Multidetector Scattering as a Probe of Local Structure in Disordered Phases

NASA Astrophysics Data System (ADS)

Clark, Noel A.; Ackerson, Bruce J.; Hurd, Alan J.

1983-05-01

The local translational structure of a two-dimensional colloidal liquid is observed by use of cross correlation of the intensity fluctuations of light scattered by the liquid through two different wave vectors. The utility of multidetector scattering in probing multipoint correlations in disordered phases is thereby demonstrated unambiguously.

Confined semiflexible polymers suppress fluctuations of soft membrane tubes.

PubMed

Mirzaeifard, Sina; Abel, Steven M

2016-02-14

We use Monte Carlo computer simulations to investigate tubular membrane structures with and without semiflexible polymers confined inside. At small values of membrane bending rigidity, empty fluid and non-fluid membrane tubes exhibit markedly different behavior, with fluid membranes adopting irregular, highly fluctuating shapes and non-fluid membranes maintaining extended tube-like structures. Fluid membranes, unlike non-fluid membranes, exhibit a local maximum in specific heat as their bending rigidity increases. The peak is coincident with a transition to extended tube-like structures. We further find that confining a semiflexible polymer within a fluid membrane tube reduces the specific heat of the membrane, which is a consequence of suppressed membrane shape fluctuations. Polymers with a sufficiently large persistence length can significantly deform the membrane tube, with long polymers leading to localized bulges in the membrane that accommodate regions in which the polymer forms loops. Analytical calculations of the energies of idealized polymer-membrane configurations provide additional insight into the formation of polymer-induced membrane deformations.

Nuclear quantum fluctuations in ice I(h).

PubMed

Moreira, Pedro Augusto Franco Pinheiro; de Koning, Maurice

2015-10-14

We discuss the role of nuclear quantum fluctuations in ice Ih, focusing on the hydrogen-bond (HB) structure and the molecular dipole-moment distribution. For this purpose we carry out DFT-based first-principles molecular dynamics and path-integral molecular dynamics simulations at T = 100 K. We analyze the HB structure in terms of a set of parameters previously employed to characterize molecular structures in the liquid phase and compute the molecular dipole moments using the maximally-localized Wannier functions. The results show that the protons experience very large digressions driven by quantum fluctuations, accompanied by major rearrangements in the electronic density. As a result of these protonic quantum fluctuations the molecular dipole-moment distribution is substantially broadened as well as shifted to a larger mean value when compared to the results obtained when such fluctuations are neglected. In terms of dielectric constants, the reconciliation between the greater mean dipole moment and experimental indications that the dielectric constant of H2O ice is lower than that of D2O ice would indicate that the topology of the HB network is sensitive to protonic quantum fluctuations.

The relation between skin friction fluctuations and turbulent fluctuating velocities in turbulent boundary layers

NASA Astrophysics Data System (ADS)

Diaz Daniel, Carlos; Laizet, Sylvain; Vassilicos, John Christos

2015-11-01

The Townsend-Perry hypothesis of wall-attached eddies relates the friction velocity uτ at the wall to velocity fluctuations at a position y from the wall, resulting in a wavenumber range where the streamwise fluctuating velocity spectrum scales as E (k) ~k-1 and the corresponding structure function scales as uτ2 in the corresponding length-scale range. However, this model does not take in account the fluctuations of the skin friction velocity, which are in fact strongly intermittent. A DNS of zero-pressure gradient turbulent boundary layer suggests a 10 to 15 degree angle from the lag of the peak in the cross-correlations between the fluctuations of the shear stress and streamwise fluctuating velocities at different heights in the boundary layer. Using this result, it is possible to refine the definition of the attached eddy range of scales, and our DNS suggests that, in this range, the second order structure function depends on filtered skin friction fluctuations in a way which is about the same at different distances from the wall and different local Reynolds numbers.

Complexity Induced Anisotropic Bimodal Intermittent Turbulence in Space Plasmas

NASA Technical Reports Server (NTRS)

Chang, Tom; Tam, Sunny W. Y.; Wu, Cheng-Chin

2004-01-01

The "physics of complexity" in space plasmas is the central theme of this exposition. It is demonstrated that the sporadic and localized interactions of magnetic coherent structures arising from the plasma resonances can be the source for the coexistence of nonpropagating spatiotemporal fluctuations and propagating modes. Non-Gaussian probability distribution functions of the intermittent fluctuations from direct numerical simulations are obtained and discussed. Power spectra and local intermittency measures using the wavelet analyses are presented to display the spottiness of the small-scale turbulent fluctuations and the non-uniformity of coarse-grained dissipation that can lead to magnetic topological reconfigurations. The technique of the dynamic renormalization group is applied to the study of the scaling properties of such type of multiscale fluctuations. Charged particle interactions with both the propagating and nonpropagating portions of the intermittent turbulence are also described.

NMR evidence for static local nematicity and its cooperative interplay with low-energy magnetic fluctuations in FeSe under pressure

DOE PAGES

Wiecki, P.; Nandi, M.; Bohmer, Anna; ...

2017-11-13

Here, we present 77Se -NMR measurements on single-crystalline FeSe under pressures up to 2 GPa. Based on the observation of the splitting and broadening of the NMR spectrum due to structural twin domains, we discovered that static, local nematic ordering exists well above the bulk nematic ordering temperature, T s. The static, local nematic order and the low-energy stripe-type antiferromagnetic spin fluctuations, as revealed by NMR spin-lattice relaxation rate measurements, are both insensitive to pressure application. Our NMR results provide clear evidence for the microscopic cooperation between magnetism and local nematicity in FeSe.

NMR evidence for static local nematicity and its cooperative interplay with low-energy magnetic fluctuations in FeSe under pressure

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

Wiecki, P.; Nandi, M.; Bohmer, Anna

Here, we present 77Se -NMR measurements on single-crystalline FeSe under pressures up to 2 GPa. Based on the observation of the splitting and broadening of the NMR spectrum due to structural twin domains, we discovered that static, local nematic ordering exists well above the bulk nematic ordering temperature, T s. The static, local nematic order and the low-energy stripe-type antiferromagnetic spin fluctuations, as revealed by NMR spin-lattice relaxation rate measurements, are both insensitive to pressure application. Our NMR results provide clear evidence for the microscopic cooperation between magnetism and local nematicity in FeSe.

Effects of experimentally measured pressure oscillations on the vibration of a solid rocket motor

NASA Technical Reports Server (NTRS)

Schoenster, J. A.; Pierce, H. B.

1972-01-01

Results are presented of firing a Nike rocket against a backstop for the purpose of obtaining pressure fluctuations in the rocket case and determining their relationship to structural vibrations of the case. Special care was required to obtain these pressure fluctuations because of the much higher static pressure generated in the rocket. Very small pressure fluctuations within the rocket case can cause significant vibration levels. A previously observed high frequency was shown to decrease with time before completely disappearing at about 1 second of burning time. The vibration of the case itself is probably related to the longitudinal structural modes at frequencies below 500 Hz and is dependent on local structural conditions at frequencies above this value.

Density Fluctuations in the Solar Wind Driven by Alfvén Wave Parametric Decay

NASA Astrophysics Data System (ADS)

Bowen, Trevor A.; Badman, Samuel; Hellinger, Petr; Bale, Stuart D.

2018-02-01

Measurements and simulations of inertial compressive turbulence in the solar wind are characterized by anti-correlated magnetic fluctuations parallel to the mean field and density structures. This signature has been interpreted as observational evidence for non-propagating pressure balanced structures, kinetic ion-acoustic waves, as well as the MHD slow-mode. Given the high damping rates of parallel propagating compressive fluctuations, their ubiquity in satellite observations is surprising and suggestive of a local driving process. One possible candidate for the generation of compressive fluctuations in the solar wind is the Alfvén wave parametric instability. Here, we test the parametric decay process as a source of compressive waves in the solar wind by comparing the collisionless damping rates of compressive fluctuations with growth rates of the parametric decay instability daughter waves. Our results suggest that generation of compressive waves through parametric decay is overdamped at 1 au, but that the presence of slow-mode-like density fluctuations is correlated with the parametric decay of Alfvén waves.

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

PubMed Central

Yoo, Jejoong; Aksimentiev, Aleksei

2013-01-01

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

PubMed

Yoo, Jejoong; Aksimentiev, Aleksei

2013-12-10

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

Aspirin locally disrupts the liquid-ordered phase

NASA Astrophysics Data System (ADS)

Alsop, Richard J.; Himbert, Sebastian; Dhaliwal, Alexander; Schmalzl, Karin; Rheinstädter, Maikel C.

2018-02-01

Local structure and dynamics of lipid membranes play an important role in membrane function. The diffusion of small molecules, the curvature of lipids around a protein and the existence of cholesterol-rich lipid domains (rafts) are examples for the membrane to serve as a functional interface. The collective fluctuations of lipid tails, in particular, are relevant for diffusion of membrane constituents and small molecules in and across membranes, and for structure and formation of membrane domains. We studied the effect of aspirin (acetylsalicylic acid, ASA) on local structure and dynamics of membranes composed of dimyristoylphosphocholine (DMPC) and cholesterol. Aspirin is a common analgesic, but is also used in the treatment of cholesterol. Using coherent inelastic neutron scattering experiments and molecular dynamics (MD) simulations, we present evidence that ASA binds to liquid-ordered, raft-like domains and disturbs domain organization and dampens collective fluctuations. By hydrogen-bonding to lipid molecules, ASA forms `superfluid' complexes with lipid molecules that can organize laterally in superlattices and suppress cholesterol's ordering effect.

Band gaps and localization of surface water waves over large-scale sand waves with random fluctuations

NASA Astrophysics Data System (ADS)

Zhang, Yu; Li, Yan; Shao, Hao; Zhong, Yaozhao; Zhang, Sai; Zhao, Zongxi

2012-06-01

Band structure and wave localization are investigated for sea surface water waves over large-scale sand wave topography. Sand wave height, sand wave width, water depth, and water width between adjacent sand waves have significant impact on band gaps. Random fluctuations of sand wave height, sand wave width, and water depth induce water wave localization. However, random water width produces a perfect transmission tunnel of water waves at a certain frequency so that localization does not occur no matter how large a disorder level is applied. Together with theoretical results, the field experimental observations in the Taiwan Bank suggest band gap and wave localization as the physical mechanism of sea surface water wave propagating over natural large-scale sand waves.

Equatorial Density Irregularity Structures at Intermediate Scales and Their Temporal Evolution

NASA Technical Reports Server (NTRS)

Kil, Hyosub; Heelis, R. A.

1998-01-01

We examine high resolution measurements of ion density in the equatorial ionosphere from the AE-E satellite during the years 1977-1981. Structure over spatial scales from 18 km to 200 m is characterized by the spectrum of irregularities at larger and smaller scales and at altitudes above 350 km and below 300 km. In the low-altitude region, only small amplitude large-scale (lambda greater than 5 km) density modulations are often observed, and thus the power spectrum of these density structures exhibits a steep spectral slope at kilometer scales. In the high-altitude region, sinusoidal density fluctuations, characterized by enhanced power near 1-km scale, are frequently observed during 2000-0200 LT. However, such fluctuations are confined to regions at the edges of larger bubble structures where the average background density is high. Small amplitude irregularity structures, observed at early local time hours, grow rapidly to high-intensity structures in about 90 min. Fully developed structures, which are observed at late local time hours, decay very slowly producing only-small differences in spectral characteristics even 4 hours later. The local time evolution of irregularity structure is investigated by using average statistics for low-(1% less than sigma less than 5%) and high-intensity (sigma greater than 10%) structures. At lower altitudes, little chance in the spectral slope is seen as a function of local time, while at higher attitudes the growth and maintenance of structures near 1 km scales dramatically affects the spectral slope.

Local Orthorhombicity in the Magnetic C 4 Phase of the Hole-Doped Iron-Arsenide Superconductor Sr 1 - x Na x Fe 2 As 2

DOE PAGES

Frandsen, Benjamin A.; Taddei, Keith M.; Yi, Ming; ...

2017-10-30

We report on temperature-dependent pair distribution function measurements of Sr 1-xNa xFe 2As 2, an iron-based superconductor system that contains a magnetic phase with reentrant tetragonal symmetry, known as the magnetic C 4 phase. Quantitative refinements indicate that the instantaneous local structure in the C 4 phase comprises fluctuating orthorhombic regions with a length scale of similar to 2 nm, despite the tetragonal symmetry of the average static structure. Additionally, local orthorhombic fluctuations exist on a similar length scale at temperatures well into the paramagnetic tetragonal phase. Furthermore, these results highlight the exceptionally large nematic susceptibility of iron-based superconductors andmore » have significant implications for the magnetic C 4 phase and the neighboring C 2 and superconducting phases.« less

Local Orthorhombicity in the Magnetic C 4 Phase of the Hole-Doped Iron-Arsenide Superconductor Sr 1 - x Na x Fe 2 As 2

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

Frandsen, Benjamin A.; Taddei, Keith M.; Yi, Ming

We report on temperature-dependent pair distribution function measurements of Sr 1-xNa xFe 2As 2, an iron-based superconductor system that contains a magnetic phase with reentrant tetragonal symmetry, known as the magnetic C 4 phase. Quantitative refinements indicate that the instantaneous local structure in the C 4 phase comprises fluctuating orthorhombic regions with a length scale of similar to 2 nm, despite the tetragonal symmetry of the average static structure. Additionally, local orthorhombic fluctuations exist on a similar length scale at temperatures well into the paramagnetic tetragonal phase. Furthermore, these results highlight the exceptionally large nematic susceptibility of iron-based superconductors andmore » have significant implications for the magnetic C 4 phase and the neighboring C 2 and superconducting phases.« less

Fluctuating exciton localization in giant π-conjugated spoked-wheel macrocycles.

PubMed

Aggarwal, A Vikas; Thiessen, Alexander; Idelson, Alissa; Kalle, Daniel; Würsch, Dominik; Stangl, Thomas; Steiner, Florian; Jester, Stefan-S; Vogelsang, Jan; Höger, Sigurd; Lupton, John M

2013-11-01

Conjugated polymers offer potential for many diverse applications, but we still lack a fundamental microscopic understanding of their electronic structure. Elementary photoexcitations (excitons) span only a few nanometres of a molecule, which itself can extend over microns, and how their behaviour is affected by molecular dimensions is not immediately obvious. For example, where is the exciton formed within a conjugated segment and is it always situated on the same repeat units? Here, we introduce structurally rigid molecular spoked wheels, 6 nm in diameter, as a model of extended π conjugation. Single-molecule fluorescence reveals random exciton localization, which leads to temporally varying emission polarization. Initially, this random localization arises after every photon absorption event because of temperature-independent spontaneous symmetry breaking. These fast fluctuations are slowed to millisecond timescales after prolonged illumination. Intramolecular heterogeneity is revealed in cryogenic spectroscopy by jumps in transition energy, but emission polarization can also switch without a spectral jump occurring, which implies long-range homogeneity in the local dielectric environment.

Fluctuating exciton localization in giant π-conjugated spoked-wheel macrocycles

NASA Astrophysics Data System (ADS)

Aggarwal, A. Vikas; Thiessen, Alexander; Idelson, Alissa; Kalle, Daniel; Würsch, Dominik; Stangl, Thomas; Steiner, Florian; Jester, Stefan-S.; Vogelsang, Jan; Höger, Sigurd; Lupton, John M.

2013-11-01

Conjugated polymers offer potential for many diverse applications, but we still lack a fundamental microscopic understanding of their electronic structure. Elementary photoexcitations (excitons) span only a few nanometres of a molecule, which itself can extend over microns, and how their behaviour is affected by molecular dimensions is not immediately obvious. For example, where is the exciton formed within a conjugated segment and is it always situated on the same repeat units? Here, we introduce structurally rigid molecular spoked wheels, 6 nm in diameter, as a model of extended π conjugation. Single-molecule fluorescence reveals random exciton localization, which leads to temporally varying emission polarization. Initially, this random localization arises after every photon absorption event because of temperature-independent spontaneous symmetry breaking. These fast fluctuations are slowed to millisecond timescales after prolonged illumination. Intramolecular heterogeneity is revealed in cryogenic spectroscopy by jumps in transition energy, but emission polarization can also switch without a spectral jump occurring, which implies long-range homogeneity in the local dielectric environment.

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

Mechanism of the high transition temperature for the 1111-type iron-based superconductors R FeAsO (R =rare earth ): Synergistic effects of local structures and 4 f electrons

NASA Astrophysics Data System (ADS)

Zhang, Lifang; Meng, Junling; Liu, Xiaojuan; Yao, Fen; Meng, Jian; Zhang, Hongjie

2017-07-01

Among the iron-based superconductors, the 1111-type Fe-As-based superconductors REFeAs O1 -xFx (RE = rare earth) exhibit high transition temperatures (Tc) above 40 K. We perform first-principles calculations based on density functional theory with the consideration of both electronic correlations and spin-orbit couplings on rare earths and Fe ions to study the underlying mechanism as the microscopic structural distortions in REFeAsO tuned by both lanthanide contraction and external strain. The electronic structures evolve similarly in both cases. It is found that there exist an optimal structural regime that will not only initialize but also optimize the orbital fluctuations due to the competing Fe-As and Fe-Fe crystal fields. We also find that the key structural features in REFeAsO, such as As-Fe-As bond angle, intrinsically induce the modification of the Fermi surface and dynamic spin fluctuation. These results suggest that the superconductivity is mediated by antiferromagnetic spin fluctuations. Simultaneously, we show that the rare-earth 4 f electrons play important roles on the high transition temperature whose behavior might be analogous to that of the heavy-fermion superconductors. The superconductivity of these 1111-type iron-based superconductors with high-Tc is considered to originate from the synergistic effects of local structures and 4 f electrons.

Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations

PubMed Central

Szczurek, Aleksander; Klewes, Ludger; Xing, Jun; Gourram, Amine; Birk, Udo; Knecht, Hans; Dobrucki, Jurek W.; Mai, Sabine

2017-01-01

Abstract Advanced light microscopy is an important tool for nanostructure analysis of chromatin. In this report we present a general concept for Single Molecule localization Microscopy (SMLM) super-resolved imaging of DNA-binding dyes based on modifying the properties of DNA and the dye. By careful adjustment of the chemical environment leading to local, reversible DNA melting and hybridization control over the fluorescence signal of the DNA-binding dye molecules can be introduced. We postulate a transient binding as the basis for our variation of binding-activated localization microscopy (BALM). We demonstrate that several intercalating and minor-groove binding DNA dyes can be used to register (optically isolate) only a few DNA-binding dye signals at a time. To highlight this DNA structure fluctuation-assisted BALM (fBALM), we applied it to measure, for the first time, nanoscale differences in nuclear architecture in model ischemia with an anticipated structural resolution of approximately 50 nm. Our data suggest that this approach may open an avenue for the enhanced microscopic analysis of chromatin nano-architecture and hence the microscopic analysis of nuclear structure aberrations occurring in various pathological conditions. It may also become possible to analyse nuclear nanostructure differences in different cell types, stages of development or environmental stress conditions. PMID:28082388

Scaling laws from geomagnetic time series

USGS Publications Warehouse

Voros, Z.; Kovacs, P.; Juhasz, A.; Kormendi, A.; Green, A.W.

1998-01-01

The notion of extended self-similarity (ESS) is applied here for the X - component time series of geomagnetic field fluctuations. Plotting nth order structure functions against the fourth order structure function we show that low-frequency geomagnetic fluctuations up to the order n = 10 follow the same scaling laws as MHD fluctuations in solar wind, however, for higher frequencies (f > l/5[h]) a clear departure from the expected universality is observed for n > 6. ESS does not allow to make an unambiguous statement about the non triviality of scaling laws in "geomagnetic" turbulence. However, we suggest to use higher order moments as promising diagnostic tools for mapping the contributions of various remote magnetospheric sources to local observatory data. Copyright 1998 by the American Geophysical Union.

On the structure of pressure fluctuations in simulated turbulent channel flow

NASA Technical Reports Server (NTRS)

Kim, John

1989-01-01

Pressure fluctuations in a turbulent channel flow are investigated by analyzing a database obtained from a direct numerical simulation. Detailed statistics associated with the pressure fluctuations are presented. Characteristics associated with the rapid (linear) and slow (nonlinear) pressure are discussed. It is found that the slow pressure fluctuations are larger than the rapid pressure fluctuations throughout the channel except very near the wall, where they are about the same magnitude. This is contrary to the common belief that the nonlinear source terms are negligible compared to the linear source terms. Probability density distributions, power spectra, and two-point correlations are examined to reveal the characteristics of the pressure fluctuations. The global dependence of the pressure fluctuations and pressure-strain correlations are also examined by evaluating the integral associated with Green's function representations of them. In the wall region where the pressure-strain terms are large, most contributions to the pressure-strain terms are from the wall region (i.e., local), whereas away from the wall where the pressure-strain terms are small, contributions are global. Structures of instantaneous pressure and pressure gradients at the wall and the corresponding vorticity field are examined.

Stability of mechanical joints in launching vehicles: Local and global stationary values of energy density

NASA Astrophysics Data System (ADS)

Chue, Ching-Hwei

A method was developed for predicting the behavior of mechanical joints in launch vehicles with particular emphasis placed on how the combined effects of loading, geometry, and materials could be optimized in terms of structure instability and/or integrity. What was considered to be essential is the fluctuation of the volume energy density with time in the structure. The peaks and valleys of the volume energy density function will be associated with failure by fracture and/or yielding while the distance between their local and global stationary values govern the structure instability. The Solid Rocket Booster (SRB) of the space shuttle was analyzed under axisymmetric and non-axisymmetric loadings. A semi-analytical finite element program was developed for solving the case of non-axisymmetric loading. Following a dynamic stress analysis, contours of the volume energy density in the structure were obtained as a function of time. The magnitudes and locations of these stationary values were then calculated locally and globally and related to possible failure by fracture. In the case of axisymmetric flight, the local and global instability behavior do not change appreciably. Fluctuations in the energy density and the dynamic stability length parameter become appreciable when the non-axisymmetric loads are considered. The magnitude of the energy in the shell structure is sensitive to alterations in the gas pressure induced by the solid propellant.

Fluctuating ideal-gas lattice Boltzmann method with fluctuation dissipation theorem for nonvanishing velocities.

PubMed

Kaehler, G; Wagner, A J

2013-06-01

Current implementations of fluctuating ideal-gas descriptions with the lattice Boltzmann methods are based on a fluctuation dissipation theorem, which, while greatly simplifying the implementation, strictly holds only for zero mean velocity and small fluctuations. We show how to derive the fluctuation dissipation theorem for all k, which was done only for k=0 in previous derivations. The consistent derivation requires, in principle, locally velocity-dependent multirelaxation time transforms. Such an implementation is computationally prohibitively expensive but, with a small computational trick, it is feasible to reproduce the correct FDT without overhead in computation time. It is then shown that the previous standard implementations perform poorly for non vanishing mean velocity as indicated by violations of Galilean invariance of measured structure factors. Results obtained with the method introduced here show a significant reduction of the Galilean invariance violations.

The seesaw space, a vector space to identify and characterize large-scale structures at 1 AU

NASA Astrophysics Data System (ADS)

Lara, A.; Niembro, T.

2017-12-01

We introduce the seesaw space, an orthonormal space formed by the local and the global fluctuations of any of the four basic solar parameters: velocity, density, magnetic field and temperature at any heliospheric distance. The fluctuations compare the standard deviation of a moving average of three hours against the running average of the parameter in a month (consider as the local fluctuations) and in a year (global fluctuations) We created this new vectorial spaces to identify the arrival of transients to any spacecraft without the need of an observer. We applied our method to the one-minute resolution data of WIND spacecraft from 1996 to 2016. To study the behavior of the seesaw norms in terms of the solar cycle, we computed annual histograms and fixed piecewise functions formed by two log-normal distributions and observed that one of the distributions is due to large-scale structures while the other to the ambient solar wind. The norm values in which the piecewise functions change vary in terms of the solar cycle. We compared the seesaw norms of each of the basic parameters due to the arrival of coronal mass ejections, co-rotating interaction regions and sector boundaries reported in literature. High seesaw norms are due to large-scale structures. We found three critical values of the norms that can be used to determined the arrival of coronal mass ejections. We present as well general comparisons of the norms during the two maxima and the minimum solar cycle periods and the differences of the norms due to large-scale structures depending on each period.

Simulation of turbulence in the divertor region of tokamak edge plasma

NASA Astrophysics Data System (ADS)

Umansky, M. V.; Rognlien, T. D.; Xu, X. Q.

2005-03-01

Results are presented for turbulence simulations with the fluid edge turbulence code BOUT [X.Q. Xu, R.H. Cohen, Contr. Plas. Phys. 36 (1998) 158]. The present study is focussed on turbulence in the divertor leg region and on the role of the X-point in the structure of turbulence. Results of the present calculations indicate that the ballooning effects are important for the divertor fluctuations. The X-point shear leads to weak correlation of turbulence across the X-point regions, in particular for large toroidal wavenumber. For the saturated amplitudes of the divertor region turbulence it is found that amplitudes of density fluctuations are roughly proportional to the local density of the background plasma. The amplitudes of electron temperature and electric potential fluctuations are roughly proportional to the local electron temperature of the background plasma.

Quantification of Nanoscale Density Fluctuations in Biological Cells/Tissues: Inverse Participation Ratio (IPR) Analysis of Transmission Electron Microscopy Images and Implications for Early-Stage Cancer Detection

NASA Astrophysics Data System (ADS)

Pradhan, Prabhakar; Damania, Dhwanil; Joshi, Hrushikesh; Taflove, Allen; Roy, Hemant; Dravid, Vinayak; Backman, Vadim

2010-03-01

We report a study of the nanoscale mass density fluctuations of biological cells and tissues by quantifying their nanoscale light-localization properties. Transmission electron microscope (TEM) images of human cells and tissues are used to construct corresponding effective disordered optical lattices. Light-localization properties are studied by statistical analysis of the inverse participation ratio (IPR) of the eigenfunctions of these optical lattices at the nanoscales. Our results indicate elevation of the nanoscale disorder strength (e.g., refractive index fluctuations) in early carcinogenesis. Importantly, our results demonstrate that the increase in the nanoscale disorder represents the earliest structural alteration in cells undergoing carcinogenesis known to-date. Potential applications of the technique for early stage cancer detection will be discussed.

Complexity and Intermittent Turbulence in Space Plasmas

NASA Technical Reports Server (NTRS)

Chang, Tom; Tam, Sunny W. Y.; Wu, Cheng-Chin

2004-01-01

Sporadic and localized interactions of coherent structures arising from plasma resonances can be the origin of "complexity" of the coexistence of non- propagating spatiotemporal fluctuations and propagating modes in space plasmas. Numerical simulation results are presented to demonstrate the intermittent character of the non-propagating fluctuations. The technique of the dynamic renormalization-group is introduced and applied to the study of scale invariance of such type of multiscale fluctuations. We also demonstrate that the particle interactions with the intermittent turbulence can lead to the efficient energization of the plasma populations. An example related to the ion acceleration processes in the auroral zone is provided.

Constancy and asynchrony of Osmoderma eremita populations in tree hollows.

PubMed

Ranius, Thomas

2001-01-01

A species rich beetle fauna is associated with old, hollow trees. Many of these species are regarded as endangered, but there is little understanding of the population structure and extinction risks of these species. In this study I show that one of the most endangered beetles, Osmoderma eremita, has a population structure which conforms to that of a metapopulation, with each tree possibly sustaining a local population. This was revealed by performing a mark-release-recapture experiment in 26 trees over a 5-year period. The spatial variability between trees was much greater than temporal variability between years. The population size was on average 11 adults tree -1 year -1 , but differed widely between trees (0-85 adults tree -1 year -1 ). The population size in each tree varied moderately between years [mean coefficient of variation (C.V.)=0.51], but more widely than from sampling errors alone (P=0.008, Monte Carlo simulation). The population size variability in all trees combined, however, was not larger than expected from sampling errors alone in a constant population (C.V.=0.15, P=0.335, Monte Carlo simulation). Thus, the fluctuations of local populations cancel each other out when they are added together. This pattern can arise only when the fluctuations occur asynchronously between trees. The asynchrony of the fluctuations justifies the assumption usually made in metapopulation modelling, that local populations within a metapopulation fluctuate independently of one another. The asynchrony might greatly increase persistence time at the metapopulation level (per stand), compared to the local population level (per tree). The total population size of O. eremita in the study area was estimated to be 3,900 individuals. Other localities sustaining O. eremita are smaller in area, and most of these must be enlarged to allow long-term metapopulation persistence and to satisfy genetic considerations of the O. eremita populations.

Role of critical fluctuations in the formation of a skyrmion lattice in MnSi

NASA Astrophysics Data System (ADS)

Chubova, N. M.; Moskvin, E. V.; Dyad'kin, V. A.; Dewhurst, Ch.; Maleev, S. V.; Grigor'ev, S. V.

2017-11-01

The region in the H- T phase diagram near the critical temperature ( T c ) of the cubic helicoidal MnSi magnet is comprehensively studied by small-angle neutron diffraction. Magnetic field H is applied along the [111] axis. The experimental geometry is chosen to simultaneously observe the following three different magnetic states of the system: (a) critical fluctuations of a spin spiral with randomly orientated wavevector k f , (b) conical structure with k c ǁ H, and (c) hexagonal skyrmion lattice with k sk ⊥ H. Both states (conical structure, and skyrmion lattice) are shown to exist above critical temperature T c = 29 K against the background of the critical fluctuations of a spin spiral. The conical lattice is present up to the temperatures where fluctuation correlation length ξ becomes comparable with pitch of spiral d s . The skyrmion lattice is localized near T c and is related to the fluctuations of a spiral with correlation length ξ ≈ 2 d s , and the propagation vector is normal to the field ( k sk ⊥ H). These spiral fluctuations are assumed to be the defects that stabilize the skyrmion lattice and promote its formation.

Correlating Structural Order with Structural Rearrangement in Dusty Plasma Liquids: Can Structural Rearrangement be Predicted by Static Structural Information?

NASA Astrophysics Data System (ADS)

Su, Yen-Shuo; Liu, Yu-Hsuan; I, Lin

2012-11-01

Whether the static microstructural order information is strongly correlated with the subsequent structural rearrangement (SR) and their predicting power for SR are investigated experimentally in the quenched dusty plasma liquid with microheterogeneities. The poor local structural order is found to be a good alarm to identify the soft spot and predict the short term SR. For the site with good structural order, the persistent time for sustaining the structural memory until SR has a large mean value but a broad distribution. The deviation of the local structural order from that averaged over nearest neighbors serves as a good second alarm to further sort out the short time SR sites. It has the similar sorting power to that using the temporal fluctuation of the local structural order over a small time interval.

Investigating the radial structure of axisymmetric fluctuations in the TCV tokamak with local and global gyrokinetic GENE simulations

NASA Astrophysics Data System (ADS)

Merlo, G.; Brunner, S.; Huang, Z.; Coda, S.; Görler, T.; Villard, L.; Bañón Navarro, A.; Dominski, J.; Fontana, M.; Jenko, F.; Porte, L.; Told, D.

2018-03-01

Axisymmetric (n = 0) density fluctuations measured in the TCV tokamak are observed to possess a frequency f 0 which is either varying (radially dispersive oscillations) or a constant over a large fraction of the plasma minor radius (radially global oscillations) as reported in a companion paper (Z Huang et al, this issue). Given that f 0 scales with the sound speed and given the poloidal structure of density fluctuations, these oscillations were interpreted as Geodesic Acoustic Modes, even though f 0 is in fact smaller than the local linear GAM frequency {f}{GAM}. In this work we employ the Eulerian gyrokinetic code GENE to simulate TCV relevant conditions and investigate the nature and properties of these oscillations, in particular their relation to the safety factor profile. Local and global simulations are carried out and a good qualitative agreement is observed between experiments and simulations. By varying also the plasma temperature and density profiles, we conclude that a variation of the edge safety factor alone is not sufficient to induce a transition from global to radially inhomogeneous oscillations, as was initially suggested by experimental results. This transition appears instead to be the combined result of variations in the different plasma profiles, collisionality and finite machine size effects. Simulations also show that radially global GAM-like oscillations can be observed in all fluxes and fluctuation fields, suggesting that they are the result of a complex nonlinear process involving also finite toroidal mode numbers and not just linear global GAM eigenmodes.

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

Li, Rong; Wu, Yongquan, E-mail: yqwu@shu.edu.cn; Xiao, Junjiang

We observed homogeneous nucleation process of supercooled liquid Fe by molecular dynamics simulations. Using bond-orientational order parameters together with Voronoi polyhedron method, we characterized local structure, calculated the volume of Voronoi polyhedra of atoms and identified the structure and density fluctuations. We monitored the formation of nucleus and analyzed its inner structure. The birth and growth of the pre-nucleus and nucleus are accompanied with aggregating and disaggregating processes in the time scale of femtosecond. Only the initial solid-like clusters (ISLC), ranging from 1 to 7 atoms, pop up directly from liquid. The relation between the logarithm of number of clustersmore » and the cluster size was found to be linear for ISLCs and was observed to be parabolic for all solid-like clusters (SLC) due to aggregating and disaggregating effects. The nucleus and pre-nuclei mainly consist of body centered cubic (BCC) and hexagonal close packed atoms, while the BCC atoms tend to be located at the surface. Medium-range structure fluctuations induce the birth of ISLCs, benefit the aggregation of embryos and remarkably promote the nucleation. But density fluctuations contribute little to nucleation. The lifetime of most icosahedral-like atoms (ICO) is shorter than 0.7 ps. No obvious relationship was found between structure/density fluctuations and the appearance of ICO atoms.« less

Transitions from trees to cycles in adaptive flow networks

NASA Astrophysics Data System (ADS)

Martens, Erik A.; Klemm, Konstantin

2017-11-01

Transport networks are crucial to the functioning of natural and technological systems. Nature features transport networks that are adaptive over a vast range of parameters, thus providing an impressive level of robustness in supply. Theoretical and experimental studies have found that real-world transport networks exhibit both tree-like motifs and cycles. When the network is subject to load fluctuations, the presence of cyclic motifs may help to reduce flow fluctuations and, thus, render supply in the network more robust. While previous studies considered network topology via optimization principles, here, we take a dynamical systems approach and study a simple model of a flow network with dynamically adapting weights (conductances). We assume a spatially non-uniform distribution of rapidly fluctuating loads in the sinks and investigate what network configurations are dynamically stable. The network converges to a spatially non-uniform stable configuration composed of both cyclic and tree-like structures. Cyclic structures emerge locally in a transcritical bifurcation as the amplitude of the load fluctuations is increased. The resulting adaptive dynamics thus partitions the network into two distinct regions with cyclic and tree-like structures. The location of the boundary between these two regions is determined by the amplitude of the fluctuations. These findings may explain why natural transport networks display cyclic structures in the micro-vascular regions near terminal nodes, but tree-like features in the regions with larger veins.

Fractal profit landscape of the stock market.

PubMed

Grönlund, Andreas; Yi, Il Gu; Kim, Beom Jun

2012-01-01

We investigate the structure of the profit landscape obtained from the most basic, fluctuation based, trading strategy applied for the daily stock price data. The strategy is parameterized by only two variables, p and q Stocks are sold and bought if the log return is bigger than p and less than -q, respectively. Repetition of this simple strategy for a long time gives the profit defined in the underlying two-dimensional parameter space of p and q. It is revealed that the local maxima in the profit landscape are spread in the form of a fractal structure. The fractal structure implies that successful strategies are not localized to any region of the profit landscape and are neither spaced evenly throughout the profit landscape, which makes the optimization notoriously hard and hypersensitive for partial or limited information. The concrete implication of this property is demonstrated by showing that optimization of one stock for future values or other stocks renders worse profit than a strategy that ignores fluctuations, i.e., a long-term buy-and-hold strategy.

Specific Features of Pressure-Fluctuation Fields in the Vicinity of a Forward-Facing Step-Backward-Facing Step Configuration

NASA Astrophysics Data System (ADS)

Golubev, A. Yu.

2018-01-01

A computational model of inhomogeneous pressure-fluctuation fields in the vicinity of a forward-facing step-backward-facing step configuration taking into account the high degree of their mutual correlation (global correlation) is generalized from experimental data. It is shown that when determining the characteristics of pressure fluctuations that act on an elastic structure, the global correlation is represented by an additional inhomogeneous field. It is demonstrated that a high degree of correlation may lead to a significant change in the main characteristics of the pressure-fluctuation field in the wake behind the configuration. This is taken into consideration in the model by correcting the local properties of this field.

ECE-imaging of the H-mode pedestal (invited).

PubMed

Tobias, B J; Austin, M E; Boom, J E; Burrell, K H; Classen, I G J; Domier, C W; Luhmann, N C; Nazikian, R; Snyder, P B

2012-10-01

A synthetic diagnostic has been developed that reproduces the highly structured electron cyclotron emission (ECE) spectrum radiated from the edge region of H-mode discharges. The modeled dependence on local perturbations of the equilibrium plasma pressure allows for interpretation of ECE data for diagnosis of local quantities. Forward modeling of the diagnostic response in this region allows for improved mapping of the observed fluctuations to flux surfaces within the plasma, allowing for the poloidal mode number of coherent structures to be resolved. In addition, other spectral features that are dependent on both T(e) and n(e) contain information about pedestal structure and the electron energy distribution of localized phenomena, such as edge filaments arising during edge-localized mode (ELM) activity.

Ultrafast Hydration Dynamics and Coupled Water-Protein Fluctuations in Apomyoglobin

NASA Astrophysics Data System (ADS)

Yang, Yi; Zhang, Luyuan; Wang, Lijuan; Zhong, Dongping

2009-06-01

Protein hydration dynamics are of fundamental importance to its structure and function. Here, we characterize the global solvation dynamics and anisotropy dynamics around the apomyoglobin surface in different conformational states (native and molten globule) by measuring the Stokes shift and anisotropy decay of tryptophan with femtosecond-resolved fluorescence upconversion. With site-directed mutagenesis, we designed sixteen mutants with one tryptophan in each, and placed the probe at a desirable position ranging from buried in the protein core to fully solvent-exposed on the protein surface. In all protein sites studied, two distinct solvation relaxations (1-8 ps and 20-200 ps) were observed, reflecting the initial collective water relaxation and subsequent hydrogen-bond network restructuring, respectively, and both are strongly correlated with protein's local structures and chemical properties. The hydration dynamics of the mutants in molten globule state are faster than those observed in native state, indicating that the protein becomes more flexible and less structured when its conformation is converted from fully-folded native state to partially-folded molten globule state. Complementary, fluorescence anisotropy dynamics of all mutants in native state show an increasing trend of wobbling times (40-260 ps) when the location of the probe is changed from a loop, to a lateral helix, and then, to the compact protein core. Such an increase in wobbling times is related to the local protein structural rigidity, which relates the interaction of water with side chains. The ultrafast hydration dynamics and related side-chain motion around the protein surface unravel the coupled water-protein fluctuations on the picosecond time scales and indicate that the local protein motions are slaved by hydrating water fluctuations.

The structure of evaporating and combusting sprays: Measurements and predictions

NASA Technical Reports Server (NTRS)

Shuen, J. S.; Solomon, A. S. P.; Faeth, F. M.

1983-01-01

The structure of particle-laden jets and nonevaporating and evaporating sprays was measured in order to evaluate models of these processes. Three models are being evaluated: (1) a locally homogeneous flow model, where slip between the phases is neglected and the flow is assumed to be in local thermodynamic equilibrium; (2) a deterministic separated flow model, where slip and finite interphase transport rates are considered but effects of particle/drop dispersion by turbulence and effects of turbulence on interphase transport rates are ignored; and (3) a stochastic separated flow model, where effects of interphase slip, turbulent dispersion and turbulent fluctuations are considered using random sampling for turbulence properties in conjunction with random-walk computations for particle motion. All three models use a k-e-g turbulence model. All testing and data reduction are completed for the particle laden jets. Mean and fluctuating velocities of the continuous phase and mean mixture fraction were measured in the evaporating sprays.

Study of relation between Pc 3 micropulsations and magnetosheath fluctuations, and multisatellite investigation of earth's bow shock

NASA Technical Reports Server (NTRS)

Greenstadt, E. W.

1975-01-01

The validity is investigated of a suggested model according to which Pc 3 and/or Pc 4 micropulsations are excited by magnetosheath field (and plasma) fluctuations arising in the quasi-parallel structure of the subsolar bow shock. The influence of solar wind plasma parameters on local shock structure and on the configuration of the entire bow shock system is included. Simultaneous data from two or more spacecraft and from multiple diagnostics is used to evaluate the geometrical factor, field-to-shock normal angle, or its B-X equivalent, and the principal plasma parameters. Results are presented and discussed.

