shifts that occur during cellularisation. The model also suggests revised patterning mechanisms for the parasegment boundaries and explains the aetiology of the even-skipped null mutant phenotype. Strikingly, a slightly modified version of the model is able to pattern segments in either simultaneous or sequential modes, depending only on initial conditions. This suggests that fundamentally similar mechanisms may underlie segmentation in short-germ and long-germ arthropods. PMID:28953896

Dissociation energy and dynamics of water clusters

NASA Astrophysics Data System (ADS)

Ch'ng, Lee Chiat

The state-to-state vibrational predissociation (VP) dynamics of water clusters were studied following excitation of a vibrational mode of each cluster. Velocity-map imaging (VMI) and resonance-enhanced multiphoton ionization (REMPI) were used to determine pair-correlated center-of-mass translational energy distributions. Product energy distributions and dissociation energies were determined. Following vibrational excitation of the HCl stretch fundamental of the HCl-H2O dimer, HCl fragments were detected by 2 + 1 REMPI via the f 3□2(nu' = 0) ← X 1Sigma+(nu'' = 0) and V1Sigma + (nu' = 11 and 12) ← X1Sigma+ (nu'' = 0) transitions. REMPI spectra clearly show HCl from dissociation produced in the ground vibrational state with J'' up to 11. The fragments' center-of-mass translational energy distributions were determined from images of selected rotational states of HCl and were converted to rotational state distributions of the water cofragment. All the distributions could be fit well when using a dimer dissociation energy of bond dissociation energy D0 = 1334 +/- 10 cm--1. The rotational distributions in the water cofragment pair-correlated with specific rotational states of HCl appear nonstatistical when compared to predictions of the statistical phase space theory. A detailed analysis of pair-correlated state distributions was complicated by the large number of water rotational states available, but the data show that the water rotational populations increase with decreasing translational energy. H2O fragments of this dimer were detected by 2 + 1 REMPI via the C˜1B1(000) ← X˜1A1(000) transition. REMPI clearly shows that H2O from dissociation is produced in the ground vibrational state. The fragment's center-of-mass translational energy distributions were determined from images of selected rotational states of H2O and were converted to rotational state distributions of the HCl cofragment. The distributions gave D0 = 1334 +/- 10 cm --1 and show a clear preference for rotational levels in the HCl fragment that minimize translational energy release. The usefulness of 2 + 1 REMPI detection of water fragment is discussed. The hydrogen bonding in water is dominated by pair-wise dimer interactions, and the predissociation of the water dimer following vibrational excitation is reported. The measured D0 values of (H 2O)2 and (D2O)2, 1105 and 1244 +/- 10 cm--1, respectively, are in excellent agreement with the calculated values of 1103 and 1244 +/- 5 cm--1. Pair-correlated water fragment rovibrational state distributions following vibrational predissociation of (H2O)2 and (D2O) 2 were obtained upon excitation of the hydrogen bonded OH and OD stretch fundamentals, respectively. Quasiclassical trajectory calculations, using an accurate full-dimensional potential energy surface, are in accord with and help to elucidate experiment. Experiment and theory find predominant excitation of the fragment bending mode upon hydrogen bond breaking. A minor channel is also observed in which both fragments are in the ground vibrational state and are highly rotationally excited. The theoretical calculations reveal equal probability of bending excitation in the donor and acceptor subunits, which is a result of interchange of donor and acceptor roles. The rotational distributions associated with the major channel, in which one water fragment has one quantum of bend, and the minor channel with both water fragments in the ground vibrational state are calculated, and are in agreement with experiment. (Abstract shortened by UMI.)

A molecular dynamics study of the role of molecular water on the structure and mechanics of amorphous geopolymer binders.

PubMed

Sadat, Mohammad Rafat; Bringuier, Stefan; Asaduzzaman, Abu; Muralidharan, Krishna; Zhang, Lianyang

2016-10-07

In this paper, molecular dynamics simulations are used to study the effect of molecular water and composition (Si/Al ratio) on the structure and mechanical properties of fully polymerized amorphous sodium aluminosilicate geopolymer binders. The X-ray pair distribution function for the simulated geopolymer binder phase showed good agreement with the experimentally determined structure in terms of bond lengths of the various atomic pairs. The elastic constants and ultimate tensile strength of the geopolymer binders were calculated as a function of water content and Si/Al ratio; while increasing the Si/Al ratio from one to three led to an increase in the respective values of the elastic stiffness and tensile strength, for a given Si/Al ratio, increasing the water content decreased the stiffness and strength of the binder phase. An atomic-scale analysis showed a direct correlation between water content and diffusion of alkali ions, resulting in the weakening of the AlO 4 tetrahedral structure due to the migration of charge balancing alkali ions away from the tetrahedra, ultimately leading to failure. In the presence of water molecules, the diffusion behavior of alkali cations was found to be particularly anomalous, showing dynamic heterogeneity. This paper, for the first time, proves the efficacy of atomistic simulations for understanding the effect of water in geopolymer binders and can thus serve as a useful design tool for optimizing composition of geopolymers with improved mechanical properties.

Hanbury Brown and Twiss correlations of Cooper pairs in helical liquids

NASA Astrophysics Data System (ADS)

Choi, Mahn-Soo

2014-01-01

We propose a Hanbury Brown and Twiss (HBT) experiment of Cooper pairs on the edge channels of quantum spin Hall insulators. The helical edge channels provide a well-defined beam of Cooper pairs and perfect Andreev reflections from superconductors. This allows our setup to be identical in spirit to the original HBT experiment. Interestingly, the cross correlation is always negative and provides no hint of the bosonic nature of Cooper pairs. This counterintuitive result is attributed to the perfect Andreev reflection and the true beam splitter in the setup.

What Do They Have in Common? Drivers of Streamflow Spatial Correlation and Prediction of Flow Regimes in Ungauged Locations

NASA Astrophysics Data System (ADS)

Betterle, A.; Radny, D.; Schirmer, M.; Botter, G.

2017-12-01

The spatial correlation of daily streamflows represents a statistical index encapsulating the similarity between hydrographs at two arbitrary catchment outlets. In this work, a process-based analytical framework is utilized to investigate the hydrological drivers of streamflow spatial correlation through an extensive application to 78 pairs of stream gauges belonging to 13 unregulated catchments in the eastern United States. The analysis provides insight on how the observed heterogeneity of the physical processes that control flow dynamics ultimately affect streamflow correlation and spatial patterns of flow regimes. Despite the variability of recession properties across the study catchments, the impact of heterogeneous drainage rates on the streamflow spatial correlation is overwhelmed by the spatial variability of frequency and intensity of effective rainfall events. Overall, model performances are satisfactory, with root mean square errors between modeled and observed streamflow spatial correlation below 10% in most cases. We also propose a method for estimating streamflow correlation in the absence of discharge data, which proves useful to predict streamflow regimes in ungauged areas. The method consists in setting a minimum threshold on the modeled flow correlation to individuate hydrologically similar sites. Catchment outlets that are most correlated (ρ>0.9) are found to be characterized by analogous streamflow distributions across a broad range of flow regimes.

Bose-Einstein correlation of kaons in Si + Au collisions at 14.6 A GeV/c

NASA Technical Reports Server (NTRS)

Akiba, Y.; Beavis, D.; Beery, P.; Britt, H. C.; Budick, B.; Chasman, C.; Chen, Z.; Chi, C. Y.; Chu, Y. Y.; Cianciolo, V.

1993-01-01

The E-802 spectrometer at the Brookhaven Alternating Gradient Synchrotron, enhanced by a trigger for selection of events with one or more specified particles, has been used to measure the momentum-space correlation between pairs of K(+)s emitted in central Si + Au collisions at 14.6 A GeV/c. This correlation has been projected onto the Lorentz-invariant relative four-momentum axis. Fits to this correlation function yield a size for the kaon source that is comparable to that found using pi(+) pairs from a similar rapidity range, once a transformation from the particle-pair frames to a single source frame is made.

Photon pair generation with tailored frequency correlations in graded-index multimode fibers.

PubMed

Pourbeyram, Hamed; Mafi, Arash

2018-05-01

We study theoretically the generation of photon pairs with controlled spectral correlations via the four-wave mixing process in graded-index multimode optical fibers (GIMFs). We show that the quantum correlations of the generated photons in GIMFs can be preserved over a wide spectral range for a tunable pump source. Therefore, GIMFs can be utilized as quantum-state-preserving tunable sources of photons. In particular, we have shown that it is possible to generate factorable two-photon states, which allow for heralding of pure-state single photons without the need for narrowband spectral post filtering. We also elaborate on the possibility of simultaneously generating correlated and uncorrelated photon pairs in the same optical fiber.

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

Wang, Yujie; Gong, Sha; Wang, Zhen

The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption ofmore » hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian.« less

Mechanical and transport properties of the poly(ethylene oxide)-poly(acrylic acid) double network hydrogel from molecular dynamic simulations.

PubMed

Jang, Seung Soon; Goddard, William A; Kalani, M Yashar S

2007-02-22

We used atomistic molecular dynamics (MD) simulations to investigate the mechanical and transport properties of the PEO-PAA double network (DN) hydrogel with 76 wt % water content. By analyzing the pair correlation functions for polymer-water pairs and for ion-water pairs and the solvent accessible surface area, we found that the solvation of polymer and ion in the DN hydrogel is enhanced in comparison with both PEO and PAA single network (SN) hydrogels. The effective mesh size of this DN hydrogel is smaller than that of the SN hydrogels with the same water content and the same molecular weight between the cross-linking points (Mc). Applying uniaxial extensions, we obtained the stress-strain curves for the hydrogels. This shows that the DN hydrogel has a sudden increase of stress above approximately 100% strain, much higher than the sum of the stresses of the two SN hydrogels at the same strain. This arises because PEO has a smaller Mc value than PAA, so that the PEO in the DN reaches fully stretched out at 100% strain that corresponds to 260% strain in the PEO SN (beyond this point, the bond stretching and the angle bending increase dramatically). We also calculated the diffusion coefficients of solutes such as D-glucose and ascorbic acid in the hydrogels, where we find that the diffusion coefficients of those solutes in the DN hydrogel are 60% of that in the PEO SN and 40% of that in the PAA SN due to its smaller effective mesh size.

Dynamically Close Pairs of Galaxies Selected in the NIR

NASA Astrophysics Data System (ADS)

Keenan, Ryan C.; Foucaud, Sebastien; De Propris, Roberto; Lin, Jing-Hua

2013-07-01

Studies of dynamically close pairs of galaxies can serve as a powerful probe of the galaxy merger rate and its evolution. Here we present a large sample of dynamically close pairs of galaxies selected in the K-band from the UKIDSS LAS. These data span ~ 175 deg2 on the sky in the 2dFGRS equatorial region (10 h < RA < 14h). Combining the 2dFGRS redshifts with those from the SDSS, our K-band selected catalog is > 90% spectroscopically complete at K AB < 16.4. In this study, we focus on quantifying the relative contributions of wet, dry, and mixed mergers to the stellar mass buildup of galaxies over the past 1-2 Gyr.

Flexible Ionic-Electronic Hybrid Oxide Synaptic TFTs with Programmable Dynamic Plasticity for Brain-Inspired Neuromorphic Computing.

PubMed

John, Rohit Abraham; Ko, Jieun; Kulkarni, Mohit R; Tiwari, Naveen; Chien, Nguyen Anh; Ing, Ng Geok; Leong, Wei Lin; Mathews, Nripan

2017-08-01

Emulation of biological synapses is necessary for future brain-inspired neuromorphic computational systems that could look beyond the standard von Neuman architecture. Here, artificial synapses based on ionic-electronic hybrid oxide-based transistors on rigid and flexible substrates are demonstrated. The flexible transistors reported here depict a high field-effect mobility of ≈9 cm 2 V -1 s -1 with good mechanical performance. Comprehensive learning abilities/synaptic rules like paired-pulse facilitation, excitatory and inhibitory postsynaptic currents, spike-time-dependent plasticity, consolidation, superlinear amplification, and dynamic logic are successfully established depicting concurrent processing and memory functionalities with spatiotemporal correlation. The results present a fully solution processable approach to fabricate artificial synapses for next-generation transparent neural circuits. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ab initio molecular dynamics simulation of binary Cu64Zr36 bulk metallic glass: Validation of the cluster-plus-glue-atom model

NASA Astrophysics Data System (ADS)

Tian, Hua; Zhang, Chong; Wang, Lu; Zhao, JiJun; Dong, Chuang; Wen, Bin; Wang, Qing

2011-06-01

We have performed ab initio molecular dynamics simulation of Cu64Zr36 alloy at descending temperatures (from 2000 K to 400 K) and discussed the evolution of short-range order with temperature. The pair-correlation functions, coordination numbers, and chemical compositions of the most abundant local clusters have been analyzed. We found that icosahedral short-range order exists in the liquid, undercooled, and glass states, and it becomes dominant in the glass states. Moreover, we demonstrated the existence of Cu-centered Cu8Zr5 icosahedral clusters as the major local structural unit in the Cu64Zr36 amorphous alloy. This finding agrees well with our previous cluster model of Cu-Zr-based BMG as well as experimental evidences from synchrotron x ray and neutron diffraction measurements.

Molecular-dynamics simulation of polymethylene chain confined in cylindrical potentials. I. Nature of the conformational defects

NASA Astrophysics Data System (ADS)

Yamamoto, Takashi; Kimikawa, Yuichi

1992-10-01

The conformational motion of a polymethylene molecule constrained by a cylindrical potential is simulated up to 100 ps. The molecule consists of 60 CH2 groups and has variable bond lengths, bond angles, and dihedral angles. Our main concern here is the excitation and the dynamics of the conformational defects: kinks, jogs, etc. Under weaker constraint a number of gauche bonds are excited; they mostly form pairs such as gtḡ kinks or gtttḡ jogs. These conformational defects show no continuous drift in space. Instead they often annihilate and then recreate at different sites showing apparently random positional changes. The conformational defects produce characteristic strain fields around them. It seems that the conformational defects interact attractively through these strain fields. This is evidenced by remarkably correlated spatial distributions of the gauche bonds.

Ecological dynamics of continuous and categorical decision-making: the regatta start in sailing.

PubMed

Araújo, Duarte; Davids, Keith; Diniz, Ana; Rocha, Luis; Santos, João Coelho; Dias, Gonçalo; Fernandes, Orlando

2015-01-01

Ecological dynamics of decision-making in the sport of sailing exemplifies emergent, conditionally coupled, co-adaptive behaviours. In this study, observation of the coupling dynamics of paired boats during competitive sailing showed that decision-making can be modelled as a self-sustained, co-adapting system of informationally coupled oscillators (boats). Bytracing the spatial-temporal displacements of the boats, time series analyses (autocorrelations, periodograms and running correlations) revealed that trajectories of match racing boats are coupled more than 88% of the time during a pre-start race, via continuous, competing co-adaptions between boats. Results showed that both the continuously selected trajectories of the sailors (12 years of age) and their categorical starting point locations were examples of emergent decisions. In this dynamical conception of decision-making behaviours, strategic positioning (categorical) and continuous displacement of a boat over the course in match-race sailing emerged as a function of interacting task, personal and environmental constraints. Results suggest how key interacting constraints could be manipulated in practice to enhance sailors' perceptual attunement to them in competition.

Dynamic mode decomposition for plasma diagnostics and validation.

PubMed

Taylor, Roy; Kutz, J Nathan; Morgan, Kyle; Nelson, Brian A

2018-05-01

We demonstrate the application of the Dynamic Mode Decomposition (DMD) for the diagnostic analysis of the nonlinear dynamics of a magnetized plasma in resistive magnetohydrodynamics. The DMD method is an ideal spatio-temporal matrix decomposition that correlates spatial features of computational or experimental data while simultaneously associating the spatial activity with periodic temporal behavior. DMD can produce low-rank, reduced order surrogate models that can be used to reconstruct the state of the system with high fidelity. This allows for a reduction in the computational cost and, at the same time, accurate approximations of the problem, even if the data are sparsely sampled. We demonstrate the use of the method on both numerical and experimental data, showing that it is a successful mathematical architecture for characterizing the helicity injected torus with steady inductive (HIT-SI) magnetohydrodynamics. Importantly, the DMD produces interpretable, dominant mode structures, including a stationary mode consistent with our understanding of a HIT-SI spheromak accompanied by a pair of injector-driven modes. In combination, the 3-mode DMD model produces excellent dynamic reconstructions across the domain of analyzed data.

Dynamic mode decomposition for plasma diagnostics and validation

NASA Astrophysics Data System (ADS)

Taylor, Roy; Kutz, J. Nathan; Morgan, Kyle; Nelson, Brian A.

2018-05-01

We demonstrate the application of the Dynamic Mode Decomposition (DMD) for the diagnostic analysis of the nonlinear dynamics of a magnetized plasma in resistive magnetohydrodynamics. The DMD method is an ideal spatio-temporal matrix decomposition that correlates spatial features of computational or experimental data while simultaneously associating the spatial activity with periodic temporal behavior. DMD can produce low-rank, reduced order surrogate models that can be used to reconstruct the state of the system with high fidelity. This allows for a reduction in the computational cost and, at the same time, accurate approximations of the problem, even if the data are sparsely sampled. We demonstrate the use of the method on both numerical and experimental data, showing that it is a successful mathematical architecture for characterizing the helicity injected torus with steady inductive (HIT-SI) magnetohydrodynamics. Importantly, the DMD produces interpretable, dominant mode structures, including a stationary mode consistent with our understanding of a HIT-SI spheromak accompanied by a pair of injector-driven modes. In combination, the 3-mode DMD model produces excellent dynamic reconstructions across the domain of analyzed data.

Anatomical connectivity influences both intra- and inter-brain synchronizations.

PubMed

Dumas, Guillaume; Chavez, Mario; Nadel, Jacqueline; Martinerie, Jacques

2012-01-01

Recent development in diffusion spectrum brain imaging combined to functional simulation has the potential to further our understanding of how structure and dynamics are intertwined in the human brain. At the intra-individual scale, neurocomputational models have already started to uncover how the human connectome constrains the coordination of brain activity across distributed brain regions. In parallel, at the inter-individual scale, nascent social neuroscience provides a new dynamical vista of the coupling between two embodied cognitive agents. Using EEG hyperscanning to record simultaneously the brain activities of subjects during their ongoing interaction, we have previously demonstrated that behavioral synchrony correlates with the emergence of inter-brain synchronization. However, the functional meaning of such synchronization remains to be specified. Here, we use a biophysical model to quantify to what extent inter-brain synchronizations are related to the anatomical and functional similarity of the two brains in interaction. Pairs of interacting brains were numerically simulated and compared to real data. Results show a potential dynamical property of the human connectome to facilitate inter-individual synchronizations and thus may partly account for our propensity to generate dynamical couplings with others.

Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics

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

Tanzi, Luana; Ramondo, Fabio, E-mail: fabio.ramondo@univaq.it; Caminiti, Ruggero

2015-09-21

We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations andmore » anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.« less

Tracking the coherent generation of polaron pairs in conjugated polymers

NASA Astrophysics Data System (ADS)

de Sio, Antonietta; Troiani, Filippo; Maiuri, Margherita; Réhault, Julien; Sommer, Ephraim; Lim, James; Huelga, Susana F.; Plenio, Martin B.; Rozzi, Carlo Andrea; Cerullo, Giulio; Molinari, Elisa; Lienau, Christoph

2016-12-01

The optical excitation of organic semiconductors not only generates charge-neutral electron-hole pairs (excitons), but also charge-separated polaron pairs with high yield. The microscopic mechanisms underlying this charge separation have been debated for many years. Here we use ultrafast two-dimensional electronic spectroscopy to study the dynamics of polaron pair formation in a prototypical polymer thin film on a sub-20-fs time scale. We observe multi-period peak oscillations persisting for up to about 1 ps as distinct signatures of vibronic quantum coherence at room temperature. The measured two-dimensional spectra show pronounced peak splittings revealing that the elementary optical excitations of this polymer are hybridized exciton-polaron-pairs, strongly coupled to a dominant underdamped vibrational mode. Coherent vibronic coupling induces ultrafast polaron pair formation, accelerates the charge separation dynamics and makes it insensitive to disorder. These findings open up new perspectives for tailoring light-to-current conversion in organic materials.

Pairing induced superconductivity in holography

NASA Astrophysics Data System (ADS)

Bagrov, Andrey; Meszena, Balazs; Schalm, Koenraad

2014-09-01

We study pairing induced superconductivity in large N strongly coupled systems at finite density using holography. In the weakly coupled dual gravitational theory the mechanism is conventional BCS theory. An IR hard wall cut-off is included to ensure that we can controllably address the dynamics of a single confined Fermi surface. We address in detail the interplay between the scalar order parameter field and fermion pairing. Adding an explicitly dynamical scalar operator with the same quantum numbers as the fermion-pair, the theory experiences a BCS/BEC crossover controlled by the relative scaling dimensions. We find the novel result that this BCS/BEC crossover exposes resonances in the canonical expectation value of the scalar operator. This occurs not only when the scaling dimension is degenerate with the Cooper pair, but also with that of higher derivative paired operators. We speculate that a proper definition of the order parameter which takes mixing with these operators into account stays finite nevertheless.

The locking-decoding frontier for generic dynamics.

PubMed

Dupuis, Frédéric; Florjanczyk, Jan; Hayden, Patrick; Leung, Debbie

2013-11-08

It is known that the maximum classical mutual information, which can be achieved between measurements on pairs of quantum systems, can drastically underestimate the quantum mutual information between them. In this article, we quantify this distinction between classical and quantum information by demonstrating that after removing a logarithmic-sized quantum system from one half of a pair of perfectly correlated bitstrings, even the most sensitive pair of measurements might yield only outcomes essentially independent of each other. This effect is a form of information locking but the definition we use is strictly stronger than those used previously. Moreover, we find that this property is generic, in the sense that it occurs when removing a random subsystem. As such, the effect might be relevant to statistical mechanics or black hole physics. While previous works had always assumed a uniform message, we assume only a min-entropy bound and also explore the effect of entanglement. We find that classical information is strongly locked almost until it can be completely decoded. Finally, we exhibit a quantum key distribution protocol that is 'secure' in the sense of accessible information but in which leakage of even a logarithmic number of bits compromises the secrecy of all others.

The locking-decoding frontier for generic dynamics

PubMed Central

Dupuis, Frédéric; Florjanczyk, Jan; Hayden, Patrick; Leung, Debbie

2013-01-01

It is known that the maximum classical mutual information, which can be achieved between measurements on pairs of quantum systems, can drastically underestimate the quantum mutual information between them. In this article, we quantify this distinction between classical and quantum information by demonstrating that after removing a logarithmic-sized quantum system from one half of a pair of perfectly correlated bitstrings, even the most sensitive pair of measurements might yield only outcomes essentially independent of each other. This effect is a form of information locking but the definition we use is strictly stronger than those used previously. Moreover, we find that this property is generic, in the sense that it occurs when removing a random subsystem. As such, the effect might be relevant to statistical mechanics or black hole physics. While previous works had always assumed a uniform message, we assume only a min-entropy bound and also explore the effect of entanglement. We find that classical information is strongly locked almost until it can be completely decoded. Finally, we exhibit a quantum key distribution protocol that is ‘secure’ in the sense of accessible information but in which leakage of even a logarithmic number of bits compromises the secrecy of all others. PMID:24204183

Pair correlation functions for identifying spatial correlation in discrete domains

NASA Astrophysics Data System (ADS)

Gavagnin, Enrico; Owen, Jennifer P.; Yates, Christian A.

2018-06-01

Identifying and quantifying spatial correlation are important aspects of studying the collective behavior of multiagent systems. Pair correlation functions (PCFs) are powerful statistical tools that can provide qualitative and quantitative information about correlation between pairs of agents. Despite the numerous PCFs defined for off-lattice domains, only a few recent studies have considered a PCF for discrete domains. Our work extends the study of spatial correlation in discrete domains by defining a new set of PCFs using two natural and intuitive definitions of distance for a square lattice: the taxicab and uniform metric. We show how these PCFs improve upon previous attempts and compare between the quantitative data acquired. We also extend our definitions of the PCF to other types of regular tessellation that have not been studied before, including hexagonal, triangular, and cuboidal. Finally, we provide a comprehensive PCF for any tessellation and metric, allowing investigation of spatial correlation in irregular lattices for which recognizing correlation is less intuitive.

Ion acoustic shock wave in collisional equal mass plasma

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

Adak, Ashish, E-mail: ashish-adak@yahoo.com; Ghosh, Samiran, E-mail: sran-g@yahoo.com; Chakrabarti, Nikhil, E-mail: nikhil.chakrabarti@saha.ac.in

The effect of ion-ion collision on the dynamics of nonlinear ion acoustic wave in an unmagnetized pair-ion plasma has been investigated. The two-fluid model has been used to describe the dynamics of both positive and negative ions with equal masses. It is well known that in the dynamics of the weakly nonlinear wave, the viscosity mediates wave dissipation in presence of weak nonlinearity and dispersion. This dissipation is responsible for the shock structures in pair-ion plasma. Here, it has been shown that the ion-ion collision in presence of collective phenomena mediated by the plasma current is the source of dissipationmore » that causes the Burgers' term which is responsible for the shock structures in equal mass pair-ion plasma. The dynamics of the weakly nonlinear wave is governed by the Korteweg-de Vries Burgers equation. The analytical and numerical investigations revealed that the ion acoustic wave exhibits both oscillatory and monotonic shock structures depending on the frequency of ion-ion collision parameter. The results have been discussed in the context of the fullerene pair-ion plasma experiments.« less

Elliptic jets, part 2. Dynamics of coherent structures: Pairing

NASA Technical Reports Server (NTRS)

Husain, Hyder S.; Hussain, Fazle

1992-01-01

The dynamics of the jet column mode of vortex pairing in the near field of an elliptic jet was investigated. Hot-wire measurements and flow visualization were used to examine the details of the pairing mechanism of nonplanar vortical elliptic structures and its effect on such turbulence measures as coherent velocities, incoherent turbulence intensities, incoherent and coherent Reynolds, stresses, turbulence production, and mass entrainment. It was found that pairing of elliptic vortices in the jet column does not occur uniformly around the entire perimeter, unlike in a circular jet. Merger occurs only in the initial major-axis plane. In the initial minor-axis plane, the trailing vortex rushes through the leading vortex without pairing and then breaks down violently, producing considerably greater entrainment and mixing than in circular or plane jets.

d -wave superconductivity in the presence of nearest-neighbor Coulomb repulsion

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

Jiang, M.; Hahner, U. R.; Schulthess, T. C.

Dynamic cluster quantum Monte Carlo calculations for a doped two-dimensional extended Hubbard model are used to study the stability and dynamics of d-wave pairing when a nearest-neighbor Coulomb repulsion V is present in addition to the on-site Coulomb repulsion U. We find that d-wave pairing and the superconducting transition temperature Tc are only weakly suppressed as long as V does not exceed U/2. This stability is traced to the strongly retarded nature of pairing that allows the d-wave pairs to minimize the repulsive effect of V. When V approaches U/2, large momentum charge fluctuations are found to become important andmore » to give rise to a more rapid suppression of d-wave pairing and T c than for smaller V.« less

A criterion for pure pair-ion plasmas and the role of quasineutrality in nonlinear dynamics

NASA Astrophysics Data System (ADS)

Saleem, H.

2007-01-01

A criterion is presented to decide whether a produced plasma can be called a pure pair-ion plasma or not. The theory is discussed in the light of recent experiments which claim that a pure pair-ion fullerene (C60±) plasma has been produced. It is also shown that the ion acoustic wave is replaced by the pair ion convective cell (PPCC) mode as the electron density becomes vanishingly small in a magnetized plasma comprised of positive and negative ions. The nonlinear dynamics of pure pair plasmas is described by two coupled equations which have no analog in electron-ion plasmas. In a stationary frame, it becomes similar to the Hasegawa-Mima equation but does not contain drift waves and ion acoustic waves.

HIV Migration Between Blood and Cerebrospinal Fluid or Semen Over Time

PubMed Central

Chaillon, Antoine; Gianella, Sara; Wertheim, Joel O.; Richman, Douglas D.; Mehta, Sanjay R.; Smith, David M.

2014-01-01

Previous studies reported associations between neuropathogenesis and human immunodeficiency virus (HIV) compartmentalization in cerebrospinal fluid (CSF) and between sexual transmission and human immunodeficiency virus type 1 (HIV) compartmentalization in semen. It remains unclear, however, how compartmentalization dynamics change over time. To address this, we used statistical methods and Bayesian phylogenetic approaches to reconstruct temporal dynamics of HIV migration between blood and CSF and between blood and the male genital tract. We investigated 11 HIV-infected individuals with paired semen and blood samples and 4 individuals with paired CSF and blood samples. Aligned partial HIV env sequences were analyzed by (1) phylogenetic reconstruction, using a Bayesian Markov-chain Monte Carlo approach; (2) evaluation of viral compartmentalization, using tree-based and distance-based methods; and (3) analysis of migration events, using a discrete Bayesian asymmetric phylogeographic approach of diffusion with Markov jump counts estimation. Finally, we evaluated potential correlates of viral gene flow across anatomical compartments. We observed bidirectional replenishment of viral compartments and asynchronous peaks of viral migration from and to blood over time, suggesting that disruption of viral compartment is transient and directionally selected. These findings imply that viral subpopulations in anatomical sites are an active part of the whole viral population and that compartmental reservoirs could have implications in future eradication studies. PMID:24302756

Ultrafast charge-transfer-to-solvent dynamics of iodide in tetrahydrofuran. 2. Photoinduced electron transfer to counterions in solution.

PubMed

Bragg, Arthur E; Schwartz, Benjamin J

2008-04-24

The excited states of atomic anions in liquids are bound only by the polarization of the surrounding solvent. Thus, the electron-detachment process following excitation to one of these solvent-bound states, known as charge-transfer-to-solvent (CTTS) states, provides a useful probe of solvent structure and dynamics. These transitions and subsequent relaxation dynamics also are influenced by other factors that alter the solution environment local to the CTTS anion, including the presence of cosolutes, cosolvents, and other ions. In this paper, we examine the ultrafast CTTS dynamics of iodide in liquid tetrahydrofuran (THF) with a particular focus on how the solvent dynamics and the CTTS electron-ejection process are altered in the presence of various counterions. In weakly polar solvents such as THF, iodide salts can be strongly ion-paired in solution; the steady-state UV-visible absorption spectroscopy of various iodide salts in liquid THF indicates that the degree of ion-pairing changes from strong to weak to none as the counterion is switched from Na+ to tetrabutylammonium (t-BA+) to crown-ether-complexed Na+, respectively. In our ultrafast experiments, we have excited the I- CTTS transition of these various iodide salts at 263 nm and probed the dynamics of the CTTS-detached electrons throughout the visible and near-IR. In the previous paper of this series (Bragg, A. E.; Schwartz, B. J. J. Phys. Chem. B 2008, 112, 483-494), we found that for "counterion-free" I- (obtained by complexing Na+ with a crown ether) the CTTS electrons were ejected approximately 6 nm from their partner iodine atoms, the result of significant nonadiabatic coupling between the CTTS excited state and extended electronic states supported by the naturally existing solvent cavities in liquid THF, which also serve as pre-existing electron traps. In contrast, for the highly ion-paired NaI/THF system, we find that approximately 90% of the CTTS electrons are "captured" by a nearby Na+ to form (Na+, e-)THF "tight-contact pairs" (TCPs), which are chemically and spectroscopically distinct from both solvated neutral sodium atoms and free solvated electrons. A simple kinetic model is able to reproduce the details of the electron capture process, with 63% of the electrons captured quickly in approximately 2.3 ps, 26% captured diffusively in approximately 63 ps, and the remaining 11% escaping out into the solution on subnanosecond time scales. We also find that the majority of the CTTS electrons are ejected to within 1 or 2 nm of the Na+. This demonstrates that the presence of the nearby cation biases the relocalization of CTTS-generated electrons from I- in THF, changing the nonadiabatic coupling to the extended, cavity-supported electronic states in THF to produce a much tighter distribution of electron-ejection distances. In the case of the more loosely ion-paired t-BA+-I-/THF system, we find that only 10-15% of the CTTS-ejected electrons associate with t-BA+ to form "loose-contact pairs" (LCPs), which are characterized by a much weaker interaction between the electron and cation than occurs in TCPs. The formation of (t-BA+, e-)THF LCPs is characterized by a Coulombically induced blue shift of the free eTHF- spectrum on a approximately 5-ps time scale. We argue that the weaker interaction between t-BA+ and the parent I- results in little change to the CTTS-ejection process, so that only those electrons that happen to localize in the vicinity of t-BA+ are captured to form LCPs. Finally, we interpret the correlation between electron capture yield and counterion-induced perturbation of the I- CTTS transition as arising from changes in the distribution of ion-pair separations with cation identity, and we discuss our results in the context of relevant solution conductivity measurements.

Electron correlations in partially filled lowest and excited Landau levels

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

Wojs, Arkadiusz

2001-03-15

The electron correlations near the half-filling of the lowest and excited Landau levels (LL's) are studied using numerical diagonalization. It is shown that in the low-lying states electrons avoid pair states with relative angular momenta R corresponding to positive anharmonicity of the interaction pseudopotential V(R). In the lowest LL, the superharmonic behavior of V(R) causes Laughlin correlations (avoiding pairs with R=1) and the Laughlin-Jain series of incompressible ground states. In the first excited LL, V(R) is harmonic at short range and a different series of incompressible states results. Similar correlations occur in the paired Moore-Read {nu}=5/2 state and in themore » {nu}=7/3 and 8/3 states, all having small total parentage from R=1 and 3 and large parentage from R=5. The {nu}=7/3 and 8/3 states are different from Laughlin {nu}=1/3 and 2/3 states and, in finite systems, occur at a different LL degeneracy (flux). The series of Laughlin-correlated states of electron pairs at {nu}=2+2/(q{sub 2}+2)=8/3, 5/2, 12/5, and 7/3 is proposed, although only in the {nu}=5/2 state pairing has been confirmed numerically. In the second excited LL, V(R) is subharmonic at short range and (near the half-filling) the electrons group into spatially separated larger {nu}=1 droplets to minimize the number of strongly repulsive pair states at R=3 and 5.« less

Entropy of finite random binary sequences with weak long-range correlations.

PubMed

Melnik, S S; Usatenko, O V

2014-11-01

We study the N-step binary stationary ergodic Markov chain and analyze its differential entropy. Supposing that the correlations are weak we express the conditional probability function of the chain through the pair correlation function and represent the entropy as a functional of the pair correlator. Since the model uses the two-point correlators instead of the block probability, it makes it possible to calculate the entropy of strings at much longer distances than using standard methods. A fluctuation contribution to the entropy due to finiteness of random chains is examined. This contribution can be of the same order as its regular part even at the relatively short lengths of subsequences. A self-similar structure of entropy with respect to the decimation transformations is revealed for some specific forms of the pair correlation function. Application of the theory to the DNA sequence of the R3 chromosome of Drosophila melanogaster is presented.

Entropy of finite random binary sequences with weak long-range correlations

NASA Astrophysics Data System (ADS)

Melnik, S. S.; Usatenko, O. V.

2014-11-01

We study the N -step binary stationary ergodic Markov chain and analyze its differential entropy. Supposing that the correlations are weak we express the conditional probability function of the chain through the pair correlation function and represent the entropy as a functional of the pair correlator. Since the model uses the two-point correlators instead of the block probability, it makes it possible to calculate the entropy of strings at much longer distances than using standard methods. A fluctuation contribution to the entropy due to finiteness of random chains is examined. This contribution can be of the same order as its regular part even at the relatively short lengths of subsequences. A self-similar structure of entropy with respect to the decimation transformations is revealed for some specific forms of the pair correlation function. Application of the theory to the DNA sequence of the R3 chromosome of Drosophila melanogaster is presented.

Orbital selective pairing and gap structures of iron-based superconductors

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

Kreisel, Andreas; Andersen, Brian M.; Sprau, P. O.

We discuss the in uence on spin-fluctuation pairing theory of orbital selective strong correlation effects in Fe-based superconductors, particularly Fe chalcogenide systems. We propose that a key ingredient for an improved itinerant pairing theory is orbital selectivity, i.e., incorporating the reduced coherence of quasiparticles occupying specific orbital states. This modifies the usual spin-fluctuation via suppression of pair scattering processes involving those less coherent states and results in orbital selective Cooper pairing of electrons in the remaining states. We show that this paradigm yields remarkably good agreement with the experimentally observed anisotropic gap structures in both bulk and monolayer FeSe, asmore » well as LiFeAs, indicating that orbital selective Cooper pairing plays a key role in the more strongly correlated iron-based superconductors.« less

Orbital selective pairing and gap structures of iron-based superconductors

DOE PAGES

Kreisel, Andreas; Andersen, Brian M.; Sprau, P. O.; ...

2017-05-08

We discuss the in uence on spin-fluctuation pairing theory of orbital selective strong correlation effects in Fe-based superconductors, particularly Fe chalcogenide systems. We propose that a key ingredient for an improved itinerant pairing theory is orbital selectivity, i.e., incorporating the reduced coherence of quasiparticles occupying specific orbital states. This modifies the usual spin-fluctuation via suppression of pair scattering processes involving those less coherent states and results in orbital selective Cooper pairing of electrons in the remaining states. We show that this paradigm yields remarkably good agreement with the experimentally observed anisotropic gap structures in both bulk and monolayer FeSe, asmore » well as LiFeAs, indicating that orbital selective Cooper pairing plays a key role in the more strongly correlated iron-based superconductors.« less

Correlation in photon pairs generated using four-wave mixing in a cold atomic ensemble

NASA Astrophysics Data System (ADS)

Ferdinand, Andrew Richard; Manjavacas, Alejandro; Becerra, Francisco Elohim

2017-04-01

Spontaneous four-wave mixing (FWM) in atomic ensembles can be used to generate narrowband entangled photon pairs at or near atomic resonances. While extensive research has been done to investigate the quantum correlations in the time and polarization of such photon pairs, the study and control of high dimensional quantum correlations contained in their spatial degrees of freedom has not been fully explored. In our work we experimentally investigate the generation of correlated light from FWM in a cold ensemble of cesium atoms as a function of the frequencies of the pump fields in the FWM process. In addition, we theoretically study the spatial correlations of the photon pairs generated in the FWM process, specifically the joint distribution of their orbital angular momentum (OAM). We investigate the width of the distribution of the OAM modes, known as the spiral bandwidth, and the purity of OAM correlations as a function of the properties of the pump fields, collected photons, and the atomic ensemble. These studies will guide experiments involving high dimensional entanglement of photons generated from this FWM process and OAM-based quantum communication with atomic ensembles. This work is supported by AFORS Grant FA9550-14-1-0300.

Asymptotic correlation functions and FFLO signature for the one-dimensional attractive Hubbard model

NASA Astrophysics Data System (ADS)

Cheng, Song; Jiang, Yuzhu; Yu, Yi-Cong; Batchelor, Murray T.; Guan, Xi-Wen

2018-04-01

We study the long-distance asymptotic behavior of various correlation functions for the one-dimensional (1D) attractive Hubbard model in a partially polarized phase through the Bethe ansatz and conformal field theory approaches. We particularly find the oscillating behavior of these correlation functions with spatial power-law decay, of which the pair (spin) correlation function oscillates with a frequency ΔkF (2 ΔkF). Here ΔkF = π (n↑ -n↓) is the mismatch in the Fermi surfaces of spin-up and spin-down particles. Consequently, the pair correlation function in momentum space has peaks at the mismatch k = ΔkF, which has been observed in recent numerical work on this model. These singular peaks in momentum space together with the spatial oscillation suggest an analog of the Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) state in the 1D Hubbard model. The parameter β representing the lattice effect becomes prominent in critical exponents which determine the power-law decay of all correlation functions. We point out that the backscattering of unpaired fermions and bound pairs within their own Fermi points gives a microscopic origin of the FFLO pairing in 1D.

Conductor gestures influence evaluations of ensemble performance

PubMed Central

Morrison, Steven J.; Price, Harry E.; Smedley, Eric M.; Meals, Cory D.

2014-01-01

Previous research has found that listener evaluations of ensemble performances vary depending on the expressivity of the conductor’s gestures, even when performances are otherwise identical. It was the purpose of the present study to test whether this effect of visual information was evident in the evaluation of specific aspects of ensemble performance: articulation and dynamics. We constructed a set of 32 music performances that combined auditory and visual information and were designed to feature a high degree of contrast along one of two target characteristics: articulation and dynamics. We paired each of four music excerpts recorded by a chamber ensemble in both a high- and low-contrast condition with video of four conductors demonstrating high- and low-contrast gesture specifically appropriate to either articulation or dynamics. Using one of two equivalent test forms, college music majors and non-majors (N = 285) viewed sixteen 30 s performances and evaluated the quality of the ensemble’s articulation, dynamics, technique, and tempo along with overall expressivity. Results showed significantly higher evaluations for performances featuring high rather than low conducting expressivity regardless of the ensemble’s performance quality. Evaluations for both articulation and dynamics were strongly and positively correlated with evaluations of overall ensemble expressivity. PMID:25104944

Molecular dynamics study of the conformational properties of cyclohexadecane

NASA Astrophysics Data System (ADS)

Zhang, Renshi; Mattice, Wayne L.

1993-06-01

Molecular dynamics has been used for the first time for the study of the conformational properties of cyclohexadecane, c-C16H32. By analyzing a long molecular dynamics trajectory (14.5 ns) at 450 K, equilibrium statistics such as the relative populations of different isomeric conformers and the probability ratios, p(gt)/p(tt), p(gg)/p(tt), and p(gg)/p(gtg), of different conformational segments, have been studied. The dynamic properties including the transition modes of gauche migration and gauche-pair creation, which have been reported before in n-alkanes, and the auto- and cross-correlations of the bond dihedral angles, have also been obtained. It was possible to make direct comparisons on some of the statistics with theory and experiment. Most of the results extracted from the molecular dynamics trajectory lie in between previously reported experimental and theoretical values. Many previously predicted conformers have been confirmed by our simulations. The results of the population probability of the most populated conformer seems to suggest that an earlier discrepancy between the theoretical works and an experimental work originates from insufficient samplings in earlier theoretical works, rather than from their inaccurate force field.

Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog

PubMed Central

Spring-Connell, Alexander M.; Evich, Marina G.; Debelak, Harald; Seela, Frank; Germann, Markus W.

2016-01-01

A truly universal nucleobase enables a host of novel applications such as simplified templates for PCR primers, randomized sequencing and DNA based devices. A universal base must pair indiscriminately to each of the canonical bases with little or preferably no destabilization of the overall duplex. In reality, many candidates either destabilize the duplex or do not base pair indiscriminatingly. The novel base 8-aza-7-deazaadenine (pyrazolo[3,4-d]pyrimidin- 4-amine) N8-(2′deoxyribonucleoside), a deoxyadenosine analog (UB), pairs with each of the natural DNA bases with little sequence preference. We have utilized NMR complemented with molecular dynamic calculations to characterize the structure and dynamics of a UB incorporated into a DNA duplex. The UB participates in base stacking with little to no perturbation of the local structure yet forms an unusual base pair that samples multiple conformations. These local dynamics result in the complete disappearance of a single UB proton resonance under native conditions. Accommodation of the UB is additionally stabilized via heightened backbone conformational sampling. NMR combined with various computational techniques has allowed for a comprehensive characterization of both structural and dynamic effects of the UB in a DNA duplex and underlines that the UB as a strong candidate for universal base applications. PMID:27566150

Nutritional correlates and mate acquisition role of multiple sexual traits in male collared flycatchers

NASA Astrophysics Data System (ADS)

Hegyi, Gergely; Szöllősi, Eszter; Jenni-Eiermann, Susanne; Török, János; Eens, Marcel; Garamszegi, László Zsolt

2010-06-01

The information content of a sexual signal may predict its importance in a multiple signal system. Many studies have correlated sexual signal expression with the absolute levels of nutrient reserves. In contrast, the changes of nutrient reserves associated with signal expression are largely unknown in the wild due to technical limitations although they are important determinants of signal information content. We compared two visual and eight acoustic sexual traits in male collared flycatchers to see whether the nutritional correlates of expression predict the role of the signal in sexual selection. We used single point assays of plasma lipid metabolites to estimate short-term changes in nutritional state in relation to sexual trait expression during courtship. As a measure of sexual selection, we estimated the relationship with pairing latency after arrival in a 4-year dataset. Males which found a mate rapidly were characterized by large wing and forehead patches, but small song strophe complexity and small figure repertoire size. Traits more strongly related to pairing latency were also more closely related to changes in nutrient reserves. This indicates a link between signal role and information content. Small wing patches and, surprisingly, complex songs seemed to indicate poor phenotypic quality and were apparently disfavoured at mate acquisition in our population. Future studies of the information content of sexual traits, especially dynamic traits such as song, may benefit from the use of plasma metabolite profiles as non-invasive indicators of short-term changes in body condition.