Charge Fluctuations in the NdO1-xFxBiS2 Superconductors

NASA Astrophysics Data System (ADS)

Athauda, Anushika; Mizuguchi, Yoshikazu; Nagao, Masanori; Neuefeind, Joerg; Louca, Despina

2017-12-01

The local atomic structure of superconducting NdO1-xFxBiS2 (x = 0.2 and 0.4) is investigated using neutron diffraction and the pair density function analysis technique. In the non-superconducting x = 0.2 composition, ferrodistortive displacements of the pyramidal sulfur ions break the tetragonal symmetry and a superlattice structure emerges with peaks appearing at h + k odd reflections superimposed on the even reflections of the P4/nmm symmetry. In the superconducting x = 0.4 composition, similar ferrodistortive displacements are observed but with different magnitudes coupled with in-plane Bi distortions which are indicative of charge fluctuations.

Potential Fluctuations and Localization Effects in CZTS Single Crystals, as Revealed by Optical Spectroscopy

NASA Astrophysics Data System (ADS)

Bleuse, Joël; Ducroquet, Frédérique; Mariette, Henri

2018-03-01

Reports on Cu_2 ZnSn(S_x Se_{1-x} )_4 (CZTSSe) solar cell devices all show an open-circuit voltage lower than expected, especially when compared to CuIn_x Ga_{1-x} (S,Se)_2 devices, which reduces their power efficiency and delays their development. A high concentration of intrinsic defects in CZTSSe, and their stabilization through neutral complex formation, which induces some local fluctuations, are at the origin of local energy shifts in the conduction and valence band edges. The implied band tail in Cu_2 ZnSnS_4 is studied in this work by combining three types of optical spectroscopy data: emission spectra compared to photoluminescence excitation spectroscopy, emission spectra as a function of excitation power, and time-resolved photoluminescence spectra. All these data converge to show that both the bandgap and the band tail of localized states just below are dependent on the degree of order/disorder in the Cu/Zn cation sublattice of the quaternary structure: in the more ordered structures, the bandgap increases by about 50 meV, and the energy range of the band tail is decreased from about 110 to 70 meV.

Localized spiraling plasma ejection contributing the ion-flux broadening in the detached linear plasma

NASA Astrophysics Data System (ADS)

Tanaka, H.; Takeyama, K.; Yoshikawa, M.; Kajita, S.; Ohno, N.; Hayashi, Y.

2018-07-01

We have performed multipoint measurements with segmented electrodes and a microwave interferometer in the linear plasma device NAGDIS-II, in order to reveal cross-field motion and axial localization of the enhanced radial transport in the detached plasma. By changing the neutral pressure successively and applying several statistical analysis techniques, it was clarified that there is axially localized ion flux broadening accompanying an enhanced plasma ejection from the center with radially elongated spiraling structure. The spiraling plasma ejection accompanies the m = 0 mode drop near the center with the similar time scale. Further, such behavior composed of f > 1 kHz fluctuations is modulated by several-hundred-hertz fluctuation with m = 0. This cross-field transport causes non-negligible effect for the reduction of the ion flux peak in the detached plasma.

Stability of synchrony against local intermittent fluctuations in tree-like power grids

NASA Astrophysics Data System (ADS)

Auer, Sabine; Hellmann, Frank; Krause, Marie; Kurths, Jürgen

2017-12-01

90% of all Renewable Energy Power in Germany is installed in tree-like distribution grids. Intermittent power fluctuations from such sources introduce new dynamics into the lower grid layers. At the same time, distributed resources will have to contribute to stabilize the grid against these fluctuations in the future. In this paper, we model a system of distributed resources as oscillators on a tree-like, lossy power grid and its ability to withstand desynchronization from localized intermittent renewable infeed. We find a remarkable interplay of the network structure and the position of the node at which the fluctuations are fed in. An important precondition for our findings is the presence of losses in distribution grids. Then, the most network central node splits the network into branches with different influence on network stability. Troublemakers, i.e., nodes at which fluctuations are especially exciting the grid, tend to be downstream branches with high net power outflow. For low coupling strength, we also find branches of nodes vulnerable to fluctuations anywhere in the network. These network regions can be predicted at high confidence using an eigenvector based network measure taking the turbulent nature of perturbations into account. While we focus here on tree-like networks, the observed effects also appear, albeit less pronounced, for weakly meshed grids. On the other hand, the observed effects disappear for lossless power grids often studied in the complex system literature.

Large-scale structure of randomly jammed spheres

NASA Astrophysics Data System (ADS)

Ikeda, Atsushi; Berthier, Ludovic; Parisi, Giorgio

2017-05-01

We numerically analyze the density field of three-dimensional randomly jammed packings of monodisperse soft frictionless spherical particles, paying special attention to fluctuations occurring at large length scales. We study in detail the two-point static structure factor at low wave vectors in Fourier space. We also analyze the nature of the density field in real space by studying the large-distance behavior of the two-point pair correlation function, of density fluctuations in subsystems of increasing sizes, and of the direct correlation function. We show that such real space analysis can be greatly improved by introducing a coarse-grained density field to disentangle genuine large-scale correlations from purely local effects. Our results confirm that both Fourier and real space signatures of vanishing density fluctuations at large scale are absent, indicating that randomly jammed packings are not hyperuniform. In addition, we establish that the pair correlation function displays a surprisingly complex structure at large distances, which is however not compatible with the long-range negative correlation of hyperuniform systems but fully compatible with an analytic form for the structure factor. This implies that the direct correlation function is short ranged, as we also demonstrate directly. Our results reveal that density fluctuations in jammed packings do not follow the behavior expected for random hyperuniform materials, but display instead a more complex behavior.

Local-structure change rendered by electronic localization-delocalization transition in cerium-based metallic glasses

NASA Astrophysics Data System (ADS)

Luo, Qiang; Schwarz, Björn; Swarbrick, Janine C.; Bednarčik, Jozef; Zhu, Yingcai; Tang, Meibo; Zheng, Lirong; Li, Ran; Shen, Jun; Eckert, Jürgen

2018-02-01

With increasing temperature, metallic glasses (MGs) undergo first glass transition without pronounced structural change and then crystallization with distinct variation in structure and properties. The present study shows a structural change of short-range order induced by an electron-delocalization transition, along with an unusual large-volume shrinkage in Ce-based MGs. An f -electron localization-delocalization transition with thermal hysteresis is observed from the temperature dependence of x-ray absorption spectroscopy and resonant inelastic x-ray scattering spectra, indicating an inheritance of the 4 f configuration of pure Ce. However, the delocalization transition becomes broadened due to the local structural heterogeneity and related fluctuation of 4 f levels in the Ce-based MGs. The amorphous structure regulated 4 f delocalization of Ce leads to bond shortening and abnormal structure change of the topological and chemical short-range orders. Due to the hierarchical bonding nature, the structure should change in a similar manner on different length scales (but not isostructurally like the Ce metal) in Ce-based MGs.

Investigating the radial structure of axisymmetric fluctuations in the TCV tokamak with local and global gyrokinetic GENE simulations

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

Merlo, Gabriele; Brunner, Stephan; Huang, Zhouji

Axisymmetric (n=0) density fluctuations measured in the TCV tokamak are observed to possess a frequency f₀ which is either varying (radially dispersive oscillations) or a constant over a large fraction of the plasma minor radius (radially global oscillations) as reported in a companion paper [Z. Huang et al., this issue]. Given that f₀ scales with the sound speed and given the poloidal structure of density fluctuations, these oscillations were interpreted as Geodesic Acoustic Modes, even though f₀ is in fact smaller than the local linear GAM frequency f_GAM . In this work we employ the Eulerian gyrokinetic code GENE tomore » simulate TCV relevant conditions and investigate the nature properties of these oscillations, in particular their relation to the safety factor profile. Local and global simulations are carried out and a good qualitative agreement is observed between experiments and simulations. By varying also the plasma temperature and density profiles, we conclude that a variation of the edge safety factor alone is not sufficient to induce a transition from global to radially inhomogeneous oscillations, as was initially suggested by experimental results. This transition appears instead to be the combined result of variations in the different plasma profiles, collisionality and finite machine size effects. In conclusion, simulations also show that radially global GAM-like oscillations can be observed in all fluxes and fluctuation fields, suggesting that they are the result of a complex nonlinear process involving also finite toroidal mode numbers and not just linear global GAM eigenmodes.« less

Investigating the radial structure of axisymmetric fluctuations in the TCV tokamak with local and global gyrokinetic GENE simulations

DOE PAGES

Merlo, Gabriele; Brunner, Stephan; Huang, Zhouji; ...

2017-12-19

Axisymmetric (n=0) density fluctuations measured in the TCV tokamak are observed to possess a frequency f₀ which is either varying (radially dispersive oscillations) or a constant over a large fraction of the plasma minor radius (radially global oscillations) as reported in a companion paper [Z. Huang et al., this issue]. Given that f₀ scales with the sound speed and given the poloidal structure of density fluctuations, these oscillations were interpreted as Geodesic Acoustic Modes, even though f₀ is in fact smaller than the local linear GAM frequency f_GAM . In this work we employ the Eulerian gyrokinetic code GENE tomore » simulate TCV relevant conditions and investigate the nature properties of these oscillations, in particular their relation to the safety factor profile. Local and global simulations are carried out and a good qualitative agreement is observed between experiments and simulations. By varying also the plasma temperature and density profiles, we conclude that a variation of the edge safety factor alone is not sufficient to induce a transition from global to radially inhomogeneous oscillations, as was initially suggested by experimental results. This transition appears instead to be the combined result of variations in the different plasma profiles, collisionality and finite machine size effects. In conclusion, simulations also show that radially global GAM-like oscillations can be observed in all fluxes and fluctuation fields, suggesting that they are the result of a complex nonlinear process involving also finite toroidal mode numbers and not just linear global GAM eigenmodes.« less

Statistical properties and correlation functions for drift waves

NASA Technical Reports Server (NTRS)

Horton, W.

1986-01-01

The dissipative one-field drift wave equation is solved using the pseudospectral method to generate steady-state fluctuations. The fluctuations are analyzed in terms of space-time correlation functions and modal probability distributions. Nearly Gaussian statistics and exponential decay of the two-time correlation functions occur in the presence of electron dissipation, while in the absence of electron dissipation long-lived vortical structures occur. Formulas from renormalized, Markovianized statistical turbulence theory are given in a local approximation to interpret the dissipative turbulence.

Magnetic intermittency of solar wind turbulence in the dissipation range

NASA Astrophysics Data System (ADS)

Pei, Zhongtian; He, Jiansen; Tu, Chuanyi; Marsch, Eckart; Wang, Linghua

2016-04-01

The feature, nature, and fate of intermittency in the dissipation range are an interesting topic in the solar wind turbulence. We calculate the distribution of flatness for the magnetic field fluctuations as a functionof angle and scale. The flatness distribution shows a "butterfly" pattern, with two wings located at angles parallel/anti-parallel to local mean magnetic field direction and main body located at angles perpendicular to local B0. This "butterfly" pattern illustrates that the flatness profile in (anti-) parallel direction approaches to the maximum value at larger scale and drops faster than that in perpendicular direction. The contours for probability distribution functions at different scales illustrate a "vase" pattern, more clear in parallel direction, which confirms the scale-variation of flatness and indicates the intermittency generation and dissipation. The angular distribution of structure function in the dissipation range shows an anisotropic pattern. The quasi-mono-fractal scaling of structure function in the dissipation range is also illustrated and investigated with the mathematical model for inhomogeneous cascading (extended p-model). Different from the inertial range, the extended p-model for the dissipation range results in approximate uniform fragmentation measure. However, more complete mathematicaland physical model involving both non-uniform cascading and dissipation is needed. The nature of intermittency may be strong structures or large amplitude fluctuations, which may be tested with magnetic helicity. In one case study, we find the heating effect in terms of entropy for large amplitude fluctuations seems to be more obvious than strong structures.

Interplay of Anderson localization and quench dynamics

NASA Astrophysics Data System (ADS)

Rahmani, Armin; Vishveshwara, Smitha

2018-06-01

In the context of an isolated three-dimensional noninteracting fermionic lattice system, we study the effects of a sudden quantum quench between a disorder-free situation and one in which disorder results in a mobility edge and associated Anderson localization. Salient post-quench features hinge upon the overlap between momentum states and post-quench eigenstates and whether these latter states are extended or localized. We find that the post-quench momentum distribution directly reflects these overlaps. For the local density, we show that disorder generically prevents the equilibration of quantum expectation values to a steady state and that the persistent fluctuations have a nonmonotonic dependence on the strength of disorder. We identify two distinct types of fluctuations, namely, temporal fluctuations describing the time-dependent fluctuations of the local density around its time average and sample-to-sample fluctuations characterizing the variations of these time averages from one realization of disorder to another. We demonstrate that both of these fluctuations vanish for extremely extended as well as extremely localized states, peaking at some intermediate value.

Independent Metrics for Protein Backbone and Side-Chain Flexibility: Time Scales and Effects of Ligand Binding.

PubMed

Fuchs, Julian E; Waldner, Birgit J; Huber, Roland G; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R

2015-03-10

Conformational dynamics are central for understanding biomolecular structure and function, since biological macromolecules are inherently flexible at room temperature and in solution. Computational methods are nowadays capable of providing valuable information on the conformational ensembles of biomolecules. However, analysis tools and intuitive metrics that capture dynamic information from in silico generated structural ensembles are limited. In standard work-flows, flexibility in a conformational ensemble is represented through residue-wise root-mean-square fluctuations or B-factors following a global alignment. Consequently, these approaches relying on global alignments discard valuable information on local dynamics. Results inherently depend on global flexibility, residue size, and connectivity. In this study we present a novel approach for capturing positional fluctuations based on multiple local alignments instead of one single global alignment. The method captures local dynamics within a structural ensemble independent of residue type by splitting individual local and global degrees of freedom of protein backbone and side-chains. Dependence on residue type and size in the side-chains is removed via normalization with the B-factors of the isolated residue. As a test case, we demonstrate its application to a molecular dynamics simulation of bovine pancreatic trypsin inhibitor (BPTI) on the millisecond time scale. This allows for illustrating different time scales of backbone and side-chain flexibility. Additionally, we demonstrate the effects of ligand binding on side-chain flexibility of three serine proteases. We expect our new methodology for quantifying local flexibility to be helpful in unraveling local changes in biomolecular dynamics.

Super-resolution binding activated localization microscopy through reversible change of DNA conformation.

PubMed

Szczurek, Aleksander; Birk, Udo; Knecht, Hans; Dobrucki, Jurek; Mai, Sabine; Cremer, Christoph

2018-01-01

Methods of super-resolving light microscopy (SRM) have found an exponentially growing range of applications in cell biology, including nuclear structure analyses. Recent developments have proven that Single Molecule Localization Microscopy (SMLM), a type of SRM, is particularly useful for enhanced spatial analysis of the cell nucleus due to its highest resolving capability combined with very specific fluorescent labeling. In this commentary we offer a brief review of the latest methodological development in the field of SMLM of chromatin designated DNA Structure Fluctuation Assisted Binding Activated Localization Microscopy (abbreviated as fBALM) as well as its potential future applications in biology and medicine.

Super-resolution binding activated localization microscopy through reversible change of DNA conformation

PubMed Central

Knecht, Hans; Dobrucki, Jurek; Mai, Sabine

2018-01-01

ABSTRACT Methods of super-resolving light microscopy (SRM) have found an exponentially growing range of applications in cell biology, including nuclear structure analyses. Recent developments have proven that Single Molecule Localization Microscopy (SMLM), a type of SRM, is particularly useful for enhanced spatial analysis of the cell nucleus due to its highest resolving capability combined with very specific fluorescent labeling. In this commentary we offer a brief review of the latest methodological development in the field of SMLM of chromatin designated DNA Structure Fluctuation Assisted Binding Activated Localization Microscopy (abbreviated as fBALM) as well as its potential future applications in biology and medicine. PMID:29297245

Low-dimensional ordering and fluctuations in methanol-{beta}-hydroquinone clathrate studied by x-ray and neutron diffraction

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

Rheinstaedter, Maikel C.; Enderle, Mechthild; Kloepperpieper, Axel

2005-01-01

Methanol-{beta}-hydroquinone clathrate has been established as a model system for dielectric ordering and fluctuations and is conceptually close to magnetic spin systems. In x-ray and neutron diffraction experiments, we investigated the ordered structure, the one-dimensional (1D) and the three-dimensional critical scattering in the paraelectric phase, and the temperature dependence of the lattice constants. Our results can be explained by microscopic models of the methanol pseudospin in the hydroquinone cage network, in consistency with previous dielectric investigations. A coupling of the 1D fluctuations to local strains leads to an anomalous temperature dependence of the 1D lattice parameter in the paraelectric regime.

Implication of Taylor's hypothesis on amplitude modulation

NASA Astrophysics Data System (ADS)

Howland, Michael; Yang, Xiang

2017-11-01

Amplitude modulation is a physical phenomenon which describes the non-linear inter-scale interaction between large and small scales in a turbulent wall-bounded flow. The amplitude of the small scale fluctuations are modulated by the large scale flow structures. Due to the increase of amplitude modulation as a function of Reynolds number (Reτ = δuτ / ν), this phenomenon is frequently studied using experimental temporal 1D signals, taken using hot-wire anemometry. Typically, Taylor's frozen turbulence hypothesis has been invoked where the convection by velocity fluctuations is neglected and the mean velocity is used as the convective velocity. At high Reynolds numbers, turbulent fluctuations are comparable to the mean velocity in the near wall region (y+ O(10)), and as a result, using a constant global convective velocity systematically locally compresses or stretches a velocity signal when converting from temporal to spatial domain given a positive or negative fluctuation respectively. Despite this, temporal hot-wire data from wind tunnel or field experiments of high Reynolds number boundary layer flows can still be used for measuring modulation provided that the local fluid velocity is used as the local convective velocity. MH is funded through the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1656518 and the Stanford Graduate Fellowship. XY is funded by the US AFOSR, Grant No. 1194592-1-TAAHO monitored by Dr. Ivett Leyva.

Fractal Profit Landscape of the Stock Market

PubMed Central

Grönlund, Andreas; Yi, Il Gu; Kim, Beom Jun

2012-01-01

We investigate the structure of the profit landscape obtained from the most basic, fluctuation based, trading strategy applied for the daily stock price data. The strategy is parameterized by only two variables, p and q Stocks are sold and bought if the log return is bigger than p and less than –q, respectively. Repetition of this simple strategy for a long time gives the profit defined in the underlying two-dimensional parameter space of p and q. It is revealed that the local maxima in the profit landscape are spread in the form of a fractal structure. The fractal structure implies that successful strategies are not localized to any region of the profit landscape and are neither spaced evenly throughout the profit landscape, which makes the optimization notoriously hard and hypersensitive for partial or limited information. The concrete implication of this property is demonstrated by showing that optimization of one stock for future values or other stocks renders worse profit than a strategy that ignores fluctuations, i.e., a long-term buy-and-hold strategy. PMID:22558079

Spatial localization of resistive drift wave structure in tokamak edge plasmas with an embedded magnetic island

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

Hu, Shilin; Qu, Hongpeng; Li, Jiquan, E-mail: lijq@energy.kyoto-u.ac.jp

Resistive drift wave instability is investigated numerically in tokamak edge plasma confined by sheared slab magnetic field geometry with an embedded magnetic island. The focus is on the structural characteristics of eigenmode inside the island, where the density profile tends to be flattened. A transition of the dominant eigenmode occurs around a critical island width w{sub c}. For thin islands with a width below w{sub c}, two global long wavelength eigenmodes with approximately the same growth rate but different eigenfrequency are excited, which are stabilized by the magnetic island through two-dimensional mode coupling in both x and y (corresponding tomore » radial and poloidal in tokamak) directions. On the other hand, a short wavelength eigenmode, which is destabilized by thick islands with a width above w{sub c}, dominates the edge fluctuation, showing a prominent structural localization in the region between the X-point and the O-point of the magnetic island. The main destabilization mechanism is identified as the mode coupling in the y direction, which is similar to the so-called toroidal coupling in tokamak plasmas. These three eigenmodes may coexist in the drift wave fluctuation for the island with a width around w{sub c}. It is demonstrated that the structural localization results mainly from the quasilinear flattening of density profile inside the magnetic island.« less

Entropic fluctuations in DNA sequences

NASA Astrophysics Data System (ADS)

Thanos, Dimitrios; Li, Wentian; Provata, Astero

2018-03-01

The Local Shannon Entropy (LSE) in blocks is used as a complexity measure to study the information fluctuations along DNA sequences. The LSE of a DNA block maps the local base arrangement information to a single numerical value. It is shown that despite this reduction of information, LSE allows to extract meaningful information related to the detection of repetitive sequences in whole chromosomes and is useful in finding evolutionary differences between organisms. More specifically, large regions of tandem repeats, such as centromeres, can be detected based on their low LSE fluctuations along the chromosome. Furthermore, an empirical investigation of the appropriate block sizes is provided and the relationship of LSE properties with the structure of the underlying repetitive units is revealed by using both computational and mathematical methods. Sequence similarity between the genomic DNA of closely related species also leads to similar LSE values at the orthologous regions. As an application, the LSE covariance function is used to measure the evolutionary distance between several primate genomes.

General framework for fluctuating dynamic density functional theory

NASA Astrophysics Data System (ADS)

Durán-Olivencia, Miguel A.; Yatsyshin, Peter; Goddard, Benjamin D.; Kalliadasis, Serafim

2017-12-01

We introduce a versatile bottom-up derivation of a formal theoretical framework to describe (passive) soft-matter systems out of equilibrium subject to fluctuations. We provide a unique connection between the constituent-particle dynamics of real systems and the time evolution equation of their measurable (coarse-grained) quantities, such as local density and velocity. The starting point is the full Hamiltonian description of a system of colloidal particles immersed in a fluid of identical bath particles. Then, we average out the bath via Zwanzig’s projection-operator techniques and obtain the stochastic Langevin equations governing the colloidal-particle dynamics. Introducing the appropriate definition of the local number and momentum density fields yields a generalisation of the Dean-Kawasaki (DK) model, which resembles the stochastic Navier-Stokes description of a fluid. Nevertheless, the DK equation still contains all the microscopic information and, for that reason, does not represent the dynamical law of observable quantities. We address this controversial feature of the DK description by carrying out a nonequilibrium ensemble average. Adopting a natural decomposition into local-equilibrium and nonequilibrium contribution, where the former is related to a generalised version of the canonical distribution, we finally obtain the fluctuating-hydrodynamic equation governing the time-evolution of the mesoscopic density and momentum fields. Along the way, we outline the connection between the ad hoc energy functional introduced in previous DK derivations and the free-energy functional from classical density-functional theory. The resultant equation has the structure of a dynamical density-functional theory (DDFT) with an additional fluctuating force coming from the random interactions with the bath. We show that our fluctuating DDFT formalism corresponds to a particular version of the fluctuating Navier-Stokes equations, originally derived by Landau and Lifshitz. Our framework thus provides the formal apparatus for ab initio derivations of fluctuating DDFT equations capable of describing the dynamics of soft-matter systems in and out of equilibrium.

Fundamental tests of galaxy formation theory

NASA Technical Reports Server (NTRS)

Silk, J.

1982-01-01

The structure of the universe as an environment where traces exist of the seed fluctuations from which galaxies formed is studied. The evolution of the density fluctuation modes that led to the eventual formation of matter inhomogeneities is reviewed, How the resulting clumps developed into galaxies and galaxy clusters acquiring characteristic masses, velocity dispersions, and metallicities, is discussed. Tests are described that utilize the large scale structure of the universe, including the dynamics of the local supercluster, the large scale matter distribution, and the anisotropy of the cosmic background radiation, to probe the earliest accessible stages of evolution. Finally, the role of particle physics is described with regard to its observable implications for galaxy formation.

Ge K-Edge Extended X-Ray Absorption Fine Structure Study of the Local Structure of Amorphous GeTe and the Crystallization

NASA Astrophysics Data System (ADS)

Maeda, Yoshihito; Wakagi, Masatoshi

1991-01-01

The local structure and crystallization of amorphous GeTe (a-GeTe) were examined by means of Ge K-edge EXAFS. In a-GeTe, both Ge-Ge and Ge-Te bonds were observed to exist in nearest neighbors of Ge. The average coordination number around Ge is 3.7, which is close to the tetrahedral structure. A random covalent network (RCN) model seems to be suitable for the local Structure. After a-GeTe crystallizes at 129°C, the Ge-Ge bond disappears and the Ge-Te bond length increases considerably. As temperature rises, in a-GeTe the Debye-Waller factor of the Ge-Te bond increases greatly, while that of the Ge-Ge bond increases only slightly. At the crystallization, it is found that the fluctuation of the Ge-Te bond length plays a major role in the change of the local structure and bonding state around Ge.

On microscopic structure of the QCD vacuum

NASA Astrophysics Data System (ADS)

Pak, D. G.; Lee, Bum-Hoon; Kim, Youngman; Tsukioka, Takuya; Zhang, P. M.

2018-05-01

We propose a new class of regular stationary axially symmetric solutions in a pure QCD which correspond to monopole-antimonopole pairs at macroscopic scale. The solutions represent vacuum field configurations which are locally stable against quantum gluon fluctuations in any small space-time vicinity. This implies that the monopole-antimonopole pair can serve as a structural element in microscopic description of QCD vacuum formation.

Mapping hydration dynamics and coupled water-protein fluctuations around a protein surface

NASA Astrophysics Data System (ADS)

Zhang, Luyuan; Wang, Lijuan; Kao, Ya-Ting; Qiu, Weihong; Yang, Yi; Okobiah, Oghaghare; Zhong, Dongping

2009-03-01

Elucidation of the molecular mechanism of water-protein interactions is critical to understanding many fundamental aspects of protein science, such as protein folding and misfolding and enzyme catalysis. We recently carried out a global mapping of protein-surface hydration dynamics around a globular α-helical protein apomyoglobin. The intrinsic optical probe tryptophan was employed to scan the protein surface one at a time by site-specific mutagenesis. With femtosecond resolution, we mapped out the dynamics of water-protein interactions with more than 20 mutants and for two states, native and molten globular. A robust bimodal distribution of time scales was observed, representing two types of water motions: local relaxation and protein-coupled fluctuations. The time scales show a strong correlation with the local protein structural rigidity and chemical identity. We also resolved two distinct contributions to the overall Stokes-shifts from the two time scales. These results are significant to understanding the role of hydration water on protein structural stability, dynamics and function.

Nanoscopic imaging of thick heterogeneous soft-matter structures in aqueous solution

PubMed Central

Bartsch, Tobias F.; Kochanczyk, Martin D.; Lissek, Emanuel N.; Lange, Janina R.; Florin, Ernst-Ludwig

2016-01-01

Precise nanometre-scale imaging of soft structures at room temperature poses a major challenge to any type of microscopy because fast thermal fluctuations lead to significant motion blur if the position of the structure is measured with insufficient bandwidth. Moreover, precise localization is also affected by optical heterogeneities, which lead to deformations in the imaged local geometry, the severity depending on the sample and its thickness. Here we introduce quantitative thermal noise imaging, a three-dimensional scanning probe technique, as a method for imaging soft, optically heterogeneous and porous matter with submicroscopic spatial resolution in aqueous solution. By imaging both individual microtubules and collagen fibrils in a network, we demonstrate that structures can be localized with a precision of ∼10 nm and that their local dynamics can be quantified with 50 kHz bandwidth and subnanometre amplitudes. Furthermore, we show how image distortions caused by optically dense structures can be corrected for. PMID:27596919

Determining Quiescent Colloidal Suspension Viscosities Using the Green-Kubo Relation and Image-Based Stress Measurements

NASA Astrophysics Data System (ADS)

Lin, Neil Y. C.; Bierbaum, Matthew; Cohen, Itai

2017-09-01

By combining confocal microscopy and stress assessment from local structural anisotropy, we directly measure stresses in 3D quiescent colloidal liquids. Our noninvasive and nonperturbative method allows us to measure forces ≲50 fN with a small and tunable probing volume, enabling us to resolve the stress fluctuations arising from particle thermal motions. We use the Green-Kubo relation to relate these measured stress fluctuations to the bulk Brownian viscosity at different volume fractions, comparing against simulations and conventional rheometry measurements. We find that the Green-Kubo analysis gives excellent agreement with these prior results, suggesting that similar methods could be applied to investigations of local flow properties in many poorly understood far-from-equilibrium systems, including suspensions that are glassy, strongly sheared, or highly confined.

Population Fluctuations and Synchrony of Grassland Butterflies in Relation to Species Traits

PubMed Central

Franzén, Markus; Nilsson, Sven G.; Johansson, Victor; Ranius, Thomas

2013-01-01

Population fluctuations and synchrony influence population persistence; species with larger fluctuations and more synchronised population fluctuations face higher extinction risks. Here, we analyse the effect of diet specialisation, mobility, length of the flight period, and distance to the northern edge of the species’ distribution in relation to between-year population fluctuations and synchrony of butterfly species. All butterfly species associated with grasslands were surveyed over five successive years at 19 grassland sites in a forest-dominated landscape (50 km2) in southern Sweden. At both the local and regional level, we found larger population fluctuations in species with longer flight periods. Population fluctuations were more synchronous among localities in diet specialists. Species with a long flight period might move more to track nectar resources compared to species with shorter flight period, and if nectar sources vary widely between years and localities it may explain that population fluctuations increase with increasing flight length. Diet generalists can use different resources (in this case host plants) at different localities and this can explain the lower synchrony in population fluctuations among generalist species. Higher degree of synchrony is one possible explanation for the higher extinction risks that have been observed for more specialised species. Therefore, diet specialists are more often threatened and require more conservation efforts than generalists. PMID:24205169

Mössbauer spectroscopy study of magnetic fluctuations in superconducting RbGd2Fe4As4O2

NASA Astrophysics Data System (ADS)

Li, Y.; Wang, Z. C.; Cao, G. H.; Zhang, J. M.; Zhang, B.; Wang, T.; Pang, H.; Li, F. S.; Li, Z. W.

2018-05-01

57Fe Mössbauer spectra were measured at different temperatures between 5.9 K and 300 K on the recently discovered self-doped superconducting RbGd2Fe4As4O2 with Tc as high as 35 K. Singlet pattern was observed down to the lowest temperature measured in this work, indicating the absence of static magnetic order on the Fe site. The intermediate isomer shift in comparison with that of the samples RbFe2As2 and GdFeAsO confirms the self doping induced local electronic structure change. Surprisingly, we observe two magnetic fluctuation induced spectral broadenings below ∼ 15 K and ∼ 100 K which are believed to be originated from the transferred magnetic fluctuations of the Gd3+ moments and that of the magnetic fluctuations of the Fe atoms, respectively.

Mapping hydration dynamics around a protein surface

PubMed Central

Zhang, Luyuan; Wang, Lijuan; Kao, Ya-Ting; Qiu, Weihong; Yang, Yi; Okobiah, Oghaghare; Zhong, Dongping

2007-01-01

Protein surface hydration is fundamental to its structure and activity. We report here the direct mapping of global hydration dynamics around a protein in its native and molten globular states, using a tryptophan scan by site-specific mutations. With 16 tryptophan mutants and in 29 different positions and states, we observed two robust, distinct water dynamics in the hydration layer on a few (≈1–8 ps) and tens to hundreds of picoseconds (≈20–200 ps), representing the initial local relaxation and subsequent collective network restructuring, respectively. Both time scales are strongly correlated with protein's structural and chemical properties. These results reveal the intimate relationship between hydration dynamics and protein fluctuations and such biologically relevant water–protein interactions fluctuate on picosecond time scales. PMID:18003912

Nonlinear reconnecting edge localized modes in current-carrying plasmas

DOE PAGES

Ebrahimi, F.

2017-05-22

Nonlinear edge localized modes in a tokamak are examined using global three-dimensional resistive magnetohydrodynamics simulations. Coherent current-carrying filament (ribbon-like) structures wrapped around the torus are nonlinearly formed due to nonaxisymmetric reconnecting current sheet instabilities, the so-called peeling-like edge localized modes. These fast growing modes saturate by breaking axisymmetric current layers isolated near the plasma edge and go through repetitive relaxation cycles by expelling current radially outward and relaxing it back. The local bidirectional fluctuation-induced electromotive force (emf) from the edge localized modes, the dynamo action, relaxes the axisymmetric current density and forms current holes near the edge. Furthermore, the three-dimensionalmore » coherent current-carrying filament structures (sometimes referred to as 3-D plasmoids) observed here should also have strong implications for solar and astrophysical reconnection.« less

Giant fluctuations and structural effects in a flocking epithelium

NASA Astrophysics Data System (ADS)

Giavazzi, Fabio; Malinverno, Chiara; Corallino, Salvatore; Ginelli, Francesco; Scita, Giorgio; Cerbino, Roberto

2017-09-01

Epithelial cells cultured in a monolayer are very motile in isolation but reach a near-jammed state when mitotic division increases their number above a critical threshold. We have recently shown that a monolayer can be reawakened by over-expression of a single protein, RAB5A, a master regulator of endocytosis. This reawakening of motility was explained in terms of a flocking transition that promotes the emergence of a large-scale collective migratory pattern. Here we focus on the impact of this reawakening on the structural properties of the monolayer. We find that the unjammed monolayer is characterised by a fluidisation at the single cell level, and by enhanced non-equilibrium large-scale number fluctuations at a larger length scale. Also, with the help of numerical simulations, we trace back the origin of these fluctuations to the self-propelled active nature of the constituents, and to the existence of a local alignment mechanism, leading to the spontaneous breaking of the orientational symmetry.

Mode localization in the cooperative dynamics of protein recognition

NASA Astrophysics Data System (ADS)

Copperman, J.; Guenza, M. G.

2016-07-01

The biological function of proteins is encoded in their structure and expressed through the mediation of their dynamics. This paper presents a study on the correlation between local fluctuations, binding, and biological function for two sample proteins, starting from the Langevin Equation for Protein Dynamics (LE4PD). The LE4PD is a microscopic and residue-specific coarse-grained approach to protein dynamics, which starts from the static structural ensemble of a protein and predicts the dynamics analytically. It has been shown to be accurate in its prediction of NMR relaxation experiments and Debye-Waller factors. The LE4PD is solved in a set of diffusive modes which span a vast range of time scales of the protein dynamics, and provides a detailed picture of the mode-dependent localization of the fluctuation as a function of the primary structure of the protein. To investigate the dynamics of protein complexes, the theory is implemented here to treat the coarse-grained dynamics of interacting macromolecules. As an example, calculations of the dynamics of monomeric and dimerized HIV protease and the free Insulin Growth Factor II Receptor (IGF2R) domain 11 and its IGF2R:IGF2 complex are presented. Either simulation-derived or experimentally measured NMR conformers are used as input structural ensembles to the theory. The picture that emerges suggests a dynamical heterogeneous protein where biologically active regions provide energetically comparable conformational states that are trapped by a reacting partner in agreement with the conformation-selection mechanism of binding.

Hole localization, water dissociation mechanisms, and band alignment at aqueous-titania interfaces

NASA Astrophysics Data System (ADS)

Lyons, John L.

Photocatalytic water splitting is a promising method for generating clean energy, but materials that can efficiently act as photocatalysts are scarce. This is in part due to the fact that exposure to water can strongly alter semiconductor surfaces and therefore photocatalyst performance. Many materials are not stable in aqueous environments; in other cases, local changes in structure may occur, affecting energy-level alignment. Even in the simplest case, dynamic fluctuations modify the organization of interface water. Accounting for such effects requires knowledge of the dominant local structural motifs and also accurate semiconductor band-edge positions, making quantitative prediction of energy-level alignments computationally challenging. Here we employ a combined theoretical approach to study the structure, energy alignment, and hole localization at aqueous-titania interfaces. We calculate the explicit aqueous-semiconductor interface using ab initio molecular dynamics, which provides the fluctuating atomic structure, the extent of water dissociation, and the resulting electrostatic potential. For both anatase and rutile TiO2 we observe spontaneous water dissociation and re-association events that occur via distinct mechanisms. We also find a higher-density water layer occurring on anatase. In both cases, we find that the second monolayer of water plays a crucial role in controlling the extent of water dissociation. Using hybrid functional calculations, we then investigate the propensity for dissociated waters to stabilize photo-excited carriers, and compare the results of rutile and anatase aqueous interfaces. Finally, we use the GW approach from many-body perturbation theory to obtain the position of semiconductor band edges relative to the occupied 1b1 level and thus the redox levels of water, and examine how local structural modifications affect these offsets. This work was performed in collaboration with N. Kharche, M. Z. Ertem, J. T. Muckerman, and M. S. Hybertsen. It made use of resources at the Center for Functional Nanomaterials, which is a U.S. DOE Office of Science Facility, at Brookhaven National Lab.

Pressure Fluctuations Induced by a Hypersonic Turbulent Boundary Layer

NASA Technical Reports Server (NTRS)

Duan, Lian; Choudhari, Meelan M.; Zhang, Chao

2016-01-01

Direct numerical simulations (DNS) are used to examine the pressure fluctuations generated by a spatially-developed Mach 5.86 turbulent boundary layer. The unsteady pressure field is analyzed at multiple wall-normal locations, including those at the wall, within the boundary layer (including inner layer, the log layer, and the outer layer), and in the free stream. The statistical and structural variations of pressure fluctuations as a function of wall-normal distance are highlighted. Computational predictions for mean velocity pro les and surface pressure spectrum are in good agreement with experimental measurements, providing a first ever comparison of this type at hypersonic Mach numbers. The simulation shows that the dominant frequency of boundary-layer-induced pressure fluctuations shifts to lower frequencies as the location of interest moves away from the wall. The pressure wave propagates with a speed nearly equal to the local mean velocity within the boundary layer (except in the immediate vicinity of the wall) while the propagation speed deviates from the Taylor's hypothesis in the free stream. Compared with the surface pressure fluctuations, which are primarily vortical, the acoustic pressure fluctuations in the free stream exhibit a significantly lower dominant frequency, a greater spatial extent, and a smaller bulk propagation speed. The freestream pressure structures are found to have similar Lagrangian time and spatial scales as the acoustic sources near the wall. As the Mach number increases, the freestream acoustic fluctuations exhibit increased radiation intensity, enhanced energy content at high frequencies, shallower orientation of wave fronts with respect to the flow direction, and larger propagation velocity.

Early structural development in melt-quenched polymer PTT from atomistic molecular dynamic simulations

NASA Astrophysics Data System (ADS)

Hsieh, Min-Kang; Lin, Shiang-Tai

2009-12-01

Molecular dynamics simulations are performed to study the initial structural development in poly(trimethylene terephthalate) (PTT) when quenched below its melting point. The development of local ordering has been observed in our simulations. The thermal properties, such as the glass transition temperature (Tg) and the melting temperature (Tm), determined from our simulations are in reasonable agreement with experimental values. It is found that, between these two temperatures, the number of local structures quickly increases during the thermal relaxation period soon after the system is quenched and starts to fluctuate afterwards. The formation and development of local structures is found to be driven mainly by the torsional and van der Waals forces and follows the classical nucleation-growth mechanism. The variation of local structures' fraction with temperature exhibits a maximum between Tg and Tm, resembling the temperature dependence of the crystallization rate for most polymers. In addition, the backbone torsion distribution for segments within the local structures preferentially reorganizes to the trans-gauche-gauche-trans (t-g-g-t) conformation, the same as that in the crystalline state. As a consequence, we believe that such local structural ordering could be the baby nuclei that have been suggested to form in the early stage of polymer crystallization.

Effect of altering local protein fluctuations using artificial intelligence

NASA Astrophysics Data System (ADS)

Nishiyama, Katsuhiko

2017-03-01

The fluctuations in Arg111, a significantly fluctuating residue in cathepsin K, were locally regulated by modifying Arg111 to Gly111. The binding properties of 15 dipeptides in the modified protein were analyzed by molecular simulations, and modeled as decision trees using artificial intelligence. The decision tree of the modified protein significantly differed from that of unmodified cathepsin K, and the Arg-to-Gly modification exerted a remarkable effect on the peptide binding properties. By locally regulating the fluctuations of a protein, we may greatly alter the original functions of the protein, enabling novel applications in several fields.

Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations

PubMed Central

Serag, Maged F.; Abadi, Maram; Habuchi, Satoshi

2014-01-01

Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields. PMID:25283876

On the Charge transport regime of crystalline organic semiconductors: diffusion limited by thermal off-diagonal electronic disorder

NASA Astrophysics Data System (ADS)

Troisi, Alessandro

2006-03-01

In organic crystalline semiconductor molecular components are held together by very weak interactions and the transfer integrals between neighboring molecular orbitals are extremely sensitive to small nuclear displacements. We used a mixed quantum chemical and molecular dynamic methodology to assess the effect of thermal structural fluctuations on the modulation of the transfer integrals between close molecules. We have found that the fluctuations of the transfer integrals are of the same order of magnitude of their average value for pentacene and anthracene. This condition makes the band description inadequate because a dynamic localization takes place and the translational symmetry is completely broken for the electronic states. We also present a simple one-dimensional semiclassical model that incorporates the effects of dynamical localization and allows the numerical computation of the charge mobility for ordered organic semiconductors. These results explain several contrasting experimental observations pointing sometimes to a delocalized ``band-like'' transport and sometimes to the existence of strongly localized charge carriers.