Anharmonicity and Octahedral Tilting in Hybrid Vacancy-Ordered Double Perovskites

DOE PAGES

Maughan, Annalise E.; Ganose, Alex M.; Candia, Andrew M.; ...

2017-11-30

The advantageous performance of hybrid organic-inorganic perovskite halide semiconduc- tors in optoelectronic applications motivates studies of their fundamental crystal-chemistry. In particular, recent studies have sought to understand how dipolar, dynamic, and organic cations, such as methylammonium (CH 3 NH 3 + ) and formamidinium (CH(NH 2 ) 2 + ) affect physical properties such as light absorption and charge transport. Here, to probe the influence of organic- inorganic coupling on charge transport, we have prepared the series of vacancy-ordered double perovskite derivatives, A 2SnI 6, where A = Cs +, CH 3NH 3 +, and CH(NH 2) 2 +. Despitemore » nearly identical cubic structures by powder X-ray diffraction, replacement of Cs + with CH 3NH 3 + or CH(NH 2) 2 + reduces conductivity through a reduction in both carrier concentration and carrier mobility. We attribute the trends in electronic behavior to anharmonic lattice dynamics from the formation of hydrogen bonds that yield coupled organic-inorganic dynamics. This anharmonicity manifests as asymmetry of the inter-octahedral I-I pair correlations in the X-ray pair distribution function of the hybrid compounds, which can be modeled by large atomistic ensembles with random rotations of rigid [SnI 6] octahedral units. The presence of soft, anharmonic lattice dynamics holds implications for electron-phonon interactions, as supported by calculation of electron-phonon coupling strength that indicates the formation of more tightly-bound polarons and reduced electron mobilities with increasing cation size. Finally, by exploiting the relatively decoupled nature of the octahedral units in these defect-ordered perovskite variants, we can interrogate the impact of organic-inorganic coupling and lattice anharmonicity on the charge transport behavior of hybrid perovskite halide semiconductors.« less

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

Maughan, Annalise E.; Ganose, Alex M.; Candia, Andrew M.

The advantageous performance of hybrid organic-inorganic perovskite halide semiconduc- tors in optoelectronic applications motivates studies of their fundamental crystal-chemistry. In particular, recent studies have sought to understand how dipolar, dynamic, and organic cations, such as methylammonium (CH 3 NH 3 + ) and formamidinium (CH(NH 2 ) 2 + ) affect physical properties such as light absorption and charge transport. Here, to probe the influence of organic- inorganic coupling on charge transport, we have prepared the series of vacancy-ordered double perovskite derivatives, A 2SnI 6, where A = Cs +, CH 3NH 3 +, and CH(NH 2) 2 +. Despitemore » nearly identical cubic structures by powder X-ray diffraction, replacement of Cs + with CH 3NH 3 + or CH(NH 2) 2 + reduces conductivity through a reduction in both carrier concentration and carrier mobility. We attribute the trends in electronic behavior to anharmonic lattice dynamics from the formation of hydrogen bonds that yield coupled organic-inorganic dynamics. This anharmonicity manifests as asymmetry of the inter-octahedral I-I pair correlations in the X-ray pair distribution function of the hybrid compounds, which can be modeled by large atomistic ensembles with random rotations of rigid [SnI 6] octahedral units. The presence of soft, anharmonic lattice dynamics holds implications for electron-phonon interactions, as supported by calculation of electron-phonon coupling strength that indicates the formation of more tightly-bound polarons and reduced electron mobilities with increasing cation size. Finally, by exploiting the relatively decoupled nature of the octahedral units in these defect-ordered perovskite variants, we can interrogate the impact of organic-inorganic coupling and lattice anharmonicity on the charge transport behavior of hybrid perovskite halide semiconductors.« less

Use of wavelet-packet transforms to develop an engineering model for multifractal characterization of mutation dynamics in pathological and nonpathological gene sequences

NASA Astrophysics Data System (ADS)

Walker, David Lee

1999-12-01

This study uses dynamical analysis to examine in a quantitative fashion the information coding mechanism in DNA sequences. This exceeds the simple dichotomy of either modeling the mechanism by comparing DNA sequence walks as Fractal Brownian Motion (fbm) processes. The 2-D mappings of the DNA sequences for this research are from Iterated Function System (IFS) (Also known as the ``Chaos Game Representation'' (CGR)) mappings of the DNA sequences. This technique converts a 1-D sequence into a 2-D representation that preserves subsequence structure and provides a visual representation. The second step of this analysis involves the application of Wavelet Packet Transforms, a recently developed technique from the field of signal processing. A multi-fractal model is built by using wavelet transforms to estimate the Hurst exponent, H. The Hurst exponent is a non-parametric measurement of the dynamism of a system. This procedure is used to evaluate gene- coding events in the DNA sequence of cystic fibrosis mutations. The H exponent is calculated for various mutation sites in this gene. The results of this study indicate the presence of anti-persistent, random walks and persistent ``sub-periods'' in the sequence. This indicates the hypothesis of a multi-fractal model of DNA information encoding warrants further consideration. This work examines the model's behavior in both pathological (mutations) and non-pathological (healthy) base pair sequences of the cystic fibrosis gene. These mutations both natural and synthetic were introduced by computer manipulation of the original base pair text files. The results show that disease severity and system ``information dynamics'' correlate. These results have implications for genetic engineering as well as in mathematical biology. They suggest that there is scope for more multi-fractal models to be developed.

Regional cerebral blood flow measurement with intravenous ( sup 15 O)water bolus and ( sup 18 F)fluoromethane inhalation

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

Herholz, K.; Pietrzyk, U.; Wienhard, K.

1989-09-01

In 20 patients with ischemic cerebrovascular disease, classic migraine, or angiomas, we compared paired dynamic positron emission tomographic measurements of regional cerebral blood flow using both ({sup 15}O)water and ({sup 18}F)fluoromethane as tracers. Cerebral blood flow was also determined according to the autoradiographic technique with a bolus injection of ({sup 15}O)water. There were reasonable overall correlations between dynamic ({sup 15}O)water and ({sup 18}F)fluoromethane values for cerebral blood flow (r = 0.82) and between dynamic and autoradiographic ({sup 15}O)water values for cerebral blood flow (r = 0.83). We found a close correspondence between abnormal pathologic findings and visually evaluated cerebral bloodmore » flow tomograms obtained with the two tracers. On average, dynamic ({sup 15}O)water cerebral blood flow was 6% lower than that measured with ({sup 18}F)fluoromethane. There also was a general trend toward a greater underestimation with ({sup 15}O)water in high-flow areas, particularly in hyperemic areas, probably due to incomplete first-pass extraction of ({sup 15}O)water. Underestimation was not detected in low-flow areas or in the cerebellum. Absolute cerebral blood flow values were less closely correlated between tracers and techniques than cerebral blood flow patterns. The variability of the relation between absolute flow values was probably caused by confounding effects of the variation in the circulatory delay time. The autoradiographic technique was most sensitive to this type error.« less

Pairing versus phase coherence of doped holes in distinct quantum spin backgrounds

NASA Astrophysics Data System (ADS)

Zhu, Zheng; Sheng, D. N.; Weng, Zheng-Yu

2018-03-01

We examine the pairing structure of holes injected into two distinct spin backgrounds: a short-range antiferromagnetic phase versus a symmetry protected topological phase. Based on density matrix renormalization group (DMRG) simulation, we find that although there is a strong binding between two holes in both phases, phase fluctuations can significantly influence the pair-pair correlation depending on the spin-spin correlation in the background. Here the phase fluctuation is identified as an intrinsic string operator nonlocally controlled by the spins. We show that while the pairing amplitude is generally large, the coherent Cooper pairing can be substantially weakened by the phase fluctuation in the symmetry-protected topological phase, in contrast to the short-range antiferromagnetic phase. It provides an example of a non-BCS mechanism for pairing, in which the paring phase coherence is determined by the underlying spin state self-consistently, bearing an interesting resemblance to the pseudogap physics in the cuprate.

The structure and resilience of financial market networks

NASA Astrophysics Data System (ADS)

Kauê Dal'Maso Peron, Thomas; da Fontoura Costa, Luciano; Rodrigues, Francisco A.

2012-03-01

Financial markets can be viewed as a highly complex evolving system that is very sensitive to economic instabilities. The complex organization of the market can be represented in a suitable fashion in terms of complex networks, which can be constructed from stock prices such that each pair of stocks is connected by a weighted edge that encodes the distance between them. In this work, we propose an approach to analyze the topological and dynamic evolution of financial networks based on the stock correlation matrices. An entropy-related measurement is adopted to quantify the robustness of the evolving financial market organization. It is verified that the network topological organization suffers strong variation during financial instabilities and the networks in such periods become less robust. A statistical robust regression model is proposed to quantity the relationship between the network structure and resilience. The obtained coefficients of such model indicate that the average shortest path length is the measurement most related to network resilience coefficient. This result indicates that a collective behavior is observed between stocks during financial crisis. More specifically, stocks tend to synchronize their price evolution, leading to a high correlation between pair of stock prices, which contributes to the increase in distance between them and, consequently, decrease the network resilience.

nth-Nearest-neighbor distribution functions of an interacting fluid from the pair correlation function: a hierarchical approach.

PubMed

Bhattacharjee, Biplab

2003-04-01

The paper presents a general formalism for the nth-nearest-neighbor distribution (NND) of identical interacting particles in a fluid confined in a nu-dimensional space. The nth-NND functions, W(n,r) (for n=1,2,3, em leader) in a fluid are obtained hierarchically in terms of the pair correlation function and W(n-1,r) alone. The radial distribution function (RDF) profiles obtained from the molecular dynamics (MD) simulation of Lennard-Jones (LJ) fluid is used to illustrate the results. It is demonstrated that the collective structural information contained in the maxima and minima of the RDF profiles being resolved in terms of individual NND functions may provide more insights about the microscopic neighborhood structure around a reference particle in a fluid. Representative comparison between the results obtained from the formalism and the MD simulation data shows good agreement. Apart from the quantities such as nth-NND functions and nth-nearest-neighbor distances, the average neighbor population number is defined. These quantities are evaluated for the LJ model system and interesting density dependence of the microscopic neighborhood shell structures are discussed in terms of them. The relevance of the NND functions in various phenomena is also pointed out.

nth-nearest-neighbor distribution functions of an interacting fluid from the pair correlation function: A hierarchical approach

NASA Astrophysics Data System (ADS)

Bhattacharjee, Biplab

2003-04-01

The paper presents a general formalism for the nth-nearest-neighbor distribution (NND) of identical interacting particles in a fluid confined in a ν-dimensional space. The nth-NND functions, W(n,r¯) (for n=1,2,3,…) in a fluid are obtained hierarchically in terms of the pair correlation function and W(n-1,r¯) alone. The radial distribution function (RDF) profiles obtained from the molecular dynamics (MD) simulation of Lennard-Jones (LJ) fluid is used to illustrate the results. It is demonstrated that the collective structural information contained in the maxima and minima of the RDF profiles being resolved in terms of individual NND functions may provide more insights about the microscopic neighborhood structure around a reference particle in a fluid. Representative comparison between the results obtained from the formalism and the MD simulation data shows good agreement. Apart from the quantities such as nth-NND functions and nth-nearest-neighbor distances, the average neighbor population number is defined. These quantities are evaluated for the LJ model system and interesting density dependence of the microscopic neighborhood shell structures are discussed in terms of them. The relevance of the NND functions in various phenomena is also pointed out.

Neural population-level memory traces in the mouse hippocampus.

PubMed

Chen, Guifen; Wang, L Phillip; Tsien, Joe Z

2009-12-16

One of the fundamental goals in neurosciences is to elucidate the formation and retrieval of brain's associative memory traces in real-time. Here, we describe real-time neural ensemble transient dynamics in the mouse hippocampal CA1 region and demonstrate their relationships with behavioral performances during both learning and recall. We employed the classic trace fear conditioning paradigm involving a neutral tone followed by a mild foot-shock 20 seconds later. Our large-scale recording and decoding methods revealed that conditioned tone responses and tone-shock association patterns were not present in CA1 during the first pairing, but emerged quickly after multiple pairings. These encoding patterns showed increased immediate-replay, correlating tightly with increased immediate-freezing during learning. Moreover, during contextual recall, these patterns reappeared in tandem six-to-fourteen times per minute, again correlating tightly with behavioral recall. Upon traced tone recall, while various fear memories were retrieved, the shock traces exhibited a unique recall-peak around the 20-second trace interval, further signifying the memory of time for the expected shock. Therefore, our study has revealed various real-time associative memory traces during learning and recall in CA1, and demonstrates that real-time memory traces can be decoded on a moment-to-moment basis over any single trial.

Classical and quantum simulations of warm dense carbon

NASA Astrophysics Data System (ADS)

Whitley, Heather; Sanchez, David; Hamel, Sebastien; Correa, Alfredo; Benedict, Lorin

We have applied classical and DFT-based molecular dynamics (MD) simulations to study the equation of state of carbon in the warm dense matter regime (ρ = 3.7 g/cc, 0.86 eV

A convergence algorithm for correlation of breech face images based on the congruent matching cells (CMC) method.

PubMed

Chen, Zhe; Song, John; Chu, Wei; Soons, Johannes A; Zhao, Xuezeng

2017-11-01

The Congruent Matching Cells (CMC) method was invented at the National Institute of Standards and Technology (NIST) for accurate firearm evidence identification and error rate estimation. The CMC method is based on the principle of discretization. The toolmark image of the reference sample is divided into correlation cells. Each cell is registered to the cell-sized area of the compared image that has maximum surface topography similarity. For each resulting cell pair, one parameter quantifies the similarity of the cell surface topography and three parameters quantify the pattern congruency of the registration position and orientation. An identification (declared match) requires a significant number of CMCs, that is, cell pairs that meet both similarity and pattern congruency requirements. The use of cell correlations reduces the effects of "invalid regions" in the compared image pairs and increases the correlation accuracy. The identification accuracy of the CMC method can be further improved by considering a feature named "convergence," that is, the tendency of the x-y registration positions of the correlated cell pairs to converge at the correct registration angle when comparing same-source samples at different relative orientations. In this paper, the difference of the convergence feature between known matching (KM) and known non-matching (KNM) image pairs is characterized, based on which an improved algorithm is developed for breech face image correlations using the CMC method. Its advantage is demonstrated by comparison with three existing CMC algorithms using four datasets. The datasets address three different brands of consecutively manufactured pistol slides, with significant differences in the distribution overlap of cell pair topography similarity for KM and KNM image pairs. For the same CMC threshold values, the convergence algorithm demonstrates noticeably improved results by reducing the number of false-positive or false-negative CMCs in a comparison. Published by Elsevier B.V.

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

Cable, J.W.

The diffuse scattering of neutrons from magnetic materials provides unique and important information regarding the spatial correlations of the atoms and the spins. Such measurements have been extensively applied to magnetically ordered systems, such as the ferromagnetic binary alloys, for which the observed correlations describe the magnetic moment fluctuations associated with local environment effects. With the advent of polarization analysis, these techniques are increasingly being applied to study disordered paramagnetic systems such as the spin-glasses and the diluted magnetic semiconductors. The spin-pair correlations obtained are essential in understanding the exchange interactions of such systems. In this paper, we describe recentmore » neutron diffuse scattering results on the atom-pair and spin-pair correlations in some of these disordered magnetic systems. 56 refs.« less

Hallux Valgus, By Nature or Nurture? A Twin Study.

PubMed

Munteanu, Shannon E; Menz, Hylton B; Wark, John D; Christie, Jemma J; Scurrah, Katrina J; Bui, Minh; Erbas, Bircan; Hopper, John L; Wluka, Anita E

2017-09-01

To evaluate the contributions of shared but unmeasured genetic and environmental factors to hallux valgus (HV). Between 2011 and 2012, 74 monozygotic (MZ) and 56 dizygotic (DZ) female twin pairs self-reported HV and putative risk factors, including footwear use across their lifespan. Estimates of casewise concordance (P C ), correlation (ρ), and odds ratios (ORs) were calculated, adjusting for age and other risk factors, and compared between MZ and DZ pairs using logistic regression, generalized estimating equations, and a maximum likelihood-based method, respectively. A total of 70 participants (27%) reported HV, with 12 MZ and 7 DZ pairs being concordant. After adjusting for age, twins were correlated (ρ = 0.27 [95% confidence interval (95% CI) 0.08, 0.46]) and concordant (P C  = 0.45 [95% CI 0.29, 0.61]; mean age 58 years), with no difference between MZ and DZ pairs (P = 0.7). HV was associated with regularly wearing footwear with a constrictive toe-box during the fourth decade (adjusted OR 2.73 [95% CI 1.12, 6.67]). This risk factor was correlated in MZ (ρ = 0.38 [95% CI 0.15, 0.60]) but not DZ (ρ = -0.20 [95% CI -0.43, 0.03]) pairs. These correlations were significantly different (P = 0.002). Twins are correlated for HV, but we found no evidence that correlation was due to shared genetic factors. We identified an environmental risk factor, footwear with a constrictive toe-box, that is not shared to the same extent by MZ and DZ pairs, contrary to the assumption of the classic twin model. Footwear, and possibly genetic factors and unknown shared environmental factors, could contribute to developing HV. © 2016, American College of Rheumatology.

Analytical pair correlations in ideal quantum gases: temperature-dependent bunching and antibunching.

PubMed

Bosse, J; Pathak, K N; Singh, G S

2011-10-01

The fluctuation-dissipation theorem together with the exact density response spectrum for ideal quantum gases has been utilized to yield a new expression for the static structure factor, which we use to derive exact analytical expressions for the temperature-dependent pair distribution function g(r) of the ideal gases. The plots of bosonic and fermionic g(r) display "Bose pile" and "Fermi hole" typically akin to bunching and antibunching as observed experimentally for ultracold atomic gases. The behavior of spin-scaled pair correlation for fermions is almost featureless, but bosons show a rich structure including long-range correlations near T(c). The coherent state at T=0 shows no correlation at all, just like single-mode lasers. The depicted decreasing trend in correlation with decrease in temperature for T

Local Genetic Correlation Gives Insights into the Shared Genetic Architecture of Complex Traits.

PubMed

Shi, Huwenbo; Mancuso, Nicholas; Spendlove, Sarah; Pasaniuc, Bogdan

2017-11-02

Although genetic correlations between complex traits provide valuable insights into epidemiological and etiological studies, a precise quantification of which genomic regions disproportionately contribute to the genome-wide correlation is currently lacking. Here, we introduce ρ-HESS, a technique to quantify the correlation between pairs of traits due to genetic variation at a small region in the genome. Our approach requires GWAS summary data only and makes no distributional assumption on the causal variant effect sizes while accounting for linkage disequilibrium (LD) and overlapping GWAS samples. We analyzed large-scale GWAS summary data across 36 quantitative traits, and identified 25 genomic regions that contribute significantly to the genetic correlation among these traits. Notably, we find 6 genomic regions that contribute to the genetic correlation of 10 pairs of traits that show negligible genome-wide correlation, further showcasing the power of local genetic correlation analyses. Finally, we report the distribution of local genetic correlations across the genome for 55 pairs of traits that show putative causal relationships. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Chromosome dynamics in meiotic prophase I in plants.

PubMed

Ronceret, A; Pawlowski, W P

2010-07-01

Early stages of meiotic prophase are characterized by complex and dramatic chromosome dynamics. Chromosome behavior during this period is associated with several critical meiotic processes that take place at the molecular level, such as recombination and homologous chromosome recognition and pairing. Studies to characterize specific patterns of chromosome dynamics and to identify their exact roles in the progression of meiotic prophase are only just beginning in plants. These studies are facilitated by advances in imaging technology in the recent years, including development of ultra-resolution three-dimensional and live microscopy methods. Studies conducted so far indicate that different chromosome regions exhibit different dynamics patterns in early prophase. In many species telomeres cluster at the nuclear envelope at the beginning of zygotene forming the telomere bouquet. The bouquet has been traditionally thought to facilitate chromosome pairing by bringing chromosome ends into close proximity, but recent studies suggest that its main role may rather be facilitating rapid movements of chromosomes during zygotene. In some species, including wheat and Arabidopsis, there is evidence that centromeres form pairs (couple) before the onset of pairing of chromosome arms. While significant advances have been achieved in elucidating the patterns of chromosome behavior in meiotic prophase I, factors controlling chromosome dynamics are still largely unknown and require further studies. Copyright 2010 S. Karger AG, Basel.

Effect of total and pair configurational entropy in determining dynamics of supercooled liquids over a range of densities

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

Banerjee, Atreyee; Nandi, Manoj Kumar; Bhattacharyya, Sarika Maitra, E-mail: mb.sarika@ncl.res.in

2016-07-21

In this paper, we present a study of supercooled liquids interacting with the Lennard Jones potential and the corresponding purely repulsive (Weeks-Chandler-Andersen) potential, over a range of densities and temperatures, in order to understand the origin of their different dynamics in spite of their structures being similar. Using the configurational entropy as the thermodynamic marker via the Adam Gibbs relation, we show that the difference in the dynamics of these two systems at low temperatures can be explained from thermodynamics. At higher densities both the thermodynamical and dynamical difference between these model systems decrease, which is quantitatively demonstrated in thismore » paper by calculating different parameters. The study also reveals the origin of the difference in pair entropy despite the similarity in the structure. Although the maximum difference in structure is obtained in the partial radial distribution function of the B type of particles, the rdf of AA pairs and AB pairs gives rise to the differences in the entropy and dynamics. This work supports the observation made in an earlier study [A. Banerjee et al., Phys. Rev. Lett. 113, 225701 (2014)] and shows that they are generic in nature, independent of density.« less

Rapidity correlations in the RHIC Beam Energy Scan Data

NASA Astrophysics Data System (ADS)

Jowzaee, Sedigheh; STAR Collaboration

2017-11-01

A pair-normalized two-particle covariance versus the rapidity of the two particles, called R2, was originally studied in ISR and FNAL data in the 1970's. This variable has recently seen renewed interest for the study of the dynamics of heavy-ion collisions in the longitudinal direction. These rapidity correlations can be decomposed into a basis set of Legendre polynomials with prefactors 〈amn 〉, which can be considered the rapidity analog of the decomposition of azimuthal anisotropies into a set of cosine functions with prefactors vn. The 〈amn 〉 values have been suggested to be sensitive to the number of particle emitting sources, baryon stopping, viscosities, and critical behavior. The rapidity correlations have been measured by the STAR collaboration as a function of the beam energy for 0-5% central Au+Au collisions with beam energies ranging from 7.7 to 200 GeV. The experimental results and comparisons to the UrQMD model are presented.

Course 4: Density Functional Theory, Methods, Techniques, and Applications

NASA Astrophysics Data System (ADS)

Chrétien, S.; Salahub, D. R.

Contents 1 Introduction 2 Density functional theory 2.1 Hohenberg and Kohn theorems 2.2 Levy's constrained search 2.3 Kohn-Sham method 3 Density matrices and pair correlation functions 4 Adiabatic connection or coupling strength integration 5 Comparing and constrasting KS-DFT and HF-CI 6 Preparing new functionals 7 Approximate exchange and correlation functionals 7.1 The Local Spin Density Approximation (LSDA) 7.2 Gradient Expansion Approximation (GEA) 7.3 Generalized Gradient Approximation (GGA) 7.4 meta-Generalized Gradient Approximation (meta-GGA) 7.5 Hybrid functionals 7.6 The Optimized Effective Potential method (OEP) 7.7 Comparison between various approximate functionals 8 LAP correlation functional 9 Solving the Kohn-Sham equations 9.1 The Kohn-Sham orbitals 9.2 Coulomb potential 9.3 Exchange-correlation potential 9.4 Core potential 9.5 Other choices and sources of error 9.6 Functionality 10 Applications 10.1 Ab initio molecular dynamics for an alanine dipeptide model 10.2 Transition metal clusters: The ecstasy, and the agony... 10.3 The conversion of acetylene to benzene on Fe clusters 11 Conclusions

The large-scale ionospheric transient current system response to upstream solar wind IMF Bz north-south and south-north turnings as seen by the WIND satellite and the full SuperMAG network of ground based magnetometers

NASA Astrophysics Data System (ADS)

Dods, Joe; Chapman, Sandra; Gjerloev, Jesper

2017-04-01

We characterise the response of the quiet-time (no substorms or storms) large scale ionospheric convection system to north-south and south-north IMF turnings by using a dynamical network of ground-based magnetometers. Canonical correlation between all pairs of SuperMAG magnetometer stations in the northern hemisphere (MLat 50-82°) is used to establish the extent of near-simultaneous magnetic response between regions of MLT-MLat. Parameters and maps that describe spatial-temporal correlation are used to characterise the system and its response to the turnings aggregated over several hundred events. We find that regions that experience large increases in correlation post-turning coincide with typical locations of a two cell convection system and are influenced by the IMF By. The time between the turnings reaching the magnetopause and a network response is found to be ˜8-10 minutes and correlation in the dayside occurs 2-8 mins before that in the nightside.

Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding.

PubMed

Csaszar, K; Spacková, N; Stefl, R; Sponer, J; Leontis, N B

2001-11-09

Molecular dynamics simulations of the frame-shifting pseudoknot from beet western yellows virus (BWYV, NDB file UR0004) were performed with explicit inclusion of solvent and counterions. In all, 33 ns of simulation were carried out, including 10 ns of the native structure with protonation of the crucial cytosine residue, C8(N3+). The native structure exhibited stable trajectories retaining all Watson-Crick and tertiary base-pairs, except for fluctuations or transient disruptions at specific sites. The most significant fluctuations involved the change or disruption of hydrogen-bonding between C8(N3+) and bases G12, A25, and C26, as well as disruption of the water bridges linking C8(N3+) with A25 and C26. To increase sampling of rare events, the native simulation was continued at 400 K. A partial, irreversible unfolding of the molecule was initiated by slippage of C8(N3+) relative to G12 and continued by sudden concerted changes in hydrogen-bonding involving A23, A24, and A25. These events were followed by a gradual loss of stacking interactions in loop 2. Of the Watson-Crick base-pairs, only the 5'-terminal pair of stem 1 dissociated at 400 K, while the trans sugar-edge/sugar-edge A20.G4 interaction remained surprisingly stable. Four additional room-temperature simulations were carried out to obtain insights into the structural and dynamic effects of selected mutations. In two of these, C8 was left unprotonated. Considerable local rearrangements occurred that were not observed in the crystal structure, thus confirming N3-protonation of C8 in the native molecule. We also investigated the effect of mutating C8(N3+) to U8, to correlate with experimental and phylogenetic studies, and of changing the G4 x C17 base-pair to A4 x U17 to weaken the trans sugar-edge interaction between positions 4 and 20 and to test models of unfolding. The simulations indicate that the C8 x G12 x C26 base-triple at the junction is the most labile region of the frame-shifting pseudoknot. They provide insights into the roles of the other non-Watson-Crick base-pairs in the early stages of unfolding of the pseudoknot, which must occur to allow readthrough of the message by the ribosome. The simulations revealed several critical, highly ordered hydration sites with close to 100 % occupancies and residency times of individual water molecules of up to 5 ns. Sodium cation coordination sites with occupancies above 50 % were also observed. Copyright 2001 Academic Press.

Solvation structures and dynamics of alkaline earth metal halides in supercritical water: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Keshri, Sonanki; Mandal, Ratnamala; Tembe, B. L.

2016-09-01

Constrained molecular dynamics simulations of alkaline earth metal halides have been carried out to investigate their structural and dynamical properties in supercritical water. Potentials of mean force (PMFs) for all the alkaline earth metal halides in supercritical water have been computed. Contact ion pairs (CIPs) are found to be more stable than all other configurations of the ion pairs except for MgI2 where solvent shared ion pair (SShIP) is more stable than the CIP. There is hardly any difference in the PMFs between the M2+ (M = Mg, Ca, Sr, Ba) and the X- (X = F, Cl, Br, I) ions whether the second X- ion is present in the first coordination shell of the M2+ ion or not. The solvent molecules in the solvation shells diffuse at a much slower rate compared to the bulk. Orientational distribution functions of solvent molecules are sharper for smaller ions.

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.

Molecular dynamics study of some non-hydrogen-bonding base pair DNA strands

NASA Astrophysics Data System (ADS)

Tiwari, Rakesh K.; Ojha, Rajendra P.; Tiwari, Gargi; Pandey, Vishnudatt; Mall, Vijaysree

2018-05-01

In order to elucidate the structural activity of hydrophobic modified DNA, the DMMO2-D5SICS, base pair is introduced as a constituent in different set of 12-mer and 14-mer DNA sequences for the molecular dynamics (MD) simulation in explicit water solvent. AMBER 14 force field was employed for each set of duplex during the 200ns production-dynamics simulation in orthogonal-box-water solvent by the Particle-Mesh-Ewald (PME) method in infinite periodic boundary conditions (PBC) to determine conformational parameters of the complex. The force-field parameters of modified base-pair were calculated by Gaussian-code using Hartree-Fock /ab-initio methodology. RMSD Results reveal that the conformation of the duplex is sequence dependent and the binding energy of the complex depends on the position of the modified base-pair in the nucleic acid strand. We found that non-bonding energy had a significant contribution to stabilising such type of duplex in comparison to electrostatic energy. The distortion produced within strands by such type of base-pair was local and destabilised the duplex integrity near to substitution, moreover the binding energy of duplex depends on the position of substitution of hydrophobic base-pair and the DNA sequence and strongly supports the corresponding experimental study.

Strong Neutron Pairing in core+4n Nuclei.

PubMed

Revel, A; Marqués, F M; Sorlin, O; Aumann, T; Caesar, C; Holl, M; Panin, V; Vandebrouck, M; Wamers, F; Alvarez-Pol, H; Atar, L; Avdeichikov, V; Beceiro-Novo, S; Bemmerer, D; Benlliure, J; Bertulani, C A; Boillos, J M; Boretzky, K; Borge, M J G; Caamaño, M; Casarejos, E; Catford, W N; Cederkäll, J; Chartier, M; Chulkov, L; Cortina-Gil, D; Cravo, E; Crespo, R; Datta Pramanik, U; Díaz Fernández, P; Dillmann, I; Elekes, Z; Enders, J; Ershova, O; Estradé, A; Farinon, F; Fraile, L M; Freer, M; Galaviz, D; Geissel, H; Gernhäuser, R; Golubev, P; Göbel, K; Hagdahl, J; Heftrich, T; Heil, M; Heine, M; Heinz, A; Henriques, A; Ignatov, A; Johansson, H T; Jonson, B; Kahlbow, J; Kalantar-Nayestanaki, N; Kanungo, R; Kelic-Heil, A; Knyazev, A; Kröll, T; Kurz, N; Labiche, M; Langer, C; Le Bleis, T; Lemmon, R; Lindberg, S; Machado, J; Marganiec, J; Movsesyan, A; Nacher, E; Najafi, M; Nilsson, T; Nociforo, C; Paschalis, S; Perea, A; Petri, M; Pietri, S; Plag, R; Reifarth, R; Ribeiro, G; Rigollet, C; Röder, M; Rossi, D; Savran, D; Scheit, H; Simon, H; Syndikus, I; Taylor, J T; Tengblad, O; Thies, R; Togano, Y; Velho, P; Volkov, V; Wagner, A; Weick, H; Wheldon, C; Wilson, G; Winfield, J S; Woods, P; Yakorev, D; Zhukov, M; Zilges, A; Zuber, K

2018-04-13

The emission of neutron pairs from the neutron-rich N=12 isotones ^{18}C and ^{20}O has been studied by high-energy nucleon knockout from ^{19}N and ^{21}O secondary beams, populating unbound states of the two isotones up to 15 MeV above their two-neutron emission thresholds. The analysis of triple fragment-n-n correlations shows that the decay ^{19}N(-1p)^{18}C^{*}→^{16}C+n+n is clearly dominated by direct pair emission. The two-neutron correlation strength, the largest ever observed, suggests the predominance of a ^{14}C core surrounded by four valence neutrons arranged in strongly correlated pairs. On the other hand, a significant competition of a sequential branch is found in the decay ^{21}O(-1n)^{20}O^{*}→^{18}O+n+n, attributed to its formation through the knockout of a deeply bound neutron that breaks the ^{16}O core and reduces the number of pairs.

How structure sculpts function: Unveiling the contribution of anatomical connectivity to the brain's spontaneous correlation structure

NASA Astrophysics Data System (ADS)

Bettinardi, R. G.; Deco, G.; Karlaftis, V. M.; Van Hartevelt, T. J.; Fernandes, H. M.; Kourtzi, Z.; Kringelbach, M. L.; Zamora-López, G.

2017-04-01

Intrinsic brain activity is characterized by highly organized co-activations between different regions, forming clustered spatial patterns referred to as resting-state networks. The observed co-activation patterns are sustained by the intricate fabric of millions of interconnected neurons constituting the brain's wiring diagram. However, as for other real networks, the relationship between the connectional structure and the emergent collective dynamics still evades complete understanding. Here, we show that it is possible to estimate the expected pair-wise correlations that a network tends to generate thanks to the underlying path structure. We start from the assumption that in order for two nodes to exhibit correlated activity, they must be exposed to similar input patterns from the entire network. We then acknowledge that information rarely spreads only along a unique route but rather travels along all possible paths. In real networks, the strength of local perturbations tends to decay as they propagate away from the sources, leading to a progressive attenuation of the original information content and, thus, of their influence. Accordingly, we define a novel graph measure, topological similarity, which quantifies the propensity of two nodes to dynamically correlate as a function of the resemblance of the overall influences they are expected to receive due to the underlying structure of the network. Applied to the human brain, we find that the similarity of whole-network inputs, estimated from the topology of the anatomical connectome, plays an important role in sculpting the backbone pattern of time-average correlations observed at rest.

MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation

PubMed Central

Wang, Luman; Mo, Qiaochu; Wang, Jianxin

2015-01-01

Most current gene coexpression databases support the analysis for linear correlation of gene pairs, but not nonlinear correlation of them, which hinders precisely evaluating the gene-gene coexpression strengths. Here, we report a new database, MIrExpress, which takes advantage of the information theory, as well as the Pearson linear correlation method, to measure the linear correlation, nonlinear correlation, and their hybrid of cell-specific gene coexpressions in immune cells. For a given gene pair or probe set pair input by web users, both mutual information (MI) and Pearson correlation coefficient (r) are calculated, and several corresponding values are reported to reflect their coexpression correlation nature, including MI and r values, their respective rank orderings, their rank comparison, and their hybrid correlation value. Furthermore, for a given gene, the top 10 most relevant genes to it are displayed with the MI, r, or their hybrid perspective, respectively. Currently, the database totally includes 16 human cell groups, involving 20,283 human genes. The expression data and the calculated correlation results from the database are interactively accessible on the web page and can be implemented for other related applications and researches. PMID:26881263

MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation.

PubMed

Wang, Luman; Mo, Qiaochu; Wang, Jianxin

2015-01-01

Most current gene coexpression databases support the analysis for linear correlation of gene pairs, but not nonlinear correlation of them, which hinders precisely evaluating the gene-gene coexpression strengths. Here, we report a new database, MIrExpress, which takes advantage of the information theory, as well as the Pearson linear correlation method, to measure the linear correlation, nonlinear correlation, and their hybrid of cell-specific gene coexpressions in immune cells. For a given gene pair or probe set pair input by web users, both mutual information (MI) and Pearson correlation coefficient (r) are calculated, and several corresponding values are reported to reflect their coexpression correlation nature, including MI and r values, their respective rank orderings, their rank comparison, and their hybrid correlation value. Furthermore, for a given gene, the top 10 most relevant genes to it are displayed with the MI, r, or their hybrid perspective, respectively. Currently, the database totally includes 16 human cell groups, involving 20,283 human genes. The expression data and the calculated correlation results from the database are interactively accessible on the web page and can be implemented for other related applications and researches.

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

Evaluation of sliding window correlation performance for characterizing dynamic functional connectivity and brain states

PubMed Central

Shakil, Sadia; Lee, Chin-Hui; Keilholz, Shella Dawn

2016-01-01

A promising recent development in the study of brain function is the dynamic analysis of resting-state functional MRI scans, which can enhance understanding of normal cognition and alterations that result from brain disorders. One widely used method of capturing the dynamics of functional connectivity is sliding window correlation (SWC). However, in the absence of a “gold standard” for comparison, evaluating the performance of the SWC in typical resting-state data is challenging. This study uses simulated networks (SNs) with known transitions to examine the effects of parameters such as window length, window offset, window type, noise, filtering, and sampling rate on the SWC performance. The SWC time course was calculated for all node pairs of each SN and then clustered using the k-means algorithm to determine how resulting brain states match known configurations and transitions in the SNs. The outcomes show that the detection of state transitions and durations in the SWC is most strongly influenced by the window length and offset, followed by noise and filtering parameters. The effect of the image sampling rate was relatively insignificant. Tapered windows provide less sensitivity to state transitions than rectangular windows, which could be the result of the sharp transitions in the SNs. Overall, the SWC gave poor estimates of correlation for each brain state. Clustering based on the SWC time course did not reliably reflect the underlying state transitions unless the window length was comparable to the state duration, highlighting the need for new adaptive window analysis techniques. PMID:26952197

Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family.

PubMed

Mottonen, James M; Xu, Minli; Jacobs, Donald J; Livesay, Dennis R

2009-05-15

We compare various predicted mechanical and thermodynamic properties of nine oxidized thioredoxins (TRX) using a Distance Constraint Model (DCM). The DCM is based on a nonadditive free energy decomposition scheme, where entropic contributions are determined from rigidity and flexibility of structure based on distance constraints. We perform averages over an ensemble of constraint topologies to calculate several thermodynamic and mechanical response functions that together yield quantitative stability/flexibility relationships (QSFR). Applied to the TRX protein family, QSFR metrics display a rich variety of similarities and differences. In particular, backbone flexibility is well conserved across the family, whereas cooperativity correlation describing mechanical and thermodynamic couplings between the residue pairs exhibit distinctive features that readily standout. The diversity in predicted QSFR metrics that describe cooperativity correlation between pairs of residues is largely explained by a global flexibility order parameter describing the amount of intrinsic flexibility within the protein. A free energy landscape is calculated as a function of the flexibility order parameter, and key values are determined where the native-state, transition-state, and unfolded-state are located. Another key value identifies a mechanical transition where the global nature of the protein changes from flexible to rigid. The key values of the flexibility order parameter help characterize how mechanical and thermodynamic response is linked. Variation in QSFR metrics and key characteristics of global flexibility are related to the native state X-ray crystal structure primarily through the hydrogen bond network. Furthermore, comparison of three TRX redox pairs reveals differences in thermodynamic response (i.e., relative melting point) and mechanical properties (i.e., backbone flexibility and cooperativity correlation) that are consistent with experimental data on thermal stabilities and NMR dynamical profiles. The results taken together demonstrate that small-scale structural variations are amplified into discernible global differences by propagating mechanical couplings through the H-bond network.

Correlation Among the Variant Group, Effective Grain Size, and Elastic Strain Energy During the Phase Transformation in 9Ni Steels

NASA Astrophysics Data System (ADS)

Terasaki, Hidenori; Moriguchi, Koji; Tomio, Yusaku; Yamagishi, Hideki; Morito, Shigekazu

2017-12-01

The effect of carbon content on the density of variant-pair boundaries was investigated in 9Ni steel using an electron backscatter diffraction patterns method. The changes in the density of variant-pair boundaries were correlated with the nondestructive measured values of shear modulus of the austenite phase at the phase transformation point. Furthermore, the effective grain size was correlated with the shear modulus and the density of variant-pair boundaries. These relations are discussed from the viewpoint of self-accommodation of elastic strain energy and the nucleation event in the bainite and martensitic transformations.

Cross-Lagged Analysis of Interplay Between Differential Traits in Sibling Pairs: Validation and Application to Parenting Behavior and ADHD Symptomatology.

PubMed

Moscati, Arden; Verhulst, Brad; McKee, Kevin; Silberg, Judy; Eaves, Lindon

2018-01-01

Understanding the factors that contribute to behavioral traits is a complex task, and partitioning variance into latent genetic and environmental components is a useful beginning, but it should not also be the end. Many constructs are influenced by their contextual milieu, and accounting for background effects (such as gene-environment correlation) is necessary to avoid bias. This study introduces a method for examining the interplay between traits, in a longitudinal design using differential items in sibling pairs. The model is validated via simulation and power analysis, and we conclude with an application to paternal praise and ADHD symptoms in a twin sample. The model can help identify what type of genetic and environmental interplay may contribute to the dynamic relationship between traits using a cross-lagged panel framework. Overall, it presents a way to estimate and explicate the developmental interplay between a set of traits, free from many common sources of bias.