Numerical evidence of fluctuating stripes in the normal state of high-Tc cuprate superconductors

NASA Astrophysics Data System (ADS)

Huang, Edwin W.; Mendl, Christian B.; Liu, Shenxiu; Johnston, Steve; Jiang, Hong-Chen; Moritz, Brian; Devereaux, Thomas P.

2017-12-01

Upon doping, Mott insulators often exhibit symmetry breaking where charge carriers and their spins organize into patterns known as stripes. For high-transition temperature cuprate superconductors, stripes are widely suspected to exist in a fluctuating form. We used numerically exact determinant quantum Monte Carlo calculations to demonstrate dynamical stripe correlations in the three-band Hubbard model, which represents the local electronic structure of the copper-oxygen plane. Our results, which are robust to varying parameters, cluster size, and boundary conditions, support the interpretation of experimental observations such as the hourglass magnetic dispersion and the Yamada plot of incommensurability versus doping in terms of the physics of fluctuating stripes. These findings provide a different perspective on the intertwined orders emerging from the cuprates’ normal state.

Temporal complexity in emission from Anderson localized lasers

NASA Astrophysics Data System (ADS)

Kumar, Randhir; Balasubrahmaniyam, M.; Alee, K. Shadak; Mujumdar, Sushil

2017-12-01

Anderson localization lasers exploit resonant cavities formed due to structural disorder. The inherent randomness in the structure of these cavities realizes a probability distribution in all cavity parameters such as quality factors, mode volumes, mode structures, and so on, implying resultant statistical fluctuations in the temporal behavior. Here we provide direct experimental measurements of temporal width distributions of Anderson localization lasing pulses in intrinsically and extrinsically disordered coupled-microresonator arrays. We first illustrate signature exponential decays in the spatial intensity distributions of the lasing modes that quantify their localized character, and then measure the temporal width distributions of the pulsed emission over several configurations. We observe a dependence of temporal widths on the disorder strength, wherein the widths show a single-peaked, left-skewed distribution in extrinsic disorder and a dual-peaked distribution in intrinsic disorder. We propose a model based on coupled rate equations for an emitter and an Anderson cavity with a random mode structure, which gives excellent quantitative and qualitative agreement with the experimental observations. The experimental and theoretical analyses bring to the fore the temporal complexity in Anderson-localization-based lasing systems.

Mass density fluctuations in quantum and classical descriptions of liquid water

NASA Astrophysics Data System (ADS)

Galib, Mirza; Duignan, Timothy T.; Misteli, Yannick; Baer, Marcel D.; Schenter, Gregory K.; Hutter, Jürg; Mundy, Christopher J.

2017-06-01

First principles molecular dynamics simulation protocol is established using revised functional of Perdew-Burke-Ernzerhof (revPBE) in conjunction with Grimme's third generation of dispersion (D3) correction to describe the properties of water at ambient conditions. This study also demonstrates the consistency of the structure of water across both isobaric (NpT) and isothermal (NVT) ensembles. Going beyond the standard structural benchmarks for liquid water, we compute properties that are connected to both local structure and mass density fluctuations that are related to concepts of solvation and hydrophobicity. We directly compare our revPBE results to the Becke-Lee-Yang-Parr (BLYP) plus Grimme dispersion corrections (D2) and both the empirical fixed charged model (SPC/E) and many body interaction potential model (MB-pol) to further our understanding of how the computed properties herein depend on the form of the interaction potential.

Mass density fluctuations in quantum and classical descriptions of liquid water

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

Galib, Mirza; Duignan, Timothy T.; Misteli, Yannick

First principles molecular dynamics simulation protocol is established using revised functional of Perdew-Burke-Ernzerhof (revPBE) in conjunction with Grimme's third generation of dispersion (D3) correction to describe properties of water at ambient conditions. This study also demonstrates the consistency of the structure of water across both isobaric (NpT) and isothermal (NVT) ensembles. Going beyond the standard structural benchmarks for liquid water, we compute properties that are connected to both local structure and mass density fluctuations that are related to concepts of solvation and hydrophobicity. We directly compare our revPBE results to the Becke-Lee-Yang-Parr (BLYP) plus Grimme dispersion corrections (D2) and bothmore » the empirical fixed charged model (SPC/E) and many body interaction potential model (MB-pol) to further our understanding of how the computed properties herein depend on the form of the interaction potential.« less

Investigation of the Dynamics of Coherent Structure, BBF, and Intermittent Turbulence in Earth's Magnetotail: A Study of Complexity in Nonlinear Space Plasmas

NASA Technical Reports Server (NTRS)

Chang, Tom

2005-01-01

We have achieved all the goals stated in our grant proposal. Specifically, these include: 1. The understanding of the complexity induced nonlinear spatiotemporal coherent structures and the coexisting propagating modes. 2. The understanding of the intermittent turbulence and energization process of the observed Bursty Bulk Flows (BBF's) in the Earth s magnetotail. 3. The development of "anisotropic three-dimensional complexity" in the plasma sheet due to localized merging and interactions of the magnetic coherent structures. 4. The study of fluctuation-induced nonlinear instabilities and their role in the reconfiguration of magnetic topologies in the magnetotail based on the concepts of the dynamic renormalization group. 5. The acceleration of ions due to the intermittent turbulence of propagating and nonpropagating fluctuations. In the following, we include lists of our published papers, invited talks, and professional activities. A detailed description of our accomplished research results is given..

Revealing Abrupt and Spontaneous Ruptures of Protein Native Structure under picoNewton Compressive Force Manipulation.

PubMed

Chowdhury, S Roy; Cao, Jin; He, Yufan; Lu, H Peter

2018-03-27

Manipulating protein conformations for exploring protein structure-function relationship has shown great promise. Although protein conformational changes under pulling force manipulation have been extensively studied, protein conformation changes under a compressive force have not been explored quantitatively. The latter is even more biologically significant and relevant in revealing protein functions in living cells associated with protein crowdedness, distribution fluctuations, and cell osmotic stress. Here we report our experimental observations on abrupt ruptures of protein native structures under compressive force, demonstrated and studied by single-molecule AFM-FRET spectroscopic nanoscopy. Our results show that the protein ruptures are abrupt and spontaneous events occurred when the compressive force reaches a threshold of 12-75 pN, a force amplitude accessible from thermal fluctuations in a living cell. The abrupt ruptures are sensitive to local environment, likely a general and important pathway of protein unfolding in living cells.

Fine-scale characteristics of interplanetary sector

NASA Technical Reports Server (NTRS)

Behannon, K. W.; Neubauer, F. M.; Barnstoff, H.

1980-01-01

The structure of the interplanetary sector boundaries observed by Helios 1 within sector transition regions was studied. Such regions consist of intermediate (nonspiral) average field orientations in some cases, as well as a number of large angle directional discontinuities (DD's) on the fine scale (time scales 1 hour). Such DD's are found to be more similar to tangential than rotational discontinuities, to be oriented on average more nearly perpendicular than parallel to the ecliptic plane to be accompanied usually by a large dip ( 80%) in B and, with a most probable thickness of 3 x 10 to the 4th power km, significantly thicker previously studied. It is hypothesized that the observed structures represent multiple traversals of the global heliospheric current sheet due to local fluctuations in the position of the sheet. There is evidence that such fluctuations are sometimes produced by wavelike motions or surface corrugations of scale length 0.05 - 0.1 AU superimposed on the large scale structure.

Topology and the universe

NASA Astrophysics Data System (ADS)

Gott, J. Richard, III

1998-09-01

Topology may play an important role in cosmology in several different ways. First, Einstein's field equations tell us about the local geometry of the universe but not about its topology. Therefore, the universe may be multiply connected. Inflation predicts that the fluctuations that made clusters and groups of galaxies arose from random quantum fluctuations in the early universe. These should be Gaussian random phase. This can be tested by quantitatively measuring the topology of large-scale structure in the universe using the genus statistic. If the original fluctuations were Gaussian random phase then the structure we see today should have a spongelike topology. A number of studies by our group and others have shown that this is indeed the case. Future tests using the Sloan Digital Sky Survey should be possible. Microwave background fluctuations should also exhibit a characteristic symmetric pattern of hot and cold spots. The COBE data are consistent with this pattern and the MAP and PLANCK satellites should provide a definitive test. If the original inflationary state was metastable then it should decay by making an infinite number of open inflationary bubble universes. This model makes a specific prediction for the power spectrum of fluctuations in the microwave background which can be checked by the MAP and PLANCK satellites. Finally, Gott and Li have proposed how a multiply connected cosmology with an early epoch of closed timelike curves might allow the universe to be its own mother.

Local thermal energy as a structural indicator in glasses.

PubMed

Zylberg, Jacques; Lerner, Edan; Bar-Sinai, Yohai; Bouchbinder, Eran

2017-07-11

Identifying heterogeneous structures in glasses-such as localized soft spots-and understanding structure-dynamics relations in these systems remain major scientific challenges. Here, we derive an exact expression for the local thermal energy of interacting particles (the mean local potential energy change caused by thermal fluctuations) in glassy systems by a systematic low-temperature expansion. We show that the local thermal energy can attain anomalously large values, inversely related to the degree of softness of localized structures in a glass, determined by a coupling between internal stresses-an intrinsic signature of glassy frustration-anharmonicity and low-frequency vibrational modes. These anomalously large values follow a fat-tailed distribution, with a universal exponent related to the recently observed universal [Formula: see text] density of states of quasilocalized low-frequency vibrational modes. When the spatial thermal energy field-a "softness field"-is considered, this power law tail manifests itself by highly localized spots, which are significantly softer than their surroundings. These soft spots are shown to be susceptible to plastic rearrangements under external driving forces, having predictive powers that surpass those of the normal modes-based approach. These results offer a general, system/model-independent, physical/observable-based approach to identify structural properties of quiescent glasses and relate them to glassy dynamics.

TESTING THE EFFECTS OF EXPANSION ON SOLAR WIND TURBULENCE

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

Vech, Daniel; Chen, Christopher H K, E-mail: dvech@umich.edu

2016-11-20

We present a multi-spacecraft approach to test the predictions of recent studies on the effect of solar wind expansion on the radial spectral, variance, and local 3D anisotropies of the turbulence. We found that on small scales (5000–10,000 km) the power levels of the B-trace structure functions do not depend on the sampling direction with respect to the radial suggesting that on this scale the effect of expansion is small possibly due to fast turbulent timescales. On larger scales (110–135 R{sub E}), the fluctuations of the radial magnetic field component are reduced by ∼20% compared to the transverse (perpendicular tomore » radial) ones, which could be due to expansion confining the fluctuations into the plane perpendicular to radial. For the local 3D spectral anisotropy, the B-trace structure functions showed dependence on the sampling direction with respect to radial. The anisotropy in the perpendicular plane is reduced when the increments are taken perpendicular with respect to radial, which could be an effect of expansion.« less

Turbulence, intermittency, and transport in the limiter shadow in LAPD and ET

NASA Astrophysics Data System (ADS)

Carter, Troy

2002-11-01

Turbulence in the scrape-off-layer (SOL) of tokamaks is often found to be intermittent, a tendency which has been attributed to the presence and transport of coherent structures (``blobs''). A recent theory [S.I. Krasheninnikov, shape Phys. Lett. A series 283, 368 (2001)] suggests that transport of these structures is controlled by nabla B and curvature drift driven polarization. I will present a study of turbulence and intermittency in limited discharges in the Large Plasma Device (LAPD) (where rotation may substitute for nabla B drift) and in the Electric Tokamak (ET) at UCLA. In LAPD, strongly intermittent turbulence in the 1-50 kHz range is observed localized to limiter produced gradients. A detailed study of these fluctuations will be presented, focusing on transport, dependencies on magnetic field, plasma density, and the presence of flows or rotation. A comparison with initial probe and imaging measurements of fluctuation characteristics in the SOL of the Electric Tokamak, in discharges with either an axisymmetric belt limiter or a toroidally localized limiter, will also be presented.

Characterizing depth-dependent refractive index of articular cartilage subjected to mechanical wear or enzymic degeneration

NASA Astrophysics Data System (ADS)

Wang, Kuyu; Wu, Jianping; Day, Robert; Kirk, Thomas Brett; Hu, Xiaozhi

2016-09-01

Utilizing a laser scanning confocal microscope system, the refractive indices of articular cartilage (AC) with mechanical or biochemical degenerations were characterized to investigate whether potential correlations exist between refractive index (RI) and cartilage degeneration. The cartilage samples collected from the medial femoral condyles of kangaroo knees were mechanically degenerated under different loading patterns or digested in trypsin solution with different concentrations. The sequences of RI were then measured from cartilage surface to deep region and the fluctuations of RI were quantified considering combined effects of fluctuating frequency and amplitude. The compositional and microstructural alterations of cartilage samples were assessed with histological methods. Along with the loss of proteoglycans, the average RI of cartilage increased and the local fluctuation of RI became stronger. Short-term high-speed test induced little influence to both the depth fluctuation and overall level of RI. Long-term low-speed test increased the fluctuation of RI but the average RI was barely changed. The results substantially demonstrate that RI of AC varies with both compositional and structural alterations and is potentially an indicator for the degeneration of AC.

Communication: On the origin of the non-Arrhenius behavior in water reorientation dynamics.

PubMed

Stirnemann, Guillaume; Laage, Damien

2012-07-21

We combine molecular dynamics simulations and analytic modeling to determine the origin of the non-Arrhenius temperature dependence of liquid water's reorientation and hydrogen-bond dynamics between 235 K and 350 K. We present a quantitative model connecting hydrogen-bond exchange dynamics to local structural fluctuations, measured by the asphericity of Voronoi cells associated with each water molecule. For a fixed local structure the regular Arrhenius behavior is recovered, and the global anomalous temperature dependence is demonstrated to essentially result from a continuous shift in the unimodal structure distribution upon cooling. The non-Arrhenius behavior can thus be explained without invoking an equilibrium between distinct structures. In addition, the large width of the homogeneous structural distribution is shown to cause a growing dynamical heterogeneity and a non-exponential relaxation at low temperature.

Protein denaturants at aqueous-hydrophobic interfaces: self-consistent correlation between induced interfacial fluctuations and denaturant stability at the interface.

PubMed

Cui, Di; Ou, Shu-Ching; Patel, Sandeep

2015-01-08

The notion of direct interaction between denaturing cosolvent and protein residues has been proposed in dialogue relevant to molecular mechanisms of protein denaturation. Here we consider the correlation between free energetic stability and induced fluctuations of an aqueous-hydrophobic interface between a model hydrophobically associating protein, HFBII, and two common protein denaturants, guanidinium cation (Gdm(+)) and urea. We compute potentials of mean force along an order parameter that brings the solute molecule close to the known hydrophobic region of the protein. We assess potentials of mean force for different relative orientations between the protein and denaturant molecule. We find that in both cases of guanidinium cation and urea relative orientations of the denaturant molecule that are parallel to the local protein-water interface exhibit greater stability compared to edge-on or perpendicular orientations. This behavior has been observed for guanidinium/methylguanidinium cations at the liquid-vapor interface of water, and thus the present results further corroborate earlier findings. Further analysis of the induced fluctuations of the aqueous-hydrophobic interface upon approach of the denaturant molecule indicates that the parallel orientation, displaying a greater stability at the interface, also induces larger fluctuations of the interface compared to the perpendicular orientations. The correlation of interfacial stability and induced interface fluctuation is a recurring theme for interface-stable solutes at hydrophobic interfaces. Moreover, observed correlations between interface stability and induced fluctuations recapitulate connections to local hydration structure and patterns around solutes as evidenced by experiment (Cooper et al., J. Phys. Chem. A 2014, 118, 5657.) and high-level ab initio/DFT calculations (Baer et al., Faraday Discuss 2013, 160, 89).

Protein Denaturants at Aqueous–Hydrophobic Interfaces: Self-Consistent Correlation between Induced Interfacial Fluctuations and Denaturant Stability at the Interface

PubMed Central

2015-01-01

The notion of direct interaction between denaturing cosolvent and protein residues has been proposed in dialogue relevant to molecular mechanisms of protein denaturation. Here we consider the correlation between free energetic stability and induced fluctuations of an aqueous–hydrophobic interface between a model hydrophobically associating protein, HFBII, and two common protein denaturants, guanidinium cation (Gdm+) and urea. We compute potentials of mean force along an order parameter that brings the solute molecule close to the known hydrophobic region of the protein. We assess potentials of mean force for different relative orientations between the protein and denaturant molecule. We find that in both cases of guanidinium cation and urea relative orientations of the denaturant molecule that are parallel to the local protein–water interface exhibit greater stability compared to edge-on or perpendicular orientations. This behavior has been observed for guanidinium/methylguanidinium cations at the liquid–vapor interface of water, and thus the present results further corroborate earlier findings. Further analysis of the induced fluctuations of the aqueous–hydrophobic interface upon approach of the denaturant molecule indicates that the parallel orientation, displaying a greater stability at the interface, also induces larger fluctuations of the interface compared to the perpendicular orientations. The correlation of interfacial stability and induced interface fluctuation is a recurring theme for interface-stable solutes at hydrophobic interfaces. Moreover, observed correlations between interface stability and induced fluctuations recapitulate connections to local hydration structure and patterns around solutes as evidenced by experiment (Cooper et al., J. Phys. Chem. A2014, 118, 5657.) and high-level ab initio/DFT calculations (Baer et al., Faraday Discuss2013, 160, 89). PMID:25536388

Electron temperature structures associated with magnetic tearing modes in the Madison Symmetric Torus

NASA Astrophysics Data System (ADS)

Stephens, Hillary Dianne

Tearing mode induced magnetic islands have a significant impact on the thermal characteristics of magnetically confined plasmas such as those in the reversed-field-pinch. Using a state-of-the-art Thomson scattering (TS) diagnostic, electron temperature fluctuations correlated with magnetic tearing modes have been observed on the Madison Symmetric Torus reversed-field-pinch. The TS diagnostic consists of two independently triggerable Nd:YAG lasers that can each pulse up to 15 times each plasma discharge and 21 General Atomics polchromators equipped with avalanche photodiode modules. Detailed calibrations focusing on accuracy, ease of use and repeatability and in-situ measurements have been performed on the system. Electron temperature (Te) profiles are acquired at 25 kHz with 2 cm or less resolution along the minor radius, sufficient to measure the effect of an island on the profile as the island rotates by the measurement point. Bayesian data analysis techniques are developed and used to detect fluctuations over an ensemble of shots. Four cases are studied; standard plasmas in quiescent periods, through sawteeth, through core reconnection events and in plasmas where the tearing mode activity is decreased. With a spectrum of unstable tearing modes, remnant islands that tend to flatten the temperature profile are present in the core between sawtooth-like reconnection events. This flattening is characteristic of rapid parallel heat conduction along helical magnetic field lines. The spatial structure of the temperature fluctuations show that the location of the rational surface of the m/n = 1/6 tearing mode is significantly further in than equilibrium suggestions predict. The fluctuations also provide a measurement of the remnant island width which is significantly smaller than the predicted full island width. These correlated fluctuations disappear during both global and core reconnection events. In striking contrast to temperature flattening, a temperature gradient within an m/m = 1/5 island is observed just after a global reconnection event. This suggests local heating and relatively good confinement within the island. Local power balance calculations suggest reduced thermal transport within this island. During improved confinement plasmas with reduced stochasticity, brought about by a reduction in tearing instability temperature fluctuations correlated with magnetic modes are small with characteristic fluctuation amplitudes of T˜e/Te ˜ 2%.

Conformational responses to changes in the state of ionization of titrable groups in proteins

NASA Astrophysics Data System (ADS)

Richman, Daniel Eric

Electrostatic energy links the structural properties of proteins with some of their important biological functions, including catalysis, energy transduction, and binding and recognition. Accurate calculation of electrostatic energy is essential for predicting and for analyzing function from structure. All proteins have many ionizable residues at the protein-water interface. These groups tend to have ionization equilibria (pK a values) shifted slightly relative to their values in water. In contrast, groups buried in the hydrophobic interior usually have highly anomalous p Ka values. These shifts are what structure-based calculations have to reproduce to allow examination of contributions from electrostatics to stability, solubility and interactions of proteins. Electrostatic energies are challenging to calculate accurately because proteins are heterogeneous dielectric materials. Any individual ionizable group can experience very different local environments with different dielectric properties. The studies in this thesis examine the hypothesis that proteins reorganize concomitant with changes in their state of ionization. It appears that the pKa value measured experimentally reflects the average of pKa values experienced in the different electrostatic environments corresponding to different conformational microstates. Current computational models fail to sample conformational reorganization of the backbone correctly. Staphyloccocal nuclease (SNase) was used as a model protein in nuclear magnetic resonance (NMR) spectroscopy studies to characterize the conformational rearrangements of the protein coupled to changes in the ionization state of titrable groups. One set of experiments tests the hypothesis that proton binding to surface Asp and Glu side chains drives local unfolding by stabilizing less-native, more water-solvated conformations in which the side chains have normalized pKa values. Increased backbone flexibility in the ps-ns timescale, hydrogen bond (H-bond) breaking on at least the mus timescale, and segmental unfolding were detected near titrating groups as pH decreased into the acidic range. The study identified local structural features and stabilities that modulate the magnitude of electrostatic effects. The data demonstrate that computational approaches to pK a calculations for surface groups must account for local fluctuations spanning a wide range of timescales. A comparative NMR spectroscopy study with the L25K and L125K variants of SNase, each with a Lys residue buried in the hydrophobic interior of the protein, determined locations, timescales, and amplitudes of backbone conformational reorganization coupled with ionization of the buried Lys residues. The L25K protein exhibited an ensemble of local fluctuations of the beta barrel in the hundreds of mus timescale and an ensemble of subglobally unfolded beta-barrel states in the hundreds of ms timescale with strong pH dependence. The L125K protein exhibited fluctuations of the helix around site 125 in the mus timescale, with negligible pH dependence. These data illustrate the diverse timescales and local structural properties of conformational reorganization coupled to ionization of buried groups, and the challenge to structure-based electrostatics calculations, which must capture these long-timescale processes.

Numerical evidence of fluctuating stripes in the normal state of high- T c cuprate superconductors

DOE PAGES

Huang, Edwin W.; Mendl, Christian B.; Liu, Shenxiu; ...

2017-12-01

Upon doping, Mott insulators often exhibit symmetry breaking where charge carriers and their spins organize into patterns known as stripes. For high–transition temperature cuprate superconductors, stripes are widely suspected to exist in a fluctuating form. We used numerically exact determinant quantum Monte Carlo calculations to demonstrate dynamical stripe correlations in the three-band Hubbard model, which represents the local electronic structure of the copper-oxygen plane. Our results, which are robust to varying parameters, cluster size, and boundary conditions, support the interpretation of experimental observations such as the hourglass magnetic dispersion and the Yamada plot of incommensurability versus doping in terms ofmore » the physics of fluctuating stripes. Furthermore, these findings provide a different perspective on the intertwined orders emerging from the cuprates’ normal state.« less

Multifractal property of Chinese stock market in the CSI 800 index based on MF-DFA approach

NASA Astrophysics Data System (ADS)

Zhu, Huijian; Zhang, Weiguo

2018-01-01

CSI 800 index consists of CSI 500 index and CSI 300 index, aiming to reflect the performance of stocks with large, mid and small size of China A share market. In this paper we analyze the multifractal structure of Chinese stock market in the CSI 800 index based on the multifractal detrended fluctuation analysis (MF-DFA) method. We find that the fluctuation of the closing logarithmic returns have multifractal properties, the shape and width of multifractal spectrum are depended on the weighing order q. More interestingly, we observe a bigger market crash in June-August 2015 than the one in 2008 based on the local Hurst exponents. The result provides important information for further study on dynamic mechanism of return fluctuation and whether it would trigger a new financial crisis.

Numerical evidence of fluctuating stripes in the normal state of high- T c cuprate superconductors

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

Huang, Edwin W.; Mendl, Christian B.; Liu, Shenxiu

Upon doping, Mott insulators often exhibit symmetry breaking where charge carriers and their spins organize into patterns known as stripes. For high–transition temperature cuprate superconductors, stripes are widely suspected to exist in a fluctuating form. We used numerically exact determinant quantum Monte Carlo calculations to demonstrate dynamical stripe correlations in the three-band Hubbard model, which represents the local electronic structure of the copper-oxygen plane. Our results, which are robust to varying parameters, cluster size, and boundary conditions, support the interpretation of experimental observations such as the hourglass magnetic dispersion and the Yamada plot of incommensurability versus doping in terms ofmore » the physics of fluctuating stripes. Furthermore, these findings provide a different perspective on the intertwined orders emerging from the cuprates’ normal state.« less

Density and magnetic fluctuations in type III-ELM pedestal evolution in JET: experimental and numerical characterization

NASA Astrophysics Data System (ADS)

De Masi, G.; Predebon, I.; Spagnolo, S.; Meneses, L.; Delabie, E.; Lupelli, I.; Hillesheim, J. C.; Maggi, C.; Contributors, JET

2018-04-01

Density and magnetic fluctuation measurements in low-β type-III ELM discharges are obtained in the Joint European Torus (JET). They are observed during the inter-ELM pedestal evolution, after the LH transition phase, at about 60-70 kHz. Density fluctuations are measured with a correlation reflectometer system installed on the low-field side and they are localized at the pedestal top. Magnetic fluctuations with a spatial scale k_yρ_i˜ 0.1 are measured through a high resolution coil array. The main features and the relations with local plasma parameters are presented. The nature of these fluctuations is discussed along with linear gyrokinetic simulations. Ion temperature gradient (ITG) modes are the dominant instabilities in the frequency range of interest. In terms of radial localization, typical oscillation frequency and qualitative relation with the possible linear drive, ITG modes are consistent with the experimental density fluctuations measurements. Micro-tearing modes (MTMs), found unstable with a lower growth rate, appear a possible explanation for magnetic fluctuations in terms of typical wavenumbers and direction of propagation.

Gaussian fluctuation of the diffusion exponent of virus capsid in a living cell nucleus

NASA Astrophysics Data System (ADS)

Itto, Yuichi

2018-05-01

In their work [4], Bosse et al. experimentally showed that virus capsid exhibits not only normal diffusion but also anomalous diffusion in nucleus of a living cell. There, it was found that the distribution of fluctuations of the diffusion exponent characterizing them takes the Gaussian form, which is, quite remarkably, the same form for two different types of the virus. This suggests high robustness of such fluctuations. Here, the statistical property of local fluctuations of the diffusion exponent of the virus capsid in the nucleus is studied. A maximum-entropy-principle approach (originally proposed for a different virus in a different cell) is applied for obtaining the fluctuation distribution of the exponent. Largeness of the number of blocks identified with local areas of interchromatin corrals is also examined based on the experimental data. It is shown that the Gaussian distribution of the local fluctuations can be derived, in accordance with the above form. In addition, it is quantified how the fluctuation distribution on a long time scale is different from the Gaussian distribution.

Complexity of low-frequency blood oxygen level-dependent fluctuations covaries with local connectivity.

PubMed

Anderson, Jeffrey S; Zielinski, Brandon A; Nielsen, Jared A; Ferguson, Michael A

2014-04-01

Very low-frequency blood oxygen level-dependent (BOLD) fluctuations have emerged as a valuable tool for describing brain anatomy, neuropathology, and development. Such fluctuations exhibit power law frequency dynamics, with largest amplitude at lowest frequencies. The biophysical mechanisms generating such fluctuations are poorly understood. Using publicly available data from 1,019 subjects of age 7-30, we show that BOLD fluctuations exhibit temporal complexity that is linearly related to local connectivity (regional homogeneity), consistently and significantly covarying across subjects and across gray matter regions. This relationship persisted independently of covariance with gray matter density or standard deviation of BOLD signal. During late neurodevelopment, BOLD fluctuations were unchanged with age in association cortex while becoming more random throughout the rest of the brain. These data suggest that local interconnectivity may play a key role in establishing the complexity of low-frequency BOLD fluctuations underlying functional magnetic resonance imaging connectivity. Stable low-frequency power dynamics may emerge through segmentation and integration of connectivity during development of distributed large-scale brain networks. Copyright © 2013 Wiley Periodicals, Inc.

Emergence of the self-similar property in gene expression dynamics

NASA Astrophysics Data System (ADS)

Ochiai, T.; Nacher, J. C.; Akutsu, T.

2007-08-01

Many theoretical models have recently been proposed to understand the structure of cellular systems composed of various types of elements (e.g., proteins, metabolites and genes) and their interactions. However, the cell is a highly dynamic system with thousands of functional elements fluctuating across temporal states. Therefore, structural analysis alone is not sufficient to reproduce the cell's observed behavior. In this article, we analyze the gene expression dynamics (i.e., how the amount of mRNA molecules in cell fluctuate in time) by using a new constructive approach, which reveals a symmetry embedded in gene expression fluctuations and characterizes the dynamical equation of gene expression (i.e., a specific stochastic differential equation). First, by using experimental data of human and yeast gene expression time series, we found a symmetry in short-time transition probability from time t to time t+1. We call it self-similarity symmetry (i.e., the gene expression short-time fluctuations contain a repeating pattern of smaller and smaller parts that are like the whole, but different in size). Secondly, we reconstruct the global behavior of the observed distribution of gene expression (i.e., scaling-law) and the local behavior of the power-law tail of this distribution. This approach may represent a step forward toward an integrated image of the basic elements of the whole cell.

A technique for plasma velocity-space cross-correlation

NASA Astrophysics Data System (ADS)

Mattingly, Sean; Skiff, Fred

2018-05-01

An advance in experimental plasma diagnostics is presented and used to make the first measurement of a plasma velocity-space cross-correlation matrix. The velocity space correlation function can detect collective fluctuations of plasmas through a localized measurement. An empirical decomposition, singular value decomposition, is applied to this Hermitian matrix in order to obtain the plasma fluctuation eigenmode structure on the ion distribution function. A basic theory is introduced and compared to the modes obtained by the experiment. A full characterization of these modes is left for future work, but an outline of this endeavor is provided. Finally, the requirements for this experimental technique in other plasma regimes are discussed.

Hierarchical Biomolecular Dynamics: Picosecond Hydrogen Bonding Regulates Microsecond Conformational Transitions.

PubMed

Buchenberg, Sebastian; Schaudinnus, Norbert; Stock, Gerhard

2015-03-10

Biomolecules exhibit structural dynamics on a number of time scales, including picosecond (ps) motions of a few atoms, nanosecond (ns) local conformational transitions, and microsecond (μs) global conformational rearrangements. Despite this substantial separation of time scales, fast and slow degrees of freedom appear to be coupled in a nonlinear manner; for example, there is theoretical and experimental evidence that fast structural fluctuations are required for slow functional motion to happen. To elucidate a microscopic mechanism of this multiscale behavior, Aib peptide is adopted as a simple model system. Combining extensive molecular dynamics simulations with principal component analysis techniques, a hierarchy of (at least) three tiers of the molecule's free energy landscape is discovered. They correspond to chiral left- to right-handed transitions of the entire peptide that happen on a μs time scale, conformational transitions of individual residues that take about 1 ns, and the opening and closing of structure-stabilizing hydrogen bonds that occur within tens of ps and are triggered by sub-ps structural fluctuations. Providing a simple mechanism of hierarchical dynamics, fast hydrogen bond dynamics is found to be a prerequisite for the ns local conformational transitions, which in turn are a prerequisite for the slow global conformational rearrangement of the peptide. As a consequence of the hierarchical coupling, the various processes exhibit a similar temperature behavior which may be interpreted as a dynamic transition.

Local fluctuations of the signed traded volumes and the dependencies of demands: a copula analysis

NASA Astrophysics Data System (ADS)

Wang, Shanshan; Guhr, Thomas

2018-03-01

We investigate how the local fluctuations of the signed traded volumes affect the dependence of demands between stocks. We analyze the empirical dependence of demands using copulas and show that they are well described by a bivariate K copula density function. We find that large local fluctuations strongly increase the positive dependence but lower slightly the negative one in the copula density. This interesting feature is due to cross-correlations of volume imbalances between stocks. Also, we explore the asymmetries of tail dependencies of the copula density, which are moderate for the negative dependencies but strong for the positive ones. For the latter, we reveal that large local fluctuations of the signed traded volumes trigger stronger dependencies of demands than of supplies, probably indicating a bull market with persistent raising of prices.

Nonlinear time series analysis of normal and pathological human walking

NASA Astrophysics Data System (ADS)

Dingwell, Jonathan B.; Cusumano, Joseph P.

2000-12-01

Characterizing locomotor dynamics is essential for understanding the neuromuscular control of locomotion. In particular, quantifying dynamic stability during walking is important for assessing people who have a greater risk of falling. However, traditional biomechanical methods of defining stability have not quantified the resistance of the neuromuscular system to perturbations, suggesting that more precise definitions are required. For the present study, average maximum finite-time Lyapunov exponents were estimated to quantify the local dynamic stability of human walking kinematics. Local scaling exponents, defined as the local slopes of the correlation sum curves, were also calculated to quantify the local scaling structure of each embedded time series. Comparisons were made between overground and motorized treadmill walking in young healthy subjects and between diabetic neuropathic (NP) patients and healthy controls (CO) during overground walking. A modification of the method of surrogate data was developed to examine the stochastic nature of the fluctuations overlying the nominally periodic patterns in these data sets. Results demonstrated that having subjects walk on a motorized treadmill artificially stabilized their natural locomotor kinematics by small but statistically significant amounts. Furthermore, a paradox previously present in the biomechanical literature that resulted from mistakenly equating variability with dynamic stability was resolved. By slowing their self-selected walking speeds, NP patients adopted more locally stable gait patterns, even though they simultaneously exhibited greater kinematic variability than CO subjects. Additionally, the loss of peripheral sensation in NP patients was associated with statistically significant differences in the local scaling structure of their walking kinematics at those length scales where it was anticipated that sensory feedback would play the greatest role. Lastly, stride-to-stride fluctuations in the walking patterns of all three subject groups were clearly distinguishable from linearly autocorrelated Gaussian noise. As a collateral benefit of the methodological approach taken in this study, some of the first steps at characterizing the underlying structure of human locomotor dynamics have been taken. Implications for understanding the neuromuscular control of locomotion are discussed.

Local self-energies for V and Pd emergent from a nonlocal LDA+FLEX implementation

NASA Astrophysics Data System (ADS)

Savrasov, Sergey Y.; Resta, Giacomo; Wan, Xiangang

2018-04-01

In the spirit of recently developed LDA+U and LDA+DMFT methods, we implement a combination of density functional theory in its local density approximation (LDA) with a k - and ω -dependent self-energy found from diagrammatic fluctuational exchange (FLEX) approximation. The active Hilbert space here is described by the correlated subset of electrons which allows one to tremendously reduce the sizes of the matrices needed to represent charge and spin susceptibilities. The method is perturbative in nature but accounts for both bubble and ladder diagrams and accumulates the physics of momentum-resolved spin fluctuations missing in such popular approach as GW. As an application, we study correlation effects on band structures in V and Pd. The d -electron self-energies emergent from this calculation are found to be remarkably k independent. However, when we compare our calculated electronic mass enhancements against LDA+DMFT, we find that for the longstanding problem of spin fluctuations in Pd, LDA+FLEX delivers a better agreement with experiment, although this conclusion depends on a particular value of the Hubbard U used in the simulation. We also discuss outcomes of a recently proposed combination of k -dependent FLEX with dynamical mean-field theory (DMFT).

Music Structure Analysis from Acoustic Signals

NASA Astrophysics Data System (ADS)

Dannenberg, Roger B.; Goto, Masataka

Music is full of structure, including sections, sequences of distinct musical textures, and the repetition of phrases or entire sections. The analysis of music audio relies upon feature vectors that convey information about music texture or pitch content. Texture generally refers to the average spectral shape and statistical fluctuation, often reflecting the set of sounding instruments, e.g., strings, vocal, or drums. Pitch content reflects melody and harmony, which is often independent of texture. Structure is found in several ways. Segment boundaries can be detected by observing marked changes in locally averaged texture.

Transition between Two Regimes Describing Internal Fluctuation of DNA in a Nanochannel

PubMed Central

Su, Tianxiang; Das, Somes K.; Xiao, Ming; Purohit, Prashant K.

2011-01-01

We measure the thermal fluctuation of the internal segments of a piece of DNA confined in a nanochannel about 50100 nm wide. This local thermodynamic property is key to accurate measurement of distances in genomic analysis. For DNA in 100 nm channels, we observe a critical length scale 10 m for the mean extension of internal segments, below which the de Gennes' theory describes the fluctuations with no fitting parameters, and above which the fluctuation data falls into Odijk's deflection theory regime. By analyzing the probability distributions of the extensions of the internal segments, we infer that folded structures of length 150250 nm, separated by 10 m exist in the confined DNA during the transition between the two regimes. For 50 nm channels we find that the fluctuation is significantly reduced since the Odijk regime appears earlier. This is critical for genomic analysis. We further propose a more detailed theory based on small fluctuations and incorporating the effects of confinement to explicitly calculate the statistical properties of the internal fluctuations. Our theory is applicable to polymers with heterogeneous mechanical properties confined in non-uniform channels. We show that existing theories for the end-to-end extension/fluctuation of polymers can be used to study the internal fluctuations only when the contour length of the polymer is many times larger than its persistence length. Finally, our results suggest that introducing nicks in the DNA will not change its fluctuation behavior when the nick density is below 1 nick per kbp DNA. PMID:21423606

Effect of supersonic molecular-beam injection on edge fluctuation and particle transport in Heliotron J

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

Zang, L., E-mail: l-zang@center.iae.kyoto-u.ac.jp; Kasajima, K.; Hashimoto, K.

Edge fluctuation in a supersonic molecular-beam injection (SMBI) fueled plasma has been measured using an electrostatic probe array. After SMBI, the plasma stored energy (W{sub p}) temporarily decreased then started to increase. The local plasma fluctuation and fluctuation induced particle transport before and after SMBI have been analyzed. In a short duration (∼4 ms) just after SMBI, the density fluctuation of broad-band low frequency increased, and the probability density function (PDF) changed from a nearly Gaussian to a positively skewed non-Gaussian one. This suggests that intermittent structures were produced due to SMBI. Also the fluctuation induced particle transport was greatly enhancedmore » during this short duration. About 4 ms after SMBI, the low frequency broad-band density fluctuation decreased, and the PDF returned to a nearly Gaussian shape. Also the fluctuation induced particle transport was reduced. Compared with conventional gas puff, W{sub p} degradation window is very short due to the short injection period of SMBI. After this short degradation window, fluctuation induced particle transport was reduced and W{sub p} started the climbing phase. Therefore, the short period of the influence to the edge fluctuation might be an advantage of this novel fueling technique. On the other hand, although their roles are not identified at present, coherent MHD modes are also suppressed as well by the application of SMBI. These MHD modes are thought to be de-exited due to a sudden change of the edge density and/or excitation conditions.« less

Local thermal energy as a structural indicator in glasses

NASA Astrophysics Data System (ADS)

Zylberg, Jacques; Lerner, Edan; Bar-Sinai, Yohai; Bouchbinder, Eran

2017-07-01

Identifying heterogeneous structures in glasses—such as localized soft spots—and understanding structure-dynamics relations in these systems remain major scientific challenges. Here, we derive an exact expression for the local thermal energy of interacting particles (the mean local potential energy change caused by thermal fluctuations) in glassy systems by a systematic low-temperature expansion. We show that the local thermal energy can attain anomalously large values, inversely related to the degree of softness of localized structures in a glass, determined by a coupling between internal stresses—an intrinsic signature of glassy frustration—anharmonicity and low-frequency vibrational modes. These anomalously large values follow a fat-tailed distribution, with a universal exponent related to the recently observed universal ω4ω4 density of states of quasilocalized low-frequency vibrational modes. When the spatial thermal energy field—a “softness field”—is considered, this power law tail manifests itself by highly localized spots, which are significantly softer than their surroundings. These soft spots are shown to be susceptible to plastic rearrangements under external driving forces, having predictive powers that surpass those of the normal modes-based approach. These results offer a general, system/model-independent, physical/observable-based approach to identify structural properties of quiescent glasses and relate them to glassy dynamics.

Edge Turbulence Imaging in Alcator C-Mod

NASA Astrophysics Data System (ADS)

Zweben, Stewart J.

2001-10-01

This talk will describe measurements and modeling of the 2-D structure of edge turbulence in Alcator C-Mod. The radial vs. poloidal structure was measured using Gas Puff Imaging (GPI) (R. Maqueda et al, RSI 72, 931 (2001), J. Terry et al, J. Nucl. Materials 290-293, 757 (2001)), in which the visible light emitted by an edge neutral gas puff (generally D or He) is viewed along the local magnetic field by a fast-gated video camera. Strong fluctuations are observed in the gas cloud light emission when the camera is gated at ~2 microsec exposure time per frame. The structure of these fluctuations is highly turbulent with a typical radial and poloidal scale of ≈1 cm, and often with local maxima in the scrape-off layer (i.e. ``blobs"). Video clips and analyses of these images will be presented along with their variation in different plasma regimes. The local time dependence of edge turbulence is measured using high-speed photodiodes viewing the gas puff emission, a scanning Langmuir probe, and also with a Princeton Scientific Instruments ultra-fast framing camera, which can make 2-D images the gas puff at up to 200,000 frames/sec. Probe measurements show that the strong turbulence region moves to the separatrix as the density limit is approached, which may be connected to the density limit (B. LaBombard et al., Phys. Plasmas 8 2107 (2001)). Comparisons of this C-Mod turbulence data will be made with results of simulations from the Drift-Ballooning Mode (DBM) (B.N. Rogers et al, Phys. Rev. Lett. 20 4396 (1998))and Non-local Edge Turbulence (NLET) codes.

Brain alterations in low-frequency fluctuations across multiple bands in obsessive compulsive disorder.

PubMed

Giménez, Mònica; Guinea-Izquierdo, Andrés; Villalta-Gil, Victoria; Martínez-Zalacaín, Ignacio; Segalàs, Cinto; Subirà, Marta; Real, Eva; Pujol, Jesús; Harrison, Ben J; Haro, Josep Maria; Sato, Joao R; Hoexter, Marcelo Q; Cardoner, Narcís; Alonso, Pino; Menchón, José Manuel; Soriano-Mas, Carles

2017-12-01

The extent of functional abnormalities in frontal-subcortical circuits in obsessive-compulsive disorder (OCD) is still unclear. Although neuroimaging studies, in general, and resting-state functional Magnetic Resonance Imaging (rs-fMRI), in particular, have provided relevant information regarding such alterations, rs-fMRI studies have been typically limited to the analysis of between-region functional connectivity alterations at low-frequency signal fluctuations (i.e., <0.08 Hz). Conversely, the local attributes of Blood Oxygen Level Dependent (BOLD) signal across different frequency bands have been seldom studied, although they may provide valuable information. Here, we evaluated local alterations in low-frequency fluctuations across different oscillation bands in OCD. Sixty-five OCD patients and 50 healthy controls underwent an rs-fMRI assessment. Alterations in the fractional amplitude of low-frequency fluctuations (fALFF) were evaluated, voxel-wise, across four different bands (from 0.01 Hz to 0.25 Hz). OCD patients showed decreased fALFF values in medial orbitofrontal regions and increased fALFF values in the dorsal-medial prefrontal cortex (DMPFC) at frequency bands <0.08 Hz. This pattern was reversed at higher frequencies, where increased fALFF values also appeared in medial temporal lobe structures and medial thalamus. Clinical variables (i.e., symptom-specific severities) were associated with fALFF values across the different frequency bands. Our findings provide novel evidence about the nature and regional distribution of functional alterations in OCD, which should contribute to refine neurobiological models of the disorder. We suggest that the evaluation of the local attributes of BOLD signal across different frequency bands may be a sensitive approach to further characterize brain functional alterations in psychiatric disorders.

Polarons and Mobile Impurities Near a Quantum Phase Transition

NASA Astrophysics Data System (ADS)

Shadkhoo, Shahriar

This dissertation aims at improving the current understanding of the physics of mobile impurities in highly correlated liquid-like phases of matter. Impurity problems pose challenging and intricate questions in different realms of many-body physics. For instance, the problem of ''solvation'' of charged solutes in polar solvents, has been the subject of longstanding debates among chemical physicists. The significant role of quantum fluctuations of the solvent, as well as the break down of linear response theory, render the ordinary treatments intractable. Inspired by this complicated problem, we first attempt to understand the role of non-specific quantum fluctuations in the solvation process. To this end, we calculate the dynamic structure factor of a model polar liquid, using the classical Molecular Dynamics (MD) simulations. We verify the failure of linear response approximation in the vicinity of a hydrated electron, by comparing the outcomes of MD simulations with the predictions of linear response theory. This nonlinear behavior is associated with the pronounced peaks of the structure factor, which reflect the strong fluctuations of the local modes. A cavity picture is constructed based on heuristic arguments, which suggests that the electron, along with the surrounding polarization cloud, behave like a frozen sphere, for which the linear response theory is broken inside and valid outside. The inverse radius of the spherical region serves as a UV momentum cutoff for the linear response approximation to be applicable. The problem of mobile impurities in polar liquids can be also addressed in the framework of the ''polaron'' problem. Polaron is a quasiparticle that typically acquires an extended state at weak couplings, and crossovers to a self-trapped state at strong couplings. Using the analytical fits to the numerically obtained charge-charge structure factor, a phenomenological approach is proposed within the Leggett's influence functional formalism, which derives the effective Euclidean action from the classical equation of motion. We calculate the effective mass of the polaron in the model polar liquid at zero and finite temperatures. The self-trapping transition of this polaron turns out to be discontinuous in certain regions of the phase diagram. In order to systematically investigate the role of quantum fluctuations on the polaron properties, we adopt a quantum field theory which supports nearly-critical local modes: the quantum Landau-Brazovskii (QLB) model, which exhibits fluctuation-induced first order transition (weak crystallization). In the vicinity of the phase transition, the quantum fluctuations are strongly correlated; one can in principle tune the strength of these fluctuations, by adjusting the parameters close to or away from the transition point. Furthermore, sufficiently close to the transition, the theory accommodates "soliton'' solutions, signaling the nonlinear response of the system. Therefore, the model seems to be a promising candidate for studying the effects of strong quantum fluctuations and also failure of linear response theory, in the polaron problem. We observe that at zero temperature, and away from the Brazovskii transition where the linear response approximation is valid, the localization transition of the polaron is discontinuous. Upon enhancing fluctuations---of either thermal or quantum nature---the gap of the effective mass closes at distinct second-order critical points. Sufficiently close to the Brazovskii transition where the nonlinear contributions of the field are significantly large, a new state appears in addition to extended and self-trapped polarons: an impurity-induced soliton. We interpret this as the break-down of linear response, reminiscent of what we observe in a polar liquid. Quantum LB model has been proposed to be realizable in ultracold Bose gases in cavities. We thus discuss the experimental feasibility, and propose a setup which is believed to exhibit the aforementioned polaronic and solitonic states. We eventually generalize the polaron formalism to the case of impurities that couple quadratically to a nearly-critical field; hence called the ''quadratic polaron''. The Hertz-Millis field theory and its generalization to the case of magnetic transition in helimagnets, is taken as a toy model. The phase diagram of the bare model contains both second-order and fluctuation-induced first-order quantum phase transitions. We propose a semi-classical scenario in which the impurity and the field couple quadratically. The polaron properties in the vicinity of these transitions are calculated in different dimensions. We observe that the quadratic coupling in three dimensions, even in the absence of the critical modes with finite wavelength, leads to a jump-like localization of the polaron. In lower dimensions, the transition behavior remains qualitatively similar to those in the case of linear coupling, namely the critical modes must have a finite wavelength to localize the particle.

Fluctuations and symmetry energy in nuclear fragmentation dynamics.

PubMed

Colonna, M

2013-01-25

Within a dynamical description of nuclear fragmentation, based on the liquid-gas phase transition scenario, we explore the relation between neutron-proton density fluctuations and nuclear symmetry energy. We show that, along the fragmentation path, isovector fluctuations follow the evolution of the local density and approach an equilibrium value connected to the local symmetry energy. Higher-density regions are characterized by smaller average asymmetry and narrower isotopic distributions. This dynamical analysis points out that fragment final state isospin fluctuations can probe the symmetry energy of the density domains from which fragments originate.

Experimental studies of toroidal correlations of plasma density fluctuations along the magnetic field lines in the T-10 tokamak and first results of numerical modeling

NASA Astrophysics Data System (ADS)

Buldakov, M. A.; Vershkov, V. A.; Isaev, M. Yu; Shelukhin, D. A.

2017-10-01

The antenna system of reflectometry diagnostics at the T-10 tokamak allows to study long-range toroidal correlations of plasma density fluctuations along the magnetic field lines. The antenna systems are installed in two poloidal cross-sections of the vacuum chamber separated by a 90° angle in the toroidal direction. The experiments, which were conducted at the low field side, showed that the high level of toroidal correlations is observed only for quasi-coherent fluctuations. However, broadband and stochastic low frequency fluctuations are not correlated. Numerical modeling of the plasma turbulence structure in the T-10 tokamak was conducted to interpret the experimental results and take into account non-locality of reflectometry measurements. In the model used, it was assumed that the magnitudes of density fluctuations are constant along the magnetic field lines. The 2D full-wave Tamic-RTH code was used to model the reflectometry signals. High level of correlations for quasi-coherent fluctuations was obtained during the modeling, which agrees with the experimental observations. However, the performed modeling also predicts high level of correlations for broadband fluctuations, which contradicts the experimental data. The modeling showed that the effective reflection radius, from which the information on quasi-coherent plasma turbulence is obtained, is shifted outwards from the reflection radius by approximately 7 mm.

Kinetic-Scale Electric and Magnetic Field Fluctuations in the Solar Wind at 1 AU: THEMIS/ARTEMIS Observations

NASA Astrophysics Data System (ADS)

Salem, C. S.; Hanson, E.; Bonnell, J. W.; Chaston, C. C.; Bale, S. D.; Mozer, F.

2017-12-01

We present here an analysis of kinetic-scale electromagnetic fluctuations in the solar wind using data from THEMIS and ARTEMIS spacecraft. We use high-time resolution electric and magnetic field measurements, as well as density fluctuations, up to 128 samples per second, as well as particle burst plasma data during carefully selected solar wind intervals. We focus our analysis on a few such intervals spanning different values of plasma beta and angles between the local magnetic field and the radial Sun-Earth direction. We discuss the careful analysis process of characterizing and removing the different instrumental effects and noise sources affecting the electric and magnetic field data at those scales, above 0.1 Hz or so, above the breakpoint marking the start of the so-called dissipation range of solar wind turbulence. We compute parameters such as the electric to magnetic field ratio, the magnetic compressibility, magnetic helicity, and other relevant quantities in order to diagnose the nature of the fluctuations at those scales between the ion and electron cyclotron frequencies, extracting information on the dominant modes composing the fluctuations. We also discuss the presence and role of coherent structures in the measured fluctuations. The nature of the fluctuations in the dissipation or dispersive scales of solar wind turbulence is still debated. This observational study is also highly relevant to the current Turbulent Dissipation Challenge.

Local time asymmetries and toroidal field line resonances: Global magnetospheric modeling in SWMF

NASA Astrophysics Data System (ADS)

Ellington, S. M.; Moldwin, M. B.; Liemohn, M. W.

2016-03-01

We present evidence of resonant wave-wave coupling via toroidal field line resonance (FLR) signatures in the Space Weather Modeling Framework's (SWMF) global, terrestrial magnetospheric model in one simulation driven by a synthetic upstream solar wind with embedded broadband dynamic pressure fluctuations. Using in situ, stationary point measurements of the radial electric field along the 1500 LT meridian, we show that SWMF reproduces a multiharmonic, continuous distribution of FLRs exemplified by 180° phase reversals and amplitude peaks across the resonant L shells. By linearly increasing the amplitude of the dynamic pressure fluctuations in time, we observe a commensurate increase in the amplitude of the radial electric and azimuthal magnetic field fluctuations, which is consistent with the solar wind driver being the dominant source of the fast mode energy. While we find no discernible local time changes in the FLR frequencies despite large-scale, monotonic variations in the dayside equatorial mass density, in selectively sampling resonant points and examining spectral resonance widths, we observe significant radial, harmonic, and time-dependent local time asymmetries in the radial electric field amplitudes. A weak but persistent local time asymmetry exists in measures of the estimated coupling efficiency between the fast mode and toroidal wave fields, which exhibits a radial dependence consistent with the coupling strength examined by Mann et al. (1999) and Zhu and Kivelson (1988). We discuss internal structural mechanisms and additional external energy sources that may account for these asymmetries as we find that local time variations in the strength of the compressional driver are not the predominant source of the FLR amplitude asymmetries. These include resonant mode coupling of observed Kelvin-Helmholtz surface wave generated Pc5 band ultralow frequency pulsations, local time differences in local ionospheric dampening rates, and variations in azimuthal mode number, which may impact the partitioning of spectral energy between the toroidal and poloidal wave modes.

An improved method to characterise the modulation of small-scale turbulent by large-scale structures

NASA Astrophysics Data System (ADS)

Agostini, Lionel; Leschziner, Michael; Gaitonde, Datta

2015-11-01

A key aspect of turbulent boundary layer dynamics is ``modulation,'' which refers to degree to which the intensity of coherent large-scale structures (LS) cause an amplification or attenuation of the intensity of the small-scale structures (SS) through large-scale-linkage. In order to identify the variation of the amplitude of the SS motion, the envelope of the fluctuations needs to be determined. Mathis et al. (2009) proposed to define this latter by low-pass filtering the modulus of the analytic signal built from the Hilbert transform of SS. The validity of this definition, as a basis for quantifying the modulated SS signal, is re-examined on the basis of DNS data for a channel flow. The analysis shows that the modulus of the analytic signal is very sensitive to the skewness of its PDF, which is dependent, in turn, on the sign of the LS fluctuation and thus of whether these fluctuations are associated with sweeps or ejections. The conclusion is that generating an envelope by use of a low-pass filtering step leads to an important loss of information associated with the effects of the local skewness of the PDF of the SS on the modulation process. An improved Hilbert-transform-based method is proposed to characterize the modulation of SS turbulence by LS structures

Complex spatial dynamics maintain northern leopard frog (Lithobates pipiens) genetic diversity in a temporally varying landscape

USGS Publications Warehouse

Mushet, David M.; Euliss, Ned H.; Chen, Yongjiu; Stockwell, Craig A.

2013-01-01

In contrast to most local amphibian populations, northeastern populations of the Northern Leopard Frog (Lithobates pipiens) have displayed uncharacteristically high levels of genetic diversity that have been attributed to large, stable populations. However, this widely distributed species also occurs in areas known for great climatic fluctuations that should be reflected in corresponding fluctuations in population sizes and reduced genetic diversity. To test our hypothesis that Northern Leopard Frog genetic diversity would be reduced in areas subjected to significant climate variability, we examined the genetic diversity of L. pipiens collected from 12 sites within the Prairie Pothole Region of North Dakota. Despite the region's fluctuating climate that includes periods of recurring drought and deluge, we found unexpectedly high levels of genetic diversity approaching that of northeastern populations. Further, genetic structure at a landscape scale was strikingly homogeneous; genetic differentiation estimates (Dest) averaged 0.10 (SD = 0.036) across the six microsatellite loci we studied, and two Bayesian assignment tests (STRUCTURE and BAPS) failed to reveal the development of significant population structure across the 68 km breadth of our study area. These results suggest that L. pipiens in the Prairie Pothole Region consists of a large, panmictic population capable of maintaining high genetic diversity in the face of marked climate variability.

Learning about the very local interstellar medium from the Voyagers

NASA Astrophysics Data System (ADS)

Florinski, V. A.; Guo, X.; Burlaga, L. F.

2017-12-01

The outer heliosheath is the region in front of the heliopause affected by the interaction between the solar wind and the flow of interstellar gas. Voyager 1 has been exploring this region for over five years uncovering a number of remarkable phenomena not present elsewhere in space directly accessible by spacecraft. The very local interstellar medium (VLISM) is characterized by remarkably low levels of magnetic fluctuation intensities presenting a nearly scatter free environment for energetic particle propagation. The fluctuations have power law spectra and probably belong to the inertial range of a turbulent cascade fed by a variety of sources, including large and kinetic scale instabilities and the inner heliosheath structures transmitted across the heliopause. While the fluxes of galactic cosmic rays are, on average, very steady in the VLISM, in agreement with theoretical expectations, they also show episodic depletions at the 90 degree pitch angle. These anisotropy events may be associated with the passage of weak compressive magnetic structures resembling shock waves, but with ramp widths orders of magnitude broader than the relevant kinetic plasma scales. The key to understanding the VLISM lies in recognizing the interconnections between the magnetic field data, which has a "local" character, the highly mobile cosmic rays that sample vast regions of space along magnetic field lines, and neutral atom populations measured by IBEX that can reveal kinetic scale physics of energetic ions produced in charge exchange events.

Self-Organized Criticality, Multifractals, and Intermittent Turbulence in Earth's Magnetotail

NASA Technical Reports Server (NTRS)

Chang, Tom

2004-01-01

We have achieved all the goals stated in our grant proposal in collaboration with Dr. C.C. Wu of the University of California at Los Angeles. Specifically, these include: The understanding of the complexity induced nonlinear spatiotemporal structures and the coexisting propagating modes. The development of plasma resonances and coherent structures in space plasmas. The study of fluctuation-induced nonlinear instabilities and their role in the reconfiguration of magnetic topologies in the magnetotail. The development of "anisotropic three-dimensional complexity" in the plasma sheet due to localized merging and interactions of the magnetic coherent structures and associated topological phase transitions. The understanding of the intermittent turbulence and energization process of the observed Bursty Bulk Flows (BBF's) in the Earth s magnetotail. The acceleration of ions due to the intermittent turbulence of propagating arid nonpropagating fluctuations In the following, we include lists of our published papers, invited talks, and professional activities. A detailed description of our accomplished research results is given in Section IV.

Dynamic Transmission of Protein Allostery without Structural Change: Spatial Pathways or Global Modes?

PubMed Central

McLeish, Tom C.B.; Cann, Martin J.; Rodgers, Thomas L.

2015-01-01

We examine the contrast between mechanisms for allosteric signaling that involve structural change, and those that do not, from the perspective of allosteric pathways. In particular we treat in detail the case of fluctuation-allostery by which amplitude modulation of the thermal fluctuations of the elastic normal modes conveys the allosteric signal, and address the question of what an allosteric pathway means in this case. We find that a perturbation theory of thermal elastic solids and nonperturbative approach (by super-coarse-graining elasticity into internal bending modes) have opposite signatures in their structure of correlated pathways. We illustrate the effect from analysis of previous results from GlxR of Corynebacterium glutamicum, an example of the CRP/FNR transcription family of allosteric homodimers. We find that the visibility of both correlated pathways and disconnected sites of correlated motion in this protein suggests that mechanisms of local elastic stretch and bend are recruited for the purpose of creating and controlling allosteric cooperativity. PMID:26338443

Observation of magnetic fluctuations and rapid density decay of magnetospheric plasma in Ring Trap 1

NASA Astrophysics Data System (ADS)

Saitoh, H.; Yoshida, Z.; Morikawa, J.; Yano, Y.; Mikami, H.; Kasaoka, N.; Sakamoto, W.

2012-06-01

The Ring Trap 1 device, a magnetospheric configuration generated by a levitated dipole field magnet, has created high-β (local β ˜ 70%) plasma by using electron cyclotron resonance heating (ECH). When a large population of energetic electrons is generated at low neutral gas pressure operation, high frequency magnetic fluctuations are observed. When the fluctuations are strongly excited, rapid loss of plasma was simultaneously observed especially in a quiet decay phase after the ECH microwave power is turned off. Although the plasma is confined in a strongly inhomogeneous dipole field configuration, the frequency spectra of the fluctuations have sharp frequency peaks, implying spatially localized sources of the fluctuations. The fluctuations are stabilized by decreasing the hot electron component below approximately 40%, realizing stable high-β confinement.

Structure and Liquid Fragility in Sodium Carbonate.

PubMed

Wilson, Mark; Ribeiro, Mauro C C; Wilding, Martin C; Benmore, Chris; Weber, J K R; Alderman, Oliver; Tamalonis, Anthony; Parise, J B

2018-02-01

The relationship between local structure and dynamics is explored for molten sodium carbonate. A flexible fluctuating-charge model, which allows for changes in the shape and charge distribution of the carbonate molecular anion, is developed. The system shows the evolution of highly temperature-dependent complex low-dimensional structures which control the dynamics (and hence the liquid fragility). By varying the molecular anion charge distribution, the key interactions responsible for the formation of these structures can be identified and rationalized. An increase in the mean charge separation within the carbonate ions increases the connectivity of the emerging structures and leads to an increase in the system fragility.

Shock Induced Chemistry: Application and Development of Ultrafast Nonlinear Probes of the Energy Dynamics of Molecules in Solids

DTIC Science & Technology

1988-01-01

crystal and in a mixed crystal. The mixed crystal data was taken with resonance enhancement by the pentacene .. ... 7 Accesiw, r)re 0IE r)) NiS cR4~ IE~) D...observations as well as their implications about the nature of the coupling of a localized defect to the bulk modes of the crystal have been analyzed [7...matter systems, in addition to phonon induced fluctuations of local mechanical properties, there can be much slower timescale structural evolution

Thermodynamic and Structural Properties of Methanol-Water Solutions Using Non-Additive Interaction Models

PubMed Central

Zhong, Yang; Warren, G. Lee; Patel, Sandeep

2014-01-01

We study bulk structural and thermodynamic properties of methanol-water solutions via molecular dynamics simulations using novel interaction potentials based on the charge equilibration (fluctuating charge) formalism to explicitly account for molecular polarization at the atomic level. The study uses the TIP4P-FQ potential for water-water interactions, and the CHARMM-based (Chemistry at HARvard Molecular Mechanics) fluctuating charge potential for methanol-methanol and methanol-water interactions. In terms of bulk solution properties, we discuss liquid densities, enthalpies of mixing, dielectric constants, self-diffusion constants, as well as structural properties related to local hydrogen bonding structure as manifested in radial distribution functions and cluster analysis. We further explore the electronic response of water and methanol in the differing local environments established by the interaction of each species predominantly with molecules of the other species. The current force field for the alcohol-water interaction performs reasonably well for most properties, with the greatest deviation from experiment observed for the excess mixing enthalpies, which are predicted to be too favorable. This is qualitatively consistent with the overestimation of the methanol-water gas-phase interaction energy for the lowest-energy conformer (methanol as proton donor). Hydration free energies for methanol in TIP4P-FQ water are predicted to be −5.6±0.2 kcal/mole, in respectable agreement with the experimental value of −5.1 kcal/mole. With respect to solution micro-structure, the present cluster analysis suggests that the micro-scale environment for concentrations where select thermodynamic quantities reach extremal values is described by a bi-percolating network structure. PMID:18074339

An experimental study of the local electronic structure of B-site gallium doped bismuth ferrite powders

NASA Astrophysics Data System (ADS)

Gholam, Turghunjan; Ablat, Abduleziz; Mamat, Mamatrishat; Wu, Rong; Aimidula, Aimierding; Bake, Muhammad Ali; Zheng, Lirong; Wang, Jiaou; Qian, Haijie; Wu, Rui; Ibrahim, Kurash

2017-08-01

The un-doped and gallium (Ga) doped multiferroic bismuth ferrite (BiFeO3) compounds were successfully synthesized by the hydrothermal technique. This is then followed by a series of detailed investigations into the influence of Ga doping on the structural, morphological, optical and magnetic properties of BiFe1 - xGaxO3 (0 ≤ x ≤ 0.15). X-ray diffraction (XRD) analyses reveal that B-site doping of Ga may lead to the transformation of its crystal structure from a rhombohedral with a space group of R3c to an orthorhombic with a space group of Pbnm phase. The scanning electron microscope (SEM) images show that doping with Ga causes a significant reduction in particle size, when compared to un-doped BiFeO3. X-ray absorption near-edge structure (XANES) spectra have also shown that as the substitution of Ga increases, the Fe K and Bi LIII-edge absorption spectra shift towards higher energy site. It also implies that doping of Ga affects the local structures of both Bi and Fe atoms. Distinct transmission band fluctuations, as shown by Fourier transform infrared (FT-IR) spectra, can provide significant evidence for a transformation in crystal structure, following the increase of Ga concentration. The magnetization hysteresis measurements show that the magnetization decreases when Ga content is x ≥ 0.05. Such a phenomenon mainly stems from the substitution of Fe for an excessive amount of Ga, resulting in reduction of both valence fluctuations and the magnetization in the BiFe1 - xGaxO3 system.

The effects of climatic fluctuations and extreme events on running water ecosystems

PubMed Central

Woodward, Guy; Bonada, Núria; Brown, Lee E.; Death, Russell G.; Durance, Isabelle; Gray, Clare; Hladyz, Sally; Ledger, Mark E.; Milner, Alexander M.; Ormerod, Steve J.; Thompson, Ross M.

2016-01-01

Most research on the effects of environmental change in freshwaters has focused on incremental changes in average conditions, rather than fluctuations or extreme events such as heatwaves, cold snaps, droughts, floods or wildfires, which may have even more profound consequences. Such events are commonly predicted to increase in frequency, intensity and duration with global climate change, with many systems being exposed to conditions with no recent historical precedent. We propose a mechanistic framework for predicting potential impacts of environmental fluctuations on running-water ecosystems by scaling up effects of fluctuations from individuals to entire ecosystems. This framework requires integration of four key components: effects of the environment on individual metabolism, metabolic and biomechanical constraints on fluctuating species interactions, assembly dynamics of local food webs, and mapping the dynamics of the meta-community onto ecosystem function. We illustrate the framework by developing a mathematical model of environmental fluctuations on dynamically assembling food webs. We highlight (currently limited) empirical evidence for emerging insights and theoretical predictions. For example, widely supported predictions about the effects of environmental fluctuations are: high vulnerability of species with high per capita metabolic demands such as large-bodied ones at the top of food webs; simplification of food web network structure and impaired energetic transfer efficiency; and reduced resilience and top-down relative to bottom-up regulation of food web and ecosystem processes. We conclude by identifying key questions and challenges that need to be addressed to develop more accurate and predictive bio-assessments of the effects of fluctuations, and implications of fluctuations for management practices in an increasingly uncertain world. PMID:27114576

Structural features that predict real-value fluctuations of globular proteins.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2012-05-01

It is crucial to consider dynamics for understanding the biological function of proteins. We used a large number of molecular dynamics (MD) trajectories of nonhomologous proteins as references and examined static structural features of proteins that are most relevant to fluctuations. We examined correlation of individual structural features with fluctuations and further investigated effective combinations of features for predicting the real value of residue fluctuations using the support vector regression (SVR). It was found that some structural features have higher correlation than crystallographic B-factors with fluctuations observed in MD trajectories. Moreover, SVR that uses combinations of static structural features showed accurate prediction of fluctuations with an average Pearson's correlation coefficient of 0.669 and a root mean square error of 1.04 Å. This correlation coefficient is higher than the one observed in predictions by the Gaussian network model (GNM). An advantage of the developed method over the GNMs is that the former predicts the real value of fluctuation. The results help improve our understanding of relationships between protein structure and fluctuation. Furthermore, the developed method provides a convienient practial way to predict fluctuations of proteins using easily computed static structural features of proteins. Copyright © 2012 Wiley Periodicals, Inc.

Structural features that predict real-value fluctuations of globular proteins

PubMed Central

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2012-01-01

It is crucial to consider dynamics for understanding the biological function of proteins. We used a large number of molecular dynamics trajectories of non-homologous proteins as references and examined static structural features of proteins that are most relevant to fluctuations. We examined correlation of individual structural features with fluctuations and further investigated effective combinations of features for predicting the real-value of residue fluctuations using the support vector regression. It was found that some structural features have higher correlation than crystallographic B-factors with fluctuations observed in molecular dynamics trajectories. Moreover, support vector regression that uses combinations of static structural features showed accurate prediction of fluctuations with an average Pearson’s correlation coefficient of 0.669 and a root mean square error of 1.04 Å. This correlation coefficient is higher than the one observed for the prediction by the Gaussian network model. An advantage of the developed method over the Gaussian network models is that the former predicts the real-value of fluctuation. The results help improve our understanding of relationships between protein structure and fluctuation. Furthermore, the developed method provides a convienient practial way to predict fluctuations of proteins using easily computed static structural features of proteins. PMID:22328193

Scaling in cognitive performance reflects multiplicative multifractal cascade dynamics

PubMed Central

Stephen, Damian G.; Anastas, Jason R.; Dixon, James A.

2012-01-01

Self-organized criticality purports to build multi-scaled structures out of local interactions. Evidence of scaling in various domains of biology may be more generally understood to reflect multiplicative interactions weaving together many disparate scales. The self-similarity of power-law scaling entails homogeneity: fluctuations distribute themselves similarly across many spatial and temporal scales. However, this apparent homogeneity can be misleading, especially as it spans more scales. Reducing biological processes to one power-law relationship neglects rich cascade dynamics. We review recent research into multifractality in executive-function cognitive tasks and propose that scaling reflects not criticality but instead interactions across multiple scales and among fluctuations of multiple sizes. PMID:22529819

Noise-induced escape in an excitable system

NASA Astrophysics Data System (ADS)

Khovanov, I. A.; Polovinkin, A. V.; Luchinsky, D. G.; McClintock, P. V. E.

2013-03-01

We consider the stochastic dynamics of escape in an excitable system, the FitzHugh-Nagumo (FHN) neuronal model, for different classes of excitability. We discuss, first, the threshold structure of the FHN model as an example of a system without a saddle state. We then develop a nonlinear (nonlocal) stability approach based on the theory of large fluctuations, including a finite-noise correction, to describe noise-induced escape in the excitable regime. We show that the threshold structure is revealed via patterns of most probable (optimal) fluctuational paths. The approach allows us to estimate the escape rate and the exit location distribution. We compare the responses of a monostable resonator and monostable integrator to stochastic input signals and to a mixture of periodic and stochastic stimuli. Unlike the commonly used local analysis of the stable state, our nonlocal approach based on optimal paths yields results that are in good agreement with direct numerical simulations of the Langevin equation.

Effect of periodic fluctuation of soil particle rotation resistance on interface shear behaviour

NASA Astrophysics Data System (ADS)

Ebrahimian, Babak; Noorzad, Asadollah

2010-06-01

The interface behaviour between infinite extended narrow granular layer and bounding structure is numerically investigated using finite element method. The micro-polar (Cosserat) continuum approach within the framework of elasto-plasticity is employed to remove the numerical difficulties caused by strain-softening of materials in classical continuum mechanics. Mechanical properties of cohesionless granular soil are described with Lade's model enhanced with polar terms including Cosserat rotations, curvatures and couple stresses via mean grain diameter as the internal length. The main attention of paper is laid on the influence of spatial periodic fluctuation of rotation resistance of soil particles interlocked with the surface of bounding structure on evolution and location of shear band developed inside granular body. The finite element results demonstrate that the location and evolution of shear localization in granular body is strongly affected by prescribed non-uniform micro-polar kinematic boundary conditions along the interface.

Fluctuating local field method probed for a description of small classical correlated lattices

NASA Astrophysics Data System (ADS)

Rubtsov, Alexey N.

2018-05-01

Thermal-equilibrated finite classical lattices are considered as a minimal model of the systems showing an interplay between low-energy collective fluctuations and single-site degrees of freedom. Standard local field approach, as well as classical limit of the bosonic DMFT method, do not provide a satisfactory description of Ising and Heisenberg small lattices subjected to an external polarizing field. We show that a dramatic improvement can be achieved within a simple approach, in which the local field appears to be a fluctuating quantity related to the low-energy degree(s) of freedom.

Origin of the non-monotonic variance of Tc in the 1111 iron based superconductors with isovalent doping

PubMed Central

Usui, Hidetomo; Suzuki, Katsuhiro; Kuroki, Kazuhiko

2015-01-01

Motivated by recent experimental investigations of the isovalent doping iron-based superconductors LaFe(AsxP1-x)O1-yFy and NdFe(AsxP1-x)O1-yFy, we theoretically study the correlation between the local lattice structure, the Fermi surface, the spin fluctuation-mediated superconductivity, and the composition ratio. In the phosphides, the dXZ and dYZ orbitals barely hybridize around the Γ point to give rise to two intersecting ellipse shape Fermi surfaces. As the arsenic content increases and the Fe-As-Fe bond angle is reduced, the hybridization increases, so that the two bands are mixed to result in concentric inner and outer Fermi surfaces, and the orbital character gradually changes to dxz and dyz, where x–y axes are rotated by 45 degrees from X–Y. This makes the orbital matching between the electron and hole Fermi surfaces better and enhances the spin fluctuation within the dxz/yz orbitals. On the other hand, the hybridization splits the two bands, resulting in a more dispersive inner band. Hence, there is a trade-off between the density of states and the orbital matching, thereby locally maximizing the dxz/yz spin fluctuation and superconductivity in the intermediate regime of As/P ratio. The consistency with the experiment strongly indicate the importance of the spin fluctuation played in this series of superconductors. PMID:26073071

Fourier and wavelet analyses of intermittent and resonant pressure components in a slot burner

NASA Astrophysics Data System (ADS)

Pagliaroli, Tiziano; Mancinelli, Matteo; Troiani, Guido; Iemma, Umberto; Camussi, Roberto

2018-01-01

In laboratory-scale burner it has been observed that the acoustic excitations change the flame topology inducing asymmetry and oscillations. Hence, an acoustic and aeroacoustic study in non reactive condition is of primary importance during the design stage of a new burner in order to avoid the development of standing waves which can force the flame. So wall pressure fluctuations inside and outside of a novel slot burner have been studied experimentally and numerically for a broad range of geometrical parameters and mass flow rates. Wall pressure fluctuations have been measured through cavity-mounted microphones, providing uni- and multi-variate pressure statistics in both the time and frequency domains. Furthermore, since the onset of combustion-driven oscillations is always presaged by intermittent bursts of high amplitude, a wavelet-based conditional sampling procedure was applied to the database in order to detect coherent signatures embedded in the pressure time signals. Since for a particular case the coherent structures identified have a multi-scale signature, a wavelet-based decomposition technique was proposed as well to separate the contribution of the large- and small-scale flow structures to the pressure fluctuation field. As a main outcome of the activity no coupling between standing waves and velocity fluctuations was observed, but only well localized pressure signatures with shape strongly affected by the neighbouring flow physics.

Muon spin relaxation study of the layered magnetoelectric FeTe2O5Br with spin amplitude modulated magnetic structure

NASA Astrophysics Data System (ADS)

Zorko, A.; Pregelj, M.; Berger, H.; Arčon, D.

2010-05-01

Local-probe weak-transverse-field and zero-field μSR measurements have been employed to investigate magnetic ordering in the new magnetoelectric compound FeTe2O5Br. Below the Néel transition temperature TN=10.6 K a static local magnetic field starts to develop at the μ+ sites. Fast μ+ polarization decay below TN speaks in favor of a broad distribution of internal magnetic fields, in agreement with the incommensurate magnetic structure suggested by neutron diffraction experiments. Above TN the presence of short-range order is detected as high as at 2TN, which suggests only weak interlayer magnetic coupling. On the other hand, strong Fe3+ spin fluctuations likely reflect geometrically frustrated structure of [Fe4O16]20- spin clusters, which are the main building blocks of the layered FeTe2O5Br structure.

Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology

PubMed Central

Lezon, Timothy R.; Bahar, Ivet

2010-01-01

Comparison of elastic network model predictions with experimental data has provided important insights on the dominant role of the network of inter-residue contacts in defining the global dynamics of proteins. Most of these studies have focused on interpreting the mean-square fluctuations of residues, or deriving the most collective, or softest, modes of motions that are known to be insensitive to structural and energetic details. However, with increasing structural data, we are in a position to perform a more critical assessment of the structure-dynamics relations in proteins, and gain a deeper understanding of the major determinants of not only the mean-square fluctuations and lowest frequency modes, but the covariance or the cross-correlations between residue fluctuations and the shapes of higher modes. A systematic study of a large set of NMR-determined proteins is analyzed using a novel method based on entropy maximization to demonstrate that the next level of refinement in the elastic network model description of proteins ought to take into consideration properties such as contact order (or sequential separation between contacting residues) and the secondary structure types of the interacting residues, whereas the types of amino acids do not play a critical role. Most importantly, an optimal description of observed cross-correlations requires the inclusion of destabilizing, as opposed to exclusively stabilizing, interactions, stipulating the functional significance of local frustration in imparting native-like dynamics. This study provides us with a deeper understanding of the structural basis of experimentally observed behavior, and opens the way to the development of more accurate models for exploring protein dynamics. PMID:20585542

Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology.

PubMed

Lezon, Timothy R; Bahar, Ivet

2010-06-17

Comparison of elastic network model predictions with experimental data has provided important insights on the dominant role of the network of inter-residue contacts in defining the global dynamics of proteins. Most of these studies have focused on interpreting the mean-square fluctuations of residues, or deriving the most collective, or softest, modes of motions that are known to be insensitive to structural and energetic details. However, with increasing structural data, we are in a position to perform a more critical assessment of the structure-dynamics relations in proteins, and gain a deeper understanding of the major determinants of not only the mean-square fluctuations and lowest frequency modes, but the covariance or the cross-correlations between residue fluctuations and the shapes of higher modes. A systematic study of a large set of NMR-determined proteins is analyzed using a novel method based on entropy maximization to demonstrate that the next level of refinement in the elastic network model description of proteins ought to take into consideration properties such as contact order (or sequential separation between contacting residues) and the secondary structure types of the interacting residues, whereas the types of amino acids do not play a critical role. Most importantly, an optimal description of observed cross-correlations requires the inclusion of destabilizing, as opposed to exclusively stabilizing, interactions, stipulating the functional significance of local frustration in imparting native-like dynamics. This study provides us with a deeper understanding of the structural basis of experimentally observed behavior, and opens the way to the development of more accurate models for exploring protein dynamics.

Images of turbulent, absorbing-emitting atmospheres and their application to windshear detection

NASA Astrophysics Data System (ADS)

Watt, David W.; Philbrick, Daniel A.

1991-03-01

The simulation of images generated by thermally-radiating, optically- thick turbulent media are discussed and the time-dependent evolution of these images is modeled. This characteristics of these images are particularly applicable to the atmosphere in the 13-15 mm band and their behavior may have application in detecting aviation hazards. The image is generated by volumetric thermal emission by atmospheric constituents within the field-of-view of the detector. The structure of the turbulent temperature field and the attenuating properties of the atmosphere interact with the field-of-view's geometry to produce a localized region which dominates the optical flow of the image. The simulations discussed in this paper model the time-dependent behavior of images generated by atmospheric flows viewed from an airborne platform. The images ar modelled by (1) generating a random field of temperature fluctuations have the proper spatial structure, (2) adding these fluctuation to the baseline temperature field of the atmospheric event, (3) accumulating the image on the detector from radiation emitted in the imaging volume, (4) allowing the individual radiating points within the imaging volume to move with the local velocity, (5) recalculating the thermal field and generating a new image. This approach was used to simulate the images generated by the temperature and velocity fields of a windshear. The simulation generated pais of images separated by a small time interval. These image paris were analyzed by image cross-correlation. The displacement of the cross-correlation peak was used to infer the velocity at the localized region. The localized region was found to depend weakly on the shape of the velocity profile. Prediction of the localized region, the effects of imaging from a moving platform, alternative image analysis schemes, and possible application to aviation hazards are discussed.

Divertor-localized fluctuations in NSTX-U L-mode discharges

NASA Astrophysics Data System (ADS)

Scotti, Filippo; Soukhanovskii, V. A.; Zweben, S.; Myra, J.; Baver, D.; Sabbagh, S. A.

2017-10-01

The 3-D structure of divertor turbulence is characterized in NSTX-U by means of fast camera imaging. Edge and divertor turbulence can be important in determining the heat flux width in fusion devices. Field-aligned filaments are found on the divertor legs via imaging of C III and D- α emission in NBI-heated diverted L-mode discharges, similar to observations in Alcator C-Mod and MAST. These flute-like fluctuations of up to 10-20% in RMS/mean are radially localized around the separatrix and limited to the region below the X-point. Poloidal and parallel correlation lengths are a few cm (10-50ρi) and several meters, respectively. For the outer leg filaments, poloidal correlation lengths decrease along the leg away from the strike point and typical effective toroidal mode numbers are in the range of 10-20. Opposite toroidal rotation is observed for inner (co-current rotation) and outer leg (counter-current rotation) filaments with apparent poloidal propagation of 1 km/s. The poloidal motion of outer leg filaments is opposite to the one typically observed for NSTX upstream blobs in the scrape-off layer. The shape, dynamics and absence of correlation with upstream turbulence suggest that these fluctuations are generated and localized in the divertor region. Supported by US DOE DE-AC52-07NA27344, DE-AC02-09CH11466, DE-FG02- 02ER54678, DE-FG02-99ER54524.

Modeling the stochastic dynamics of moving turbulent spots over a slender cone at Mach 5 during laminar-turbulent transition

NASA Astrophysics Data System (ADS)

Robbins, Brian; Field, Rich; Grigoriu, Mircea; Jamison, Ryan; Mesh, Mikhail; Casper, Katya; Dechant, Lawrence

2016-11-01

During reentry, a hypersonic vehicle undergoes a period in which the flow about the vehicle transitions from laminar to turbulent flow. During this transitional phase, the flow is characterized by intermittent formations of localized turbulent behavior. These localized regions of turbulence are born at the onset of transition and grow as they move to the aft end of the flight vehicle. Throughout laminar-turbulent transition, the moving turbulent spots cause pressure fluctuations on the outer surface of the vehicle, which leads to the random vibration of the structure and its internal components. In light of this, it is of great interest to study the dynamical response of a flight vehicle undergoing transitional flow so that aircraft can be better designed to prevent structural failure. In this talk, we present a statistical model that calculates the birth, evolution, and pressure field of turbulent spots over a generic slender cone structure. We then illustrate that the model appropriately quantifies intermittency behavior and pressure loading by comparing the intermittency and root-mean-square pressure fluctuations produced by the model with theory and experiment. Finally, we present results pertaining to the structural response of a housing panel on the slender cone. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under Contract DE-AC04-94AL85000.