Freeze-out dynamics via charged kaon femtoscopy in sNN=200 GeV central Au + Au collisions

NASA Astrophysics Data System (ADS)

Adamczyk, L.; Adkins, J. K.; Agakishiev, G.; Aggarwal, M. M.; Ahammed, Z.; Alekseev, I.; Alford, J.; Anson, C. D.; Aparin, A.; Arkhipkin, D.; Aschenauer, E.; Averichev, G. S.; Balewski, J.; Banerjee, A.; Barnovska, Z.; Beavis, D. R.; Bellwied, R.; Betancourt, M. J.; Betts, R. R.; Bhasin, A.; Bhati, A. K.; Bhattarai; Bichsel, H.; Bielcik, J.; Bielcikova, J.; Bland, L. C.; Bordyuzhin, I. G.; Borowski, W.; Bouchet, J.; Brandin, A. V.; Brovko, S. G.; Bruna, E.; Bültmann, S.; Bunzarov, I.; Burton, T. P.; Butterworth, J.; Caines, H.; Calderón de la Barca Sánchez, M.; Cebra, D.; Cendejas, R.; Cervantes, M. C.; Chaloupka, P.; Chang, Z.; Chattopadhyay, S.; Chen, H. F.; Chen, J. H.; Chen, J. Y.; Chen, L.; Cheng, J.; Cherney, M.; Chikanian, A.; Christie, W.; Chung, P.; Chwastowski, J.; Codrington, M. J. M.; Corliss, R.; Cramer, J. G.; Crawford, H. J.; Cui, X.; Das, S.; Davila Leyva, A.; De Silva, L. C.; Debbe, R. R.; Dedovich, T. G.; Deng, J.; Derradi de Souza, R.; Dhamija, S.; di Ruzza, B.; Didenko, L.; Dilks; Ding, F.; Dion, A.; Djawotho, P.; Dong, X.; Drachenberg, J. L.; Draper, J. E.; Du, C. M.; Dunkelberger, L. E.; Dunlop, J. C.; Efimov, L. G.; Elnimr, M.; Engelage, J.; Engle, K. S.; Eppley, G.; Eun, L.; Evdokimov, O.; Fatemi, R.; Fazio, S.; Fedorisin, J.; Fersch, R. G.; Filip, P.; Finch, E.; Fisyak, Y.; Flores, C. E.; Gagliardi, C. A.; Gangadharan, D. R.; Garand, D.; Geurts, F.; Gibson, A.; Gliske, S.; Grebenyuk, O. G.; Grosnick, D.; Guo, Y.; Gupta, A.; Gupta, S.; Guryn, W.; Haag, B.; Hajkova, O.; Hamed, A.; Han, L.-X.; Haque, R.; Harris, J. W.; Hays-Wehle, J. P.; Heppelmann, S.; Hirsch, A.; Hoffmann, G. W.; Hofman, D. J.; Horvat, S.; Huang, B.; Huang, H. Z.; Huck, P.; Humanic, T. J.; Igo, G.; Jacobs, W. W.; Jena, C.; Judd, E. G.; Kabana, S.; Kang, K.; Kauder, K.; Ke, H. W.; Keane, D.; Kechechyan, A.; Kesich, A.; Kikola, D. P.; Kiryluk, J.; Kisel, I.; Kisiel, A.; Koetke, D. D.; Kollegger, T.; Konzer, J.; Koralt, I.; Korsch, W.; Kotchenda, L.; Kravtsov, P.; Krueger, K.; Kulakov, I.; Kumar, L.; Kycia, R. A.; Lamont, M. A. C.; Landgraf, J. M.; Landry, K. D.; LaPointe, S.; Lauret, J.; Lebedev, A.; Lednicky, R.; Lee, J. H.; Leight, W.; LeVine, M. J.; Li, C.; Li, W.; Li, X.; Li, X.; Li, Y.; Li, Z. M.; Lima, L. M.; Lisa, M. A.; Liu, F.; Ljubicic, T.; Llope, W. J.; Longacre, R. S.; Luo, X.; Ma, G. L.; Ma, Y. G.; Madagodagettige Don, D. M. M. D.; Mahapatra, D. P.; Majka, R.; Margetis, S.; Markert, C.; Masui, H.; Matis, H. S.; McDonald, D.; McShane, T. S.; Mioduszewski, S.; Mitrovski, M. K.; Mohammed, Y.; Mohanty, B.; Mondal, M. M.; Munhoz, M. G.; Mustafa, M. K.; Naglis, M.; Nandi, B. K.; Nasim, Md.; Nayak, T. K.; Nelson, J. M.; Nogach, L. V.; Novak, J.; Odyniec, G.; Ogawa, A.; Oh, K.; Ohlson, A.; Okorokov, V.; Oldag, E. W.; Oliveira, R. A. N.; Olson, D.; Pachr, M.; Page, B. S.; Pal, S. K.; Pan, Y. X.; Pandit, Y.; Panebratsev, Y.; Pawlak, T.; Pawlik, B.; Pei, H.; Perkins, C.; Peryt, W.; Pile, P.; Planinic, M.; Pluta, J.; Plyku, D.; Poljak, N.; Porter, J.; Poskanzer, A. M.; Powell, C. B.; Pruneau, C.; Pruthi, N. K.; Przybycien, M.; Pujahari, P. R.; Putschke, J.; Qiu, H.; Ramachandran, S.; Raniwala, R.; Raniwala, S.; Ray, R. L.; Riley, C. K.; Ritter, H. G.; Roberts, J. B.; Rogachevskiy, O. V.; Romero, J. L.; Ross, J. F.; Roy, A.; Ruan, L.; Rusnak, J.; Sahoo, N. R.; Sahu, P. K.; Sakrejda, I.; Salur, S.; Sandacz, A.; Sandweiss, J.; Sangaline, E.; Sarkar, A.; Schambach, J.; Scharenberg, R. P.; Schmah, A. M.; Schmidke, B.; Schmitz, N.; Schuster, T. R.; Seger, J.; Seyboth, P.; Shah, N.; Shahaliev, E.; Shao, M.; Sharma, B.; Sharma, M.; Shen, W. Q.; Shi, S. S.; Shou, Q. Y.; Sichtermann, E. P.; Singaraju, R. N.; Skoby, M. J.; Smirnov, D.; Smirnov, N.; Solanki, D.; Sorensen, P.; deSouza, U. G.; Spinka, H. M.; Srivastava, B.; Stanislaus, T. D. S.; Stevens, J. R.; Stock, R.; Strikhanov, M.; Stringfellow, B.; Suaide, A. A. P.; Suarez, M. C.; Sumbera, M.; Sun, X. M.; Sun, Y.; Sun, Z.; Surrow, B.; Svirida, D. N.; Symons, T. J. M.; Szanto de Toledo, A.; Takahashi, J.; Tang, A. H.; Tang, Z.; Tarini, L. H.; Tarnowsky, T.; Thomas, J. H.; Timmins, A. R.; Tlusty, D.; Tokarev, M.; Trentalange, S.; Tribble, R. E.; Tribedy, P.; Trzeciak, B. A.; Tsai, O. D.; Turnau, J.; Ullrich, T.; Underwood, D. G.; Van Buren, G.; van Nieuwenhuizen, G.; Vanfossen, J. A., Jr.; Varma, R.; Vasconcelos, G. M. S.; Vertesi, R.; Videbæk, F.; Viyogi, Y. P.; Vokal, S.; Voloshin, S. A.; Vossen, A.; Wada, M.; Walker, M.; Wang, F.; Wang, G.; Wang, H.; Wang, J. S.; Wang, Q.; Wang, X. L.; Wang, Y.; Webb, G.; Webb, J. C.; Westfall, G. D.; Wieman, H.; Wissink, S. W.; Witt, R.; Wu, Y. F.; Xiao, Z.; Xie, W.; Xin, K.; Xu, H.; Xu, N.; Xu, Q. H.; Xu, W.; Xu, Y.; Xu, Z.; Yan; Yang, C.; Yang, Y.; Yang, Y.; Yepes, P.; Yi, L.; Yip, K.; Yoo, I.-K.; Zawisza, Y.; Zbroszczyk, H.; Zha, W.; Zhang, J. B.; Zhang, S.; Zhang, X. P.; Zhang, Y.; Zhang, Z. P.; Zhao, F.; Zhao, J.; Zhong, C.; Zhu, X.; Zhu, Y. H.; Zoulkarneeva, Y.; Zyzak, M.

2013-09-01

We present measurements of three-dimensional correlation functions of like-sign, low-transverse-momentum kaon pairs from sNN=200 GeV Au+Au collisions. A Cartesian surface-spherical harmonic decomposition technique was used to extract the kaon source function. The latter was found to have a three-dimensional Gaussian shape and can be adequately reproduced by Therminator event-generator simulations with resonance contributions taken into account. Compared to the pion one, the kaon source function is generally narrower and does not have the long tail along the pair transverse momentum direction. The kaon Gaussian radii display a monotonic decrease with increasing transverse mass mT over the interval of 0.55≤mT≤1.15 GeV/c2. While the kaon radii are adequately described by the mT -scaling in the outward and sideward directions, in the longitudinal direction the lowest mT value exceeds the expectations from a pure hydrodynamical model prediction.

Pair 2-electron reduced density matrix theory using localized orbitals

NASA Astrophysics Data System (ADS)

Head-Marsden, Kade; Mazziotti, David A.

2017-08-01

Full configuration interaction (FCI) restricted to a pairing space yields size-extensive correlation energies but its cost scales exponentially with molecular size. Restricting the variational two-electron reduced-density-matrix (2-RDM) method to represent the same pairing space yields an accurate lower bound to the pair FCI energy at a mean-field-like computational scaling of O (r3) where r is the number of orbitals. In this paper, we show that localized molecular orbitals can be employed to generate an efficient, approximately size-extensive pair 2-RDM method. The use of localized orbitals eliminates the substantial cost of optimizing iteratively the orbitals defining the pairing space without compromising accuracy. In contrast to the localized orbitals, the use of canonical Hartree-Fock molecular orbitals is shown to be both inaccurate and non-size-extensive. The pair 2-RDM has the flexibility to describe the spectra of one-electron RDM occupation numbers from all quantum states that are invariant to time-reversal symmetry. Applications are made to hydrogen chains and their dissociation, n-acene from naphthalene through octacene, and cadmium telluride 2-, 3-, and 4-unit polymers. For the hydrogen chains, the pair 2-RDM method recovers the majority of the energy obtained from similar calculations that iteratively optimize the orbitals. The localized-orbital pair 2-RDM method with its mean-field-like computational scaling and its ability to describe multi-reference correlation has important applications to a range of strongly correlated phenomena in chemistry and physics.

Geometrical correlations in the nucleosomal DNA conformation and the role of the covalent bonds rigidity

PubMed Central

Ghorbani, Maryam; Mohammad-Rafiee, Farshid

2011-01-01

We develop a simple elastic model to study the conformation of DNA in the nucleosome core particle. In this model, the changes in the energy of the covalent bonds that connect the base pairs of each strand of the DNA double helix, as well as the lateral displacements and the rotation of adjacent base pairs are considered. We show that because of the rigidity of the covalent bonds in the sugar-phosphate backbones, the base pair parameters are highly correlated, especially, strong twist-roll-slide correlation in the conformation of the nucleosomal DNA is vividly observed in the calculated results. This simple model succeeds to account for the detailed features of the structure of the nucleosomal DNA, particularly, its more important base pair parameters, roll and slide, in good agreement with the experimental results. PMID:20972223

Hole pairing and ground state properties of high-Tc superconductivity within the t-t'-J-V model

NASA Astrophysics Data System (ADS)

Roy, Krishanu; Pal, Papiya; Nath, Subhadip; Ghosh, Nanda Kumar

2018-04-01

The t-t'-J-V model, one of the realistic models for studying high-Tc cuprates, has been investigated to explore the hole pairing and other ground state properties using exact diagonalization (ED) technique with 2 holes in a small 8-site cluster. The role of next-nearest-neighbor (NNN) hopping and nearest-neighbor (NN) Coulomb repulsion has been considered. It appears that qualitative behavior of the ground state energies of an 8-site and 16- or 18-site cluster is similar. Results show that a small short-ranged antiferromagnetic (AF) correlation exists in the 2 hole case which is favored by large V/t. A superconducting phase emerges at 0 ≤ V/t ≤ 4J. Hole-hole correlation calculation also suggests that the two holes of the pair are either at |i - j| = 1 or √2. Negative t'/t suppresses the possibility of pairing of holes. Though s-wave pairing susceptibility is dominant, pairing correlation length calculation indicates that the long range pairing, which is suitable for superconductivity, is in the d-wave channel. Both s- and d-wave pairing susceptibility gets suppressed by V/t while d-(s-) wave susceptibility gets favored (suppressed) by t'/t. The charge gap shows a gapped behavior while a spin-gapless region exists at small V/t for finite t'/t.

Multiplicity evolution of identified particle charge-dependent correlations in Pb-Pb, p-Pb and pp collisions at the LHC with ALICE

NASA Astrophysics Data System (ADS)

Pan, Jinjin; Alice Collaboration

2017-09-01

The charge pair creation and transport processes in heavy-ion collisions are investigated experimentally by measurements of charge-dependent correlations of identified particle pairs, related to the Balance Function. The produced pair separation in rapidity is expected to be larger for hadrons arising from quark-antiquark pair creation in the early stages of the collision than for hadrons emerging from the later hadronization stage. Correlations are reported for charged-pion pairs in Pb-Pb, p-Pb and pp collisions at √{sNN } = 2.76, 5.02 and 7 TeV, respectively; and for charged-kaon pairs in Pb-Pb collisions at √{sNN } = 2.76 TeV. The correlations are measured as a function of relative rapidity Δy and azimuthal angle Δϕ , and are dominated by a peak centered at Δy = Δϕ = 0. We observe that the peak widths in Δy and Δϕ are narrower in higher multiplicity events in Pb-Pb, p-Pb, and pp collisions, which is consistent with the effects of radial flow, as well as the two-wave quark production mechanism. We investigate the charge transport and system evolution further by studying the Δϕ width of the peak as a function of Δy. Funded by the US Department of Energy.

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.

Utilizing Molecular Dynamics ' Multipotent Methodologies to Measure Microscopic Motions of DNA Molecules: A Magniloquent Manuscript On DNA's Means and Mannerisms

NASA Astrophysics Data System (ADS)

Kingsland, Addie

DNA is an amazing molecule which is the basic template for all genetics. It is the primary molecule for storing biological information, and has many applications in nanotechnology. Double-stranded DNA may contain mismatched base pairs beyond the Watson-Crick pairs guanine-cytosine and adenine-thymine. To date, no one has found a physical property of base pair mismatches which describes the behavior of naturally occurring mismatch repair enzymes. Many materials properties of DNA are also unknown, for instance, when pulling DNA in different configurations, different energy differences are observed with no obvious reason why. DNA mismatches also affect their local environment, for instance changing the quantum yield of nearby azobenzene moieties. We utilize molecular dynamics computer simulations to study the structure and dynamics for both matched and mismatched base pairs, within both biological and materials contexts, and in both equilibrium and biased dynamics. We show that mismatched pairs shift further in the plane normal to the DNA strand and are more likely to exhibit non-canonical structures, including the e-motif. Base pair mismatches alter their local environment, affecting the trans- to cis- photoisomerization quantum yield of azobenzene, as well as increasing the likelihood of observing the e-motif. We also show that by using simulated data, we can give new insights on theoretical models to calculate the energetics of pulling DNA strands apart. These results, all relatively inexpensive on modern computer hardware, can help guide the design of DNA-based nanotechnologies, as well as give new insights into the functioning of mismatch repair systems in cancer prevention.

Evidence that pairing with genetically similar mates is maladaptive in a monogamous bird

USGS Publications Warehouse

Mulard, Hervé; Danchin, E.; Talbot, S.L.; Ramey, A.M.; Hatch, Shyla A.; White, J.F.; Helfenstein, F.; Wagner, R.H.

2009-01-01

Background. Evidence of multiple genetic criteria of mate choice is accumulating in numerous taxa. In many species, females have been shown to pair with genetically dissimilar mates or with extra-pair partners that are more genetically compatible than their social mates, thereby increasing their offsprings' heterozygosity which often correlates with offspring fitness. While most studies have focused on genetically promiscuous species, few studies have addressed genetically monogamous species, in which mate choice tends to be mutual. Results. Here, we used microsatellite markers to assess individual global heterozygosity and genetic similarity of pairs in a socially and genetically monogamous seabird, the black-legged kittiwake Rissa tridactyla. We found that pairs were more genetically dissimilar than expected by chance. We also identified fitness costs of breeding with genetically similar partners: (i) genetic similarity of pairs was negatively correlated with the number of chicks hatched, and (ii) offspring heterozygosity was positively correlated with growth rate and survival. Conclusion. These findings provide evidence that breeders in a genetically monogamous species may avoid the fitness costs of reproducing with a genetically similar mate. In such species that lack the opportunity to obtain extra-pair fertilizations, mate choice may therefore be under high selective pressure. ?? 2009 Mulard et al; licensee BioMed Central Ltd.

Correlates of genetic monogamy in socially monogamous mammals: insights from Azara's owl monkeys

PubMed Central

Huck, Maren; Fernandez-Duque, Eduardo; Babb, Paul; Schurr, Theodore

2014-01-01

Understanding the evolution of mating systems, a central topic in evolutionary biology for more than 50 years, requires examining the genetic consequences of mating and the relationships between social systems and mating systems. Among pair-living mammals, where genetic monogamy is extremely rare, the extent of extra-group paternity rates has been associated with male participation in infant care, strength of the pair bond and length of the breeding season. This study evaluated the relationship between two of those factors and the genetic mating system of socially monogamous mammals, testing predictions that male care and strength of pair bond would be negatively correlated with rates of extra-pair paternity (EPP). Autosomal microsatellite analyses provide evidence for genetic monogamy in a pair-living primate with bi-parental care, the Azara's owl monkey (Aotus azarae). A phylogenetically corrected generalized least square analysis was used to relate male care and strength of the pair bond to their genetic mating system (i.e. proportions of EPP) in 15 socially monogamous mammalian species. The intensity of male care was correlated with EPP rates in mammals, while strength of pair bond failed to reach statistical significance. Our analyses show that, once social monogamy has evolved, paternal care, and potentially also close bonds, may facilitate the evolution of genetic monogamy. PMID:24648230

Correlates of genetic monogamy in socially monogamous mammals: insights from Azara's owl monkeys.

PubMed

Huck, Maren; Fernandez-Duque, Eduardo; Babb, Paul; Schurr, Theodore

2014-05-07

Understanding the evolution of mating systems, a central topic in evolutionary biology for more than 50 years, requires examining the genetic consequences of mating and the relationships between social systems and mating systems. Among pair-living mammals, where genetic monogamy is extremely rare, the extent of extra-group paternity rates has been associated with male participation in infant care, strength of the pair bond and length of the breeding season. This study evaluated the relationship between two of those factors and the genetic mating system of socially monogamous mammals, testing predictions that male care and strength of pair bond would be negatively correlated with rates of extra-pair paternity (EPP). Autosomal microsatellite analyses provide evidence for genetic monogamy in a pair-living primate with bi-parental care, the Azara's owl monkey (Aotus azarae). A phylogenetically corrected generalized least square analysis was used to relate male care and strength of the pair bond to their genetic mating system (i.e. proportions of EPP) in 15 socially monogamous mammalian species. The intensity of male care was correlated with EPP rates in mammals, while strength of pair bond failed to reach statistical significance. Our analyses show that, once social monogamy has evolved, paternal care, and potentially also close bonds, may facilitate the evolution of genetic monogamy.

Entangle Accelerating Universe

NASA Astrophysics Data System (ADS)

González-Díaz, Pedro F.; Robles-Pérez, Salvador a. i. e.

We show that there exists a T-duality symmetry between two-dimensional warp drives and two dimensional Tolman-Hawking and Gidding-Strominger baby universes respectively correlated in pairs, so that the creation of warp drives is also equivalent to space-time squeezing. It has been also seen that the nucleation of warp drives entails a violation of the Bell's inequalities. These results are generalized to the case of any dynamically accelerating universe whose creation is also physically equivalent to spacetime squeezing and to the violation of the Bell's inequalities, so that the universe we are living in should be governed by essential sharp quantum theory laws and must be a quantum entangled system.

Modal survey of the space shuttle solid rocket motor using multiple input methods

NASA Technical Reports Server (NTRS)

Brillhart, Ralph; Hunt, David L.; Jensen, Brent M.; Mason, Donald R.

1987-01-01

The ability to accurately characterize propellant in a finite element model is a concern of engineers tasked with studying the dynamic response of the Space Shuttle Solid Rocket Motor (SRM). THe uncertainties arising from propellant characterization through specimem testing led to the decision to perform a model survey and model correlation of a single segment of the Shuttle SRM. Multiple input methods were used to excite and define case/propellant modes of both an inert segment and, later, a live propellant segment. These tests were successful at defining highly damped, flexible modes, several pairs of which occured with frequency spacing of less than two percent.

Understanding ion association states and molecular dynamics using infrared spectroscopy

NASA Astrophysics Data System (ADS)

Masser, Hanqing

A molecular level understanding of the ion transport mechanism within polymer electrolytes is crucial to the further development for advanced energy storage applications. This can be achieved by the identification and quantitative measurement of different ion species in the system and further relating them to the ion conductivity. In the first part of this thesis, research is presented towards understanding the ion association states (free ions, ion pairs and ion aggregates) in ionomer systems, and the correlation of ion association states, ion conduction, polymer dynamics, and morphology. Ion conductivity in ionomers can be improved by lowering glass transition temperature, increasing polymer ion solvation ability, and adjusting ionomer structural variables such as ion content, cation type and side chain structure. These effects are studied in three ionomer systems respectively, using a combination of characterization methods. Fourier Transform Infrared Spectroscopy (FTIR) identifies and quantifies the ion association states. Dielectric Spectroscopy (DRS) characterizes ion conductivity and polymer and ion dynamics. X-ray scattering reveals changes in morphology. The influence of a cation solvating plasticizer on a polyester ionomer is systematically investigated with respect to ion association states, ion and polymer dynamics and morphology. A decrease in the number ratio of ion aggregates with increased plasticizer content and a slight increase at elevated temperature are observed in FTIR. Similar results are also detected by X-ray scattering. As determined from dielectric spectroscopy, ion conductivity increases with plasticizer content, in accordance with the decrease in glass transition temperature. Research on copolymer of poly(ethylene oxide) (PEO) and poly(tetramethylene oxide) (PTMO) based ionomers further develops an understanding of the trade-off between ion solvation and segmental dynamics. Upon the incorporation of PTMO, the majority of the PTMO microphase separates from the PEO-rich microphase, and ionic groups are preferentially solvated by PEO chains and reside in the PEO-rich microphase. As the ratio of PTMO increases, the fraction of aggregates increases, resulting in more highly coordinated aggregation states. Results on ion association states are in good agreement with previous results on ion conductivity, polymer dynamics and morphology. The effects of ion content, cation type and ionic side chain structure on ion association states are systemically studied in a series of ionomers with short ethylene oxide and ionic sulfonated styrene side chains, and then correlated to the ion and polymer dynamic characterization. It is found that ionomers with modest ion content, large cation and styrene ionic side chain have the most "free ions" and ion pairs, and highest ion conductivity. Ion conduction in ionomers is optimized by systematically changing their chemical structures. In addition to knowledge of ion association states, a IR band shape also contains information on molecular dynamics. In companion investigation, the vibrational relaxation and dynamic transitions of conformationally insensitive normal modes in two different polymer systems (atactic polystyrene and deuterated poly(methyl methacrylate)) are studied. The information on vibrational relaxations is resolved by conducting precisely controlled FTIR experiments, applying specialized curve resolving data analysis, and calculating time correlation functions through numerical Fourier transformation. The vibrational relaxations of these modes can be described by a two process model: a fast process on the time scale of 0.01 ps, which is inhomogeneously broadened by a slow process on the time scale of picoseconds.

Investigation of Dynamic Force/Vibration Transmission Characteristics of Four-Square Type Gear Durability Test Machines

NASA Technical Reports Server (NTRS)

Kahraman, Ahmet

2002-01-01

In this study, design requirements for a dynamically viable, four-square type gear test machine are investigated. Variations of four-square type gear test machines have been in use for durability and dynamics testing of both parallel- and cross-axis gear set. The basic layout of these machines is illustrated. The test rig is formed by two gear pairs, of the same reduction ratio, a test gear pair and a reaction gear pair, connected to each other through shafts of certain torsional flexibility to form an efficient, closed-loop system. A desired level of constant torque is input to the circuit through mechanical (a split coupling with a torque arm) or hydraulic (a hydraulic actuator) means. The system is then driven at any desired speed by a small DC motor. The main task in hand is the isolation of the test gear pair from the reaction gear pair under dynamic conditions. Any disturbances originated at the reaction gear mesh might potentially travel to the test gearbox, altering the dynamic loading conditions of the test gear mesh, and hence, influencing the outcome of the durability or dynamics test. Therefore, a proper design of connecting structures becomes a major priority. Also, equally important is the issue of how close the operating speed of the machine is to the resonant frequencies of the gear meshes. This study focuses on a detailed analysis of the current NASA Glenn Research Center gear pitting test machine for evaluation of its resonance and vibration isolation characteristics. A number of these machines as the one illustrated has been used over last 30 years to establish an extensive database regarding the influence of the gear materials, processes surface treatments and lubricants on gear durability. This study is intended to guide an optimum design of next generation test machines for the most desirable dynamic characteristics.

EPR paradox, quantum nonlocality and physical reality

NASA Astrophysics Data System (ADS)

Kupczynski, M.

2016-03-01

Eighty years ago Einstein, Podolsky and Rosen demonstrated that instantaneous reduction of wave function, believed to describe completely a pair of entangled physical systems, led to EPR paradox. The paradox disappears in statistical interpretation of quantum mechanics (QM) according to which a wave function describes only an ensemble of identically prepared physical systems. QM predicts strong correlations between outcomes of measurements performed on different members of EPR pairs in far-away locations. Searching for an intuitive explanation of these correlations John Bell analysed so called local realistic hidden variable models and proved that correlations consistent with these models satisfy Bell inequalities which are violated by some predictions of QM and by experimental data. Several different local models were constructed and inequalities proven. Some eminent physicists concluded that Nature is definitely nonlocal and that it is acting according to a law of nonlocal randomness. According to these law perfectly random, but strongly correlated events, can be produced at the same time in far away locations and a local and causal explanation of their occurrence cannot be given. We strongly disagree with this conclusion and we prove the contrary by analysing in detail some influential finite sample proofs of Bell and CHSH inequalities and so called Quantum Randi Challenges. We also show how one can win so called Bell's game without violating locality of Nature. Nonlocal randomness is inconsistent with local quantum field theory, with standard model in elementary particle physics and with causal laws and adaptive dynamics prevailing in the surrounding us world. The experimental violation of Bell-type inequalities does not prove the nonlocality of Nature but it only confirms a contextual character of quantum observables and gives a strong argument against counterfactual definiteness and against a point of view according to which experimental outcomes are produced in irreducible random way.

m1A and m1G Potently Disrupt A-RNA Structure Due to the Intrinsic Instability of Hoogsteen Base Pairs

PubMed Central

Zhou, Huiqing; Kimsey, Isaac J.; Nikolova, Evgenia N.; Sathyamoorthy, Bharathwaj; Grazioli, Gianmarc; McSally, James; Bai, Tianyu; Wunderlich, Christoph H.; Kreutz, Christoph; Andricioaei, Ioan; Al-Hashimi, Hashim M.

2016-01-01

The B-DNA double helix can dynamically accommodate G–C and A–T base pairs in either Watson-Crick or Hoogsteen configurations. Here, we show that G–C+ and A–U Hoogsteen base pairs are strongly disfavored in A-RNA. As a result, N1-methyl adenosine and N1-methyl guanosine, which occur in DNA as a form of alkylation damage, and in RNA as a posttranscriptional modification, have dramatically different consequences. They create G–C+ and A–U Hoogsteen base pairs in duplex DNA that maintain the structural integrity of the double helix, but block base pairing all together and induce local duplex melting in RNA, providing a mechanism for potently disrupting RNA structure through posttranscriptional modifications. The markedly different propensities to form Hoogsteen base pairs in B-DNA and A-RNA may help meet the opposing requirements of maintaining genome stability on one hand, and dynamically modulating the structure of the epitranscriptome on the other. PMID:27478929

Solvation and Ion Pair Association in Aqueous Metal Sulfates: Interpretation of NDIS raw data by isobaric-isothermal molecular dynamics simulation.

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

Chialvo, Ariel A; Simonson, J Michael

2010-01-01

We analyzed the solvation behavior of aqueous lithium, nickel, and ytterbium sulfates at ambient conditions in terms of the relevant radial distributions functions and the corresponding first-order difference of the sulfur-site neutronweighted distribution functions generated by isothermal-isobaric molecular dynamics simulation. We determined of the partial contributions to the neutronweighted distribution functions, to identify the main peaks, and the effect of the contact ion-pair configuration on the resulting H ! S coordination number. Finally, we assessed the extent of the ion-pair formation according to Poirier- DeLap formalism and highlighted the significant increase of the ion-pair association exhibited by these salts withmore » cation charge.« less

Quantifying the spatio-temporal pattern of the ground impact of space weather events using dynamical networks formed from the SuperMAG database of ground based magnetometer stations.

NASA Astrophysics Data System (ADS)

Dods, Joe; Chapman, Sandra; Gjerloev, Jesper

2016-04-01

Quantitative understanding of the full spatial-temporal pattern of space weather is important in order to estimate the ground impact. Geomagnetic indices such as AE track the peak of a geomagnetic storm or substorm, but cannot capture the full spatial-temporal pattern. Observations by the ~100 ground based magnetometers in the northern hemisphere have the potential to capture the detailed evolution of a given space weather event. We present the first analysis of the full available set of ground based magnetometer observations of substorms using dynamical networks. SuperMAG offers a database containing ground station magnetometer data at a cadence of 1min from 100s stations situated across the globe. We use this data to form dynamic networks which capture spatial dynamics on timescales from the fast reconfiguration seen in the aurora, to that of the substorm cycle. Windowed linear cross-correlation between pairs of magnetometer time series along with a threshold is used to determine which stations are correlated and hence connected in the network. Variations in ground conductivity and differences in the response functions of magnetometers at individual stations are overcome by normalizing to long term averages of the cross-correlation. These results are tested against surrogate data in which phases have been randomised. The network is then a collection of connected points (ground stations); the structure of the network and its variation as a function of time quantify the detailed dynamical processes of the substorm. The network properties can be captured quantitatively in time dependent dimensionless network parameters and we will discuss their behaviour for examples of 'typical' substorms and storms. The network parameters provide a detailed benchmark to compare data with models of substorm dynamics, and can provide new insights on the similarities and differences between substorms and how they correlate with external driving and the internal state of the magnetosphere. We can also investigate the solar wind control of the magnetospheric-ionospheric convection system using dynamical networks. The dynamical networks are first interpolated onto a regular grid. Statistically averaged network responses are then formed for a variety of solar wind conditions, including investigating the network response to southward turnings. [1] Dods, J., S. C. Chapman, and J. W. Gjerloev (2015), Network analysis of geomagnetic substorms using the SuperMAG database of ground-based magnetometer stations, J. Geophys. Res. Space Physics, 120, 7774-7784, doi:10.1002/2015JA021456

Automated Radiology-Pathology Module Correlation Using a Novel Report Matching Algorithm by Organ System.

PubMed

Dane, Bari; Doshi, Ankur; Gfytopoulos, Soterios; Bhattacharji, Priya; Recht, Michael; Moore, William

2018-05-01

Radiology-pathology correlation is time-consuming and is not feasible in most clinical settings, with the notable exception of breast imaging. The purpose of this study was to determine if an automated radiology-pathology report pairing system could accurately match radiology and pathology reports, thus creating a feedback loop allowing for more frequent and timely radiology-pathology correlation. An experienced radiologist created a matching matrix of radiology and pathology reports. These matching rules were then exported to a novel comprehensive radiology-pathology module. All distinct radiology-pathology pairings at our institution from January 1, 2016 to July 1, 2016 were included (n = 8999). The appropriateness of each radiology-pathology report pairing was scored as either "correlative" or "non-correlative." Pathology reports relating to anatomy imaged in the specific imaging study were deemed correlative, whereas pathology reports describing anatomy not imaged with the particular study were denoted non-correlative. Overall, there was 88.3% correlation (accuracy) of the radiology and pathology reports (n = 8999). Subset analysis demonstrated that computed tomography (CT) abdomen/pelvis, CT head/neck/face, CT chest, musculoskeletal CT (excluding spine), mammography, magnetic resonance imaging (MRI) abdomen/pelvis, MRI brain, musculoskeletal MRI (excluding spine), breast MRI, positron emission tomography (PET), breast ultrasound, and head/neck ultrasound all demonstrated greater than 91% correlation. When further stratified by imaging modality, CT, MRI, mammography, and PET demonstrated excellent correlation (greater than 96.3%). Ultrasound and non-PET nuclear medicine studies demonstrated poorer correlation (80%). There is excellent correlation of radiology imaging reports and appropriate pathology reports when matched by organ system. Rapid, appropriate radiology-pathology report pairings provide an excellent opportunity to close feedback loop to the interpreting radiologist. Copyright © 2018 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

Singlet-to-triplet intermediates and triplet exciton dynamics in pentacene thinfilms

NASA Astrophysics Data System (ADS)

Thorsmolle, Verner; Korber, Michael; Obergfell, Emanuel; Kuhlman, Thomas; Campbell, Ian; Crone, Brian; Taylor, Antoinette; Averitt, Richard; Demsar, Jure

Singlet-to-triplet fission in organic semiconductors is a spin-conserving multiexciton process in which one spin-zero singlet excitation is converted into two spin-one triplet excitations on an ultrafast timescale. Current scientific interest into this carrier multiplication process is largely driven by prospects of enhancing the efficiency in photovoltaic applications by generating two long-lived triplet excitons by one photon. The fission process is known to involve intermediate states, known as correlated triplet pairs, with an overall singlet character, before being interchanged into uncorrelated triplets. Here we use broadband femtosecond real-time spectroscopy to study the excited state dynamics in pentacene thin films, elucidating the fission process and the role of intermediate triplet states. VKT and AJT acknowledge support by the LDRD program at Los Alamos National Laboratory and the Department of Energy, Grant No. DE-FG02-04ER118. MK, MO and JD acknowledge support by the Alexander von Humboldt Foundation.

Molecular dynamics study of linear and comb-like polyelectrolytes in aqueous solution: effect of Ca2+ ions

NASA Astrophysics Data System (ADS)

Tong, Kefeng; Song, Xingfu; Sun, Shuying; Xu, Yanxia; Yu, Jianguo

2014-08-01

All-atom molecular dynamics simulations were employed to provide microscopic mechanism for the salt tolerance of polyelectrolytes dispersants. The conformational variation of polyelectrolytes and interactions between COO- groups and counterions/water molecules were also studied via radius of gyration and pair correlations functions. Sodium polyacrylate (NaPA) and sodium salts of poly(acrylic acid)-poly(ethylene oxide) (NaPA-PEO) were selected as the representative linear and comb-like polyelectrolyte, respectively. The results show that Ca2+ ions interact with COO- groups much stronger than Na+ ions and can bring ion-bridging interaction between intermolecular COO- groups in the NaPA systems. While in the NaPA-PEO systems, the introduced PEO side chains can prevent backbone chains from ion-bridging interactions and weaken the conformational changes. The present results can help in selecting and designing new-type efficient polyelectrolyte dispersants with good salt tolerance.

AB INITIO Molecular Dynamics Simulations on Local Structure and Electronic Properties in Liquid Sb from 913 K to 1193 K

NASA Astrophysics Data System (ADS)

Hao, Qing-Hai; Li, Y. D.; Kong, Xiang-Shan; Liu, C. S.

2013-02-01

Ab initio molecular dynamics simulations on liquid Sb have been carried out at five different temperatures from 913 K to 1193 K. We have investigated the temperature dependence of structure properties including structural factor S(Q), pair correlation function g(r), bond-angle distribution function g3(θ), cluster properties and bond order parameter Q4 and Q6. A shoulder was reproduced in the high wave number side of the first peak in the S(Q) implying that the residual structure units of crystalline Sb remain in liquid Sb. There is a noticeable bend at around 1023 K in the temperature dependence of the first-peak height of S(Q), the cluster properties and bond order parameter Q4, respectively, indicating that an abnormal structural change may occur at 973-1023 K.

The atomic scale structure of CXV carbon: wide-angle x-ray scattering and modeling studies.

PubMed

Hawelek, L; Brodka, A; Dore, J C; Honkimaki, V; Burian, A

2013-11-13

The disordered structure of commercially available CXV activated carbon produced from finely powdered wood-based carbon has been studied using the wide-angle x-ray scattering technique, molecular dynamics and density functional theory simulations. The x-ray scattering data has been converted to the real space representation in the form of the pair correlation function via the Fourier transform. Geometry optimizations using classical molecular dynamics based on the reactive empirical bond order potential and density functional theory at the B3LYP/6-31g* level have been performed to generate nanoscale models of CXV carbon consistent with the experimental data. The final model of the structure comprises four chain-like and buckled graphitic layers containing a small percentage of four-fold coordinated atoms (sp(3) defects) in each layer. The presence of non-hexagonal rings in the atomic arrangement has been also considered.

Liquid-to-liquid crossover in the GaIn eutectic alloy

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

Yu, Q.; Wang, X. D.; Su, Y.

Liquid-liquid crossover is promising and closely related to the atomic dynamics during heating and cooling processes. Here we reveal a reversible structural crossover in the liquid Ga85.8In14.2 eutectic alloys by using in situ synchrotron x-ray diffraction and ab initio molecular dynamics simulation. A kink always appears on the temperature dependent behaviors of density, ratio of the second peak position to the first in the pair correlation function, coordination number, heat capacity, free energy, and atomic diffusivity in the temperature range of about 400–550 K. It is likely ascribed to atomic rearrangements of Ga and In atoms from a relative randommore » packing at high temperatures to a relative nonuniform packing at low temperatures, in which In atoms prefer to have more In neighbors. This observation will promote more understanding of the liquid structure of eutectic alloys« less

Onset of jamming for gas-fluidized grains

NASA Astrophysics Data System (ADS)

Abate, Adam

2006-03-01

Upon approach to jamming, whether for molecular liquids or colloidal particles or grains of sand, the microscopic dynamics can develop dramatic long-ranged correlations while the microscopic structure remains relatively unchanged. Experimentally, it has been difficult to study such phenomena in full detail due to the range of temporal and spatial scales involved. Here we introduce a new model system that is both easier to image and to manipulate at the microscale: a bidisperse system of steel beads rolling stochastically due to a nearly-levitating upflow of air. At fixed air flow, we demonstrate that this system exhibits all the hallmarks of a jamming transition as spheres are added and the area fraction increases toward close-packing. In terms of structure, the pair correlation function and the Voronoi cell shape distribution functions exhibit peak splitting. In terms of dynamics, the mean-squared displacement develops a plateau separating the short-time ballistic from the long-time diffusive motions; in this plateau the displacement distribution is non-Gaussian, due to spatial heterogeneities. While this phenomenology is familiar, one feature observed previously only in simulation is the presence of string-like swirls of rearranging grains. We highlight these by movies of an appropriately time-averaged velocity field. We hope to connect such dynamics both to a microscopic measure of effective temperature and to the macroscopic viscosity of the system.

Visual stimulation synchronizes or desynchronizes the activity of neuron pairs between the caudate nucleus and the posterior thalamus.

PubMed

Rokszin, Alice; Gombköto, Péter; Berényi, Antal; Márkus, Zita; Braunitzer, Gábor; Benedek, György; Nagy, Attila

2011-10-18

Recent morphological and physiological studies have suggested a strong relationship between the suprageniculate nucleus (Sg) of the posterior thalamus and the input structure of the basal ganglia, the caudate nucleus (CN) of the feline brain. Accordingly, to clarify if there is a real functional relationship between Sg and CN during visual information processing, we investigated the temporal relations of simultaneously recorded neuronal spike trains of these two structures, looking for any significant cross-correlation between the spiking of the simultaneously recorded neurons. For the purposes of statistical analysis, we used the shuffle and jittering resampling methods. Of the recorded 288 Sg-CN neuron pairs, 26 (9.2%) showed significantly correlated spontaneous activity. Nineteen pairs (6.7%) showed correlated activity during stationary visual stimulation, while 21 (7.4%) pairs during stimulus movement. There was no overlap between the neuron pairs that showed cross-correlated spontaneous activity and the pairs that synchronized their activity during visual stimulation. Thus visual stimulation seems to have been able to synchronize, and also, by other neuron pairs, desynchronize the activity of CN and Sg. In about half of the cases, the activation of Sg preceded the activation of CN by a few milliseconds, while in the other half, CN was activated earlier. Our results provide the first piece of evidence for the existence of a functional cooperation between Sg and CN. We argue that either a monosynaptic bidirectional direct connection should exist between these structures, or a common input comprising of parallel pathways synchronizing them. Copyright © 2011 Elsevier B.V. All rights reserved.

Defect-Engineered Heat Transport in Graphene: A Route to High Efficient Thermal Rectification

PubMed Central

Zhao, Weiwei; Wang, Yanlei; Wu, Zhangting; Wang, Wenhui; Bi, Kedong; Liang, Zheng; Yang, Juekuan; Chen, Yunfei; Xu, Zhiping; Ni, Zhenhua

2015-01-01

Low-dimensional materials such as graphene provide an ideal platform to probe the correlation between thermal transport and lattice defects, which could be engineered at the molecular level. In this work, we perform molecular dynamics simulations and non-contact optothermal Raman measurements to study this correlation. We find that oxygen plasma treatment could reduce the thermal conductivity of graphene significantly even at extremely low defect concentration (∼83% reduction for ∼0.1% defects), which could be attributed mainly to the creation of carbonyl pair defects. Other types of defects such as hydroxyl, epoxy groups and nano-holes demonstrate much weaker effects on the reduction where the sp2 nature of graphene is better preserved. With the capability of selectively functionalizing graphene, we propose an asymmetric junction between graphene and defective graphene with a high thermal rectification ratio of ∼46%, as demonstrated by our molecular dynamics simulation results. Our findings provide fundamental insights into the physics of thermal transport in defective graphene, and two-dimensional materials in general, which could help on the future design of functional applications such as optothermal and electrothermal devices. PMID:26132747

Pairing phase diagram of three holes in the generalized Hubbard model

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

Navarro, O.; Espinosa, J.E.

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

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.

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.

Prediction of regulatory gene pairs using dynamic time warping and gene ontology.

PubMed

Yang, Andy C; Hsu, Hui-Huang; Lu, Ming-Da; Tseng, Vincent S; Shih, Timothy K

2014-01-01

Selecting informative genes is the most important task for data analysis on microarray gene expression data. In this work, we aim at identifying regulatory gene pairs from microarray gene expression data. However, microarray data often contain multiple missing expression values. Missing value imputation is thus needed before further processing for regulatory gene pairs becomes possible. We develop a novel approach to first impute missing values in microarray time series data by combining k-Nearest Neighbour (KNN), Dynamic Time Warping (DTW) and Gene Ontology (GO). After missing values are imputed, we then perform gene regulation prediction based on our proposed DTW-GO distance measurement of gene pairs. Experimental results show that our approach is more accurate when compared with existing missing value imputation methods on real microarray data sets. Furthermore, our approach can also discover more regulatory gene pairs that are known in the literature than other methods.

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

NASA Astrophysics Data System (ADS)

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

2014-07-01

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

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

PubMed Central

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

2014-01-01

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

A longitudinal twin study of physical aggression during early childhood: evidence for a developmentally dynamic genome.

PubMed

Lacourse, E; Boivin, M; Brendgen, M; Petitclerc, A; Girard, A; Vitaro, F; Paquin, S; Ouellet-Morin, I; Dionne, G; Tremblay, R E

2014-09-01

Physical aggression (PA) tends to have its onset in infancy and to increase rapidly in frequency. Very little is known about the genetic and environmental etiology of PA development during early childhood. We investigated the temporal pattern of genetic and environmental etiology of PA during this crucial developmental period. Participants were 667 twin pairs, including 254 monozygotic and 413 dizygotic pairs, from the ongoing longitudinal Quebec Newborn Twin Study. Maternal reports of PA were obtained from three waves of data at 20, 32 and 50 months. These reports were analysed using a biometric Cholesky decomposition and linear latent growth curve model. The best-fitting Cholesky model revealed developmentally dynamic effects, mostly genetic attenuation and innovation. The contribution of genetic factors at 20 months substantially decreased over time, while new genetic effects appeared later on. The linear latent growth curve model revealed a significant moderate increase in PA from 20 to 50 months. Two separate sets of uncorrelated genetic factors accounted for the variation in initial level and growth rate. Non-shared and shared environments had no effect on the stability, initial status and growth rate in PA. Genetic factors underlie PA frequency and stability during early childhood; they are also responsible for initial status and growth rate in PA. The contribution of shared environment is modest, and perhaps limited, as it appears only at 50 months. Future research should investigate the complex nature of these dynamic genetic factors through genetic-environment correlation (r GE) and interaction (G×E) analyses.

Estimating the distance separating fluorescent protein FRET pairs

PubMed Central

van der Meer, B. Wieb; Blank, Paul S.