Coherent wave transmission in quasi-one-dimensional systems with Lévy disorder

NASA Astrophysics Data System (ADS)

Amanatidis, Ilias; Kleftogiannis, Ioannis; Falceto, Fernando; Gopar, Víctor A.

2017-12-01

We study the random fluctuations of the transmission in disordered quasi-one-dimensional systems such as disordered waveguides and/or quantum wires whose random configurations of disorder are characterized by density distributions with a long tail known as Lévy distributions. The presence of Lévy disorder leads to large fluctuations of the transmission and anomalous localization, in relation to the standard exponential localization (Anderson localization). We calculate the complete distribution of the transmission fluctuations for a different number of transmission channels in the presence and absence of time-reversal symmetry. Significant differences in the transmission statistics between disordered systems with Anderson and anomalous localizations are revealed. The theoretical predictions are independently confirmed by tight-binding numerical simulations.

Conductance fluctuation of edge-disordered graphene nanoribbons: Crossover from diffusive transport to Anderson localization

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

Takashima, Kengo; Yamamoto, Takahiro, E-mail: takahiro@rs.tus.ac.jp; Department of Liberal Arts

Conductance fluctuation of edge-disordered graphene nanoribbons (ED-GNRs) is examined using the non-equilibrium Green's function technique combined with the extended Hückel approximation. The mean free path λ and the localization length ξ of the ED-GNRs are determined to classify the quantum transport regimes. In the diffusive regime where the length L{sub c} of the ED-GNRs is much longer than λ and much shorter than ξ, the conductance histogram is given by a Gaussian distribution function with universal conductance fluctuation. In the localization regime where L{sub c}≫ξ, the histogram is no longer the universal Gaussian distribution but a lognormal distribution that characterizesmore » Anderson localization.« less

Role of local network oscillations in resting-state functional connectivity.

PubMed

Cabral, Joana; Hugues, Etienne; Sporns, Olaf; Deco, Gustavo

2011-07-01

Spatio-temporally organized low-frequency fluctuations (<0.1 Hz), observed in BOLD fMRI signal during rest, suggest the existence of underlying network dynamics that emerge spontaneously from intrinsic brain processes. Furthermore, significant correlations between distinct anatomical regions-or functional connectivity (FC)-have led to the identification of several widely distributed resting-state networks (RSNs). This slow dynamics seems to be highly structured by anatomical connectivity but the mechanism behind it and its relationship with neural activity, particularly in the gamma frequency range, remains largely unknown. Indeed, direct measurements of neuronal activity have revealed similar large-scale correlations, particularly in slow power fluctuations of local field potential gamma frequency range oscillations. To address these questions, we investigated neural dynamics in a large-scale model of the human brain's neural activity. A key ingredient of the model was a structural brain network defined by empirically derived long-range brain connectivity together with the corresponding conduction delays. A neural population, assumed to spontaneously oscillate in the gamma frequency range, was placed at each network node. When these oscillatory units are integrated in the network, they behave as weakly coupled oscillators. The time-delayed interaction between nodes is described by the Kuramoto model of phase oscillators, a biologically-based model of coupled oscillatory systems. For a realistic setting of axonal conduction speed, we show that time-delayed network interaction leads to the emergence of slow neural activity fluctuations, whose patterns correlate significantly with the empirically measured FC. The best agreement of the simulated FC with the empirically measured FC is found for a set of parameters where subsets of nodes tend to synchronize although the network is not globally synchronized. Inside such clusters, the simulated BOLD signal between nodes is found to be correlated, instantiating the empirically observed RSNs. Between clusters, patterns of positive and negative correlations are observed, as described in experimental studies. These results are found to be robust with respect to a biologically plausible range of model parameters. In conclusion, our model suggests how resting-state neural activity can originate from the interplay between the local neural dynamics and the large-scale structure of the brain. Copyright © 2011 Elsevier Inc. All rights reserved.

Spatial fluctuations of helical Dirac fermions on the surface of topological insulators

NASA Astrophysics Data System (ADS)

Beidenkopf, Haim

2013-03-01

Strong topological insulators are materials that host exotic states on their surfaces due to a topological band inversion in their bulk band structure. These surface states have Dirac dispersion as if they were massless relativistic particles, and are assured to remain metallic by time reversal symmetry. The helical spin texture associated with the Dirac dispersion prohibits backscattering, which we have imaged using scanning tunneling microscopy (STM) and spectroscopic mappings. This topological protection can be lifted by time-reversal breaking perturbations that induce a gap at the Dirac point and cant the helical spin texture. Massive Dirac electrons had been visualized by angular resolved photo emission spectroscopy in magnetically doped topological insulators. While we do not identify a gapped spectrum in our STM measurements of similar compounds, we do find a dominating electrostatic response to the charged content of those dopants. In their presence the Dirac spectrum exhibits strong spatial fluctuations. As a result translational invariance is broken over a characteristic length scale and the Dirac-point energy is only locally defined. Possible global manifestations of these local fluctuations will be discussed, as well as alternative avenues for breaking time reversal symmetry while maintaining the integrity of the Dirac spectrum. This work was supported by NSF, NSF-MRSEC, and DARPA.

Fluctuation spectroscopy: From Rayleigh-Jeans waves to Abrikosov vortex clusters

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

Varlamov, A. A.; Galda, A.; Glatz, A.

Superconducting (SC) fluctuations, discovered in the late 1960s, have constituted an important research area in superconductivity as they are manifest in a variety of phenomena. Indeed, the underlying physics of SC fluctuations makes it possible to elucidate the fundamental properties of the superconducting state. The interest in SC fluctuation phenomena was further enhanced with the discovery of cuprate high-temperature superconductors (HTSs). In these materials, superconducting fluctuations appear over a wide range of temperatures due to the superconductors extremely short coherence lengths and low effective dimensionality of the electron systems. These strong fluctuations lead to anomalous properties of the normal statemore » in some HTS materials. Within the framework of the phenomenological Ginzburg-Landau theory, and more extensively in the diagrammatic microscopic approach based on BCS theory, SC fluctuations as well as other quantum contributions (weak localization, etc.) enabled a new way to investigate and characterize disordered electron systems, granular metals, Josephson structures, artificial superlattices, and others. The characteristic feature of SC fluctuations is its strong dependence on temperature and magnetic field in the vicinity of the superconducting phase transition. This dependence allows the separation of fluctuation effects from other contributions and provides information about the microscopic parameters of a material, in particular, the critical temperature and the zero-temperature critical magnetic field. As such, SC fluctuations are very sensitive to the relaxation processes that break phase coherence and can be used as a versatile characterization instrument for SCs: Fluctuation spectroscopy has emerged as a powerful tool for studying the properties of superconducting systems on a quantitative level. Here the physics of SC fluctuations is reviewed, commencing from a qualitative description of thermodynamic fluctuations close to the critical temperature and quantum fluctuations at zero temperature in the vicinity of the second critical field. The analysis of the latter allows us to present fluctuation formation as a fragmentation of the Abrikosov lattice. Finally, this review highlights a series of experimental findings followed by microscopic description and numerical analysis of the effects of fluctuations on numerous properties of superconductors in the entire phase diagram and beyond the superconducting phase.« less

Fluctuation spectroscopy: From Rayleigh-Jeans waves to Abrikosov vortex clusters

DOE PAGES

Varlamov, A. A.; Galda, A.; Glatz, A.

2018-03-27

Superconducting (SC) fluctuations, discovered in the late 1960s, have constituted an important research area in superconductivity as they are manifest in a variety of phenomena. Indeed, the underlying physics of SC fluctuations makes it possible to elucidate the fundamental properties of the superconducting state. The interest in SC fluctuation phenomena was further enhanced with the discovery of cuprate high-temperature superconductors (HTSs). In these materials, superconducting fluctuations appear over a wide range of temperatures due to the superconductors extremely short coherence lengths and low effective dimensionality of the electron systems. These strong fluctuations lead to anomalous properties of the normal statemore » in some HTS materials. Within the framework of the phenomenological Ginzburg-Landau theory, and more extensively in the diagrammatic microscopic approach based on BCS theory, SC fluctuations as well as other quantum contributions (weak localization, etc.) enabled a new way to investigate and characterize disordered electron systems, granular metals, Josephson structures, artificial superlattices, and others. The characteristic feature of SC fluctuations is its strong dependence on temperature and magnetic field in the vicinity of the superconducting phase transition. This dependence allows the separation of fluctuation effects from other contributions and provides information about the microscopic parameters of a material, in particular, the critical temperature and the zero-temperature critical magnetic field. As such, SC fluctuations are very sensitive to the relaxation processes that break phase coherence and can be used as a versatile characterization instrument for SCs: Fluctuation spectroscopy has emerged as a powerful tool for studying the properties of superconducting systems on a quantitative level. Here the physics of SC fluctuations is reviewed, commencing from a qualitative description of thermodynamic fluctuations close to the critical temperature and quantum fluctuations at zero temperature in the vicinity of the second critical field. The analysis of the latter allows us to present fluctuation formation as a fragmentation of the Abrikosov lattice. Finally, this review highlights a series of experimental findings followed by microscopic description and numerical analysis of the effects of fluctuations on numerous properties of superconductors in the entire phase diagram and beyond the superconducting phase.« less

Fluctuation spectroscopy: From Rayleigh-Jeans waves to Abrikosov vortex clusters

NASA Astrophysics Data System (ADS)

Varlamov, A. A.; Galda, A.; Glatz, A.

2018-01-01

Superconducting (SC) fluctuations, discovered in the late 1960s, have constituted an important research area in superconductivity as they are manifest in a variety of phenomena. Indeed, the underlying physics of SC fluctuations makes it possible to elucidate the fundamental properties of the superconducting state. The interest in SC fluctuation phenomena was further enhanced with the discovery of cuprate high-temperature superconductors (HTSs). In these materials, superconducting fluctuations appear over a wide range of temperatures due to the superconductors extremely short coherence lengths and low effective dimensionality of the electron systems. These strong fluctuations lead to anomalous properties of the normal state in some HTS materials. Within the framework of the phenomenological Ginzburg-Landau theory, and more extensively in the diagrammatic microscopic approach based on BCS theory, SC fluctuations as well as other quantum contributions (weak localization, etc.) enabled a new way to investigate and characterize disordered electron systems, granular metals, Josephson structures, artificial superlattices, and others. The characteristic feature of SC fluctuations is its strong dependence on temperature and magnetic field in the vicinity of the superconducting phase transition. This dependence allows the separation of fluctuation effects from other contributions and provides information about the microscopic parameters of a material, in particular, the critical temperature and the zero-temperature critical magnetic field. As such, SC fluctuations are very sensitive to the relaxation processes that break phase coherence and can be used as a versatile characterization instrument for SCs: Fluctuation spectroscopy has emerged as a powerful tool for studying the properties of superconducting systems on a quantitative level. Here the physics of SC fluctuations is reviewed, commencing from a qualitative description of thermodynamic fluctuations close to the critical temperature and quantum fluctuations at zero temperature in the vicinity of the second critical field. The analysis of the latter allows us to present fluctuation formation as a fragmentation of the Abrikosov lattice. This review highlights a series of experimental findings followed by microscopic description and numerical analysis of the effects of fluctuations on numerous properties of superconductors in the entire phase diagram and beyond the superconducting phase.

Förster-type energy transfer as a probe for changes in local fluctuations of the protein matrix.

PubMed

Somogyi, B; Matkó, J; Papp, S; Hevessy, J; Welch, G R; Damjanovich, S

1984-07-17

Much evidence, on both theoretical and experimental sides, indicates the importance of local fluctuations (in energy levels, conformational substates, etc.) of the macromolecular matrix in the biological activity of proteins. We describe here a novel application of the Förster-type energy-transfer process capable of monitoring changes both in local fluctuations and in conformational states of macromolecules. A new energy-transfer parameter, f, is defined as an average transfer efficiency, [E], normalized by the actual average quantum efficiency of the donor fluorescence, [phi D]. A simple oscillator model (for a one donor-one acceptor system) is presented to show the sensitivity of this parameter to changes in amplitudes of local fluctuations. The different modes of averaging (static, dynamic, and intermediate cases) occurring for a given value of the average transfer rate, [kt], and the experimental requirements as well as limitations of the method are also discussed. The experimental tests were performed on the ribonuclease T1-pyridoxamine 5'-phosphate conjugate (a one donor-one acceptor system) by studying the change of the f parameter with temperature, an environmental parameter expectedly perturbing local fluctuations of proteins. The parameter f increased with increasing temperature as expected on the basis of the oscillator model, suggesting that it really reflects changes of fluctuation amplitudes (significant changes in the orientation factor, k2, as well as in the spectral properties of the fluorophores can be excluded by anisotropy measurements and spectral investigations). Possibilities of the general applicability of the method are also discussed.

Thermodynamic properties of paramagnetic α - and β -Mn from first principles: The effect of transverse spin fluctuations

NASA Astrophysics Data System (ADS)

Ehteshami, Hossein; Korzhavyi, Pavel A.

2017-12-01

First-principles-based thermodynamic modeling of cubic α and β phases of Mn represent a challenge due to their structural complexity and the necessity of simultaneous treatment of several types of disorder (electronic, magnetic, and vibrational) that have very different characteristic time scales. Here we employ mean-field theoretical models to describe the different types of disorder and then we connect each layer of theory to the others using the adiabatic principle of separating faster and slower degrees of freedom. The slowest (vibrational) degrees of freedom are treated using the Moruzzi, Janak, and Schwarz formalism [Phys. Rev. B 37, 790 (1988), 10.1103/PhysRevB.37.790] of the Debye-Grüneisen model parametrized based on the first-principles calculated equation of state which includes the free-energy contributions due to the fast (electronic and magnetic) degrees of freedom via the Fermi-Dirac distribution function and a mean-field theory of transverse spin fluctuations. The magnetic contribution due to transverse spin fluctuations has been computed self-consistently within the disordered local moment picture of the paramagnetic state. The obtained results for thermodynamic properties such as lattice parameter, linear thermal expansion coefficient, and heat capacity of both phases show a good agreement with available experimental data. We also tested the assumption about the nature (localized versus delocalized) of magnetic moment on site IV in α -Mn and site I in β -Mn on the thermodynamic properties of these two phases. Similar to the findings of experimental studies, we conclude that magnetic moment on site IV in α -Mn is not of a localized character. However, a similar analysis suggests that the magnetic moment of site I in β -Mn should be treated as localized.

Two-terminal conductance fluctuations in the integer quantum Hall regime

NASA Astrophysics Data System (ADS)

Ho, Chang-Ming

1999-09-01

Motivated by recent experiments on the conductance fluctuations in mesoscopic integer quantum Hall systems, we consider a model in which the Coulomb interactions are incorporated into the picture of edge-state transport through a single saddle point. The occupancies of classical localized states in the two-dimensional electron system change due to the interactions between electrons when the gate voltage on top of the device is varied. The electrostatic potential between the localized states and the saddle point causes fluctuations of the saddle-point potential and thus fluctuations of the transmission probability of edge states. This simple model is studied numerically and compared with the observation.

Rotation of Guanine Amino Groups in G-Quadruplexes: A Probe for Local Structure and Ligand Binding.

PubMed

Adrian, Michael; Winnerdy, Fernaldo Richtia; Heddi, Brahim; Phan, Anh Tuân

2017-08-22

Nucleic acids are dynamic molecules whose functions may depend on their conformational fluctuations and local motions. In particular, amino groups are dynamic components of nucleic acids that participate in the formation of various secondary structures such as G-quadruplexes. Here, we present a cost-efficient NMR method to quantify the rotational dynamics of guanine amino groups in G-quadruplex nucleic acids. An isolated spectrum of amino protons from a specific tetrad-bound guanine can be extracted from the nuclear Overhauser effect spectroscopy spectrum based on the close proximity between the intra-residue imino and amino protons. We apply the method in different structural contexts of G-quadruplexes and their complexes. Our results highlight the role of stacking and hydrogen-bond interactions in restraining amino-group rotation. The measurement of the rotation rate of individual amino groups could give insight into the dynamic processes occurring at specific locations within G-quadruplex nucleic acids, providing valuable probes for local structure, dynamics, and ligand binding. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Frequency Response of a Protein to Local Conformational Perturbations

PubMed Central

Eren, Dilek; Alakent, Burak

2013-01-01

Signals created by local perturbations are known to propagate long distances through proteins via backbone connectivity and nonbonded interactions. In the current study, signal propagation from the flexible ligand binding loop to the rest of Protein Tyrosine Phosphatase 1B (PTP1B) was investigated using frequency response techniques. Using restrained Targeted Molecular Dynamics (TMD) potential on WPD and R loops, PTP1B was driven between its crystal structure conformations at different frequencies. Propagation of the local perturbation signal was manifested via peaks at the fundamental frequency and upper harmonics of 1/f distributed spectral density of atomic variables, such as Cα atoms, dihedral angles, or polar interaction distances. Frequency of perturbation was adjusted high enough (simulation length >∼10×period of a perturbation cycle) not to be clouded by random diffusional fluctuations, and low enough (<∼0.8 ns−1) not to attenuate the propagating signal and enhance the contribution of the side-chains to the dissipation of the signals. Employing Discrete Fourier Transform (DFT) to TMD simulation trajectories of 16 cycles of conformational transitions at periods of 1.2 to 5 ns yielded Cα displacements consistent with those obtained from crystal structures. Identification of the perturbed atomic variables by statistical t-tests on log-log scale spectral densities revealed the extent of signal propagation in PTP1B, while phase angles of the filtered trajectories at the fundamental frequency were used to cluster collectively fluctuating elements. Hydrophobic interactions were found to have a higher contribution to signal transduction between side-chains compared to the role of polar interactions. Most of in-phase fluctuating residues on the signaling pathway were found to have high identity among PTP domains, and located over a wide region of PTP1B including the allosteric site. Due to its simplicity and efficiency, the suggested technique may find wide applications in identification of signaling pathways of different proteins. PMID:24086121

Reynolds stress of localized toroidal modes

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

Zhang, Y.Z.; Mahajan, S.M.

1995-02-01

An investigation of the 2D toroidal eigenmode problem reveals the possibility of a new consistent 2D structure, the dissipative BM-II mode. In contrast to the conventional ballooning mode, the new mode is poloidally localized at {pi}/2 (or -{pi}/2), and possesses significant radial asymmetry. The radial asymmetry, in turn, allows the dissipative BM-II to generate considerably larger Reynolds stress as compared to the standard slab drift type modes. It is also shown that a wide class of localized dissipative toroidal modes are likely to be of the dissipative BM-II nature, suggesting that at the tokamak edge, the fluctuation generated Reynolds stressmore » (a possible source of poloidal flow) can be significant.« less

Changes of statistical structural fluctuations unveils an early compacted degraded stage of PNS myelin

NASA Astrophysics Data System (ADS)

Poccia, Nicola; Campi, Gaetano; Ricci, Alessandro; Caporale, Alessandra S.; di Cola, Emanuela; Hawkins, Thomas A.; Bianconi, Antonio

2014-06-01

Degradation of the myelin sheath is a common pathology underlying demyelinating neurological diseases from Multiple Sclerosis to Leukodistrophies. Although large malformations of myelin ultrastructure in the advanced stages of Wallerian degradation is known, its subtle structural variations at early stages of demyelination remains poorly characterized. This is partly due to the lack of suitable and non-invasive experimental probes possessing sufficient resolution to detect the degradation. Here we report the feasibility of the application of an innovative non-invasive local structure experimental approach for imaging the changes of statistical structural fluctuations in the first stage of myelin degeneration. Scanning micro X-ray diffraction, using advances in synchrotron x-ray beam focusing, fast data collection, paired with spatial statistical analysis, has been used to unveil temporal changes in the myelin structure of dissected nerves following extraction of the Xenopus laevis sciatic nerve. The early myelin degeneration is a specific ordered compacted phase preceding the swollen myelin phase of Wallerian degradation. Our demonstration of the feasibility of the statistical analysis of SµXRD measurements using biological tissue paves the way for further structural investigations of degradation and death of neurons and other cells and tissues in diverse pathological states where nanoscale structural changes may be uncovered.

Recent progress of TAMA300

NASA Astrophysics Data System (ADS)

Arai, K.; TAMA Collaboration

2008-07-01

Current effort of the TAMA project is focused on establishment of the interferometer operation with a new vibration isolation system, called 'Seismic Attenuation System' (SAS). The SAS employs a multiple stage structure to realize soft spring for all of directions, as well as utilizes active control systems to stabilize mechanical resonances in the low frequency region below 1 Hz. The SASs were installed for four test masses, resulting in improvement of cavity length fluctuation below 150 Hz. We describe the structure of the SAS and its local active control system, and the status of the interferometer.

Spatially resolved speckle-correlometry of sol-gel transition

NASA Astrophysics Data System (ADS)

Isaeva, A. A.; Isaeva, E. A.; Pantyukov, A. V.; Zimnyakov, D. A.

2018-04-01

Sol-gel transition was studied using the speckle correlometry method with a localized light source and spatial filtering of backscattered radiation. Water solutions of technical or food gelatin with added TiO2 nanoparticles were used as studied objects. Structural transformation of "sol-gel" system was studied at various temperatures from 25°C to 50°C using analysis of the correlation and structure functions of speckle intensity fluctuations. The characteristic temperatures of "sol - gel" transition were evaluated for studied systems. Obtained results can be used for various applications in biomedicine and food industry.

Intermittent fluctuations in the Alcator C-Mod scrape-off layer for ohmic and high confinement mode plasmas

NASA Astrophysics Data System (ADS)

Garcia, O. E.; Kube, R.; Theodorsen, A.; LaBombard, B.; Terry, J. L.

2018-05-01

Plasma fluctuations in the scrape-off layer of the Alcator C-Mod tokamak in ohmic and high confinement modes have been analyzed using gas puff imaging data. In all cases investigated, the time series of emission from a single spatially resolved view into the gas puff are dominated by large-amplitude bursts, attributed to blob-like filament structures moving radially outwards and poloidally. There is a remarkable similarity of the fluctuation statistics in ohmic plasmas and in edge localized mode-free and enhanced D-alpha high confinement mode plasmas. Conditionally averaged waveforms have a two-sided exponential shape with comparable temporal scales and asymmetry, while the burst amplitudes and the waiting times between them are exponentially distributed. The probability density functions and the frequency power spectral densities are similar for all these confinement modes. These results provide strong evidence in support of a stochastic model describing the plasma fluctuations in the scrape-off layer as a super-position of uncorrelated exponential pulses. Predictions of this model are in excellent agreement with experimental measurements in both ohmic and high confinement mode plasmas. The stochastic model thus provides a valuable tool for predicting fluctuation-induced plasma-wall interactions in magnetically confined fusion plasmas.

Local time dependence of turbulent magnetic fields in Saturn's magnetodisc

NASA Astrophysics Data System (ADS)

Kaminker, V.; Delamere, P. A.; Ng, C. S.; Dennis, T.; Otto, A.; Ma, X.

2017-04-01

Net plasma transport in magnetodiscs around giant planets is outward. Observations of plasma temperature have shown that the expanding plasma is heating nonadiabatically during this process. Turbulence has been suggested as a source of heating. However, the mechanism and distribution of magnetic fluctuations in giant magnetospheres are poorly understood. In this study we attempt to quantify the radial and local time dependence of fluctuating magnetic field signatures that are suggestive of turbulence, quantifying the fluctuations in terms of a plasma heating rate density. In addition, the inferred heating rate density is correlated with magnetic field configurations that include azimuthal bend forward/back and magnitude of the equatorial normal component of magnetic field relative to the dipole. We find a significant local time dependence in magnetic fluctuations that is consistent with flux transport triggered in the subsolar and dusk sectors due to magnetodisc reconnection.

Numerical simulation of a helical shape electric arc in the external axial magnetic field

NASA Astrophysics Data System (ADS)

Urusov, R. M.; Urusova, I. R.

2016-10-01

Within the frameworks of non-stationary three-dimensional mathematical model, in approximation of a partial local thermodynamic equilibrium, a numerical calculation was made of characteristics of DC electric arc burning in a cylindrical channel in the uniform external axial magnetic field. The method of numerical simulation of the arc of helical shape in a uniform external axial magnetic field was proposed. This method consists in that that in the computational algorithm, a "scheme" analog of fluctuations for electrons temperature is supplemented. The "scheme" analogue of fluctuations increases a weak numerical asymmetry of electrons temperature distribution, which occurs randomly in the course of computing. This asymmetry can be "picked up" by the external magnetic field that continues to increase up to a certain value, which is sufficient for the formation of helical structure of the arc column. In the absence of fluctuations in the computational algorithm, the arc column in the external axial magnetic field maintains cylindrical axial symmetry, and a helical form of the arc is not observed.

Relation between self-organized criticality and grain aspect ratio in granular piles

NASA Astrophysics Data System (ADS)

Denisov, D. V.; Villanueva, Y. Y.; Lőrincz, K. A.; May, S.; Wijngaarden, R. J.

2012-05-01

We investigate experimentally whether self-organized criticality (SOC) occurs in granular piles composed of different grains, namely, rice, lentils, quinoa, and mung beans. These four grains were selected to have different aspect ratios, from oblong to oblate. As a function of aspect ratio, we determined the growth (β) and roughness (α) exponents, the avalanche fractal dimension (D), the avalanche size distribution exponent (τ), the critical angle (γ), and its fluctuation. At superficial inspection, three types of grains seem to have power-law-distributed avalanches with a well-defined τ. However, only rice is truly SOC if we take three criteria into account: a power-law-shaped avalanche size distribution, finite size scaling, and a universal scaling relation relating characteristic exponents. We study SOC as a spatiotemporal fractal; in particular, we study the spatial structure of criticality from local observation of the slope angle. From the fluctuation of the slope angle we conclude that greater fluctuation (and thus bigger avalanches) happen in piles consisting of grains with larger aspect ratio.

An assessment of memristor intrinsic fluctuations: a measurement of single atomic motion

NASA Astrophysics Data System (ADS)

Borghetti, Julien; Yang, J. Joshua; Medeiros-Ribeiro, Gilberto; Williams, R. Stanley

2010-03-01

Memristors provides electrically tunable resistance for upcoming non-volatile memory and future neuromorphic computing. One of the key benefits of such a device is its scalability, which can be demonstrated from an architectural perspective as well as from a fundamental physics limit. 4D addressing schemes utilizing cross bar structures that can be stacked several layers high above the chip embodies unlimited addressing space. On the other limit, the basic operating principles of memristive devices allow one to reach storage of information in a single atom. In this report of nanoscale (sub 50nm) devices, we detect single atom fluctuations, which would then represent the ultimate limit for noise sources thus delineating the boundary conditions for circuit design. We show that electrically induced individual atom migrations do not affect the overall device atomic configuration until a critical bias where a single local fluctuation triggers a general atomic reconfiguration. This instability illustrates the robustness of the device non-volatility upon small electrical stress.

Non-gaussianity versus nonlinearity of cosmological perturbations.

PubMed

Verde, L

2001-06-01

Following the discovery of the cosmic microwave background, the hot big-bang model has become the standard cosmological model. In this theory, small primordial fluctuations are subsequently amplified by gravity to form the large-scale structure seen today. Different theories for unified models of particle physics, lead to different predictions for the statistical properties of the primordial fluctuations, that can be divided in two classes: gaussian and non-gaussian. Convincing evidence against or for gaussian initial conditions would rule out many scenarios and point us toward a physical theory for the origin of structures. The statistical distribution of cosmological perturbations, as we observe them, can deviate from the gaussian distribution in several different ways. Even if perturbations start off gaussian, nonlinear gravitational evolution can introduce non-gaussian features. Additionally, our knowledge of the Universe comes principally from the study of luminous material such as galaxies, but galaxies might not be faithful tracers of the underlying mass distribution. The relationship between fluctuations in the mass and in the galaxies distribution (bias), is often assumed to be local, but could well be nonlinear. Moreover, galaxy catalogues use the redshift as third spatial coordinate: the resulting redshift-space map of the galaxy distribution is nonlinearly distorted by peculiar velocities. Nonlinear gravitational evolution, biasing, and redshift-space distortion introduce non-gaussianity, even in an initially gaussian fluctuation field. I investigate the statistical tools that allow us, in principle, to disentangle the above different effects, and the observational datasets we require to do so in practice.

X-ray and simulation studies of water

NASA Astrophysics Data System (ADS)

Nilsson, A.; Schlesinger, D.; G. M. Pettersson, L.

Here we present a picture that combines discussions regarding the thermodynamic anomalies in ambient and supercooled water with recent interpretations of X-ray spectroscopy and scattering data of water. At ambient temperatures most molecules favor a closer packing than tetrahedral, with strongly distorted hydrogen bonds, which allows the quantized librational modes to be excited and contribute to the entropy, but with enthalpically favored tetrahedrally bonded water patches appearing as fluctuations, a competition between entropy and enthalpy. Upon cooling water the amount of molecules participating in tetrahedral structures and the size of the tetrahedral patches increase. The two local structures are connected to the liquid-liquid critical point hypothesis in supercooled water corresponding to high-density liquid (HDL) and low-density liquid (LDL). We demonstrate that the HDL local structure deviates from a tetrahedral coordination not only through a collapse of the 2nd shell but also through severe distortions around the 1st coordination shell.

Generation of intermittent gravitocapillary waves via parametric forcing

NASA Astrophysics Data System (ADS)

Castillo, Gustavo; Falcón, Claudio

2018-04-01

We report on the generation of an intermittent wave field driven by a horizontally moving wave maker interacting with Faraday waves. The spectrum of the local gravitocapillary surface wave fluctuations displays a power law in frequency for a wide range of forcing parameters. We compute the probability density function of the local surface height increments, which show that they change strongly across time scales. The structure functions of these increments are shown to display power laws as a function of the time lag, with exponents that are nonlinear functions of the order of the structure function. We argue that the origin of this scale-invariant intermittent spectrum is the Faraday wave pattern breakup due to its advection by the propagating gravity waves. Finally, some interpretations are proposed to explain the appearance of this intermittent spectrum.

Near-field optical technique applied for investigation of the characteristics of polymer fiber and waveguide structures.

PubMed

Ming, Hai; Tang, Lin; Sun, Xiaohong; Zhang, Jiangying; Wang, Pei; Lu, Yonghua; Bai, Ming; Guo, Yang; Xie, Aifang; Zhang, Zebo

2004-01-01

This article summarizes the near-field optical technique applied for investigating the characteristics of polymer fiber and waveguide structures. The near-field optical technique is used to analyze multimode interference structures of fiber. The localized fluctuation of the transmission caused by fractal cluster is carried out in Nd3+- and Eu3+-doped polymer fiber and film by means of a scanning near-field optical microscopy. The near-field optical spectrum of Nd3+-doped polymer fiber is investigated. The topography and near-field intensity images of Azo-polymer liquid crystal film for waveguide are obtained simultaneously.

Conformational Analysis on structural perturbations of the zinc finger NEMO

NASA Astrophysics Data System (ADS)

Godwin, Ryan; Salsbury, Freddie; Salsbury Group Team

2014-03-01

The NEMO (NF-kB Essential Modulator) Zinc Finger protein (2jvx) is a functional Ubiquitin-binding domain, and plays a role in signaling pathways for immune/inflammatory responses, apoptosis, and oncogenesis [Cordier et al., 2008]. Characterized by 3 cysteines and 1 histidine residue at the active site, the biologically occurring, bound zinc configuration is a stable structural motif. Perturbations of the zinc binding residues suggest conformational changes in the 423-atom protein characterized via analysis of all-atom molecular dynamics simulations. Structural perturbations include simulations with and without a zinc ion and with and without de-protonated cysteines, resulting in four distinct configurations. Simulations of various time scales show consistent results, yet the longest, GPU driven, microsecond runs show more drastic structural and dynamic fluctuations when compared to shorter duration time-scales. The last cysteine residue (26 of 28) and the helix on which it resides exhibit a secondary, locally unfolded conformation in addition to its normal bound conformation. Combined analytics elucidate how the presence of zinc and/or protonated cysteines impact the dynamics and energetic fluctuations of NEMO. Comprehensive Cancer Center of Wake Forest University Computational Biosciences shared resource supported by NCI CCSG P30CA012197.

Theory of dynamic barriers, activated hopping, and the glass transition in polymer melts

NASA Astrophysics Data System (ADS)

Schweizer, Kenneth S.; Saltzman, Erica J.

2004-07-01

A statistical mechanical theory of collective dynamic barriers, slow segmental relaxation, and the glass transition of polymer melts is developed by combining, and in some aspects extending, methods of mode coupling, density functional, and activated hopping transport theories. A coarse-grained description of polymer chains is adopted and the melt is treated as a liquid of segments. The theory is built on the idea that collective density fluctuations on length scales considerably longer than the local cage scale are of primary importance in the deeply supercooled regime. The barrier hopping or segmental relaxation time is predicted to be a function primarily of a single parameter that is chemical structure, temperature, and pressure dependent. This parameter depends on the material-specific dimensionless amplitude of thermal density fluctuations (compressibility) and a reduced segmental density determined by the packing length and backbone characteristic ratio. Analytic results are derived for a crossover temperature Tc, collective barrier, and glass transition temperature Tg. The relation of these quantities to structural and thermodynamic properties of the polymer melt is established. A universal power-law scaling behavior of the relaxation time below Tc is predicted based on identification of a reduced temperature variable that quantifies the breadth of the supercooled regime. Connections between the ratio Tc/Tg, two measures of dynamic fragility, and the magnitude of the local relaxation time at Tg logically follow. Excellent agreement with experiment is found for these generic aspects, and the crucial importance of the experimentally observed near universality of the dynamic crossover time is established. Extensions of the theory to treat the full chain dynamics, heterogeneity, barrier fluctuations, and nonpolymeric thermal glass forming liquids are briefly discussed.

Quantitative Boltzmann-Gibbs Principles via Orthogonal Polynomial Duality

NASA Astrophysics Data System (ADS)

Ayala, Mario; Carinci, Gioia; Redig, Frank

2018-06-01

We study fluctuation fields of orthogonal polynomials in the context of particle systems with duality. We thereby obtain a systematic orthogonal decomposition of the fluctuation fields of local functions, where the order of every term can be quantified. This implies a quantitative generalization of the Boltzmann-Gibbs principle. In the context of independent random walkers, we complete this program, including also fluctuation fields in non-stationary context (local equilibrium). For other interacting particle systems with duality such as the symmetric exclusion process, similar results can be obtained, under precise conditions on the n particle dynamics.

Sequence composition and environment effects on residue fluctuations in protein structures

NASA Astrophysics Data System (ADS)

Ruvinsky, Anatoly M.; Vakser, Ilya A.

2010-10-01

Structure fluctuations in proteins affect a broad range of cell phenomena, including stability of proteins and their fragments, allosteric transitions, and energy transfer. This study presents a statistical-thermodynamic analysis of relationship between the sequence composition and the distribution of residue fluctuations in protein-protein complexes. A one-node-per-residue elastic network model accounting for the nonhomogeneous protein mass distribution and the interatomic interactions through the renormalized inter-residue potential is developed. Two factors, a protein mass distribution and a residue environment, were found to determine the scale of residue fluctuations. Surface residues undergo larger fluctuations than core residues in agreement with experimental observations. Ranking residues over the normalized scale of fluctuations yields a distinct classification of amino acids into three groups: (i) highly fluctuating-Gly, Ala, Ser, Pro, and Asp, (ii) moderately fluctuating-Thr, Asn, Gln, Lys, Glu, Arg, Val, and Cys, and (iii) weakly fluctuating-Ile, Leu, Met, Phe, Tyr, Trp, and His. The structural instability in proteins possibly relates to the high content of the highly fluctuating residues and a deficiency of the weakly fluctuating residues in irregular secondary structure elements (loops), chameleon sequences, and disordered proteins. Strong correlation between residue fluctuations and the sequence composition of protein loops supports this hypothesis. Comparing fluctuations of binding site residues (interface residues) with other surface residues shows that, on average, the interface is more rigid than the rest of the protein surface and Gly, Ala, Ser, Cys, Leu, and Trp have a propensity to form more stable docking patches on the interface. The findings have broad implications for understanding mechanisms of protein association and stability of protein structures.

Zero-Point Spin-Fluctuations of Single Adatoms.

PubMed

Ibañez-Azpiroz, Julen; Dos Santos Dias, Manuel; Blügel, Stefan; Lounis, Samir

2016-07-13

Stabilizing the magnetic signal of single adatoms is a crucial step toward their successful usage in widespread technological applications such as high-density magnetic data storage devices. The quantum mechanical nature of these tiny objects, however, introduces intrinsic zero-point spin-fluctuations that tend to destabilize the local magnetic moment of interest by dwindling the magnetic anisotropy potential barrier even at absolute zero temperature. Here, we elucidate the origins and quantify the effect of the fundamental ingredients determining the magnitude of the fluctuations, namely, the (i) local magnetic moment, (ii) spin-orbit coupling, and (iii) electron-hole Stoner excitations. Based on a systematic first-principles study of 3d and 4d adatoms, we demonstrate that the transverse contribution of the fluctuations is comparable in size to the magnetic moment itself, leading to a remarkable ≳50% reduction of the magnetic anisotropy energy. Our analysis gives rise to a comprehensible diagram relating the fluctuation magnitude to characteristic features of adatoms, providing practical guidelines for designing magnetically stable nanomagnets with minimal quantum fluctuations.

Fluctuation dynamics in reconnecting current sheets

NASA Astrophysics Data System (ADS)

von Stechow, Adrian; Grulke, Olaf; Ji, Hantao; Yamada, Masaaki; Klinger, Thomas

2015-11-01

During magnetic reconnection, a highly localized current sheet forms at the boundary between opposed magnetic fields. Its steep perpendicular gradients and fast parallel drifts can give rise to a range of instabilities which can contribute to the overall reconnection dynamics. In two complementary laboratory reconnection experiments, MRX (PPPL, Princeton) and VINETA.II (IPP, Greifswald, Germany), magnetic fluctuations are observed within the current sheet. Despite the large differences in geometries (toroidal vs. linear), plasma parameters (high vs. low beta) and magnetic configuration (low vs. high magnetic guide field), similar broadband fluctuation characteristics are observed in both experiments. These are identified as Whistler-like fluctuations in the lower hybrid frequency range that propagate along the current sheet in the electron drift direction. They are intrinsic to the localized current sheet and largely independent of the slower reconnection dynamics. This contribution characterizes these magnetic fluctuations within the wide parameter range accessible by both experiments. Specifically, the fluctuation spectra and wave dispersion are characterized with respect to the magnetic topology and plasma parameters of the reconnecting current sheet.

Coulomb spin liquid in anion-disordered pyrochlore Tb 2Hf 2O 7

DOE PAGES

Sibille, Romain; Lhotel, Elsa; Hatnean, Monica Ciomaga; ...

2017-10-12

Here, the charge ordered structure of ions and vacancies characterizing rare-earth pyrochlore oxides serves as a model for the study of geometrically frustrated magnetism. The organization of magnetic ions into networks of corner-sharing tetrahedra gives rise to highly correlated magnetic phases with strong fluctuations, including spin liquids and spin ices. It is an open question how these ground states governed by local rules are affected by disorder. Here we demonstrate in the pyrochlore Tb 2Hf 2O 7, that the vicinity of the disordering transition towards a defective fluorite structure translates into a tunable density of anion Frenkel disorder while cationsmore » remain ordered. Quenched random crystal fields and disordered exchange interactions can therefore be introduced into otherwise perfect pyrochlore lattices of magnetic ions. We show that disorder can play a crucial role in preventing long-range magnetic order at low temperatures, and instead induces a strongly fluctuating Coulomb spin liquid with defect-induced frozen magnetic degrees of freedom.« less

Electronic Structure and Magnetic Phase Transition in Helicoidal Fe1 - x Co x Si Ferromagnets

NASA Astrophysics Data System (ADS)

Povzner, A. A.; Volkov, A. G.; Nogovitsyna, T. A.

2018-02-01

LSDA + U + SO calculations of the electronic structure of helicoidal Fe1 - x Co x Si ferromagnets within the virtual crystal approximation have been supplemented with the consideration of the Dzyaloshinski-Moriya interaction and ferromagnetic fluctuations of the spin density of collective d electrons with the Hubbard interactions at Fe and Co atoms randomly distributed over sites. The magnetic-state equation in the developed model describes helicoidal ferromagnetism and its disappearance accompanied by the occurrence of a maximum of uniform magnetic susceptibility at temperature T C and chiral fluctuations of the local magnetization at T > T C . The reasons why the magnetic contribution to the specific heat at the magnetic phase transition changes monotonically and the volume coefficient of thermal expansion (VCTE) at low temperatures is negative and has a wide minimum near T C have been investigated. It is shown that the VCTE changes sign when passing to the paramagnetic state (at temperature T S ).