2014-01-01

Förster resonance energy transfer (FRET) describes a physical phenomenon widely applied in biomedical research to estimate separations between biological molecules. Routinely, genetic engineering is used to incorporate spectral variants of the green fluorescent protein (GFPs), into cellular expressed proteins. The transfer efficiency or rate of energy transfer between donor and acceptor FPs is then assayed. As appreciable FRET occurs only when donors and acceptors are in close proximity (1–10 nm), the presence of FRET may indicate that the engineered proteins associate as interacting species. For a homogeneous population of FRET pairs the separations between FRET donors and acceptors can be estimated from a measured FRET efficiency if it is assumed that donors and acceptors are randomly oriented and rotate extensively during their excited state (dynamic regime). Unlike typical organic fluorophores, the rotational correlation-times of FPs are typically much longer than their fluorescence lifetime; accordingly FPs are virtually static during their excited state. Thus, estimating separations between FP FRET pairs is problematic. To overcome this obstacle, we present here a simple method for estimating separations between FPs using the experimentally measured average FRET efficiency. This approach assumes that donor and acceptor fluorophores are randomly oriented, but do not rotate during their excited state (static regime). This approach utilizes a Monte-Carlo simulation generated look-up table that allows one to estimate the separation, normalized to the Förster distance, from the average FRET efficiency. Assuming a dynamic regime overestimates the separation significantly (by 10% near 0.5 and 30% near 0.75 efficiencies) compared to assuming a static regime, which is more appropriate for estimates of separations between FPs. PMID:23811334

Improved automatic estimation of winds at the cloud top of Venus using superposition of cross-correlation surfaces

NASA Astrophysics Data System (ADS)

Ikegawa, Shinichi; Horinouchi, Takeshi

2016-06-01

Accurate wind observation is a key to study atmospheric dynamics. A new automated cloud tracking method for the dayside of Venus is proposed and evaluated by using the ultraviolet images obtained by the Venus Monitoring Camera onboard the Venus Express orbiter. It uses multiple images obtained successively over a few hours. Cross-correlations are computed from the pair combinations of the images and are superposed to identify cloud advection. It is shown that the superposition improves the accuracy of velocity estimation and significantly reduces false pattern matches that cause large errors. Two methods to evaluate the accuracy of each of the obtained cloud motion vectors are proposed. One relies on the confidence bounds of cross-correlation with consideration of anisotropic cloud morphology. The other relies on the comparison of two independent estimations obtained by separating the successive images into two groups. The two evaluations can be combined to screen the results. It is shown that the accuracy of the screened vectors are very high to the equatorward of 30 degree, while it is relatively low at higher latitudes. Analysis of them supports the previously reported existence of day-to-day large-scale variability at the cloud deck of Venus, and it further suggests smaller-scale features. The product of this study is expected to advance the dynamics of venusian atmosphere.

Sauter-Schwinger pair creation dynamically assisted by a plane wave

NASA Astrophysics Data System (ADS)

Torgrimsson, Greger; Schneider, Christian; Schützhold, Ralf

2018-05-01

We study electron-positron pair creation by a strong and constant electric field superimposed with a weaker transversal plane wave which is incident perpendicularly (or under some angle). Comparing the fully nonperturbative approach based on the world-line instanton method with a perturbative expansion into powers of the strength of the weaker plane wave, we find good agreement—provided that the latter is carried out to sufficiently high orders. As usual for the dynamically assisted Sauter-Schwinger effect, the additional plane wave induces an exponential enhancement of the pair-creation probability if the combined Keldysh parameter exceeds a certain threshold.

Measurement of $$B\\bar{B}$$ Angular Correlations based on Secondary Vertex Reconstruction at $$\\sqrt{s}=7$$ TeV

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

Khachatryan, Vardan; et al.

2011-03-01

A measurement of the angular correlations between beauty and anti-beauty hadrons (B B-bar) produced in pp collisions at a centre-of-mass energy of 7 TeV at the CERN LHC is presented, probing for the first time the region of small angular separation. The B hadrons are identified by the presence of displaced secondary vertices from their decays. The B hadron angular separation is reconstructed from the decay vertices and the primary-interaction vertex. The differential B B-bar production cross section, measured from a data sample collected by CMS and corresponding to an integrated luminosity of 3.1 inverse picobarns, shows that a sizablemore » fraction of the B B-bar pairs are produced with small opening angles. These studies provide a test of QCD and further insight into the dynamics of b b-bar production.« less

Self-consistent implementation of ensemble density functional theory method for multiple strongly correlated electron pairs

DOE PAGES

Filatov, Michael; Liu, Fang; Kim, Kwang S.; ...

2016-12-22

Here, the spin-restricted ensemble-referenced Kohn-Sham (REKS) method is based on an ensemble representation of the density and is capable of correctly describing the non-dynamic electron correlation stemming from (near-)degeneracy of several electronic configurations. The existing REKS methodology describes systems with two electrons in two fractionally occupied orbitals. In this work, the REKS methodology is extended to treat systems with four fractionally occupied orbitals accommodating four electrons and self-consistent implementation of the REKS(4,4) method with simultaneous optimization of the orbitals and their fractional occupation numbers is reported. The new method is applied to a number of molecular systems where simultaneous dissociationmore » of several chemical bonds takes place, as well as to the singlet ground states of organic tetraradicals 2,4-didehydrometaxylylene and 1,4,6,9-spiro[4.4]nonatetrayl.« less

Solvation effects on like-charge attraction.

PubMed

Ghanbarian, Shahzad; Rottler, Jörg

2013-02-28

We present results of molecular dynamics simulations of the electrostatic interaction between two parallel charged rods in the presence of divalent counterions. Such polyelectrolytes have been considered as a simple model for understanding electrostatic interactions in highly charged biomolecules such as DNA. Since there are correlations between the free charge carriers, the phenomenon of like charge attraction appears for specific parameters. We explore the role of solvation effects and the resulting deviations from Coulomb's law on the nanoscale on this peculiar phenomenon. The behavior of the force between the charged rods in a simulation with atomistic representation of water molecules is completely different from a model in which water is modeled as a continuum dielectric. By calculating counterion-rodion pair correlation functions, we find that the presence of water molecules changes the structure of the counterion cloud and results in both qualitative and quantitative changes of the force between highly charged polyelectrolytes.

Anomalous Protein-Protein Interactions in Multivalent Salt Solution.

PubMed

Pasquier, Coralie; Vazdar, Mario; Forsman, Jan; Jungwirth, Pavel; Lund, Mikael

2017-04-13

The stability of aqueous protein solutions is strongly affected by multivalent ions, which induce ion-ion correlations beyond the scope of classical mean-field theory. Using all-atom molecular dynamics (MD) and coarse grained Monte Carlo (MC) simulations, we investigate the interaction between a pair of protein molecules in 3:1 electrolyte solution. In agreement with available experimental findings of "reentrant protein condensation", we observe an anomalous trend in the protein-protein potential of mean force with increasing electrolyte concentration in the order: (i) double-layer repulsion, (ii) ion-ion correlation attraction, (iii) overcharge repulsion, and in excess of 1:1 salt, (iv) non Coulombic attraction. To efficiently sample configurational space we explore hybrid continuum solvent models, applicable to many-protein systems, where weakly coupled ions are treated implicitly, while strongly coupled ones are treated explicitly. Good agreement is found with the primitive model of electrolytes, as well as with atomic models of protein and solvent.

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.

Monte Carlo study of four dimensional binary hard hypersphere mixtures

NASA Astrophysics Data System (ADS)

Bishop, Marvin; Whitlock, Paula A.

2012-01-01

A multithreaded Monte Carlo code was used to study the properties of binary mixtures of hard hyperspheres in four dimensions. The ratios of the diameters of the hyperspheres examined were 0.4, 0.5, 0.6, and 0.8. Many total densities of the binary mixtures were investigated. The pair correlation functions and the equations of state were determined and compared with other simulation results and theoretical predictions. At lower diameter ratios the pair correlation functions of the mixture agree with the pair correlation function of a one component fluid at an appropriately scaled density. The theoretical results for the equation of state compare well to the Monte Carlo calculations for all but the highest densities studied.

Differential stabilities and sequence-dependent base pair opening dynamics of Watson-Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine.

PubMed

Szulik, Marta W; Pallan, Pradeep S; Nocek, Boguslaw; Voehler, Markus; Banerjee, Surajit; Brooks, Sonja; Joachimiak, Andrzej; Egli, Martin; Eichman, Brandt F; Stone, Michael P

2015-02-10

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson-Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5'-CG-3' sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5'-T(8)X(9)G(10)-3' sequence of the DDD, were compared. The presence of 5caC at the X(9) base increased the stability of the DDD, whereas 5hmC or 5fC did not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A(5):T(8), whereas 5caC did not. At the oxidized base pair G(4):X(9), 5fC exhibited an increase in the imino proton exchange rate and the calculated kop. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C(3):G(10). No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G(4):X(9); each favored Watson-Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N(4) exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. However, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes.

Differential stabilities and sequence-dependent base pair opening dynamics of Watson–Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine

DOE PAGES

Szulik, Marta W.; Pallan, Pradeep S.; Nocek, Boguslaw; ...

2015-01-29

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson–Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5'-CG-3' sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5'-T 8X 9G 10-3' sequence of the DDD, were compared. The presence of 5caC at the X9 base increased the stability of the DDD, whereas 5hmC or 5fC didmore » not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A 5:T 8, whereas 5caC did not. At the oxidized base pair G 4:X 9, 5fC exhibited an increase in the imino proton exchange rate and the calculated k op. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C 3:G 10. No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G 4:X 9; each favored Watson–Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N 4 exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. Furthermore, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes.« less

Differential Stabilities and Sequence-Dependent Base Pair Opening Dynamics of Watson–Crick Base Pairs with 5-Hydroxymethylcytosine, 5-Formylcytosine, or 5-Carboxylcytosine

PubMed Central

2016-01-01

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson–Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5′-CG-3′ sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5′-T8X9G10-3′ sequence of the DDD, were compared. The presence of 5caC at the X9 base increased the stability of the DDD, whereas 5hmC or 5fC did not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A5:T8, whereas 5caC did not. At the oxidized base pair G4:X9, 5fC exhibited an increase in the imino proton exchange rate and the calculated kop. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C3:G10. No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G4:X9; each favored Watson–Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N4 exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. However, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes. PMID:25632825

Generation of Synthetic Spike Trains with Defined Pairwise Correlations

PubMed Central

Niebur, Ernst

2008-01-01

Recent technological advances as well as progress in theoretical understanding of neural systems have created a need for synthetic spike trains with controlled mean rate and pairwise cross-correlation. This report introduces and analyzes a novel algorithm for the generation of discretized spike trains with arbitrary mean rates and controlled cross correlation. Pairs of spike trains with any pairwise correlation can be generated, and higher-order correlations are compatible with common synaptic input. Relations between allowable mean rates and correlations within a population are discussed. The algorithm is highly efficient, its complexity increasing linearly with the number of spike trains generated and therefore inversely with the number of cross-correlated pairs. PMID:17521277

Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

NASA Astrophysics Data System (ADS)

Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

2018-06-01

We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

Dynamic Tunnel Usability Study: Format Recommendations for Synthetic Vision System Primary Flight Displays

NASA Technical Reports Server (NTRS)

Arthur, Jarvis J., III; Prinzel, Lawrence J., III; Kramer, Lynda J.; Bailey, Randall E.

2006-01-01

A usability study evaluating dynamic tunnel concepts has been completed under the Aviation Safety and Security Program, Synthetic Vision Systems Project. The usability study was conducted in the Visual Imaging Simulator for Transport Aircraft Systems (VISTAS) III simulator in the form of questionnaires and pilot-in-the-loop simulation sessions. Twelve commercial pilots participated in the study to determine their preferences via paired comparisons and subjective rankings regarding the color, line thickness and sensitivity of the dynamic tunnel. The results of the study showed that color was not significant in pilot preference paired comparisons or in pilot rankings. Line thickness was significant for both pilot preference paired comparisons and in pilot rankings. The preferred line/halo thickness combination was a line width of 3 pixels and a halo of 4 pixels. Finally, pilots were asked their preference for the current dynamic tunnel compared to a less sensitive dynamic tunnel. The current dynamic tunnel constantly gives feedback to the pilot with regard to path error while the less sensitive tunnel only changes as the path error approaches the edges of the tunnel. The tunnel sensitivity comparison results were not statistically significant.

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.

Hurricane impacts on a pair of coastal forested watersheds: implications of selective hurricane damage to forest structure and streamflow dynamics

Treesearch

A.D. Jayakaran; T.M. Williams; H. Ssegane; D.M. Amatya; B. Song; C.C. Trettin

2014-01-01

Hurricanes are infrequent but influential disruptors of ecosystem processes in the southeastern Atlantic and Gulf coasts. Every southeastern forested wetland has the potential to be struck by a tropical cyclone. We examined the impact of Hurricane Hugo on two paired coastal South Carolina watersheds in terms of streamflow and vegetation dynamics, both before and after...

Molecular dynamics investigation of dynamical heterogeneity and local structure in the supercooled liquid and glass states of Al

NASA Astrophysics Data System (ADS)

Li, Maozhi; Wang, Cai-Zhuang; Mendelev, Mikhail I.; Ho, Kai-Ming

2008-05-01

Molecular dynamics simulations are performed to study the structure and dynamical heterogeneity in the liquid and glass states of Al using a frequently employed embedded atom potential. While the pair correlation function of the glass and liquid states displays only minor differences, the icosahedral short-range order (ISRO) and the dynamics of the two states are very different. The ISRO is much stronger in the glass than in the liquid. It is also found that both the most mobile and the most immobile atoms in the glass state tend to form clusters, and the clusters formed by the immobile atoms are more compact. In order to investigate the local environment of each atom in the liquid and glass states, a local density is defined to characterize the local atomic packing. There is a strong correlation between the local packing density and the mobility of the atoms. These results indicate that dynamical heterogeneity in glasses is directly correlated to the local structure. We also analyze the diffusion mechanisms of atoms in the liquid and glass states. It is found that for the mobile atoms in the glass state, initially they are confined in the cages formed by their nearest neighbors and vibrating. On the time scale of β relaxation, the mobile atoms try to break up the cage confinement and hop into new cages. In the supercooled liquid states, however, atoms continuously diffuse. Furthermore, it is found that on the time scale of β relaxation, some of the mobile atoms in the glass state cooperatively hop, which is facilitated by the stringlike cluster structures. On the longer time scale, it is found that a certain fraction of atoms can simultaneously hop, although they are not nearest neighbors. Further analysis shows that these hopping atoms form big and more compact clusters than the characterized most mobile atoms. The cooperative rearrangement of these big compact clusters might facilitate the simultaneous hopping of atoms in the glass states on the long time scale.

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.

Multiconfiguration pair-density functional theory: barrier heights and main group and transition metal energetics.

PubMed

Carlson, Rebecca K; Li Manni, Giovanni; Sonnenberger, Andrew L; Truhlar, Donald G; Gagliardi, Laura

2015-01-13

Kohn-Sham density functional theory, resting on the representation of the electronic density and kinetic energy by a single Slater determinant, has revolutionized chemistry, but for open-shell systems, the Kohn-Sham Slater determinant has the wrong symmetry properties as compared to an accurate wave function. We have recently proposed a theory, called multiconfiguration pair-density functional theory (MC-PDFT), in which the electronic kinetic energy and classical Coulomb energy are calculated from a multiconfiguration wave function with the correct symmetry properties, and the rest of the energy is calculated from a density functional, called the on-top density functional, that depends on the density and the on-top pair density calculated from this wave function. We also proposed a simple way to approximate the on-top density functional by translation of Kohn-Sham exchange-correlation functionals. The method is much less expensive than other post-SCF methods for calculating the dynamical correlation energy starting with a multiconfiguration self-consistent-field wave function as the reference wave function, and initial tests of the theory were quite encouraging. Here, we provide a broader test of the theory by applying it to bond energies of main-group molecules and transition metal complexes, barrier heights and reaction energies for diverse chemical reactions, proton affinities, and the water dimerization energy. Averaged over 56 data points, the mean unsigned error is 3.2 kcal/mol for MC-PDFT, as compared to 6.9 kcal/mol for Kohn-Sham theory with a comparable density functional. MC-PDFT is more accurate on average than complete active space second-order perturbation theory (CASPT2) for main-group small-molecule bond energies, alkyl bond dissociation energies, transition-metal-ligand bond energies, proton affinities, and the water dimerization energy.

The shift from a response strategy to object-in-place strategy during learning is accompanied by a matching shift in neural firing correlates in the hippocampus.

PubMed

Lee, Inah; Kim, Jangjin

2010-08-01

Hippocampal-dependent tasks often involve specific associations among stimuli (including egocentric information), and such tasks are therefore prone to interference from irrelevant task strategies before a correct strategy is found. Using an object-place paired-associate task, we investigated changes in neural firing patterns in the hippocampus in association with a shift in strategy during learning. We used an object-place paired-associate task in which a pair of objects was presented in two different arms of a radial maze. Each object was associated with reward only in one of the arms, thus requiring the rats to consider both object identity and its location in the maze. Hippocampal neurons recorded in CA1 displayed a dynamic transition in their firing patterns during the acquisition of the task across days, and this corresponded to a shift in strategy manifested in behavioral data. Specifically, before the rats learned the task, they chose an object that maintained a particular egocentric relationship with their body (response strategy) irrespective of the object identity. However, as the animal acquired the task, it chose an object according to both its identity and the associated location in the maze (object-in-place strategy). We report that CA1 neurons in the hippocampus changed their prospective firing correlates according to the dominant strategy (i.e., response versus object-in-place strategy) employed at a given stage of learning. The results suggest that neural firing pattern in the hippocampus is heavily influenced by the task demand hypothesized by the animal and the firing pattern changes flexibly as the perceived task demand changes.

Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.

PubMed

Wu, Johnny C; Gardner, David P; Ozer, Stuart; Gutell, Robin R; Ren, Pengyu

2009-08-28

The accurate prediction of the secondary and tertiary structure of an RNA with different folding algorithms is dependent on several factors, including the energy functions. However, an RNA higher-order structure cannot be predicted accurately from its sequence based on a limited set of energy parameters. The inter- and intramolecular forces between this RNA and other small molecules and macromolecules, in addition to other factors in the cell such as pH, ionic strength, and temperature, influence the complex dynamics associated with transition of a single stranded RNA to its secondary and tertiary structure. Since all of the factors that affect the formation of an RNAs 3D structure cannot be determined experimentally, statistically derived potential energy has been used in the prediction of protein structure. In the current work, we evaluate the statistical free energy of various secondary structure motifs, including base-pair stacks, hairpin loops, and internal loops, using their statistical frequency obtained from the comparative analysis of more than 50,000 RNA sequences stored in the RNA Comparative Analysis Database (rCAD) at the Comparative RNA Web (CRW) Site. Statistical energy was computed from the structural statistics for several datasets. While the statistical energy for a base-pair stack correlates with experimentally derived free energy values, suggesting a Boltzmann-like distribution, variation is observed between different molecules and their location on the phylogenetic tree of life. Our statistical energy values calculated for several structural elements were utilized in the Mfold RNA-folding algorithm. The combined statistical energy values for base-pair stacks, hairpins and internal loop flanks result in a significant improvement in the accuracy of secondary structure prediction; the hairpin flanks contribute the most.

Electrical Conductivity through a Single Atomic Step Measured with the Proximity-Induced Superconducting Pair Correlation

DOE PAGES

Kim, Howon; Lin, Shi -Zeng; Graf, Matthias J.; ...

2016-09-08

Local disordered nanostructures in an atomically thick metallic layer on a semiconducting substrate play significant and decisive roles in transport properties of two-dimensional (2D) conductive systems. We measured the electrical conductivity through a step of monoatomic height in a truly microscopic manner by using as a signal the superconducting pair correlation induced by the proximity effect. The transport property across a step of a one-monolayer Pb surface metallic phase, formed on a Si(111) substrate, was evaluated by inducing the pair correlation around the local defect and measuring its response, i.e., the reduced density of states at the Fermi energy usingmore » scanning tunneling microscopy. We found that the step resistance has a significant contribution to the total resistance on a nominally flat surface. Our study also revealed that steps in the 2D metallic layer terminate the propagation of the pair correlation. Furthermore, superconductivity is enhanced between the first surface step and the superconductor–normal-metal interface by reflectionless tunneling when the step is located within a coherence length.« less

Electrical Conductivity through a Single Atomic Step Measured with the Proximity-Induced Superconducting Pair Correlation.

PubMed

Kim, Howon; Lin, Shi-Zeng; Graf, Matthias J; Miyata, Yoshinori; Nagai, Yuki; Kato, Takeo; Hasegawa, Yukio

2016-09-09

Local disordered nanostructures in an atomically thick metallic layer on a semiconducting substrate play significant and decisive roles in transport properties of two-dimensional (2D) conductive systems. We measured the electrical conductivity through a step of monoatomic height in a truly microscopic manner by using as a signal the superconducting pair correlation induced by the proximity effect. The transport property across a step of a one-monolayer Pb surface metallic phase, formed on a Si(111) substrate, was evaluated by inducing the pair correlation around the local defect and measuring its response, i.e., the reduced density of states at the Fermi energy using scanning tunneling microscopy. We found that the step resistance has a significant contribution to the total resistance on a nominally flat surface. Our study also revealed that steps in the 2D metallic layer terminate the propagation of the pair correlation. Superconductivity is enhanced between the first surface step and the superconductor-normal-metal interface by reflectionless tunneling when the step is located within a coherence length.

Evidence that the association of childhood trauma with psychosis and related psychopathology is not explained by gene-environment correlation: A monozygotic twin differences approach.

PubMed

Lecei, Aleksandra; Decoster, Jeroen; De Hert, Marc; Derom, Catherine; Jacobs, Nele; Menne-Lothmann, Claudia; van Os, Jim; Thiery, Evert; Rutten, Bart P F; Wichers, Marieke; van Winkel, Ruud

2018-05-21

Converging evidence supports childhood trauma as possible causal risk for psychosis and related psychopathology. However, studies have shown that baseline psychotic symptoms may actually increase risk for subsequent victimization, suggesting that exposure to CT is not random but may result from pre-existing vulnerability. Therefore, studies testing whether the association between CT and psychopathology persists when accounting for gene-environment correlation are much needed. A monozygotic (MZ) twin differences approach was used to examine whether differences in CT exposure among MZ twin pairs would be associated with MZ differences in symptoms. As MZ twins are genetically identical, within-pair correlations between CT exposure and psychopathology rule out the possibility that the association is solely attributable to gene-environment correlation. 266 monozygotic twins (133 pairs) from a larger general population study were available for analysis. CT was associated with symptoms of psychosis (B = 0.62; SE = 0.08, p < .001) and overall psychopathology (B = 43.13; SE = 6.27; p < .001). There were measurable differences within pairs in CT exposure and symptoms, allowing for meaningful within-pair differences. Within-pair differences in CT exposure were associated with within-pair differences in symptoms of psychosis (B = 0.35; SE = 0.16; p = .024), as well as with overall psychopathology (B = 29.22; SE = 12.24; p = .018), anxiety (B = 0.65; SE = 0.21; p = .002) and depression (B = 0.37; SE = 0.18; p = .043). While it is not unlikely that pre-existing vulnerability may increase the risk for traumatic exposures, such gene-environment correlation does not explain away the association between CT and psychopathology. The present findings thus suggest that at least part of the association between CT and psychopathology may be causal. Copyright © 2018. Published by Elsevier B.V.