Contingency and statistical laws in replicate microbial closed ecosystems.

PubMed

Hekstra, Doeke R; Leibler, Stanislas

2012-05-25

Contingency, the persistent influence of past random events, pervades biology. To what extent, then, is each course of ecological or evolutionary dynamics unique, and to what extent are these dynamics subject to a common statistical structure? Addressing this question requires replicate measurements to search for emergent statistical laws. We establish a readily replicated microbial closed ecosystem (CES), sustaining its three species for years. We precisely measure the local population density of each species in many CES replicates, started from the same initial conditions and kept under constant light and temperature. The covariation among replicates of the three species densities acquires a stable structure, which could be decomposed into discrete eigenvectors, or "ecomodes." The largest ecomode dominates population density fluctuations around the replicate-average dynamics. These fluctuations follow simple power laws consistent with a geometric random walk. Thus, variability in ecological dynamics can be studied with CES replicates and described by simple statistical laws. Copyright © 2012 Elsevier Inc. All rights reserved.

Testing Inflation with Large Scale Structure: Connecting Hopes with Reality

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

Alvarez, Marcello; Baldauf, T.; Bond, J. Richard

2014-12-15

The statistics of primordial curvature fluctuations are our window into the period of inflation, where these fluctuations were generated. To date, the cosmic microwave background has been the dominant source of information about these perturbations. Large-scale structure is, however, from where drastic improvements should originate. In this paper, we explain the theoretical motivations for pursuing such measurements and the challenges that lie ahead. In particular, we discuss and identify theoretical targets regarding the measurement of primordial non-Gaussianity. We argue that when quantified in terms of the local (equilateral) template amplitude fmore » $$loc\\atop{NL}$$ (f$$eq\\atop{NL}$$), natural target levels of sensitivity are Δf$$loc, eq\\atop{NL}$$ ≃ 1. We highlight that such levels are within reach of future surveys by measuring 2-, 3- and 4-point statistics of the galaxy spatial distribution. This paper summarizes a workshop held at CITA (University of Toronto) on October 23-24, 2014.« less

Exploring the Influence of Dynamic Disorder on Excitons in Solid Pentacene

NASA Astrophysics Data System (ADS)

Wang, Zhiping; Sharifzadeh, Sahar; Doak, Peter; Lu, Zhenfei; Neaton, Jeffrey

2014-03-01

A complete understanding of the spectroscopic and charge transport properties of organic semiconductors requires knowledge of the role of thermal fluctuations and dynamic disorder. We present a first-principles theoretical study aimed at understanding the degree to which dynamic disorder at room temperature results in energy level broadening and excited-state localization within bulk crystalline pentacene. Ab initio molecular dynamics simulations are well-equilibrated for 7-9 ps and tens of thousands of structural snapshots, taken at 0.5 fs intervals, provide input for many-body perturbation theory within the GW approximation and Bethe-Salpeter equation (BSE) approach. The GW-corrected density of states, including thousands of snapshots, indicates that thermal fluctuations significantly broaden the valence and conduction states by >0.2 eV. Additionally, we investigate the nature and energy of the lowest energy singlet and triplet excitons, computed for a set of uncorrelated and energetically preferred structures. This work supported by DOE; computational resources provided by NERSC.

Changes in Phosphatidylcholine Headgroup Tilt and Water Order Induced by Monovalent Salts: Molecular Dynamics Simulations

PubMed Central

Sachs, Jonathan N.; Nanda, Hirsh; Petrache, Horia I.; Woolf, Thomas B.

2004-01-01

The association between monovalent salts and neutral lipid bilayers is known to influence global bilayer structural properties such as headgroup conformational fluctuations and the dipole potential. The local influence of the ions, however, has been unknown due to limited structural resolution of experimental methods. Molecular dynamics simulations are used here to elucidate local structural rearrangements upon association of a series of monovalent Na+ salts to a palmitoyl-oleoyl-phosphatidylcholine bilayer. We observe association of all ion types in the interfacial region. Larger anions, which are meant to rationalize data regarding a Hofmeister series of anions, bind more deeply within the bilayer than either Cl− or Na+. Although the simulations are able to reproduce experimentally measured quantities, the analysis is focused on local properties currently invisible to experiments, which may be critical to biological systems. As such, for all ion types, including Cl−, we show local ion-induced perturbations to headgroup tilt, the extent and direction of which is sensitive to ion charge and size. Additionally, we report salt-induced ordering of the water well beyond the interfacial region, which may be significant in terms of hydration repulsion between stacked bilayers. PMID:15189873

Cosmic structure and dynamics of the local Universe

NASA Astrophysics Data System (ADS)

Kitaura, Francisco-Shu; Erdoǧdu, Pirin; Nuza, Sebastián. E.; Khalatyan, Arman; Angulo, Raul E.; Hoffman, Yehuda; Gottlöber, Stefan

2012-11-01

We present a cosmography analysis of the local Universe based on the recently released Two-Micron All-Sky Redshift Survey catalogue. Our method is based on a Bayesian Networks Machine Learning algorithm (the KIGEN-code) which self-consistently samples the initial density fluctuations compatible with the observed galaxy distribution and a structure formation model given by second-order Lagrangian perturbation theory (2LPT). From the initial conditions we obtain an ensemble of reconstructed density and peculiar velocity fields which characterize the local cosmic structure with high accuracy unveiling non-linear structures like filaments and voids in detail. Coherent redshift-space distortions are consistently corrected within 2LPT. From the ensemble of cross-correlations between the reconstructions and the galaxy field and the variance of the recovered density fields, we find that our method is extremely accurate up to k˜ 1 h Mpc-1 and still yields reliable results down to scales of about 3-4 h-1 Mpc. The motion of the Local Group we obtain within ˜80 h-1 Mpc (vLG = 522 ± 86 km s-1, lLG = 291° ± 16°, bLG = 34° ± 8°) is in good agreement with measurements derived from the cosmic microwave background and from direct observations of peculiar motions and is consistent with the predictions of ΛCDM.

A Local Quantum Phase Transition in YFe 2Al 10

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

Gannon, W J.; Zaliznyak, Igor A.; Wu, L. S.

Here, a phase transition occurs when correlated regions of a new phase grow to span the system and the fluctuations within the correlated regions become long-lived. Here we present neutron scattering measurements showing that this conventional picture must be replaced by a new paradigm in YFe 2Al 10, a compound that forms naturally very close to a T = 0 quantum phase transition. Fully quantum mechanical fluctuations of localized moments are found to diverge at low energies and temperatures, however the fluctuating moments are entirely without spatial correlations. Zero temperature order in YFe 2Al 10 is achieved by a newmore » and entirely local type of quantum phase transition that may originate with the creation of the moments themselves.« less

A Local Quantum Phase Transition in YFe 2Al 10

DOE PAGES

Gannon, W J.; Zaliznyak, Igor A.; Wu, L. S.; ...

2018-06-29

Here, a phase transition occurs when correlated regions of a new phase grow to span the system and the fluctuations within the correlated regions become long-lived. Here we present neutron scattering measurements showing that this conventional picture must be replaced by a new paradigm in YFe 2Al 10, a compound that forms naturally very close to a T = 0 quantum phase transition. Fully quantum mechanical fluctuations of localized moments are found to diverge at low energies and temperatures, however the fluctuating moments are entirely without spatial correlations. Zero temperature order in YFe 2Al 10 is achieved by a newmore » and entirely local type of quantum phase transition that may originate with the creation of the moments themselves.« less

The Impact of Structural Heterogeneity on Excitation-Inhibition Balance in Cortical Networks.

PubMed

Landau, Itamar D; Egger, Robert; Dercksen, Vincent J; Oberlaender, Marcel; Sompolinsky, Haim

2016-12-07

Models of cortical dynamics often assume a homogeneous connectivity structure. However, we show that heterogeneous input connectivity can prevent the dynamic balance between excitation and inhibition, a hallmark of cortical dynamics, and yield unrealistically sparse and temporally regular firing. Anatomically based estimates of the connectivity of layer 4 (L4) rat barrel cortex and numerical simulations of this circuit indicate that the local network possesses substantial heterogeneity in input connectivity, sufficient to disrupt excitation-inhibition balance. We show that homeostatic plasticity in inhibitory synapses can align the functional connectivity to compensate for structural heterogeneity. Alternatively, spike-frequency adaptation can give rise to a novel state in which local firing rates adjust dynamically so that adaptation currents and synaptic inputs are balanced. This theory is supported by simulations of L4 barrel cortex during spontaneous and stimulus-evoked conditions. Our study shows how synaptic and cellular mechanisms yield fluctuation-driven dynamics despite structural heterogeneity in cortical circuits. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Multiscale structure of time series revealed by the monotony spectrum.

PubMed

Vamoş, Călin

2017-03-01

Observation of complex systems produces time series with specific dynamics at different time scales. The majority of the existing numerical methods for multiscale analysis first decompose the time series into several simpler components and the multiscale structure is given by the properties of their components. We present a numerical method which describes the multiscale structure of arbitrary time series without decomposing them. It is based on the monotony spectrum defined as the variation of the mean amplitude of the monotonic segments with respect to the mean local time scale during successive averagings of the time series, the local time scales being the durations of the monotonic segments. The maxima of the monotony spectrum indicate the time scales which dominate the variations of the time series. We show that the monotony spectrum can correctly analyze a diversity of artificial time series and can discriminate the existence of deterministic variations at large time scales from the random fluctuations. As an application we analyze the multifractal structure of some hydrological time series.

Radiative transitions in highly doped and compensated chalcopyrites and kesterites: The case of Cu2ZnSnS4

NASA Astrophysics Data System (ADS)

Teixeira, J. P.; Sousa, R. A.; Sousa, M. G.; da Cunha, A. F.; Fernandes, P. A.; Salomé, P. M. P.; Leitão, J. P.

2014-12-01

The theoretical models of radiative recombinations in both CuIn1 -xGaxSe2 chalcopyrite and Cu2ZnSnS4 kesterite, and related compounds, were revised. For heavily doped materials, electrons are free or bound to large donor agglomerates which hinders the involvement of single donors in the radiative recombination channels. In this work, we investigated the temperature and excitation power dependencies of the photoluminescence of Cu2ZnSnS4-based solar cells in which the absorber layer was grown through sulphurization of multiperiod structures of precursor layers. For both samples the luminescence is dominated by an asymmetric band with peak energy at ˜1.22 eV, which is influenced by fluctuating potentials in both conduction and valence bands. A value of ˜60 meV was estimated for the root-mean-square depth of the tails in the conduction band. The radiative transitions involve the recombination of electrons captured by localized states in tails of the conduction band with holes localized in neighboring acceptors that follow the fluctuations in the valence band. The same acceptor level with an ionization energy of ˜280 meV was identified in both absorber layers. The influence of fluctuating potentials in the electrical performance of the solar cells was discussed.

Energy transfer between two vacuum-gapped metal plates: Coulomb fluctuations and electron tunneling

NASA Astrophysics Data System (ADS)

Zhang, Zu-Quan; Lü, Jing-Tao; Wang, Jian-Sheng

2018-05-01

Recent experimental measurements for near-field radiative heat transfer between two bodies have been able to approach the gap distance within 2 nm , where the contributions of Coulomb fluctuation and electron tunneling are comparable. Using the nonequilibrium Green's function method in the G0W0 approximation, based on a tight-binding model, we obtain for the energy current a Caroli formula from the Meir-Wingreen formula in the local equilibrium approximation. Also, the Caroli formula is consistent with the evanescent part of the heat transfer from the theory of fluctuational electrodynamics. We go beyond the local equilibrium approximation to study the energy transfer in the crossover region from electron tunneling to Coulomb fluctuation based on a numerical calculation.

Ion aggregation in high salt solutions. III. Computational vibrational spectroscopy of HDO in aqueous salt solutions

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

Choi, Jun-Ho; Lim, Sohee; Chon, Bonghwan

The vibrational frequency, frequency fluctuation dynamics, and transition dipole moment of the O—D stretch mode of HDO molecule in aqueous solutions are strongly dependent on its local electrostatic environment and hydrogen-bond network structure. Therefore, the time-resolved vibrational spectroscopy the O—D stretch mode has been particularly used to investigate specific ion effects on water structure. Despite prolonged efforts to understand the interplay of O—D vibrational dynamics with local water hydrogen-bond network and ion aggregate structures in high salt solutions, still there exists a gap between theory and experiment due to a lack of quantitative model for accurately describing O—D stretch frequencymore » in high salt solutions. To fill this gap, we have performed numerical simulations of Raman scattering and IR absorption spectra of the O—D stretch mode of HDO in highly concentrated NaCl and KSCN solutions and compared them with experimental results. Carrying out extensive quantum chemistry calculations on not only water clusters but also ion-water clusters, we first developed a distributed vibrational solvatochromic charge model for the O—D stretch mode in aqueous salt solutions. Furthermore, the non-Condon effect on the vibrational transition dipole moment of the O—D stretch mode was fully taken into consideration with the charge response kernel that is non-local polarizability density. From the fluctuating O—D stretch mode frequencies and transition dipole vectors obtained from the molecular dynamics simulations, the O—D stretch Raman scattering and IR absorption spectra of HDO in salt solutions could be calculated. The polarization effect on the transition dipole vector of the O—D stretch mode is shown to be important and the asymmetric line shapes of the O—D stretch Raman scattering and IR absorption spectra of HDO especially in highly concentrated NaCl and KSCN solutions are in quantitative agreement with experimental results. We anticipate that this computational approach will be of critical use in interpreting linear and nonlinear vibrational spectroscopies of HDO molecule that is considered as an excellent local probe for monitoring local electrostatic and hydrogen-bonding environment in not just salt but also other confined and crowded solutions.« less

Convective Propagation Characteristics Using a Simple Representation of Convective Organization

NASA Astrophysics Data System (ADS)

Neale, R. B.; Mapes, B. E.

2016-12-01

Observed equatorial wave propagation is intimately linked to convective organization and it's coupling to features of the larger-scale flow. In this talk we a use simple 4 level model to accommodate vertical modes of a mass flux convection scheme (shallow, mid-level and deep). Two paradigms of convection are used to represent convective processes. One that has only both random (unorganized) diagnosed fluctuations of convective properties and one with organized fluctuations of convective properties that are amplified by previously existing convection and has an explicit moistening impact on the local convecting environment We show a series of model simulations in single-column, 2D and 3D configurations, where the role of convective organization in wave propagation is shown to be fundamental. For the optimal choice of parameters linking organization to local atmospheric state, a broad array of convective wave propagation emerges. Interestingly the key characteristics of propagating modes are the low-level moistening followed by deep convection followed by mature 'large-scale' heating. This organization structure appears to hold firm across timescales from 5-day wave disturbances to MJO-like wave propagation.

Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Pandey, R. B.; Jacobs, D. J.; Farmer, B. L.

2017-05-01

The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ˜ 1.3), random-coil (D ˜ 1.75), and globular (D ˜ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.

Modifications to intermittent turbulent structures by sheared flow in LAPD

NASA Astrophysics Data System (ADS)

Rossi, Giovanni; Schaffner, David; Carter, Troy; Guice, Danny; Bengtson, Roger

2012-10-01

Turbulence in the edge of the Large Plasma Device is generally observed to be intermittent with the production of filamentary structures. Density-enhancement events (called ``blobs'') are localized to the region radially outside the edge of the cathode source while density-depletion events (called ``holes'') are localized to the region radially inward. A flow-shear layer is also observed to be localized to this same spatial region. Control over the edge flow and shear in LAPD is now possible using a biasable limiter. Edge intermittency is observed to be strongly affected by variations in the edge flow, with intermittency (as measured by skewness of the fluctuation amplitude PDF) increasing with edge flow (in either direction) and reaching a minimum when spontaneous edge flow is zeroed-out using biasing. This trend is counter to the observed changes in turbulent particle flux, which peaks at low flow/shear. Two-dimensional cross-conditional averaging confirms the blobs to be detached filamentary structures with a clear dipolar potential structure and a geometry also dependent on the magnitude of sheared flow. More detailed measurements are made to connect the occurrence of these blobs to observed flow-driven coherent modes and their contribution to radial particle flux.

The effects of local blowing perturbations on thermal turbulent structures

NASA Astrophysics Data System (ADS)

Liu, Can; Araya, Guillermo; Leonardi, Stefano; Castillo, Luciano

2013-11-01

Blowing is an active flow control technique with several industrial applications, particularly in film cooling of turbine blades. In the past, the effects of localized blowing have been mostly analyzed on the velocity field and its influence of the flow parameters and turbulence structures (Krogstad and Kourakine, 2000). However, little literature can be found on the effects of blowing on the coherent thermal structures. In the present study, an incompressible turbulent channel flow with given steady blowing at the wall is simulated via DNS by means of five spanwise holes. The Reynolds number based on the friction velocity and half channel height is approximately Re = 394 and the molecular Prandtl number is Pr = 0.71. Temperature is considered a passive scalar with isothermal conditions at the wall. Different blowing amplitudes and perturbing angles (with respect to the streamwise direction) are applied to find out their effects on the turbulent thermal structures by means of a two-point correlation analysis. In addition, local reduction and increase of drag are connected to vorticity. The corresponding influence of perturbing amplitudes and angles on the energy budget of thermal fluctuations and turbulent Prandtl numbers are also shown and discussed.

An association of magnetospheric whistler dispersion characteristics with changes in local plasma density.

NASA Technical Reports Server (NTRS)

Scarf, F. L.; Chappell, C. R.

1973-01-01

We use OGO 5 measurements made within the plasmapause on May 15, 1969, to investigate the possible association between changes in lightning whistler dispersion characteristics and local density fluctuations. It is shown that groups of whistlers with relatively constant dispersions tended to be detected in regions where the local ion concentration was significantly enhanced. It is assumed that these local density fluctuations represent characteristics of large-scale field-aligned variations. The results are then compared with ray refraction estimates appropriate for low-frequency whistler mode propagation (wave components with frequencies comparable to the local lower hybrid frequency) in a nonuniform medium.

Dispersion Measure Variation of Repeating Fast Radio Burst Sources

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

Yang, Yuan-Pei; Zhang, Bing, E-mail: yypspore@gmail.com, E-mail: zhang@physics.unlv.edu

The repeating fast radio burst (FRB) 121102 was recently localized in a dwarf galaxy at a cosmological distance. The dispersion measure (DM) derived for each burst from FRB 121102 so far has not shown significant evolution, even though an apparent increase was recently seen with newly detected VLA bursts. It is expected that more repeating FRB sources may be detected in the future. In this work, we investigate a list of possible astrophysical processes that might cause DM variation of a particular FRB source. The processes include (1) cosmological scale effects such as Hubble expansion and large-scale structure fluctuations; (2)more » FRB local effects such as gas density fluctuation, expansion of a supernova remnant (SNR), a pulsar wind nebula, and an H ii region; and (3) the propagation effect due to plasma lensing. We find that the DM variations contributed by the large-scale structure are extremely small, and any observable DM variation is likely caused by the plasma local to the FRB source. In addition to mechanisms that decrease DM over time, we suggest that an FRB source in an expanding SNR around a nearly neutral ambient medium during the deceleration (Sedov–Taylor and snowplow) phases or in a growing H ii region can increase DM. Some effects (e.g., an FRB source moving in an H ii region or plasma lensing) can produce either positive or negative DM variations. Future observations of DM variations of FRB 121102 and other repeating FRB sources can provide important clues regarding the physical origin of these sources.« less

Detrended fluctuation analysis of short datasets: An application to fetal cardiac data

NASA Astrophysics Data System (ADS)

Govindan, R. B.; Wilson, J. D.; Preißl, H.; Eswaran, H.; Campbell, J. Q.; Lowery, C. L.

2007-02-01

Using detrended fluctuation analysis (DFA) we perform scaling analysis of short datasets of length 500-1500 data points. We quantify the long range correlation (exponent α) by computing the mean value of the local exponents αL (in the asymptotic regime). The local exponents are obtained as the (numerical) derivative of the logarithm of the fluctuation function F(s) with respect to the logarithm of the scale factor s:αL=dlog10F(s)/dlog10s. These local exponents display huge variations and complicate the correct quantification of the underlying correlations. We propose the use of the phase randomized surrogate (PRS), which preserves the long range correlations of the original data, to minimize the variations in the local exponents. Using the numerically generated uncorrelated and long range correlated data, we show that performing DFA on several realizations of PRS and estimating αL from the averaged fluctuation functions (of all realizations) can minimize the variations in αL. The application of this approach to the fetal cardiac data (RR intervals) is discussed and we show that there is a statistically significant correlation between α and the gestation age.

Conformational Fluctuations in G-Protein-Coupled Receptors

NASA Astrophysics Data System (ADS)

Brown, Michael F.

2014-03-01

G-protein-coupled receptors (GPCRs) comprise almost 50% of pharmaceutical drug targets, where rhodopsin is an important prototype and occurs naturally in a lipid membrane. Rhodopsin photoactivation entails 11-cis to all-trans isomerization of the retinal cofactor, yielding an equilibrium between inactive Meta-I and active Meta-II states. Two important questions are: (1) Is rhodopsin is a simple two-state switch? Or (2) does isomerization of retinal unlock an activated conformational ensemble? For an ensemble-based activation mechanism (EAM) a role for conformational fluctuations is clearly indicated. Solid-state NMR data together with theoretical molecular dynamics (MD) simulations detect increased local mobility of retinal after light activation. Resultant changes in local dynamics of the cofactor initiate large-scale fluctuations of transmembrane helices that expose recognition sites for the signal-transducing G-protein. Time-resolved FTIR studies and electronic spectroscopy further show the conformational ensemble is strongly biased by the membrane lipid composition, as well as pH and osmotic pressure. A new flexible surface model (FSM) describes how the curvature stress field of the membrane governs the energetics of active rhodopsin, due to the spontaneous monolayer curvature of the lipids. Furthermore, influences of osmotic pressure dictate that a large number of bulk water molecules are implicated in rhodopsin activation. Around 60 bulk water molecules activate rhodopsin, which is much larger than the number of structural waters seen in X-ray crystallography, or inferred from studies of bulk hydrostatic pressure. Conformational selection and promoting vibrational motions of rhodopsin lead to activation of the G-protein (transducin). Our biophysical data give a paradigm shift in understanding GPCR activation. The new view is: dynamics and conformational fluctuations involve an ensemble of substates that activate the cognate G-protein in the amplified visual response.

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

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

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

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

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

NASA Astrophysics Data System (ADS)

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

2016-03-01

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

Microscopic structural descriptor of liquid water

NASA Astrophysics Data System (ADS)

Shi, Rui; Tanaka, Hajime

2018-03-01

The microscopic structure of liquid water has been believed to be the key to the understanding of the unique properties of this extremely important substance. Many structural descriptors have been developed for revealing local structural order in water, but their properties are still not well understood. The essential difficulty comes from structural fluctuations due to thermal noise, which are intrinsic to the liquid state. The most popular and widely used descriptors are the local structure index (LSI) and d5. Recently, Russo and Tanaka [Nat. Commun. 3, 3556 (2014)] introduced a new descriptor ζ which measures the translational order between the first and second shells considering hydrogen bonding (H-bonding) in the first shell. In this work, we compare the performance of these three structural descriptors for a popular water model known as TIP5P water. We show that local structural ordering can be properly captured only by the structural descriptor ζ, but not by the other two descriptors particularly at a high temperature, where thermal noise effects are severe. The key difference of ζ from LSI and d5 is that only ζ considers H-bonding which is crucial to detect high translational and tetrahedral order of not only oxygen but also hydrogen atoms. The importance of H-bonding is very natural, considering the fact that the locally favored structures are stabilized by energy gain due to the formation of four hydrogen bonds between the central water molecule and its neighboring ones in the first shell. Our analysis of the water structure by using ζ strongly supports the two-state model of water: water is a dynamic mixture of locally favored (ordered) and normal-liquid (disordered) structures. This work demonstrates the importance of H-bonding in the characterization of water's structures and provides a useful structural descriptor for water-type tetrahedral liquids to study their structure and dynamics.

Single Molecular Level Probing of Structure and Dynamics of Papain Under Denaturation.

PubMed

Sengupta, Bhaswati; Chaudhury, Apala; Das, Nilimesh; Sen, Pratik

2017-01-01

Papain is a cysteine protease enzyme present in papaya and known to help in digesting peptide. Thus the structure and function of the active site of papain is of interest. The objective of present study is to unveil the overall structural transformation and the local structural change around the active site of papain as a function of chemical denaturant. Papain has been tagged at Cys-25 with a thiol specific fluorescence probe N-(7- dimethylamino-4-methylcoumarin-3-yl) iodoacetamide (DACIA). Guanidine hydrochloride (GnHCl) has been used as the chemical denaturant. Steady state, time-resolved, and single molecular level fluorescence techniques was applied to map the change in the local environment. It is found that papain undergoes a two-step denaturation in the presence of GnHCl. Fluorescence correlation spectroscopic (FCS) data indicate that the size (hydrodynamic diameter) of native papain is ~36.8 Å, which steadily increases to ~53 Å in the presence of 6M GnHCl. FCS study also reveals that the conformational fluctuation time of papain is 6.3 µs in its native state, which decreased to 2.7 µs in the presence of 0.75 M GnHCl. Upon further increase in GnHCl concentration the conformational fluctuation time increase monotonically till 6 M GnHCl, where the time constant is measured as 14 µs. On the other hand, the measurement of ellipticity, hence the helical structure, by circular dichroism spectroscopy is found to be incapable to capture such structural transformation. It is concluded that in the presence of small amount of GnHCl the active site of papain takes up a more compact structure (although the overall size increases) than in the native state, which has been designated as the intermediate state. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Thermonuclear runaways in nova outbursts. 2: Effect of strong, instantaneous, local fluctuations

NASA Technical Reports Server (NTRS)

Shankar, Anurag; Arnett, David

1994-01-01

In an attempt to understand the manner in which nova outbursts are initiated on the surface of a white dwarf, we investigate the effects fluctuations have on the evolution of a thermonuclear runaway. Fluctuations in temperature density, or the composition of material in the burning shell may arise due to the chaotic flow field generated by convection when it occurs, or by the accretion process itself. With the aid of two-dimensional reactive flow calculations, we consider cases where a strong fluctutation in temperature arises during the early, quiescent accretion phase or during the later, more dynamic, explosion phase. In all cases we find that an instantaneous, local temperature fluctuation causes the affected material to become Rayleigh-Taylor unstable. The rapid rise and subsequent expansion of matter immediately cools the hot blob, which prevents the lateral propagation of burning. This suggests that local temperature fluctuations do not play a significant role in directly initiating the runaway, especially during the early stages. However, they may provide an efficient mechanism of mixing core material into the envelope (thereby pre-enriching the fuel for subsequent episodes of explosive hydrogen burning) and of mixing substantial amounts of the radioactive nucleus N-13 into the surface layers, making novae potential gamma-ray sources. This suggests that it is the global not the local, evolution of the core-envelope interface to high temperatures which dominates the development of the runaway. We also present a possible new scenario for the initiation of nova outbursts based on our results.

Large Amplitude IMF Fluctuations in Corotating Interaction Regions: Ulysses at Midlatitudes

NASA Technical Reports Server (NTRS)

Tsurutani, Bruce T.; Ho, Christian M.; Arballo, John K.; Goldstein, Bruce E.; Balogh, Andre

1995-01-01

Corotating Interaction Regions (CIRs), formed by high-speed corotating streams interacting with slow speed streams, have been examined from -20 deg to -36 deg heliolatitudes. The high-speed streams emanate from a polar coronal hole that Ulysses eventually becomes fully embedded in as it travels towards the south pole. We find that the trailing portion of the CIR, from the interface surface (IF) to the reverse shock (RS), contains both large amplitude transverse fluctuations and magnitude fluctuations. Similar fluctuations have been previously noted to exist within CIRs detected in the ecliptic plane, but their existence has not been explained. The normalized magnetic field component variances within this portion of the CIR and in the trailing high-speed stream are approximately the same, indicating that the fluctuations in the CIR are compressed Alfven waves. Mirror mode structures with lower intensities are also observed in the trailing portion of the CIR, presumably generated from a local instability driven by free energy associated with compression of the high-speed solar wind plasma. The mixture of these two modes (compressed Alfven waves and mirror modes) plus other modes generated by three wave processes (wave-shock interactions) lead to a lower Alfvenicity within the trailing portion of the CfR than in the high-speed stream proper. The results presented in this paper suggest a mechanism for generation of large amplitude B(sub z) fluctuations within CIRS. Such phenomena have been noted to be responsible for the generation of moderate geomagnetic storms during the declining phase of the solar cycle.

3D Anisotropy of Solar Wind Turbulence, Tubes, or Ribbons?

NASA Astrophysics Data System (ADS)

Verdini, Andrea; Grappin, Roland; Alexandrova, Olga; Lion, Sonny

2018-01-01

We study the anisotropy with respect to the local magnetic field of turbulent magnetic fluctuations at magnetofluid scales in the solar wind. Previous measurements in the fast solar wind obtained axisymmetric anisotropy, despite that the analysis method allows nonaxisymmetric structures. These results are probably contaminated by the wind expansion that introduces another symmetry axis, namely, the radial direction, as indicated by recent numerical simulations. These simulations also show that while the expansion is strong, the principal fluctuations are in the plane perpendicular to the radial direction. Using this property, we separate 11 yr of Wind spacecraft data into two subsets characterized by strong and weak expansion and determine the corresponding turbulence anisotropy. Under strong expansion, the small-scale anisotropy is consistent with the Goldreich & Sridhar critical balance. As in previous works, when the radial symmetry axis is not eliminated, the turbulent structures are field-aligned tubes. Under weak expansion, we find 3D anisotropy predicted by the Boldyrev model, that is, turbulent structures are ribbons and not tubes. However, the very basis of the Boldyrev phenomenology, namely, a cross-helicity increasing at small scales, is not observed in the solar wind: the origin of the ribbon formation is unknown.

Application of wavelet based MFDFA on Mueller matrix images for cervical pre-cancer detection

NASA Astrophysics Data System (ADS)

Zaffar, Mohammad; Pradhan, Asima

2018-02-01

A systematic study has been conducted on application of wavelet based multifractal de-trended fluctuation analysis (MFDFA) on Mueller matrix (MM) images of cervical tissue sections for early cancer detection. Changes in multiple scattering and orientation of fibers are observed by utilizing a discrete wavelet transform (Daubechies) which identifies fluctuations over polynomial trends. Fluctuation profiles, after 9th level decomposition, for all elements of MM qualitatively establish a demarcation of different grades of cancer from normal tissue. Moreover, applying MFDFA on MM images, Hurst exponent profiles for images of MM qualitatively are seen to display differences. In addition, the values of Hurst exponent increase for the diagonal elements of MM with increasing grades of the cervical cancer, while the value for the elements which correspond to linear polarizance decrease. However, for circular polarizance the value increases with increasing grades. These fluctuation profiles reveal the trend of local variation of refractive -indices and along with Hurst exponent profile, may serve as a useful biological metric in the early detection of cervical cancer. The quantitative measurements of Hurst exponent for diagonal and first column (polarizance governing elements) elements which reflect changes in multiple scattering and structural anisotropy in stroma, may be sensitive indicators of pre-cancer.

A New Look at Some Solar Wind Turbulence Puzzles

NASA Technical Reports Server (NTRS)

Roberts, Aaron

2006-01-01

Some aspects of solar wind turbulence have defied explanation. While it seems likely that the evolution of Alfvenicity and power spectra are largely explained by the shearing of an initial population of solar-generated Alfvenic fluctuations, the evolution of the anisotropies of the turbulence does not fit into the model so far. A two-component model, consisting of slab waves and quasi-two-dimensional fluctuations, offers some ideas, but does not account for the turning of both wave-vector-space power anisotropies and minimum variance directions in the fluctuating vectors as the Parker spiral turns. We will show observations that indicate that the minimum variance evolution is likely not due to traditional turbulence mechanisms, and offer arguments that the idea of two-component turbulence is at best a local approximation that is of little help in explaining the evolution of the fluctuations. Finally, time-permitting, we will discuss some observations that suggest that the low Alfvenicity of many regions of the solar wind in the inner heliosphere is not due to turbulent evolution, but rather to the existence of convected structures, including mini-clouds and other twisted flux tubes, that were formed with low Alfvenicity. There is still a role for turbulence in the above picture, but it is highly modified from the traditional views.

Role of large thermal fluctuations and magnesium ions in t-RNA selectivity of the ribosome

PubMed Central

Guo, Zuojun; Gibson, Meghan; Sitha, Sanyasi; Chu, Steven; Mohanty, Udayan

2011-01-01

The fidelity of translation selection begins with the base pairing of codon-anticodon complex between the m-RNA and tRNAs. Binding of cognate and near-cognate tRNAs induces 30S subunit of the ribosome to wrap around the ternary complex, EF-Tu(GTP)aa-tRNA. We have proposed that large thermal fluctuations play a crucial role in the selection process. To test this conjecture, we have developed a theoretical technique to determine the probability that the ternary complex, as a result of large thermal fluctuations, forms contacts leading to stabilization of the GTPase activated state. We argue that the configurational searches for such processes are in the tail end of the probability distribution and show that the probability for this event is localized around the most likely configuration. Small variations in the repositioning of cognate relative to near-cognate complexes lead to rate enhancement of the cognate complex. The binding energies of over a dozen unique site-bound magnesium structural motifs are investigated and provide insights into the nature of interaction of divalent metal ions with the ribosome. PMID:21368154

Superconductivity-localization interplay and fluctuation magnetoresistance in epitaxial BaPb1 -xBixO3 thin films

NASA Astrophysics Data System (ADS)

Harris, D. T.; Campbell, N.; Uecker, R.; Brützam, M.; Schlom, D. G.; Levchenko, A.; Rzchowski, M. S.; Eom, C.-B.

2018-04-01

BaPb1 -xBixO3 is a superconductor, with transition temperature Tc=11 K, whose parent compound BaBiO3 possesses a charge ordering phase and perovskite crystal structure reminiscent of the cuprates. The lack of magnetism simplifies the BaPb1 -xBixO3 phase diagram, making this system an ideal platform for contrasting high-Tc systems with isotropic superconductors. Here we use high-quality epitaxial thin films and magnetotransport to demonstrate superconducting fluctuations that extend well beyond Tc. For the thickest films (thickness above ˜100 nm ) this region extends to ˜27 K , well above the bulk Tc and remarkably close to the higher Tc of Ba1 -xKxBiO3 (Tc=31 K). We drive the system through a superconductor-insulator transition by decreasing thickness and find the observed Tc correlates strongly with disorder. This material manifests strong fluctuations across a wide range of thicknesses, temperatures, and disorder presenting new opportunities for understanding the precursor of superconductivity near the 2D-3D dimensionality crossover.

Are the Formation and Abundances of Metal-poor Stars the Result of Dust Dynamics?

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

Hopkins, Philip F.; Conroy, Charlie, E-mail: phopkins@caltech.edu

Large dust grains can fluctuate dramatically in their local density, relative to the gas, in neutral turbulent disks. Small, high-redshift galaxies (before reionization) represent ideal environments for this process. We show via simple arguments and simulations that order-of-magnitude fluctuations are expected in local abundances of large grains (>100 Å) under these conditions. This can have important consequences for star formation and stellar metal abundances in extremely metal-poor stars. Low-mass stars can form in dust-enhanced regions almost immediately after some dust forms even if the galaxy-average metallicity is too low for fragmentation to occur. We argue that the metal abundances ofmore » these “promoted” stars may contain interesting signatures as the CNO abundances (concentrated in large carbonaceous grains and ices) and Mg and Si (in large silicate grains) can be enhanced and/or fluctuate almost independently. Remarkably, the otherwise puzzling abundance patterns of some metal-poor stars can be well fit by standard IMF-averaged core-collapse SNe yields if we allow for fluctuating local dust-to-gas ratios. We also show that the observed log-normal distribution of enhancements in pure SNe yields, shows very large enhancements and variations up to factors of ≳100 as expected in the dust-promoted model, preferentially in the [C/Fe]-enhanced metal-poor stars. Together, this suggests that (1) dust exists in second-generation star formation, (2) local dust-to-gas ratio fluctuations occur in protogalaxies and can be important for star formation, and (3) the light element abundances of these stars may be affected by the local chemistry of dust where they formed, rather than directly tracing nucleosynthesis from earlier populations.« less

1/ f noise from the laws of thermodynamics for finite-size fluctuations.

PubMed

Chamberlin, Ralph V; Nasir, Derek M

2014-07-01

Computer simulations of the Ising model exhibit white noise if thermal fluctuations are governed by Boltzmann's factor alone; whereas we find that the same model exhibits 1/f noise if Boltzmann's factor is extended to include local alignment entropy to all orders. We show that this nonlinear correction maintains maximum entropy during equilibrium fluctuations. Indeed, as with the usual way to resolve Gibbs' paradox that avoids entropy reduction during reversible processes, the correction yields the statistics of indistinguishable particles. The correction also ensures conservation of energy if an instantaneous contribution from local entropy is included. Thus, a common mechanism for 1/f noise comes from assuming that finite-size fluctuations strictly obey the laws of thermodynamics, even in small parts of a large system. Empirical evidence for the model comes from its ability to match the measured temperature dependence of the spectral-density exponents in several metals and to show non-Gaussian fluctuations characteristic of nanoscale systems.

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

Barada, K., E-mail: kshitish@ucla.edu; Rhodes, T. L.; Crocker, N. A.

We present new measurements of internal magnetic fluctuations obtained with a novel eight channel cross polarization scattering (CPS) system installed on the DIII-D tokamak. Measurements of internal, localized magnetic fluctuations provide a window on an important physics quantity that we heretofore have had little information on. Importantly, these measurements provide a new ability to challenge and test linear and nonlinear simulations and basic theory. The CPS method, based upon the scattering of an incident microwave beam into the opposite polarization by magnetic fluctuations, has been significantly extended and improved over the method as originally developed on the Tore Supra tokamak.more » A new scattering geometry, provided by a unique probe beam, is utilized to improve the spatial localization and wavenumber range. Remotely controllable polarizer and mirror angles allow polarization matching and wavenumber selection for a range of plasma conditions. The quasi-optical system design, its advantages and challenges, as well as important physics validation tests are presented and discussed. Effect of plasma beta (ratio of kinetic to magnetic pressure) on both density and magnetic fluctuations is studied and it is observed that internal magnetic fluctuations increase with beta. During certain quiescent high confinement operational regimes, coherent low frequency modes not detected by magnetic probes are detected locally by CPS diagnostics.« less

Measurements of surface-pressure fluctuations on the XB-70 airplane at local Mach numbers up to 2.45

NASA Technical Reports Server (NTRS)

Lewis, T. L.; Dods, J. B., Jr.; Hanly, R. D.

1973-01-01

Measurements of surface-pressure fluctuations were made at two locations on the XB-70 airplane for nine flight-test conditions encompassing a local Mach number range from 0.35 to 2.45. These measurements are presented in the form of estimated power spectral densities, coherence functions, and narrow-band-convection velocities. The estimated power spectral densities compared favorably with wind-tunnel data obtained by other experimenters. The coherence function and convection velocity data supported conclusions by other experimenters that low-frequency surface-pressure fluctuations consist of small-scale turbulence components with low convection velocity.

Multidimensional Visualization of MHD and Turbulence in Fusion Plasmas [Multi-dimensional Visualization of Turbulence in Fusion Plasmas

DOE PAGES

Muscatello, Christopher M.; Domier, Calvin W.; Hu, Xing; ...

2014-08-13

Here, quasi-optical imaging at sub-THz frequencies has had a major impact on fusion plasma diagnostics. Mm-wave imaging reflectometry utilizes microwaves to actively probe fusion plasmas, inferring the local properties of electron density fluctuations. Electron cyclotron emission imaging is a multichannel radiometer that passively measures the spontaneous emission of microwaves from the plasma to infer local properties of electron temperature fluctuations. These imaging diagnostics work together to diagnose the characteristics of turbulence. Important quantities such as amplitude and wavenumber of coherent fluctuations, correlation lengths and decor relation times of turbulence, and poloidal flow velocity of the plasma are readily inferred.

Fluctuation dynamics of exchange rates on Polish financial market

NASA Astrophysics Data System (ADS)

Orłowski, A.; Struzik, Z. R.; Syczewska, E.; Załuska-Kotur, M. A.

2004-12-01

We show results of local fluctuation analysis, probability distributions, and fractional integration analysis for nominal exchange rates of the Polish zloty versus two foreign currencies (US dollar and German mark/euro). The results confirm the rapid change of the volatility pattern in August 1997. We compare the type of the fluctuation behavior before and after this date.

"Fluctuoscopy" of Superconductors

NASA Astrophysics Data System (ADS)

Varlamov, A. A.

Study of fluctuation phenomena in superconductors (SCs) is the subject of great fundamental and practical importance. Understanding of their physics allowed to clear up the fundamental properties of SC state. Being predicted in 1968, one of the fluctuation effects, namely paraconductivity, was experimentally observed almost simultaneously. Since this time, fluctuations became a noticeable part of research in the field of superconductivity, and a variety of fluctuation effects have been discovered. The new wave of interest to fluctuations (FL) in superconductors was generated by the discovery of cuprate oxide superconductors (high-temperature superconductors, HTS), where, due to extremely short coherence length and low effective dimensionality of the electron system, superconductive fluctuations manifest themselves in a wide range of temperatures. Moreover, anomalous properties of the normal state of HTS were attributed by many theorists to strong FL in these systems. Being studied in the framework of the phenomenological Ginzburg-Landau theory and, more extensively, in diagrammatic microscopic approach, SC FLs side by side with other quantum corrections (weak localization, etc.) became a new tool for investigation and characterization of such new systems as HTS, disordered electron systems, granular metals, Josephson structures, artificial super-lattices, etc. The characteristic feature of SC FL is their strong dependence on temperature and magnetic fields in the vicinity of phase transition. This allows one to definitely separate the fluctuation effects from other contributions and to use them as the source of information about the microscopic parameters of a material. By their origin, SC FLs are very sensitive to relaxation processes, which break phase coherence. This allows using them for versatile characterization of SC. Today, one can speak about the " fluctuoscopy" of superconductive systems. In review, we present the qualitative picture both of thermodynamic fluctuations close to critical temperature T c0and quantum fluctuations at zero temperature and in vicinity of the second critical field H c2(0). Then in the frameworks of the Ginzburg-Landau theory, we discuss the characteristic crossovers in fluctuation properties of superconductive nanoparticles and layered superconductors. We present the general expression for fluctuation magneto-conductivity valid through all phase diagram of superconductor and apply it to study of the quantum phase transition close to H c2(0). Fluctuation analysis of this transition allows us to present the scenario of fluctuation defragmentation of the Abrikosov lattice.

Spatial and mesoscopic fluctuations in glassy dynamics

NASA Astrophysics Data System (ADS)

Chamon, Claudio C.; Cugliandolo, Leticia F.

2004-05-01

One of the striking properties of a glassy system is that many material properties depend on its age, i.e., the time since the system entered its glassy phase. In this this talk we shall review some recent progress (work in collaboration with H. E. Castillo, P. Charbonneau, J. L. Iguain, M. P. Kennett, D. R. Reichman and M. Sellitto) in understanding local aging, through the study of local observable quantities, which reveal that there are spatial heterogeneities and fluctuations in the aging process of macroscopic systems. We show that a number of universal properties are shared by many non-equilibrium systems, both with and without quenched disorder, such as the 3D Edwards-Anderson model and some kinetically constrained non-interacting 2D and 3D spin models, for example. Similar scaling relations are found for mesoscopic sample-to-sample fluctuations of global quantities in small size systems. We discuss how the emergence of a symmetry in aging systems, time-reparametrization invariance, could be responsible for the observed universal behavior of the local and mesoscopic non-equilibrium fluctuations.

Single to Multiquasiparticle Excitations in the Itinerant Helical Magnet CeRhIn 5

DOE PAGES

Stock, C.; Rodriguez-Rivera, J. A.; Schmalzl, K.; ...

2015-06-19

Neutron scattering is used to measure the quantum spin fluctuations in CeRhIn 5 - the parent material of the eXIn 5 superconducting series. Out-of-plane spin fluctuations are gapped and localized in momentum, similar to the spin excitons in CeCoIn5. The in-plane fluctuations consist of sharp spin-wave excitations parameterized by a nearest neighbor exchange J RKKY =0.88 ± 0.05 meV that crossover to a temporally and spatially broad multiparticle spectrum with energies of ~ 2 × J RKKY . This continuum represents composite fluctuations that illustrate the breakdown of single magnons originating from the delicate energy balance between localized 4f andmore » itinerant behavior in a heavy metal. The experiment therefore shows how quasiparticle behavior is changed by the close proximity of quantum criticality.« less

Influence of static habitat attributes on local and regional Rocky intertidal community structure

USGS Publications Warehouse

Konar, B.; Iken, K.; Coletti, H.; Monson, Daniel H.; Weitzman, Ben P.

2016-01-01

Rocky intertidal communities are structured by local environmental drivers, which can be dynamic, fluctuating on various temporal scales, or static and not greatly varying across years. We examined the role of six static drivers (distance to freshwater, tidewater glacial presence, wave exposure, fetch, beach slope, and substrate composition) on intertidal community structure across the northern Gulf of Alaska. We hypothesized that community structure is less similar at the local scale compared with the regional scale, coinciding with static drivers being less similar on smaller than larger scales. We also hypothesized that static attributes mainly drive local biological community structure. For this, we surveyed five to six sites in each of the six regions in the mid and low intertidal strata. Across regions, static attributes were not consistently different and only small clusters of sites had similar attributes. Additionally, intertidal communities were less similar on the site compared with the region level. These results suggest that these biological communities are not strongly influenced by the local static attributes measured in this study. An alternative explanation is that static attributes among our regions are not different enough to influence the biological communities. This lack of evidence for a strong static driver may be a result of our site selection, which targeted rocky sheltered communities. This suggests that this habitat may be ideal to examine the influence of dynamic drivers. We recommend that future analyses of dynamic attributes may best be performed after analyses have demonstrated that sites do not differ in static attributes.

Nanoscale visualization of electronic properties of AlxGa1-xN/AlyGa1-yN multiple quantum-well heterostructure by spreading resistance microscopy

NASA Astrophysics Data System (ADS)

Sviridov, D. E.; Kozlovsky, V. I.; Rong, X.; Chen, G.; Wang, X.; Jmerik, V. N.; Kirilenko, D. A.; Ivanov, S. V.

2017-01-01

Cross-sectional spreading resistance microscopy has been used to investigate nanoscale variations in electronic properties of an undoped Al0.75Ga0.25N/Al0.95Ga0.05N multiple quantum well (MQW) heterostructure grown by plasma-assisted molecular beam epitaxy on an AlN/c-sapphire template, prepared by metalorganic vapor phase epitaxy. It is found that a current signal from the MQWs can be detected only at a negative sample bias. Moreover, its value changes periodically from one quantum well (QW) to another. Analysis of the current-voltage characteristics of the contacts of a tip with the structure layers showed that periodic contrast of MQWs is the result of fluctuations of the chemical composition of the QWs and the concentration of electrons accumulated in them. Mathematical simulations indicate that this modulation is associated with the periodic fluctuations of an Al-mole fraction in the barrier layers of the structure due to counter gradients of the intensity of Al and Ga molecular fluxes across the surface of a substrate rotating slowly during growth. The nanoscale fluctuations of the current contrast observed along the QW layers are caused, most likely, by the presence of the areas of lateral carrier localization, which originate during the formation of QWs by sub-monolayer digital alloying technique.

Simulation of ultrasonic pulse propagation, distortion, and attenuation in the human chest wall.

PubMed

Mast, T D; Hinkelman, L M; Metlay, L A; Orr, M J; Waag, R C

1999-12-01

A finite-difference time-domain model for ultrasonic pulse propagation through soft tissue has been extended to incorporate absorption effects as well as longitudinal-wave propagation in cartilage and bone. This extended model has been used to simulate ultrasonic propagation through anatomically detailed representations of chest wall structure. The inhomogeneous chest wall tissue is represented by two-dimensional maps determined by staining chest wall cross sections to distinguish between tissue types, digitally scanning the stained cross sections, and mapping each pixel of the scanned images to fat, muscle, connective tissue, cartilage, or bone. Each pixel of the tissue map is then assigned a sound speed, density, and absorption value determined from published measurements and assumed to be representative of the local tissue type. Computational results for energy level fluctuations and arrival time fluctuations show qualitative agreement with measurements performed on the same specimens, but show significantly less waveform distortion than measurements. Visualization of simulated tissue-ultrasound interactions in the chest wall shows possible mechanisms for image aberration in echocardiography, including effects associated with reflection and diffraction caused by rib structures. A comparison of distortion effects for varying pulse center frequencies shows that, for soft tissue paths through the chest wall, energy level and waveform distortion increase markedly with rising ultrasonic frequency and that arrival-time fluctuations increase to a lesser degree.

Role of local assembly in the hierarchical crystallization of associating colloidal hard hemispheres

NASA Astrophysics Data System (ADS)

Lei, Qun-li; Hadinoto, Kunn; Ni, Ran

2017-10-01

Hierarchical self-assembly consisting of local associations of simple building blocks for the formation of complex structures widely exists in nature, while the essential role of local assembly remains unknown. In this work, by using computer simulations, we study a simple model system consisting of associating colloidal hemispheres crystallizing into face-centered-cubic crystals comprised of spherical dimers of hemispheres, focusing on the effect of dimer formation on the hierarchical crystallization. We found that besides assisting the crystal nucleation because of increasing the symmetry of building blocks, the association between hemispheres can also induce both reentrant melting and reentrant crystallization depending on the range of interaction. Especially when the interaction is highly sticky, we observe a novel reentrant crystallization of identical crystals, which melt only in a certain temperature range. This offers another axis in fabricating responsive crystalline materials by tuning the fluctuation of local association.

Widely accessible method for superresolution fluorescence imaging of living systems

PubMed Central

Dedecker, Peter; Mo, Gary C. H.; Dertinger, Thomas; Zhang, Jin

2012-01-01

Superresolution fluorescence microscopy overcomes the diffraction resolution barrier and allows the molecular intricacies of life to be revealed with greatly enhanced detail. However, many current superresolution techniques still face limitations and their implementation is typically associated with a steep learning curve. Patterned illumination-based superresolution techniques [e.g., stimulated emission depletion (STED), reversible optically-linear fluorescence transitions (RESOLFT), and saturated structured illumination microscopy (SSIM)] require specialized equipment, whereas single-molecule–based approaches [e.g., stochastic optical reconstruction microscopy (STORM), photo-activation localization microscopy (PALM), and fluorescence-PALM (F-PALM)] involve repetitive single-molecule localization, which requires its own set of expertise and is also temporally demanding. Here we present a superresolution fluorescence imaging method, photochromic stochastic optical fluctuation imaging (pcSOFI). In this method, irradiating a reversibly photoswitching fluorescent protein at an appropriate wavelength produces robust single-molecule intensity fluctuations, from which a superresolution picture can be extracted by a statistical analysis of the fluctuations in each pixel as a function of time, as previously demonstrated in SOFI. This method, which uses off-the-shelf equipment, genetically encodable labels, and simple and rapid data acquisition, is capable of providing two- to threefold-enhanced spatial resolution, significant background rejection, markedly improved contrast, and favorable temporal resolution in living cells. Furthermore, both 3D and multicolor imaging are readily achievable. Because of its ease of use and high performance, we anticipate that pcSOFI will prove an attractive approach for superresolution imaging. PMID:22711840

Properties of Asymmetric Detrended Fluctuation Analysis in the time series of RR intervals

NASA Astrophysics Data System (ADS)

Piskorski, J.; Kosmider, M.; Mieszkowski, D.; Krauze, T.; Wykretowicz, A.; Guzik, P.

2018-02-01

Heart rate asymmetry is a phenomenon by which the accelerations and decelerations of heart rate behave differently, and this difference is consistent and unidirectional, i.e. in most of the analyzed recordings the inequalities have the same directions. So far, it has been established for variance and runs based types of descriptors of RR intervals time series. In this paper we apply the newly developed method of Asymmetric Detrended Fluctuation Analysis, which so far has mainly been used with economic time series, to the set of 420 stationary 30 min time series of RR intervals from young, healthy individuals aged between 20 and 40. This asymmetric approach introduces separate scaling exponents for rising and falling trends. We systematically study the presence of asymmetry in both global and local versions of this method. In this study global means "applying to the whole time series" and local means "applying to windows jumping along the recording". It is found that the correlation structure of the fluctuations left over after detrending in physiological time series shows strong asymmetric features in both magnitude, with α+ <α-, where α+ is related to heart rate decelerations and α- to heart rate accelerations, and the proportion of the signal in which the above inequality holds. A very similar effect is observed if asymmetric noise is added to a symmetric self-affine function. No such phenomena are observed in the same physiological data after shuffling or with a group of symmetric synthetic time series.

Directed self-organization of single DNA molecules in a nanoslit via embedded nanopit arrays

PubMed Central

Reisner, Walter; Larsen, Niels B.; Flyvbjerg, Henrik; Tegenfeldt, Jonas O.; Kristensen, Anders

2009-01-01

We show that arrays of nanopit structures etched in a nanoslit can control the positioning and conformation of single DNA molecules in nanofluidic devices. By adjusting the spacing, organization and placement of the nanopits it is possible to immobilize DNA at predetermined regions of a device without additional chemical modification and achieve a high degree of control over local DNA conformation. DNA can be extended between two nanopits and in closely spaced arrays will self-assemble into “connect-the-dots” conformations consisting of locally pinned segments joined by fluctuating linkers. These results have broad implications for nanotechnology fields that require methods for the nanoscale positioning and manipulation of DNA. PMID:19122138

Does a Growing Static Length Scale Control the Glass Transition?

NASA Astrophysics Data System (ADS)

Wyart, Matthieu; Cates, Michael E.

2017-11-01

Several theories of the glass transition propose that the structural relaxation time τα is controlled by a growing static length scale ξ that is determined by the free energy landscape but not by the local dynamic rules governing its exploration. We argue, based on recent simulations using particle-radius-swap dynamics, that only a modest factor in the increase in τα on approach to the glass transition may stem from the growth of a static length, with a vastly larger contribution attributable, instead, to a slowdown of local dynamics. This reinforces arguments that we base on the observed strong coupling of particle diffusion and density fluctuations in real glasses.

The structural changes in the bone tissue and regional lymph nodes when using bone cement

NASA Astrophysics Data System (ADS)

Zhukov, D. V.; Zajdman, A. M.; Prohorenko, V. M.; Ustikova, N. V.

2017-09-01

In orthopedics bone cement is used to replace defects. However, it is known that it possesses toxic properties, due to its composition monomer methyl methacrylate. There are some unresolved issues, in particular its local action, not investigated reaction of the immune system to respond to any fluctuations of endoecological equilibrium. All this helps to explain not only the intraoperative complications such as acute heart and lung failure, but also many deferred pathological processes, complications in the postoperative period.

Euclidean scalar field theory in the bilocal approximation

NASA Astrophysics Data System (ADS)

Nagy, S.; Polonyi, J.; Steib, I.

2018-04-01

The blocking step of the renormalization group method is usually carried out by restricting it to fluctuations and to local blocked action. The tree-level, bilocal saddle point contribution to the blocking, defined by the infinitesimal decrease of the sharp cutoff in momentum space, is followed within the three dimensional Euclidean ϕ6 model in this work. The phase structure is changed, new phases and relevant operators are found, and certain universality classes are restricted by the bilocal saddle point.

Investigation of the Temperature Fluctuation of Single-Phase Fluid Based Microchannel Heat Sink.

PubMed

Wang, Tao; Wang, Jiejun; He, Jian; Wu, Chuangui; Luo, Wenbo; Shuai, Yao; Zhang, Wanli; Lee, Chengkuo

2018-05-10

The temperature fluctuation in a single-phase microchannel heat sink (MCHS) is investigated using the integrated temperature sensors with deionized water as the coolant. Results show that the temperature fluctuation in single phase is not negligible. The causes of the temperature fluctuation are revealed based on both simulation and experiment. It is found that the inlet temperature fluctuation and the gas bubbles separated out from coolant are the main causes. The effect of the inlet temperature fluctuation is global, where the temperatures at different locations change simultaneously. Meanwhile, the gas bubble effect is localized where the temperature changes at different locations are not synchronized. In addition, the relation between temperature fluctuation and temperature gradient is established. The temperature fluctuation increases with the temperature gradient accordingly.

A simple phenomenological model for grain clustering in turbulence

NASA Astrophysics Data System (ADS)

Hopkins, Philip F.

2016-01-01

We propose a simple model for density fluctuations of aerodynamic grains, embedded in a turbulent, gravitating gas disc. The model combines a calculation for the behaviour of a group of grains encountering a single turbulent eddy, with a hierarchical approximation of the eddy statistics. This makes analytic predictions for a range of quantities including: distributions of grain densities, power spectra and correlation functions of fluctuations, and maximum grain densities reached. We predict how these scale as a function of grain drag time ts, spatial scale, grain-to-gas mass ratio tilde{ρ }, strength of turbulence α, and detailed disc properties. We test these against numerical simulations with various turbulence-driving mechanisms. The simulations agree well with the predictions, spanning ts Ω ˜ 10-4-10, tilde{ρ }˜ 0{-}3, α ˜ 10-10-10-2. Results from `turbulent concentration' simulations and laboratory experiments are also predicted as a special case. Vortices on a wide range of scales disperse and concentrate grains hierarchically. For small grains this is most efficient in eddies with turnover time comparable to the stopping time, but fluctuations are also damped by local gas-grain drift. For large grains, shear and gravity lead to a much broader range of eddy scales driving fluctuations, with most power on the largest scales. The grain density distribution has a log-Poisson shape, with fluctuations for large grains up to factors ≳1000. We provide simple analytic expressions for the predictions, and discuss implications for planetesimal formation, grain growth, and the structure of turbulence.

Methods for Evaluating the Temperature Structure-Function Parameter Using Unmanned Aerial Systems and Large-Eddy Simulation

NASA Astrophysics Data System (ADS)

Wainwright, Charlotte E.; Bonin, Timothy A.; Chilson, Phillip B.; Gibbs, Jeremy A.; Fedorovich, Evgeni; Palmer, Robert D.

2015-05-01

Small-scale turbulent fluctuations of temperature are known to affect the propagation of both electromagnetic and acoustic waves. Within the inertial-subrange scale, where the turbulence is locally homogeneous and isotropic, these temperature perturbations can be described, in a statistical sense, using the structure-function parameter for temperature, . Here we investigate different methods of evaluating , using data from a numerical large-eddy simulation together with atmospheric observations collected by an unmanned aerial system and a sodar. An example case using data from a late afternoon unmanned aerial system flight on April 24 2013 and corresponding large-eddy simulation data is presented and discussed.

Second harmonic generation from small particle aggregates

NASA Astrophysics Data System (ADS)

Mochan, W. Luis; Ortiz, Guillermo P.; Mendoza, Bernardo S.; Brudny, Vera L.

2001-03-01

Novel nanofabrication techniques are capable of producing nanoparticles with controled structures which include small clusters, self-assembled particles, quantum dots, vesicles, etc. The non-linear optical scattering of these structures are important for applications, and can be used for their physical characterization. The second harmonic (SH) field radiated by a single small spherical particle has surface and bulk, dipolar and quadrupolar contributions of similar intensities and is strongly dependent of the local environment of the particle [1], in contrast to the linear case. In this work we calculate the nonlinear scattering by particle aggregates and we investigate the effects on the SH generation of the disorder induced field fluctuations and of the localization of light. We acknowledge the partial support from DGAPA-UNAM (grant IN110999), Conacyt (31120-E and 26651-E), CIP and UBACyT. [1] Vera L. Brudny, Bernardo S. Mendoza, and W. Luis Mochán, Phys. Rev. B 62, 11152 (2000).

Chimera States in Continuous Media: Existence and Distinctness

NASA Astrophysics Data System (ADS)

Nicolaou, Zachary G.; Riecke, Hermann; Motter, Adilson E.

2017-12-01

The defining property of chimera states is the coexistence of coherent and incoherent domains in systems that are structurally and spatially homogeneous. The recent realization that such states might be common in oscillator networks raises the question of whether an analogous phenomenon can occur in continuous media. Here, we show that chimera states can exist in continuous systems even when the coupling is strictly local, as in many fluid and pattern forming media. Using the complex Ginzburg-Landau equation as a model system, we characterize chimera states consisting of a coherent domain of a frozen spiral structure and an incoherent domain of amplitude turbulence. We show that in this case, in contrast with discrete network systems, fluctuations in the local coupling field play a crucial role in limiting the coherent regions. We suggest these findings shed light on new possible forms of coexisting order and disorder in fluid systems.

Stability and dynamics of membrane-spanning DNA nanopores

NASA Astrophysics Data System (ADS)

Maingi, Vishal; Burns, Jonathan R.; Uusitalo, Jaakko J.; Howorka, Stefan; Marrink, Siewert J.; Sansom, Mark S. P.

2017-03-01

Recently developed DNA-based analogues of membrane proteins have advanced synthetic biology. A fundamental question is how hydrophilic nanostructures reside in the hydrophobic environment of the membrane. Here, we use multiscale molecular dynamics (MD) simulations to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer. Coarse-grained MD reveals that the lipids reorganize locally to interact closely with the membrane-spanning section of the DNA tube. Steered simulations along the bilayer normal establish the metastable nature of the inserted pore, yielding a force profile with barriers for membrane exit due to the membrane anchors. Atomistic, equilibrium simulations at two salt concentrations confirm the close packing of lipid around of the stably inserted DNA pore and its cation selectivity, while revealing localized structural fluctuations. The wide-ranging and detailed insight informs the design of next-generation DNA pores for synthetic biology or biomedicine.

Topsoil structure stability in a restored floodplain: Impacts of fluctuating water levels, soil parameters and ecosystem engineers.

PubMed

Schomburg, A; Schilling, O S; Guenat, C; Schirmer, M; Le Bayon, R C; Brunner, P

2018-10-15

Ecosystem services provided by floodplains are strongly controlled by the structural stability of soils. The development of a stable structure in floodplain soils is affected by a complex and poorly understood interplay of hydrological, physico-chemical and biological processes. This paper aims at analysing relations between fluctuating groundwater levels, soil physico-chemical and biological parameters on soil structure stability in a restored floodplain. Water level fluctuations in the soil are modelled using a numerical surface-water-groundwater flow model and correlated to soil physico-chemical parameters and abundances of plants and earthworms. Causal relations and multiple interactions between the investigated parameters are tested through structural equation modelling (SEM). Fluctuating water levels in the soil did not directly affect the topsoil structure stability, but indirectly through affecting plant roots and soil parameters that in turn determine topsoil structure stability. These relations remain significant for mean annual days of complete and partial (>25%) water saturation. Ecosystem functioning of a restored floodplain might already be affected by the fluctuation of groundwater levels alone, and not only through complete flooding by surface water during a flood period. Surprisingly, abundances of earthworms did not show any relation to other variables in the SEM. These findings emphasise that earthworms have efficiently adapted to periodic stress and harsh environmental conditions. Variability of the topsoil structure stability is thus stronger driven by the influence of fluctuating water levels on plants than by the abundance of earthworms. This knowledge about the functional network of soil engineering organisms, soil parameters and fluctuating water levels and how they affect soil structural stability is of fundamental importance to define management strategies of near-natural or restored floodplains in the future. Copyright © 2018 Elsevier B.V. All rights reserved.

Interfacial layering and capillary roughness in immiscible liquids.

PubMed

Geysermans, P; Pontikis, V

2010-08-21

The capillary roughness and the atomic density profiles of extended interfaces between immiscible liquids are determined as a function of the interface area by using molecular dynamics and Lennard-Jones (12-6) potentials. We found that with increasing area, the interface roughness diverges logarithmically, thus fitting the theoretical mean-field prediction. In systems small enough for the interfacial roughness not to blur the structural details, atomic density profiles across the fluid interface are layered with correlation length in the range of molecular correlations in liquids. On increasing the system size, the amplitude of the thermally excited position fluctuations of the interface increases, thus causing layering to rapidly vanish, if density profiles are computed without special care. In this work, we present and validate a simple method, operating in the direct space, for extracting from molecular dynamics trajectories the "intrinsic" structure of a fluid interface that is the local density profile of the interface cleaned from capillary wave effects. Estimated values of interfacial properties such as the tension, the intrinsic width, and the lower wavelength limit of position fluctuations are in agreement with results collected from the literature.

Theoretical Study of near Neutrality. II. Effect of Subdivided Population Structure with Local Extinction and Recolonization

PubMed Central

Ohta, T.

1992-01-01

There are several unsolved problems concerning the model of nearly neutral mutations. One is the interaction of subdivided population structure and weak selection that spatially fluctuates. The model of nearly neutral mutations whose selection coefficient spatially fluctuates has been studied by adopting the island model with periodic extinction-recolonization. Both the number of colonies and the migration rate play significant roles in determining mutants' behavior, and selection is ineffective when the extinction-recolonization is frequent with low migration rate. In summary, the number of mutant substitutions decreases and the polymorphism increases by increasing the total population size, and/or decreasing the extinction-recolonization rate. However, by increasing the total size of the population, the mutant substitution rate does not become as low when compared with that in panmictic populations, because of the extinction-recolonization, especially when the migration rate is limited. It is also found that the model satisfactorily explains the contrasting patterns of molecular polymorphisms observed in sibling species of Drosophila, including heterozygosity, proportion of polymorphism and fixation index. PMID:1582566

Characterizing Atomistic Geometries and Potential Functions Using Strain Functionals

NASA Astrophysics Data System (ADS)

Kober, Edward; Mathew, Nithin; Rudin, Sven

2017-06-01

We demonstrate the use of strain tensor functionals for characterizing arbitrarily ordered atomistic structures. This approach defines a Gaussian-weighted neighborhood around each atom and characterizes that local geometry in terms of n-th order strain tensors, which are equivalent to the n-th order moments/derivatives of the neighborhood. Fourth order expansions can distinguish the cubic structures (and deformations thereof), but sixth order expansions are required to fully characterize hexagonal structures. These functions are continuous and smooth and much less sensitive to thermal fluctuations than other descriptors based on discrete neighborhoods. Reducing these metrics to rotational invariant descriptors allows a large number of defect structures to be readily identified and forms the basis of a classification scheme that allows molecular dynamics simulations to be readily analyzed. Applications to the analysis of shock waves impinging on samples of Cu, Ta and Ti will be presented. The method has been extended to vector fields as well, enabling the local stress to be cast in terms of rotationally invariant functions as well. The stress-strain correlations can then be used as the basis for developing and analyzing potential functions.

Hierarchical structure of stock price fluctuations in financial markets

NASA Astrophysics Data System (ADS)

Gao, Ya-Chun; Cai, Shi-Min; Wang, Bing-Hong

2012-12-01

The financial market and turbulence have been broadly compared on account of the same quantitative methods and several common stylized facts they share. In this paper, the She-Leveque (SL) hierarchy, proposed to explain the anomalous scaling exponents deviating from Kolmogorov monofractal scaling of the velocity fluctuation in fluid turbulence, is applied to study and quantify the hierarchical structure of stock price fluctuations in financial markets. We therefore observed certain interesting results: (i) the hierarchical structure related to multifractal scaling generally presents in all the stock price fluctuations we investigated. (ii) The quantitatively statistical parameters that describe SL hierarchy are different between developed financial markets and emerging ones, distinctively. (iii) For the high-frequency stock price fluctuation, the hierarchical structure varies with different time periods. All these results provide a novel analogy in turbulence and financial market dynamics and an insight to deeply understand multifractality in financial markets.

Statistics of spatial derivatives of velocity and pressure in turbulent channel flow

NASA Astrophysics Data System (ADS)

Vreman, A. W.; Kuerten, J. G. M.

2014-08-01

Statistical profiles of the first- and second-order spatial derivatives of velocity and pressure are reported for turbulent channel flow at Reτ = 590. The statistics were extracted from a high-resolution direct numerical simulation. To quantify the anisotropic behavior of fine-scale structures, the variances of the derivatives are compared with the theoretical values for isotropic turbulence. It is shown that appropriate combinations of first- and second-order velocity derivatives lead to (directional) viscous length scales without explicit occurrence of the viscosity in the definitions. To quantify the non-Gaussian and intermittent behavior of fine-scale structures, higher-order moments and probability density functions of spatial derivatives are reported. Absolute skewnesses and flatnesses of several spatial derivatives display high peaks in the near wall region. In the logarithmic and central regions of the channel flow, all first-order derivatives appear to be significantly more intermittent than in isotropic turbulence at the same Taylor Reynolds number. Since the nine variances of first-order velocity derivatives are the distinct elements of the turbulence dissipation, the budgets of these nine variances are shown, together with the budget of the turbulence dissipation. The comparison of the budgets in the near-wall region indicates that the normal derivative of the fluctuating streamwise velocity (∂u'/∂y) plays a more important role than other components of the fluctuating velocity gradient. The small-scale generation term formed by triple correlations of fluctuations of first-order velocity derivatives is analyzed. A typical mechanism of small-scale generation near the wall (around y+ = 1), the intensification of positive ∂u'/∂y by local strain fluctuation (compression in normal and stretching in spanwise direction), is illustrated and discussed.

Ultrafast phosphate hydration dynamics in bulk H{sub 2}O

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

Costard, Rene, E-mail: costard@mbi-berlin.de; Tyborski, Tobias; Fingerhut, Benjamin P., E-mail: fingerhut@mbi-berlin.de

2015-06-07

Phosphate vibrations serve as local probes of hydrogen bonding and structural fluctuations of hydration shells around ions. Interactions of H{sub 2}PO{sub 4}{sup −} ions and their aqueous environment are studied combining femtosecond 2D infrared spectroscopy, ab-initio calculations, and hybrid quantum-classical molecular dynamics (MD) simulations. Two-dimensional infrared spectra of the symmetric (ν{sub S}(PO{sub 2}{sup −})) and asymmetric (ν{sub AS}(PO{sub 2}{sup −})) PO{sub 2}{sup −} stretching vibrations display nearly homogeneous lineshapes and pronounced anharmonic couplings between the two modes and with the δ(P-(OH){sub 2}) bending modes. The frequency-time correlation function derived from the 2D spectra consists of a predominant 50 fs decaymore » and a weak constant component accounting for a residual inhomogeneous broadening. MD simulations show that the fluctuating electric field of the aqueous environment induces strong fluctuations of the ν{sub S}(PO{sub 2}{sup −}) and ν{sub AS}(PO{sub 2}{sup −}) transition frequencies with larger frequency excursions for ν{sub AS}(PO{sub 2}{sup −}). The calculated frequency-time correlation function is in good agreement with the experiment. The ν(PO{sub 2}{sup −}) frequencies are mainly determined by polarization contributions induced by electrostatic phosphate-water interactions. H{sub 2}PO{sub 4}{sup −}/H{sub 2}O cluster calculations reveal substantial frequency shifts and mode mixing with increasing hydration. Predicted phosphate-water hydrogen bond (HB) lifetimes have values on the order of 10 ps, substantially longer than water-water HB lifetimes. The ultrafast phosphate-water interactions observed here are in marked contrast to hydration dynamics of phospholipids where a quasi-static inhomogeneous broadening of phosphate vibrations suggests minor structural fluctuations of interfacial water.« less

Reply to ``Comment on `Relative locality and the soccer ball problem'''

NASA Astrophysics Data System (ADS)

Amelino-Camelia, Giovanni; Freidel, Laurent; Kowalski-Glikman, Jerzy; Smolin, Lee

2013-07-01

In a Comment [S. Hossenfelder Phys. Rev. D 88, 028701 (2013)], Hossenfelder proposes a generalization of the results we reported in [Phys. Rev. D 84, 087702 (2011)] and argues that thermal fluctuations introduce incurable pathologies for the description of macroscopic bodies in the relative-locality framework. We here show that Hossenfelder’s analysis, while raising a very interesting point, is incomplete and leads to incorrect conclusions. Her estimate for the fluctuations did not take into account some contributions from the geometry of momentum space, which must be included at the relevant order of approximation. Using the full expression here derived, one finds that thermal fluctuations are not, in general, large for macroscopic bodies in the relative-locality framework. We find that such corrections can be unexpectedly large only for some choices of momentum-space geometry, and we comment on the possibility of developing a phenomenology suitable for possibly ruling out such geometries of momentum space.

Transport behaviors of locally fractional coupled Brownian motors with fluctuating interactions

NASA Astrophysics Data System (ADS)

Wang, Huiqi; Ni, Feixiang; Lin, Lifeng; Lv, Wangyong; Zhu, Hongqiang

2018-09-01

In some complex viscoelastic mediums, it is ubiquitous that absorbing and desorbing surrounding Brownian particles randomly occur in coupled systems. The conventional method is to model a variable-mass system driven by both multiplicative and additive noises. In this paper, an improved mathematical model is created based on generalized Langevin equations (GLE) to characterize the random interaction with locally fluctuating number of coupled particles in the elastically coupled factional Brownian motors (FBM). By the numerical simulations, the effect of fluctuating interactions on collective transport behaviors is investigated, and some abnormal phenomena, such as cooperative behaviors, stochastic resonance (SR) and anomalous transport, are observed in the regime of sub-diffusion.

Quantum dot-like emitters formed due to alloy fluctuations in GaNAs-based nanowires.

NASA Astrophysics Data System (ADS)

Buyanova, Irina; Jansson, M.; Filippov, S.; Stehr, J.; Palisaitis, J.; Persson, P.; Ishikawa, F.; Chen, Weimin

Group III-V semiconductor nanowires with embedded quantum dots (QDs) are currently attracting increasing attention as a highly attractive platform for a variety of advanced applications ranging from third generation photovoltaics to quantum information technologies. In this work, we show that local fluctuations in N composition inside coaxial GaAs/GaNAs nanowires induces three-dimensional confining potentials equivalent to that for QDs thus forming optically active and highly localized states inside the GaNAs shell. Principal quantization axis of these states is concluded to mainly coincide with the nanowire axis, based on the strong polarization of the detected emission orthogonal to the nanowire axis revealed from polarization-resolved micro-photoluminescence studies. This is partly attributed to a predominantly uniaxial tensile strain field in the GaNAs shell caused by lattice mismatch with the GaAs core. GaNAs alloys can, therefore, be used as an active material in hybrid QD-NW structures utilized for fabrication of nanoscale polarized-light sources that are efficient within the near-infrared spectral range. Financial support by the Swedish Energy Agency (Grant # P40119-1) and the Swedish Research Council (Grant # 2015-05532) is greatly appreciated.

Radiative instabilities in sheared magnetic field

NASA Technical Reports Server (NTRS)

Drake, J. F.; Sparks, L.; Van Hoven, G.

1988-01-01

The structure and growth rate of the radiative instability in a sheared magnetic field B have been calculated analytically using the Braginskii fluid equations. In a shear layer, temperature and density perturbations are linked by the propagation of sound waves parallel to the local magnetic field. As a consequence, density clumping or condensation plays an important role in driving the instability. Parallel thermal conduction localizes the mode to a narrow layer where K(parallel) is small and stabilizes short wavelengths k larger-than(c) where k(c) depends on the local radiation and conduction rates. Thermal coupling to ions also limits the width of the unstable spectrum. It is shown that a broad spectrum of modes is typically unstable in tokamak edge plasmas and it is argued that this instability is sufficiently robust to drive the large-amplitude density fluctuations often measured there.

Refractometric sensitivity and thermal stabilization of fluorescent core microcapillary sensors: theory and experiment.

PubMed

Lane, S; Marsiglio, F; Zhi, Y; Meldrum, A

2015-02-20

Fluorescent-core microcapillaries (FCMs) present a robust basis for the application of optical whispering gallery modes toward refractometric sensing. An important question concerns whether these devices can be rendered insensitive to local temperature fluctuations, which may otherwise limit their refractometric detection limits, mainly as a result of thermorefractive effects. Here, we first use a standard cylindrical cavity formalism to develop the refractometric and thermally limited detection limits for the FCM structure. We then measure the thermal response of a real device with different analytes in the channel and compare the result to the theory. Good stability against temperature fluctuations was obtained for an ethanol solvent, with a near-zero observed thermal shift for the transverse magnetic modes. Similarly good results could in principle be obtained for any other solvent (e.g., water), if the thickness of the fluorescent layer can be sufficiently well controlled.

Simulation of electric double-layer capacitors: evaluation of constant potential method

NASA Astrophysics Data System (ADS)

Wang, Zhenxing; Laird, Brian; Yang, Yang; Olmsted, David; Asta, Mark

2014-03-01

Atomistic simulations can play an important role in understanding electric double-layer capacitors (EDLCs) at a molecular level. In such simulations, typically the electrode surface is modeled using fixed surface charges, which ignores the charge fluctuation induced by local fluctuations in the electrolyte solution. In this work we evaluate an explicit treatment of charges, namely constant potential method (CPM)[1], in which the electrode charges are dynamically updated to maintain constant electrode potential. We employ a model system with a graphite electrode and a LiClO4/acetonitrile electrolyte, examined as a function of electrode potential differences. Using various molecular and macroscopic properties as metrics, we compare CPM simulations on this system to results using fixed surface charges. Specifically, results for predicted capacity, electric potential gradient and solvent density profile are identical between the two methods; However, ion density profiles and solvation structure yield significantly different results.

Tissue fusion over nonadhering surfaces

PubMed Central

Nier, Vincent; Deforet, Maxime; Duclos, Guillaume; Yevick, Hannah G.; Cochet-Escartin, Olivier; Marcq, Philippe; Silberzan, Pascal

2015-01-01

Tissue fusion eliminates physical voids in a tissue to form a continuous structure and is central to many processes in development and repair. Fusion events in vivo, particularly in embryonic development, often involve the purse-string contraction of a pluricellular actomyosin cable at the free edge. However, in vitro, adhesion of the cells to their substrate favors a closure mechanism mediated by lamellipodial protrusions, which has prevented a systematic study of the purse-string mechanism. Here, we show that monolayers can cover well-controlled mesoscopic nonadherent areas much larger than a cell size by purse-string closure and that active epithelial fluctuations are required for this process. We have formulated a simple stochastic model that includes purse-string contractility, tissue fluctuations, and effective friction to qualitatively and quantitatively account for the dynamics of closure. Our data suggest that, in vivo, tissue fusion adapts to the local environment by coordinating lamellipodial protrusions and purse-string contractions. PMID:26199417

The structure of evaporating and combusting sprays: Measurements and predictions

NASA Technical Reports Server (NTRS)

Shuen, J. S.; Solomon, A. S. P.; Faeth, G. M.

1982-01-01

An apparatus was constructed to provide measurements in open sprays with no zones of recirculation, in order to provide well-defined conditions for use in evaluating spray models. Measurements were completed in a gas jet, in order to test experimental methods, and are currently in progress for nonevaporating sprays. A locally homogeneous flow (LHF) model where interphase transport rates are assumed to be infinitely fast; a separated flow (SF) model which allows for finite interphase transport rates but neglects effects of turbulent fluctuations on drop motion; and a stochastic SF model which considers effects of turbulent fluctuations on drop motion were evaluated using existing data on particle-laden jets. The LHF model generally overestimates rates of particle dispersion while the SF model underestimates dispersion rates. The stochastic SF flow yield satisfactory predictions except at high particle mass loadings where effects of turbulence modulation may have caused the model to overestimate turbulence levels.

Effect of wave localization on plasma instabilities

NASA Astrophysics Data System (ADS)

Levedahl, William Kirk

1987-10-01

The Anderson model of wave localization in random media is involved to study the effect of solar wind density turbulence on plasma processes associated with the solar type III radio burst. ISEE-3 satellite data indicate that a possible model for the type III process is the parametric decay of Langmuir waves excited by solar flare electron streams into daughter electromagnetic and ion acoustic waves. The threshold for this instability, however, is much higher than observed Langmuir wave levels because of rapid wave convection of the transverse electromagnetic daughter wave in the case where the solar wind is assumed homogeneous. Langmuir and transverse waves near critical density satisfy the Ioffe-Reigel criteria for wave localization in the solar wind with observed density fluctuations -1 percent. Numerical simulations of wave propagation in random media confirm the localization length predictions of Escande and Souillard for stationary density fluctations. For mobile density fluctuations localized wave packets spread at the propagation velocity of the density fluctuations rather than the group velocity of the waves. Computer simulations using a linearized hybrid code show that an electron beam will excite localized Langmuir waves in a plasma with density turbulence. An action principle approach is used to develop a theory of non-linear wave processes when waves are localized. A theory of resonant particles diffusion by localized waves is developed to explain the saturation of the beam-plasma instability. It is argued that localization of electromagnetic waves will allow the instability threshold to be exceeded for the parametric decay discussed above.

Exact master equation and non-Markovian decoherence dynamics of Majorana zero modes under gate-induced charge fluctuations

NASA Astrophysics Data System (ADS)

Lai, Hon-Lam; Yang, Pei-Yun; Huang, Yu-Wei; Zhang, Wei-Min

2018-02-01

In this paper, we use the exact master equation approach to investigate the decoherence dynamics of Majorana zero modes in the Kitaev model, a 1D p -wave spinless topological superconducting chain (TSC) that is disturbed by gate-induced charge fluctuations. The exact master equation is derived by extending Feynman-Vernon influence functional technique to fermionic open systems involving pairing excitations. We obtain the exact master equation for the zero-energy Bogoliubov quasiparticle (bogoliubon) in the TSC, and then transfer it into the master equation for the Majorana zero modes. Within this exact master equation formalism, we can describe in detail the non-Markovian decoherence dynamics of the zero-energy bogoliubon as well as Majorana zero modes under local perturbations. We find that at zero temperature, local charge fluctuations induce level broadening to one of the Majorana zero modes but there is an isolated peak (localized bound state) located at zero energy that partially protects the Majorana zero mode from decoherence. At finite temperatures, the zero-energy localized bound state does not precisely exist, but the coherence of the Majorana zero mode can still be partially but weakly protected, due to the sharp dip of the spectral density near the zero frequency. The decoherence will be enhanced as one increases the charge fluctuations and/or the temperature of the gate.