The relationships between age, associative memory performance and the neural correlates of successful associative memory encoding

PubMed Central

de Chastelaine, Marianne; Mattson, Julia T.; Wang, Tracy H.; Donley, Brian E.; Rugg, Michael D.

2016-01-01

Using fMRI, subsequent memory effects (greater activity for later remembered than later forgotten study items) predictive of associative encoding were compared across samples of young, middle-aged and older adults (total n = 136). During scanning, participants studied visually presented word pairs. In a later test phase, they discriminated between studied pairs, ‘rearranged’ pairs (items studied on different trials) and new pairs. Subsequent memory effects were identified by contrasting activity elicited by study pairs that went on to be correctly judged intact or incorrectly judged rearranged. Effects in the hippocampus were age-invariant and positively correlated across participants with associative memory performance. Subsequent memory effects in the right IFG were greater in the older than the young group. In older participants only, both left and, in contrast to prior reports, right IFG subsequent memory effects correlated positively with memory performance. We suggest that the IFG is especially vulnerable to age-related decline in functional integrity, and that the relationship between encoding-related activity in right IFG and memory performance depends on the experimental context. PMID:27143433

Cluster fusion-fission dynamics in the Singapore stock exchange

NASA Astrophysics Data System (ADS)

Teh, Boon Kin; Cheong, Siew Ann

2015-10-01

In this paper, we investigate how the cross-correlations between stocks in the Singapore stock exchange (SGX) evolve over 2008 and 2009 within overlapping one-month time windows. In particular, we examine how these cross-correlations change before, during, and after the Sep-Oct 2008 Lehman Brothers Crisis. To do this, we extend the complete-linkage hierarchical clustering algorithm, to obtain robust clusters of stocks with stronger intracluster correlations, and weaker intercluster correlations. After we identify the robust clusters in all time windows, we visualize how these change in the form of a fusion-fission diagram. Such a diagram depicts graphically how the cluster sizes evolve, the exchange of stocks between clusters, as well as how strongly the clusters mix. From the fusion-fission diagram, we see a giant cluster growing and disintegrating in the SGX, up till the Lehman Brothers Crisis in September 2008 and the market crashes of October 2008. After the Lehman Brothers Crisis, clusters in the SGX remain small for few months before giant clusters emerge once again. In the aftermath of the crisis, we also find strong mixing of component stocks between clusters. As a result, the correlation between initially strongly-correlated pairs of stocks decay exponentially with average life time of about a month. These observations impact strongly how portfolios and trading strategies should be formulated.

A digital correlator upgrade for the Arcminute MicroKelvin Imager

NASA Astrophysics Data System (ADS)

Hickish, Jack; Razavi-Ghods, Nima; Perrott, Yvette C.; Titterington, David J.; Carey, Steve H.; Scott, Paul F.; Grainge, Keith J. B.; Scaife, Anna M. M.; Alexander, Paul; Saunders, Richard D. E.; Crofts, Mike; Javid, Kamran; Rumsey, Clare; Jin, Terry Z.; Ely, John A.; Shaw, Clive; Northrop, Ian G.; Pooley, Guy; D'Alessandro, Robert; Doherty, Peter; Willatt, Greg P.

2018-04-01

The Arcminute Microkelvin Imager (AMI) telescopes located at the Mullard Radio Astronomy Observatory near Cambridge have been significantly enhanced by the implementation of a new digital correlator with 1.2 MHz spectral resolution. This system has replaced a 750-MHz resolution analogue lag-based correlator, and was designed to mitigate the effects of radio frequency interference, particularly that from geostationary satellites which are visible from the AMI site when observing at low declinations. The upgraded instrument consists of 18 ROACH2 Field Programmable Gate Array platforms used to implement a pair of real-time FX correlators - one for each of AMI's two arrays. The new system separates the down-converted RF baseband signal from each AMI receiver into two sub-bands, each of which are filtered to a width of 2.3 GHz and digitized at 5-Gsps with 8 bits of precision. These digital data streams are filtered into 2048 frequency channels and cross-correlated using FPGA hardware, with a commercial 10 Gb Ethernet switch providing high-speed data interconnect. Images formed using data from the new digital correlator show over an order of magnitude improvement in dynamic range over the previous system. The ability to observe at low declinations has also been significantly improved.

Protein Phosphatase 4 Promotes Chromosome Pairing and Synapsis, and Contributes to Maintaining Crossover Competence with Increasing Age

PubMed Central

Sato-Carlton, Aya; Li, Xuan; Crawley, Oliver; Testori, Sarah; Martinez-Perez, Enrique; Sugimoto, Asako; Carlton, Peter M.

2014-01-01

Prior to the meiotic divisions, dynamic chromosome reorganizations including pairing, synapsis, and recombination of maternal and paternal chromosome pairs must occur in a highly regulated fashion during meiotic prophase. How chromosomes identify each other's homology and exclusively pair and synapse with their homologous partners, while rejecting illegitimate synapsis with non-homologous chromosomes, remains obscure. In addition, how the levels of recombination initiation and crossover formation are regulated so that sufficient, but not deleterious, levels of DNA breaks are made and processed into crossovers is not understood well. We show that in Caenorhabditis elegans, the highly conserved Serine/Threonine protein phosphatase PP4 homolog, PPH-4.1, is required independently to carry out four separate functions involving meiotic chromosome dynamics: (1) synapsis-independent chromosome pairing, (2) restriction of synapsis to homologous chromosomes, (3) programmed DNA double-strand break initiation, and (4) crossover formation. Using quantitative imaging of mutant strains, including super-resolution (3D-SIM) microscopy of chromosomes and the synaptonemal complex, we show that independently-arising defects in each of these processes in the absence of PPH-4.1 activity ultimately lead to meiotic nondisjunction and embryonic lethality. Interestingly, we find that defects in double-strand break initiation and crossover formation, but not pairing or synapsis, become even more severe in the germlines of older mutant animals, indicating an increased dependence on PPH-4.1 with increasing maternal age. Our results demonstrate that PPH-4.1 plays multiple, independent roles in meiotic prophase chromosome dynamics and maintaining meiotic competence in aging germlines. PP4's high degree of conservation suggests it may be a universal regulator of meiotic prophase chromosome dynamics. PMID:25340746

Distinct epigenetic signatures elucidate enhancer-gene relationships that delineate CIMP and non-CIMP colorectal cancers.

PubMed

Chong, Allen; Teo, Jing Xian; Ban, Kenneth H K

2016-05-10

Epigenetic changes, like DNA methylation, affect gene expression and in colorectal cancer (CRC), a distinct phenotype called the CpG island methylator phenotype ("CIMP") has significantly higher levels of DNA methylation at so-called "Type C loci" within the genome. We postulate that enhancer-gene pairs are coordinately controlled through DNA methylation in order to regulate the expression of key genes/biomarkers for a particular phenotype.Firstly, we found 24 experimentally-validated enhancers (VISTA enhancer browser) that contained statistically significant (FDR-adjusted q-value of <0.01) differentially methylated regions (DMRs) (1000bp) in a study of CIMP versus non-CIMP CRCs. Of these, the methylation of 2 enhancers, 1702 and 1944, were found to be very well correlated with the methylation of the genes Wnt3A and IGDCC3, respectively, in two separate and independent datasets.We show for the first time that there are indeed distinct and dynamic changes in the methylation pattern of specific enhancer-gene pairs in CRCs. Such a coordinated epigenetic event could be indicative of an interaction between (1) enhancer 1702 and Wnt3A and (2) enhancer 1944 and IGDCC3. Moreover, our study shows that the methylation patterns of these 2 enhancer-gene pairs can potentially be used as biomarkers to delineate CIMP from non-CIMP CRCs.

Effective interactions between soft-repulsive colloids: experiments, theory, and simulations.

PubMed

Mohanty, Priti S; Paloli, Divya; Crassous, Jérôme J; Zaccarelli, Emanuela; Schurtenberger, Peter

2014-03-07

We describe a combined experimental, theoretical, and simulation study of the structural correlations between cross-linked highly monodisperse and swollen Poly(N-isopropylacrylamide) microgel dispersions in the fluid phase in order to obtain the effective pair-interaction potential between the microgels. The density-dependent experimental pair distribution functions g(r)'s are deduced from real space studies using fluorescent confocal microscopy and compared with integral equation theory and molecular dynamics computer simulations. We use a model of Hertzian spheres that is capable to well reproduce the experimental pair distribution functions throughout the fluid phase, having fixed the particle size and the repulsive strength. Theoretically, a monodisperse system is considered whose properties are calculated within the Rogers-Young closure relation, while in the simulations the role of polydispersity is taken into account. We also discuss the various effects arising from the finite resolution of the microscope and from the noise coming from the fast Brownian motion of the particles at low densities, and compare the information content from data taken in 2D and 3D through a comparison with the corresponding simulations. Finally different potential shapes, recently adopted in studies of microgels, are also taken into account to assess which ones could also be used to describe the structure of the microgel fluid.

Role of five-fold symmetry in undercooled Al-Cu binary alloys

NASA Astrophysics Data System (ADS)

Pasturel, A.; Jakse, N.

2018-04-01

We investigate the role of five-fold symmetry (FFS) in undercooled Al1-xCux liquids (x = 0.3 and 0.4) using ab initio molecular dynamics simulations. We show that the structure factors and pair-correlation functions display characteristic features which are compatible with the occurrence of FFS and the emergence of a medium range order (MRO) below a temperature TX located close to the liquidus temperature. Then, we demonstrate that the formation of MRO is associated with a strong increase in local FFS-motifs which become more and more connected with decreasing temperature. From the temperature dependence of dynamic properties, we find that TX corresponds also to the onset of dynamic phenomena, like the non-Arrhenius temperature dependence of transport properties and the emergence of dynamical heterogeneities (DHs). Finally, we clearly identify a relationship between the fivefold topology at the medium-range scale (IMRO) and the spatial distribution of DHs using isoconfigurational ensemble simulations. This questions the direct role of the connectivity of five-fold-based motifs found in IMRO in nucleation of the parent crystalline ground states, namely, Al2Cu and Al3Cu2, which also display local ordering with a significant degree of FFS.

Dynamically assisted Schwinger effect beyond the spatially-uniform-field approximation

NASA Astrophysics Data System (ADS)

Aleksandrov, I. A.; Plunien, G.; Shabaev, V. M.

2018-06-01

We investigate the phenomenon of electron-positron pair production from vacuum in the presence of a strong electric field superimposed by a weak but fast varying pulse which substantially increases the total particle yield. We employ a nonperturbative numerical technique and perform the calculations beyond the spatially-uniform-field approximation, i.e., dipole approximation, taking into account the coordinate dependence of the fast component. The analysis of the main characteristics of the pair-production process (momentum spectra of particles and total amount of pairs) reveals a number of important features which are absent within the previously used approximation. In particular, the structure of the momentum distribution is modified both qualitatively and quantitatively, and the total number of pairs created as well as the enhancement factor due to dynamical assistance become significantly smaller.

Critical temperature for shape transition in hot nuclei within covariant density functional theory

NASA Astrophysics Data System (ADS)

Zhang, W.; Niu, Y. F.

2018-05-01

Prompted by the simple proportional relation between critical temperature for pairing transition and pairing gap at zero temperature, we investigate the relation between critical temperature for shape transition and ground-state deformation by taking even-even Cm-304286 isotopes as examples. The finite-temperature axially deformed covariant density functional theory with BCS pairing correlation is used. Since the Cm isotopes are the newly proposed nuclei with octupole correlations, we studied in detail the free energy surface, the Nilsson single-particle (s.p.) levels, and the components of s.p. levels near the Fermi level in 292Cm. Through this study, the formation of octupole equilibrium is understood by the contribution coming from the octupole driving pairs with Ω [N ,nz,ml] and Ω [N +1 ,nz±3 ,ml] for single-particle levels near the Fermi surfaces as it provides a good manifestation of the octupole correlation. Furthermore, the systematics of deformations, pairing gaps, and the specific heat as functions of temperature for even-even Cm-304286 isotopes are discussed. Similar to the relation between the critical pairing transition temperature and the pairing gap at zero temperature Tc=0.6 Δ (0 ) , a proportional relation between the critical shape transition temperature and the deformation at zero temperature Tc=6.6 β (0 ) is found for both octupole shape transition and quadrupole shape transition for the isotopes considered.

Variance in population firing rate as a measure of slow time-scale correlation

PubMed Central

Snyder, Adam C.; Morais, Michael J.; Smith, Matthew A.

2013-01-01

Correlated variability in the spiking responses of pairs of neurons, also known as spike count correlation, is a key indicator of functional connectivity and a critical factor in population coding. Underscoring the importance of correlation as a measure for cognitive neuroscience research is the observation that spike count correlations are not fixed, but are rather modulated by perceptual and cognitive context. Yet while this context fluctuates from moment to moment, correlation must be calculated over multiple trials. This property undermines its utility as a dependent measure for investigations of cognitive processes which fluctuate on a trial-to-trial basis, such as selective attention. A measure of functional connectivity that can be assayed on a moment-to-moment basis is needed to investigate the single-trial dynamics of populations of spiking neurons. Here, we introduce the measure of population variance in normalized firing rate for this goal. We show using mathematical analysis, computer simulations and in vivo data how population variance in normalized firing rate is inversely related to the latent correlation in the population, and how this measure can be used to reliably classify trials from different typical correlation conditions, even when firing rate is held constant. We discuss the potential advantages for using population variance in normalized firing rate as a dependent measure for both basic and applied neuroscience research. PMID:24367326

Interactome analysis of longitudinal pharyngeal infection of cynomolgus macaques by group A Streptococcus.

PubMed

Shea, Patrick R; Virtaneva, Kimmo; Kupko, John J; Porcella, Stephen F; Barry, William T; Wright, Fred A; Kobayashi, Scott D; Carmody, Aaron; Ireland, Robin M; Sturdevant, Daniel E; Ricklefs, Stacy M; Babar, Imran; Johnson, Claire A; Graham, Morag R; Gardner, Donald J; Bailey, John R; Parnell, Michael J; Deleo, Frank R; Musser, James M

2010-03-09

Relatively little is understood about the dynamics of global host-pathogen transcriptome changes that occur during bacterial infection of mucosal surfaces. To test the hypothesis that group A Streptococcus (GAS) infection of the oropharynx provokes a distinct host transcriptome response, we performed genome-wide transcriptome analysis using a nonhuman primate model of experimental pharyngitis. We also identified host and pathogen biological processes and individual host and pathogen gene pairs with correlated patterns of expression, suggesting interaction. For this study, 509 host genes and seven biological pathways were differentially expressed throughout the entire 32-day infection cycle. GAS infection produced an initial widespread significant decrease in expression of many host genes, including those involved in cytokine production, vesicle formation, metabolism, and signal transduction. This repression lasted until day 4, at which time a large increase in expression of host genes was observed, including those involved in protein translation, antigen presentation, and GTP-mediated signaling. The interactome analysis identified 73 host and pathogen gene pairs with correlated expression levels. We discovered significant correlations between transcripts of GAS genes involved in hyaluronic capsule production and host endocytic vesicle formation, GAS GTPases and host fibrinolytic genes, and GAS response to interaction with neutrophils. We also identified a strong signal, suggesting interaction between host gammadelta T cells and genes in the GAS mevalonic acid synthesis pathway responsible for production of isopentenyl-pyrophosphate, a short-chain phospholipid that stimulates these T cells. Taken together, our results are unique in providing a comprehensive understanding of the host-pathogen interactome during mucosal infection by a bacterial pathogen.

The Choice of PCR Primers Has Great Impact on Assessments of Bacterial Community Diversity and Dynamics in a Wastewater Treatment Plant

PubMed Central

Fredriksson, Nils Johan; Hermansson, Malte; Wilén, Britt-Marie

2013-01-01

Assessments of bacterial community diversity and dynamics are fundamental for the understanding of microbial ecology as well as biotechnological applications. We show that the choice of PCR primers has great impact on the results of analyses of diversity and dynamics using gene libraries and DNA fingerprinting. Two universal primer pairs targeting the 16S rRNA gene, 27F&1492R and 63F&M1387R, were compared and evaluated by analyzing the bacterial community in the activated sludge of a large-scale wastewater treatment plant. The two primer pairs targeted distinct parts of the bacterial community, none encompassing the other, both with similar richness. Had only one primer pair been used, very different conclusions had been drawn regarding dominant phylogenetic and putative functional groups. With 27F&1492R, Betaproteobacteria would have been determined to be the dominating taxa while 63F&M1387R would have described Alphaproteobacteria as the most common taxa. Microscopy and fluorescence in situ hybridization analysis showed that both Alphaproteobacteria and Betaproteobacteria were abundant in the activated sludge, confirming that the two primer pairs target two different fractions of the bacterial community. Furthermore, terminal restriction fragment polymorphism analyses of a series of four activated sludge samples showed that the two primer pairs would have resulted in different conclusions about community stability and the factors contributing to changes in community composition. In conclusion, different PCR primer pairs, although considered universal, target different ranges of bacteria and will thus show the diversity and dynamics of different fractions of the bacterial community in the analyzed sample. We also show that while a database search can serve as an indicator of how universal a primer pair is, an experimental assessment is necessary to evaluate the suitability for a specific environmental sample. PMID:24098498

The influence of pairing correlations on the isospin symmetry breaking corrections of superallowed Fermi beta decays

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

Cal Latin-Small-Letter-Dotless-I k, A. E., E-mail: engincalik@yahoo.com; Gerceklioglu, M.; Selam, C.

2013-05-15

Within the framework of quasi-particle random phase approximation, the isospin breaking correction of superallowed 0{sup +} {yields} 0{sup +} beta decay and unitarity of Cabibbo-Kobayashi-Maskawa mixing matrix have been investigated. The broken isotopic symmetry of nuclear part of Hamiltonian has been restored by Pyatov's method. The isospin symmetry breaking correction with pairing correlations has been compared with the previous results without pairing. The effect of pairing interactions has been examined for nine superallowed Fermi beta decays; their parent nuclei are {sup 26}Al, {sup 34}Cl, {sup 38}K, {sup 42}Sc, {sup 46}V, {sup 50}Mn, {sup 54}Co, {sup 62}Ga, {sup 74}Rb.

Digging into the Elusive Localised Solutions of (2+1) Dimensional sine-Gordon Equation

NASA Astrophysics Data System (ADS)

Radha, R.; Senthil Kumar, C.

2018-05-01

In this paper, we revisit the (2+1) dimensional sine-Gordon equation analysed earlier [R. Radha and M. Lakshmanan, J. Phys. A Math. Gen. 29, 1551 (1996)] employing the Truncated Painlevé Approach. We then generate the solutions in terms of lower dimensional arbitrary functions of space and time. By suitably harnessing the arbitrary functions present in the closed form of the solution, we have constructed dromion solutions and studied their collisional dynamics. We have also constructed dromion pairs and shown that the dynamics of the dromion pairs can be turned ON or OFF desirably. In addition, we have also shown that the orientation of the dromion pairs can be changed. Apart from the above classes of solutions, we have also generated compactons, rogue waves and lumps and studied their dynamics.

Correlation between three color coordinates of human teeth.

PubMed

Lee, Yong-Keun

2014-11-01

The objective was to determine whether there were significant correlations in the three color coordinates within each of two color coordinate systems, such as the Commission Internationale de l’Eclairage (CIE) L*a*b* system, and the lightness, chroma, and hue angle system, of human vital teeth. The color of six maxillary and six mandibular anterior teeth was measured by the Shade Vision System. Pearson correlations between each pair of the color coordinates were determined (α=0.01 ). The influence of two color coordinates on the other color coordinate was determined with a multiple regression analysis (α=0.01 ). Based on correlation analyses, all the color coordinate pairs showed significant correlations except for the chroma and hue angle pair. The CIE L* was negatively correlated with the CIE a*,b*, and chroma, but positively correlated with the hue angle. The CIE a* was positively correlated with the CIE b* and chroma. Tooth color coordinates were correlated each other. Lighter teeth were less chromatic both in the CIE a* and b* coordinates. Therefore, it was postulated that the three color coordinates of human teeth were harmonized within certain color attribute ranges, and a lack of correlations in these coordinates might indicate external/internal discolorations and/or anomalies of teeth.

Correlation between three color coordinates of human teeth

NASA Astrophysics Data System (ADS)

Lee, Yong-Keun

2014-11-01

The objective was to determine whether there were significant correlations in the three color coordinates within each of two color coordinate systems, such as the Commission Internationale de l'Eclairage (CIE) L*a*b* system, and the lightness, chroma, and hue angle system, of human vital teeth. The color of six maxillary and six mandibular anterior teeth was measured by the Shade Vision System. Pearson correlations between each pair of the color coordinates were determined (α=0.01). The influence of two color coordinates on the other color coordinate was determined with a multiple regression analysis (α=0.01). Based on correlation analyses, all the color coordinate pairs showed significant correlations except for the chroma and hue angle pair. The CIE L* was negatively correlated with the CIE a*, b*, and chroma, but positively correlated with the hue angle. The CIE a* was positively correlated with the CIE b* and chroma. Tooth color coordinates were correlated each other. Lighter teeth were less chromatic both in the CIE a* and b* coordinates. Therefore, it was postulated that the three color coordinates of human teeth were harmonized within certain color attribute ranges, and a lack of correlations in these coordinates might indicate external/internal discolorations and/or anomalies of teeth.