Evolution of the Orszag-Tang vortex system in a compressible medium. II - Supersonic flow

NASA Technical Reports Server (NTRS)

Picone, J. Michael; Dahlburg, Russell B.

1991-01-01

A study is presented on the effect of embedded supersonic flows and the resulting emerging shock waves on phenomena associated with MHD turbulence, including reconnection, the formation of current sheets and vortex structures, and the evolution of spatial and temporal correlations among physical variables. A two-dimensional model problem, the Orszag-Tang (1979) vortex system, is chosen, which involves decay from nonrandom initial conditions. The system is doubly periodic, and the initial conditions consist of single-mode solenoidal velocity and magnetic fields, each containing X points and O points. The initial mass density is flat, and the initial pressure fluctuations are incompressible, balancing the local forces for a magnetofluid of unit mass density. Results on the evolution of the local structure of the flow field, the global properties of the system, and spectral correlations are presented. The important dynamical properties and observational consequences of embedded supersonic regions and emerging shocks in the Orszag-Tang model of an MHD system undergoing reconnection are discussed. Conclusions are drawn regarding the effects of local supersonic regions on MHD turbulence.

Small-scale behavior in distorted turbulent boundary layers at low Reynolds number

NASA Technical Reports Server (NTRS)

Saddoughi, Seyed G.

1994-01-01

During the last three years we have conducted high- and low-Reynolds-number experiments, including hot-wire measurements of the velocity fluctuations, in the test-section-ceiling boundary layer of the 80- by 120-foot Full-Scale Aerodynamics Facility at NASA Ames Research Center, to test the local-isotropy predictions of Kolmogorov's universal equilibrium theory. This hypothesis, which states that at sufficiently high Reynolds numbers the small-scale structures of turbulent motions are independent of large-scale structures and mean deformations, has been used in theoretical studies of turbulence and computational methods such as large-eddy simulation; however, its range of validity in shear flows has been a subject of controversy. The present experiments were planned to enhance our understanding of the local-isotropy hypothesis. Our experiments were divided into two sets. First, measurements were taken at different Reynolds numbers in a plane boundary layer, which is a 'simple' shear flow. Second, experiments were designed to address this question: will our criteria for the existence of local isotropy hold for 'complex' nonequilibrium flows in which extra rates of mean strain are added to the basic mean shear?

Spatiotemporal dynamics of Puumala hantavirus associated with its rodent host, Myodes glareolus

PubMed Central

Weber de Melo, Vanessa; Sheikh Ali, Hanan; Freise, Jona; Kühnert, Denise; Essbauer, Sandra; Mertens, Marc; Wanka, Konrad M; Drewes, Stephan; Ulrich, Rainer G; Heckel, Gerald

2015-01-01

Many viruses significantly impact human and animal health. Understanding the population dynamics of these viruses and their hosts can provide important insights for epidemiology and virus evolution. Puumala virus (PUUV) is a European hantavirus that may cause regional outbreaks of hemorrhagic fever with renal syndrome in humans. Here, we analyzed the spatiotemporal dynamics of PUUV circulating in local populations of its rodent reservoir host, the bank vole (Myodes glareolus) during eight years. Phylogenetic and population genetic analyses of all three genome segments of PUUV showed strong geographical structuring at a very local scale. There was a high temporal turnover of virus strains in the local bank vole populations, but several virus strains persisted through multiple years. Phylodynamic analyses showed no significant changes in the local effective population sizes of PUUV, although vole numbers and virus prevalence fluctuated widely. Microsatellite data demonstrated also a temporally persisting subdivision between local vole populations, but these groups did not correspond to the subdivision in the virus strains. We conclude that restricted transmission between vole populations and genetic drift play important roles in shaping the genetic structure and temporal dynamics of PUUV in its natural host which has several implications for zoonotic risks of the human population. PMID:26136821

A model for characterizing residential ground current and magnetic field fluctuations.

PubMed

Mader, D L; Peralta, S B; Sherar, M D

1994-01-01

The current through the residential grounding circuit is an important source for magnetic fields; field variations near the grounding circuit accurately track fluctuations in this ground current. In this paper, a model is presented which permits calculation of the range of these fluctuations. A discrete network model is used to simulate a local distribution system for a single street, and a statistical model to simulate unbalanced currents in the system. Simulations of three-house and ten-house networks show that random appliance operation leads to ground current fluctuations which can be quite large, on the order of 600%. This is consistent with measured fluctuations in an actual house.

Evidence of toroidally localized turbulence with applied 3D fields in the DIII-D tokamak

DOE PAGES

Wilcox, R. S.; Shafer, M. W.; Ferraro, N. M.; ...

2016-09-21

New evidence indicates that there is significant 3D variation in density fluctuations near the boundary of weakly 3D tokamak plasmas when resonant magnetic perturbations are applied to suppress transient edge instabilities. The increase in fluctuations is concomitant with an increase in the measured density gradient, suggesting that this toroidally localized gradient increase could be a mechanism for turbulence destabilization in localized flux tubes. Two-fluid magnetohydrodynamic simulations find that, although changes to the magnetic field topology are small, there is a significant 3D variation of the density gradient within the flux surfaces that is extended along field lines. This modeling agreesmore » qualitatively with the measurements. The observed gradient and fluctuation asymmetries are proposed as a mechanism by which global profile gradients in the pedestal could be relaxed due to a local change in the 3D equilibrium. In conclusion, these processes may play an important role in pedestal and scrape-off layer transport in ITER and other future tokamak devices with small applied 3D fields.« less

A versatile phenomenological model for the S-shaped temperature dependence of photoluminescence energy for an accurate determination of the exciton localization energy in bulk and quantum well structures

NASA Astrophysics Data System (ADS)

Dixit, V. K.; Porwal, S.; Singh, S. D.; Sharma, T. K.; Ghosh, Sandip; Oak, S. M.

2014-02-01

Temperature dependence of the photoluminescence (PL) peak energy of bulk and quantum well (QW) structures is studied by using a new phenomenological model for including the effect of localized states. In general an anomalous S-shaped temperature dependence of the PL peak energy is observed for many materials which is usually associated with the localization of excitons in band-tail states that are formed due to potential fluctuations. Under such conditions, the conventional models of Varshni, Viña and Passler fail to replicate the S-shaped temperature dependence of the PL peak energy and provide inconsistent and unrealistic values of the fitting parameters. The proposed formalism persuasively reproduces the S-shaped temperature dependence of the PL peak energy and provides an accurate determination of the exciton localization energy in bulk and QW structures along with the appropriate values of material parameters. An example of a strained InAs0.38P0.62/InP QW is presented by performing detailed temperature and excitation intensity dependent PL measurements and subsequent in-depth analysis using the proposed model. Versatility of the new formalism is tested on a few other semiconductor materials, e.g. GaN, nanotextured GaN, AlGaN and InGaN, which are known to have a significant contribution from the localized states. A quantitative evaluation of the fractional contribution of the localized states is essential for understanding the temperature dependence of the PL peak energy of bulk and QW well structures having a large contribution of the band-tail states.

Season-modulated responses of Neotropical bats to forest fragmentation.

PubMed

Ferreira, Diogo F; Rocha, Ricardo; López-Baucells, Adrià; Farneda, Fábio Z; Carreiras, João M B; Palmeirim, Jorge M; Meyer, Christoph F J

2017-06-01

Seasonality causes fluctuations in resource availability, affecting the presence and abundance of animal species. The impacts of these oscillations on wildlife populations can be exacerbated by habitat fragmentation. We assessed differences in bat species abundance between the wet and dry season in a fragmented landscape in the Central Amazon characterized by primary forest fragments embedded in a secondary forest matrix. We also evaluated whether the relative importance of local vegetation structure versus landscape characteristics (composition and configuration) in shaping bat abundance patterns varied between seasons. Our working hypotheses were that abundance responses are species as well as season specific, and that in the wet season, local vegetation structure is a stronger determinant of bat abundance than landscape-scale attributes. Generalized linear mixed-effects models in combination with hierarchical partitioning revealed that relationships between species abundances and local vegetation structure and landscape characteristics were both season specific and scale dependent. Overall, landscape characteristics were more important than local vegetation characteristics, suggesting that landscape structure is likely to play an even more important role in landscapes with higher fragment-matrix contrast. Responses varied between frugivores and animalivores. In the dry season, frugivores responded more to compositional metrics, whereas during the wet season, local and configurational metrics were more important. Animalivores showed similar patterns in both seasons, responding to the same group of metrics in both seasons. Differences in responses likely reflect seasonal differences in the phenology of flowering and fruiting between primary and secondary forests, which affected the foraging behavior and habitat use of bats. Management actions should encompass multiscale approaches to account for the idiosyncratic responses of species to seasonal variation in resource abundance and consequently to local and landscape scale attributes.

Nonisothermal fluctuating hydrodynamics and Brownian motion

NASA Astrophysics Data System (ADS)

Falasco, G.; Kroy, K.

2016-03-01

The classical theory of Brownian dynamics follows from coarse graining the underlying linearized fluctuating hydrodynamics of the solvent. We extend this procedure to globally nonisothermal conditions, requiring only a local thermal equilibration of the solvent. Starting from the conservation laws, we establish the stochastic equations of motion for the fluid momentum fluctuations in the presence of a suspended Brownian particle. These are then contracted to the nonisothermal generalized Langevin description of the suspended particle alone, for which the coupling to stochastic temperature fluctuations is found to be negligible under typical experimental conditions.

Citrate synthase proteins in extremophilic organisms: Studies within a structure-based model

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

Różycki, Bartosz, E-mail: rozycki@ifpan.edu.pl; Cieplak, Marek

2014-12-21

We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the closed and two in the open conformations. Even though the proteins belong to the same fold, the model distinguishes the properties of these proteins in a way which is consistent with experiments. For instance, the thermophilic proteins are more stable thermodynamically than their mesophilic and cryophilic homologues, which we observe both in the magnitude of thermal fluctuations near the native state and in the kineticsmore » of thermal unfolding. The level of stability correlates with the average coordination number for amino acid contacts and with the degree of structural compactness. The pattern of positional fluctuations along the sequence in the closed conformation is different than in the open conformation, including within the active site. The modes of correlated and anticorrelated movements of pairs of amino acids forming the active site are very different in the open and closed conformations. Taken together, our results show that the precise location of amino acid contacts in the native structure appears to be a critical element in explaining the similarities and differences in the thermodynamic properties, local flexibility, and collective motions of the different forms of the enzyme.« less

Citrate synthase proteins in extremophilic organisms: Studies within a structure-based model

NASA Astrophysics Data System (ADS)

RóŻycki, Bartosz; Cieplak, Marek

2014-12-01

We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the closed and two in the open conformations. Even though the proteins belong to the same fold, the model distinguishes the properties of these proteins in a way which is consistent with experiments. For instance, the thermophilic proteins are more stable thermodynamically than their mesophilic and cryophilic homologues, which we observe both in the magnitude of thermal fluctuations near the native state and in the kinetics of thermal unfolding. The level of stability correlates with the average coordination number for amino acid contacts and with the degree of structural compactness. The pattern of positional fluctuations along the sequence in the closed conformation is different than in the open conformation, including within the active site. The modes of correlated and anticorrelated movements of pairs of amino acids forming the active site are very different in the open and closed conformations. Taken together, our results show that the precise location of amino acid contacts in the native structure appears to be a critical element in explaining the similarities and differences in the thermodynamic properties, local flexibility, and collective motions of the different forms of the enzyme.

Insights on dramatic radial fluctuations in track formation by energetic ions

DOE PAGES

Sachan, Ritesh; Lang, Maik; Trautmann, Christina; ...

2016-06-02

We discuss the insights on the unexpected dramatic radial variations in the ion tracks formed by energetic ion (2.3 GeV 208Pb) irradiation at a constant electronic energy-loss (~42 keV/nm) in pyrochlore structured Gd 2TiZrO 7. Though previous studies have shown track formation and average track diameter measurements, this work brings further clarity on why quantitative analysis of ion track formation in Gd 2Ti xZr (1-x)O 7 systems can be more complicated than the currently accepted behavior for ion tracks. The ion track profile is usually considered to be diametrically uniform at constant values of the electronic energy-loss. This study showsmore » the diameter variations to be as large as ~40% within an extremely short incremental track length of ~20 nm. Our molecular dynamics simulations show that these fluctuations in diameter of amorphous core and overall track diameter are attributed to (i) the stochastic nature of inelastic energy loss along the track and (ii) the random substitution of Ti atoms by Zr atoms on the B-site in the pyrochlore lattice. Furthermore, the partial substitution of Ti by Zr increases the favorability of the defect-fluorite structure formation over amorphous phase stochastically, by introducing localized inhomogeneity in atomic structure, density and strain.« less

Insights on dramatic radial fluctuations in track formation by energetic ions

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

Sachan, Ritesh; Lang, Maik; Trautmann, Christina

We discuss the insights on the unexpected dramatic radial variations in the ion tracks formed by energetic ion (2.3 GeV 208Pb) irradiation at a constant electronic energy-loss (~42 keV/nm) in pyrochlore structured Gd 2TiZrO 7. Though previous studies have shown track formation and average track diameter measurements, this work brings further clarity on why quantitative analysis of ion track formation in Gd 2Ti xZr (1-x)O 7 systems can be more complicated than the currently accepted behavior for ion tracks. The ion track profile is usually considered to be diametrically uniform at constant values of the electronic energy-loss. This study showsmore » the diameter variations to be as large as ~40% within an extremely short incremental track length of ~20 nm. Our molecular dynamics simulations show that these fluctuations in diameter of amorphous core and overall track diameter are attributed to (i) the stochastic nature of inelastic energy loss along the track and (ii) the random substitution of Ti atoms by Zr atoms on the B-site in the pyrochlore lattice. Furthermore, the partial substitution of Ti by Zr increases the favorability of the defect-fluorite structure formation over amorphous phase stochastically, by introducing localized inhomogeneity in atomic structure, density and strain.« less

Characterizing multi-scale self-similar behavior and non-statistical properties of fluctuations in financial time series

NASA Astrophysics Data System (ADS)

Ghosh, Sayantan; Manimaran, P.; Panigrahi, Prasanta K.

2011-11-01

We make use of wavelet transform to study the multi-scale, self-similar behavior and deviations thereof, in the stock prices of large companies, belonging to different economic sectors. The stock market returns exhibit multi-fractal characteristics, with some of the companies showing deviations at small and large scales. The fact that, the wavelets belonging to the Daubechies’ (Db) basis enables one to isolate local polynomial trends of different degrees, plays the key role in isolating fluctuations at different scales. One of the primary motivations of this work is to study the emergence of the k-3 behavior [X. Gabaix, P. Gopikrishnan, V. Plerou, H. Stanley, A theory of power law distributions in financial market fluctuations, Nature 423 (2003) 267-270] of the fluctuations starting with high frequency fluctuations. We make use of Db4 and Db6 basis sets to respectively isolate local linear and quadratic trends at different scales in order to study the statistical characteristics of these financial time series. The fluctuations reveal fat tail non-Gaussian behavior, unstable periodic modulations, at finer scales, from which the characteristic k-3 power law behavior emerges at sufficiently large scales. We further identify stable periodic behavior through the continuous Morlet wavelet.

Edge transport and mode structure of a QCM-like fluctuation driven by the Shoelace antenna

NASA Astrophysics Data System (ADS)

Golfinopoulos, T.; LaBombard, B.; Brunner, D.; Terry, J. L.; Baek, S. G.; Ennever, P.; Edlund, E.; Han, W.; Burke, W. M.; Wolfe, S. M.; Irby, J. H.; Hughes, J. W.; Fitzgerald, E. W.; Granetz, R. S.; Greenwald, M. J.; Leccacorvi, R.; Marmar, E. S.; Pierson, S. Z.; Porkolab, M.; Vieira, R. F.; Wukitch, S. J.; The Alcator C-Mod Team

2018-05-01

The Shoelace antenna was built to drive edge fluctuations in the Alcator C-Mod tokamak, matching the wavenumber (k\\perp≈1.5 cm‑1) and frequency (30≲ f ≲ 200 kHz) of the quasi-coherent mode (QCM), which is responsible for regulating transport across the plasma boundary in the steady-state, ELM-free Enhanced D α (EDA) H-mode. Initial experiments in 2012 demonstrated that the antenna drove a resonant response in the edge plasma in steady-state EDA and transient, non-ELMy H-modes, but transport measurements were unavailable. In 2016, the Shoelace antenna was relocated to enable direct measurements of driven transport by a reciprocating Mirror Langmuir Probe, while also making available gas puff imaging and reflectometer data to provide additional radial localization of the driven fluctuation. This new data suggests a  ∼4 mm-wide mode layer centered on or just outside the separatrix. Fluctuations coherent with the antenna produced a radial electron flux with {Γ_e}/{n_e}∼4 m s‑1 in EDA H-mode, smaller than but comparable to the QCM level. But in transient ELM-free H-mode, {Γ_e}/{n_e} was an order of magnitude smaller, and driven fluctuations reduced by a factor of ≳ 3. The driven mode is quantitatively similar to the intrinsic QCM across measured spectral quantities, except that it is more coherent and weaker. This work informs the prospect of achieving control of edge transport by direct coupling to edge modes, as well as the use of such active coupling for diagnostic purposes.

New Insights into the Nature of Turbulence in the Earth's Magnetosheath Using Magnetospheric MultiScale Mission Data

NASA Astrophysics Data System (ADS)

Breuillard, H.; Matteini, L.; Argall, M. R.; Sahraoui, F.; Andriopoulou, M.; Le Contel, O.; Retinò, A.; Mirioni, L.; Huang, S. Y.; Gershman, D. J.; Ergun, R. E.; Wilder, F. D.; Goodrich, K. A.; Ahmadi, N.; Yordanova, E.; Vaivads, A.; Turner, D. L.; Khotyaintsev, Yu. V.; Graham, D. B.; Lindqvist, P.-A.; Chasapis, A.; Burch, J. L.; Torbert, R. B.; Russell, C. T.; Magnes, W.; Strangeway, R. J.; Plaschke, F.; Moore, T. E.; Giles, B. L.; Paterson, W. R.; Pollock, C. J.; Lavraud, B.; Fuselier, S. A.; Cohen, I. J.

2018-06-01

The Earth’s magnetosheath, which is characterized by highly turbulent fluctuations, is usually divided into two regions of different properties as a function of the angle between the interplanetary magnetic field and the shock normal. In this study, we make use of high-time resolution instruments on board the Magnetospheric MultiScale spacecraft to determine and compare the properties of subsolar magnetosheath turbulence in both regions, i.e., downstream of the quasi-parallel and quasi-perpendicular bow shocks. In particular, we take advantage of the unprecedented temporal resolution of the Fast Plasma Investigation instrument to show the density fluctuations down to sub-ion scales for the first time. We show that the nature of turbulence is highly compressible down to electron scales, particularly in the quasi-parallel magnetosheath. In this region, the magnetic turbulence also shows an inertial (Kolmogorov-like) range, indicating that the fluctuations are not formed locally, in contrast with the quasi-perpendicular magnetosheath. We also show that the electromagnetic turbulence is dominated by electric fluctuations at sub-ion scales (f > 1 Hz) and that magnetic and electric spectra steepen at the largest-electron scale. The latter indicates a change in the nature of turbulence at electron scales. Finally, we show that the electric fluctuations around the electron gyrofrequency are mostly parallel in the quasi-perpendicular magnetosheath, where intense whistlers are observed. This result suggests that energy dissipation, plasma heating, and acceleration might be driven by intense electrostatic parallel structures/waves, which can be linked to whistler waves.

Magnetic Field Fluctuations in the High Ionosphere at Polar Latitudes: Impact of the IMF Conditions

NASA Astrophysics Data System (ADS)

De Michelis, P.; Consolini, G.; Tozzi, R.

2016-12-01

The characterization of ionospheric turbulence plays an important role for all those communication systems affected by the ionospheric medium. For instance, independently of geomagnetic latitude, ionospheric turbulence represents a considerable issue for all Global Navigation Satellite Systems (GNSS). Swarm constellation measurements of the Earth's magnetic field allow a precise characterization of ionospheric turbulence. This is possible using a range of indices derived from the analysis of the scaling properties of the geomagnetic field. In particular, by the scaling properties of the 1st order structure function, a scale index can be obtained, with a consequent characterization of the degree of persistence of the fluctuations and of their spectral properties. The knowledge of this index provides a global characterization of the nature and level of ionospheric turbulence on a local scale, which can be displayed along a single satellite orbit or through maps over the region of interest. The present work focuses on the analysis of the scaling properties of the 1st order structure function of magnetic field fluctuations measured by Swarm constellation at polar latitudes in the Northern Hemisphere. They are studied according to different interplanetary magnetic field conditions and Earth's seasons to characterize the possible drivers of magnetic field variability. The obtained results are discussed in the framework of Sun-Earth relationship and ionospheric polar convection. This work is supported by the Italian National Program for Antarctic Research (PNRA) Research Project 2013/AC3.08

Fluctuating micro-heterogeneity in water-tert-butyl alcohol mixtures and lambda-type divergence of the mean cluster size with phase transition-like multiple anomalies

NASA Astrophysics Data System (ADS)

Banerjee, Saikat; Furtado, Jonathan; Bagchi, Biman

2014-05-01

Water-tert-butyl alcohol (TBA) binary mixture exhibits a large number of thermodynamic and dynamic anomalies. These anomalies are observed at surprisingly low TBA mole fraction, with xTBA ≈ 0.03-0.07. We demonstrate here that the origin of the anomalies lies in the local structural changes that occur due to self-aggregation of TBA molecules. We observe a percolation transition of the TBA molecules at xTBA ≈ 0.05. We note that "islands" of TBA clusters form even below this mole fraction, while a large spanning cluster emerges above that mole fraction. At this percolation threshold, we observe a lambda-type divergence in the fluctuation of the size of the largest TBA cluster, reminiscent of a critical point. Alongside, the structure of water is also perturbed, albeit weakly, by the aggregation of TBA molecules. There is a monotonic decrease in the tetrahedral order parameter of water, while the dipole moment correlation shows a weak nonlinearity. Interestingly, water molecules themselves exhibit a reverse percolation transition at higher TBA concentration, xTBA ≈ 0.45, where large spanning water clusters now break-up into small clusters. This is accompanied by significant divergence of the fluctuations in the size of largest water cluster. This second transition gives rise to another set of anomalies around. Both the percolation transitions can be regarded as manifestations of Janus effect at small molecular level.

Fluctuating micro-heterogeneity in water-tert-butyl alcohol mixtures and lambda-type divergence of the mean cluster size with phase transition-like multiple anomalies.

PubMed

Banerjee, Saikat; Furtado, Jonathan; Bagchi, Biman

2014-05-21

Water-tert-butyl alcohol (TBA) binary mixture exhibits a large number of thermodynamic and dynamic anomalies. These anomalies are observed at surprisingly low TBA mole fraction, with x(TBA) ≈ 0.03-0.07. We demonstrate here that the origin of the anomalies lies in the local structural changes that occur due to self-aggregation of TBA molecules. We observe a percolation transition of the TBA molecules at x(TBA) ≈ 0.05. We note that "islands" of TBA clusters form even below this mole fraction, while a large spanning cluster emerges above that mole fraction. At this percolation threshold, we observe a lambda-type divergence in the fluctuation of the size of the largest TBA cluster, reminiscent of a critical point. Alongside, the structure of water is also perturbed, albeit weakly, by the aggregation of TBA molecules. There is a monotonic decrease in the tetrahedral order parameter of water, while the dipole moment correlation shows a weak nonlinearity. Interestingly, water molecules themselves exhibit a reverse percolation transition at higher TBA concentration, x(TBA) ≈ 0.45, where large spanning water clusters now break-up into small clusters. This is accompanied by significant divergence of the fluctuations in the size of largest water cluster. This second transition gives rise to another set of anomalies around. Both the percolation transitions can be regarded as manifestations of Janus effect at small molecular level.

Self-Consistent Monte Carlo Study of the Coulomb Interaction under Nano-Scale Device Structures

NASA Astrophysics Data System (ADS)

Sano, Nobuyuki

2011-03-01

It has been pointed that the Coulomb interaction between the electrons is expected to be of crucial importance to predict reliable device characteristics. In particular, the device performance is greatly degraded due to the plasmon excitation represented by dynamical potential fluctuations in high-doped source and drain regions by the channel electrons. We employ the self-consistent 3D Monte Carlo (MC) simulations, which could reproduce both the correct mobility under various electron concentrations and the collective plasma waves, to study the physical impact of dynamical potential fluctuations on device performance under the Double-gate MOSFETs. The average force experienced by an electron due to the Coulomb interaction inside the device is evaluated by performing the self-consistent MC simulations and the fixed-potential MC simulations without the Coulomb interaction. Also, the band-tailing associated with the local potential fluctuations in high-doped source region is quantitatively evaluated and it is found that the band-tailing becomes strongly dependent of position in real space even inside the uniform source region. This work was partially supported by Grants-in-Aid for Scientific Research B (No. 2160160) from the Ministry of Education, Culture, Sports, Science and Technology in Japan.

Performance Comparison of Systematic Methods for Rigorous Definition of Coarse-Grained Sites of Large Biomolecules.

PubMed

Zhang, Yuwei; Cao, Zexing; Zhang, John Zenghui; Xia, Fei

2017-02-27

Construction of coarse-grained (CG) models for large biomolecules used for multiscale simulations demands a rigorous definition of CG sites for them. Several coarse-graining methods such as the simulated annealing and steepest descent (SASD) based on the essential dynamics coarse-graining (ED-CG) or the stepwise local iterative optimization (SLIO) based on the fluctuation maximization coarse-graining (FM-CG), were developed to do it. However, the practical applications of these methods such as SASD based on ED-CG are subject to limitations because they are too expensive. In this work, we extend the applicability of ED-CG by combining it with the SLIO algorithm. A comprehensive comparison of optimized results and accuracy of various algorithms based on ED-CG show that SLIO is the fastest as well as the most accurate algorithm among them. ED-CG combined with SLIO could give converged results as the number of CG sites increases, which demonstrates that it is another efficient method for coarse-graining large biomolecules. The construction of CG sites for Ras protein by using MD fluctuations demonstrates that the CG sites derived from FM-CG can reflect the fluctuation properties of secondary structures in Ras accurately.

Charge ordering transition in GdBaCo2O5: Evidence of reentrant behavior

NASA Astrophysics Data System (ADS)

Allieta, M.; Scavini, M.; Lo Presti, L.; Coduri, M.; Loconte, L.; Cappelli, S.; Oliva, C.; Ghigna, P.; Pattison, P.; Scagnoli, V.

2013-12-01

We present a detailed study on the charge ordering transition in a GdBaCo2O5.0 system by combining high-resolution synchrotron powder/single-crystal diffraction with electron paramagnetic resonance experiments as a function of temperature. We found a second-order structural phase transition at TCO = 247 K (Pmmm to Pmma) associated with the onset of long-range charge ordering. At Tmin ≈ 1.2TCO, the electron paramagnetic resonance linewidth rapidly broadens, providing evidence of antiferromagnetic spin fluctuations. This likely indicates that, analogously to manganites, the long-range antiferromagnetic order in GdBaCo2O5.0 sets in at ≈TCO. Pair distribution function analysis of diffraction data revealed signatures of structural inhomogeneities at low temperature. By comparing the average and local bond valences, we found that above TCO the local structure is consistent with a fully random occupation of Co2+ and Co3+ in a 1:1 ratio and with a complete charge ordering below TCO. Below T ≈ 100 K the charge localization is partially melted at the local scale, suggesting a reentrant behavior of charge ordering. This result is supported by the weakening of superstructure reflections and the temperature evolution of electron paramagnetic resonance linewidth that is consistent with paramagnetic reentrant behavior reported in the GdBaCo2O5.5 parent compound.

Local fluctuations of ozone from 16 km to 45 km deduced from in situ vertical ozone profile

NASA Technical Reports Server (NTRS)

Moreau, G.; Robert, C.

1994-01-01

A vertical ozone profile obtained by an in situ ozone sonde from 16 km to 45 km, has allowed to observe local ozone concentration variations. These variations can be observed, thanks to a fast measurement system based on a UV absorption KrF excimer laser beam in a multipass cell. Ozone standard deviation versus altitude calculated from the mean is derived. Ozone variations or fluctuations are correlated with the different dynamic zones of the stratosphere.

Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis.

PubMed

Martínez, Leandro

2015-01-01

The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO) strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit.

Automatic Identification of Mobile and Rigid Substructures in Molecular Dynamics Simulations and Fractional Structural Fluctuation Analysis

PubMed Central

Martínez, Leandro

2015-01-01

The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO) strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit PMID:25816325

Hydrated Electron Transfer to Nucleobases in Aqueous Solutions Revealed by Ab Initio Molecular Dynamics Simulations.

PubMed

Zhao, Jing; Wang, Mei; Fu, Aiyun; Yang, Hongfang; Bu, Yuxiang

2015-08-03

We present an ab initio molecular dynamics (AIMD) simulation study into the transfer dynamics of an excess electron from its cavity-shaped hydrated electron state to a hydrated nucleobase (NB)-bound state. In contrast to the traditional view that electron localization at NBs (G/A/C/T), which is the first step for electron-induced DNA damage, is related only to dry or prehydrated electrons, and a fully hydrated electron no longer transfers to NBs, our AIMD simulations indicate that a fully hydrated electron can still transfer to NBs. We monitored the transfer dynamics of fully hydrated electrons towards hydrated NBs in aqueous solutions by using AIMD simulations and found that due to solution-structure fluctuation and attraction of NBs, a fully hydrated electron can transfer to a NB gradually over time. Concurrently, the hydrated electron cavity gradually reorganizes, distorts, and even breaks. The transfer could be completed in about 120-200 fs in four aqueous NB solutions, depending on the electron-binding ability of hydrated NBs and the structural fluctuation of the solution. The transferring electron resides in the π*-type lowest unoccupied molecular orbital of the NB, which leads to a hydrated NB anion. Clearly, the observed transfer of hydrated electrons can be attributed to the strong electron-binding ability of hydrated NBs over the hydrated electron cavity, which is the driving force, and the transfer dynamics is structure-fluctuation controlled. This work provides new insights into the evolution dynamics of hydrated electrons and provides some helpful information for understanding the DNA-damage mechanism in solution. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

50 years of DNA ‘Breathing’: Reflections on Old and New Approaches

PubMed Central

von Hippel, Peter H.; Johnson, Neil P.; Marcus, Andrew H.

2015-01-01

Summary The coding sequences for genes, and much other regulatory information involved in genome expression, are located ‘inside’ the DNA duplex. Thus the ‘macromolecular machines’ that read-out this information from the base sequence of the DNA must somehow access the DNA ‘interior’. Double-stranded (ds) DNA is a highly structured and cooperatively stabilized system at physiological temperatures, but is also only marginally stable and undergoes a cooperative ‘melting phase transition’ at temperatures not far above physiological. Furthermore, due to its length and heterogeneous sequence, with AT-rich segments being less stable than GC-rich segments, the DNA genome ‘melts’ in a multistate fashion. Therefore the DNA genome must also manifest thermally driven structural (‘breathing’) fluctuations at physiological temperatures that should reflect the heterogeneity of the dsDNA stability near the melting temperature. Thus many of the breathing fluctuations of dsDNA are likely also to be sequence dependent, and could well contain information that should be ‘readable’ and useable by regulatory proteins and protein complexes in site-specific binding reactions involving dsDNA ‘opening’. Our laboratory has been involved in studying the breathing fluctuations of duplex DNA for about 50 years. In this ‘Reflections’ article we present a relatively chronological overview of these studies, starting with the use of simple chemical probes (such as hydrogen exchange, formaldehyde and simple DNA ‘melting’ proteins) to examine the local stability of the dsDNA structure, and culminating in sophisticated spectroscopic approaches that can be used to monitor the breathing-dependent interactions of regulatory complexes with their duplex DNA targets in ‘real time’. PMID:23840028

Investigation on relationship between epicentral distance and growth curve of initial P-wave propagating in local heterogeneous media for earthquake early warning system

NASA Astrophysics Data System (ADS)

Okamoto, Kyosuke; Tsuno, Seiji

2015-10-01

In the earthquake early warning (EEW) system, the epicenter location and magnitude of earthquakes are estimated using the amplitude growth rate of initial P-waves. It has been empirically pointed out that the growth rate becomes smaller as epicentral distance becomes far regardless of the magnitude of earthquakes. So, the epicentral distance can be estimated from the growth rate using this empirical relationship. However, the growth rates calculated from different earthquakes at the same epicentral distance mark considerably different values from each other. Sometimes the growth rates of earthquakes having the same epicentral distance vary by 104 times. Qualitatively, it has been considered that the gap in the growth rates is due to differences in the local heterogeneities that the P-waves propagate through. In this study, we demonstrate theoretically how local heterogeneities in the subsurface disturb the relationship between the growth rate and the epicentral distance. Firstly, we calculate seismic scattered waves in a heterogeneous medium. First-ordered PP, PS, SP, and SS scatterings are considered. The correlation distance of the heterogeneities and fractional fluctuation of elastic parameters control the heterogeneous conditions for the calculation. From the synthesized waves, the growth rate of the initial P-wave is obtained. As a result, we find that a parameter (in this study, correlation distance) controlling heterogeneities plays a key role in the magnitude of the fluctuation of the growth rate. Then, we calculate the regional correlation distances in Japan that can account for the fluctuation of the growth rate of real earthquakes from 1997 to 2011 observed by K-NET and KiK-net. As a result, the spatial distribution of the correlation distance shows locality. So, it is revealed that the growth rates fluctuate according to the locality. When this local fluctuation is taken into account, the accuracy of the estimation of epicentral distances from initial P-waves can improve, which will in turn improve the accuracy of the EEW system.

Stress-induced electric current fluctuations in rocks: a superstatistical model

NASA Astrophysics Data System (ADS)

Cartwright-Taylor, Alexis; Vallianatos, Filippos; Sammonds, Peter

2017-04-01

We recorded spontaneous electric current flow in non-piezoelectric Carrara marble samples during triaxial deformation. Mechanical data, ultrasonic velocities and acoustic emissions were acquired simultaneously with electric current to constrain the relationship between electric current flow, differential stress and damage. Under strain-controlled loading, spontaneous electric current signals (nA) were generated and sustained under all conditions tested. In dry samples, a detectable electric current arises only during dilatancy and the overall signal is correlated with the damage induced by microcracking. Our results show that fracture plays a key role in the generation of electric currents in deforming rocks (Cartwright-Taylor et al., in prep). We also analysed the high-frequency fluctuations of these electric current signals and found that they are not normally distributed - they exhibit power-law tails (Cartwright-Taylor et al., 2014). We modelled these distributions with q-Gaussian statistics, derived by maximising the Tsallis entropy. This definition of entropy is particularly applicable to systems which are strongly correlated and far from equilibrium. Good agreement, at all experimental conditions, between the distributions of electric current fluctuations and the q-Gaussian function with q-values far from one, illustrates the highly correlated, fractal nature of the electric source network within the samples and provides further evidence that the source of the electric signals is the developing fractal network of cracks. It has been shown (Beck, 2001) that q-Gaussian distributions can arise from the superposition of local relaxations in the presence of a slowly varying driving force, thus providing a dynamic reason for the appearance of Tsallis statistics in systems with a fluctuating energy dissipation rate. So, the probability distribution for a dynamic variable, u under some external slow forcing, β, can be obtained as a superposition of temporary local equilibrium processes whose variance fluctuates over time. The appearance of q-Gaussian statistics are caused by the fluctuating β parameter, which effectively models the fluctuating energy dissipation rate in the system. This concept is known as superstatistics and is physically relevant for modelling driven non-equilibrium systems where the environmental conditions fluctuate on a large scale. The idea is that the environmental variable, such as temperature or pressure, changes so slowly that a rapidly fluctuating variable within that environment has time to relax back to equilibrium between each change in the environment. The application of superstatistical techniques to our experimental electric current fluctuations show that they can indeed be described, to good approximation, by the superposition of local Gaussian processes with fluctuating variance. We conclude, then, that the measured electric current fluctuates in response to intermittent energy dissipation and is driven to varying temporary local equilibria during deformation by the variations in stress intensity. The advantage of this technique is that, once the model has been established to be a good description of the system in question, the average β parameter (a measure of the average energy dissipation rate) for the system can be obtained simply from the macroscopic q-Gaussian distribution parameters.

Relaxation and collective excitations of cluster nano-plasmas

NASA Astrophysics Data System (ADS)

Reinholz, Heidi; Röpke, Gerd; Broda, Ingrid; Morozov, Igor; Bystryi, Roman; Lavrinenko, Yaroslav

2018-01-01

Nano-plasmas produced, for example, in clusters after short-pulse laser irradiation, can show collective excitations, as derived from the time evolution of fluctuations in thermodynamic equilibrium. Molecular dynamical simulations are performed for various cluster sizes. New data are obtained for the minimum value of the stationary cluster charge. The bi-local autocorrelation function gives the spatial structure of the eigenmodes, for which energy eigenvalues are obtained. By varying the cluster size, starting from a few-particle cluster, the emergence of macroscopic properties such as collective excitations is shown.

Structural predictions for Correlated Electron Materials Using the Functional Dynamical Mean Field Theory Approach

NASA Astrophysics Data System (ADS)

Haule, Kristjan

2018-04-01

The Dynamical Mean Field Theory (DMFT) in combination with the band structure methods has been able to address reach physics of correlated materials, such as the fluctuating local moments, spin and orbital fluctuations, atomic multiplet physics and band formation on equal footing. Recently it is getting increasingly recognized that more predictive ab-initio theory of correlated systems needs to also address the feedback effect of the correlated electronic structure on the ionic positions, as the metal-insulator transition is almost always accompanied with considerable structural distortions. We will review recently developed extension of merger between the Density Functional Theory (DFT) and DMFT method, dubbed DFT+ embedded DMFT (DFT+eDMFT), whichsuccessfully addresses this challenge. It is based on the stationary Luttinger-Ward functional to minimize the numerical error, it subtracts the exact double-counting of DFT and DMFT, and implements self-consistent forces on all atoms in the unit cell. In a few examples, we will also show how the method elucidated the important feedback effect of correlations on crystal structure in rare earth nickelates to explain the mechanism of the metal-insulator transition. The method showed that such feedback effect is also essential to understand the dynamic stability of the high-temperature body-centered cubic phase of elemental iron, and in particular it predicted strong enhancement of the electron-phonon coupling over DFT values in FeSe, which was very recently verified by pioneering time-domain experiment.

Fluctuation scaling, Taylor's law, and crime.

PubMed

Hanley, Quentin S; Khatun, Suniya; Yosef, Amal; Dyer, Rachel-May

2014-01-01

Fluctuation scaling relationships have been observed in a wide range of processes ranging from internet router traffic to measles cases. Taylor's law is one such scaling relationship and has been widely applied in ecology to understand communities including trees, birds, human populations, and insects. We show that monthly crime reports in the UK show complex fluctuation scaling which can be approximated by Taylor's law relationships corresponding to local policing neighborhoods and larger regional and countrywide scales. Regression models applied to local scale data from Derbyshire and Nottinghamshire found that different categories of crime exhibited different scaling exponents with no significant difference between the two regions. On this scale, violence reports were close to a Poisson distribution (α = 1.057 ± 0.026) while burglary exhibited a greater exponent (α = 1.292 ± 0.029) indicative of temporal clustering. These two regions exhibited significantly different pre-exponential factors for the categories of anti-social behavior and burglary indicating that local variations in crime reports can be assessed using fluctuation scaling methods. At regional and countrywide scales, all categories exhibited scaling behavior indicative of temporal clustering evidenced by Taylor's law exponents from 1.43 ± 0.12 (Drugs) to 2.094 ± 0081 (Other Crimes). Investigating crime behavior via fluctuation scaling gives insight beyond that of raw numbers and is unique in reporting on all processes contributing to the observed variance and is either robust to or exhibits signs of many types of data manipulation.

Fluctuation Scaling, Taylor’s Law, and Crime

PubMed Central

Hanley, Quentin S.; Khatun, Suniya; Yosef, Amal; Dyer, Rachel-May

2014-01-01

Fluctuation scaling relationships have been observed in a wide range of processes ranging from internet router traffic to measles cases. Taylor’s law is one such scaling relationship and has been widely applied in ecology to understand communities including trees, birds, human populations, and insects. We show that monthly crime reports in the UK show complex fluctuation scaling which can be approximated by Taylor’s law relationships corresponding to local policing neighborhoods and larger regional and countrywide scales. Regression models applied to local scale data from Derbyshire and Nottinghamshire found that different categories of crime exhibited different scaling exponents with no significant difference between the two regions. On this scale, violence reports were close to a Poisson distribution (α = 1.057±0.026) while burglary exhibited a greater exponent (α = 1.292±0.029) indicative of temporal clustering. These two regions exhibited significantly different pre-exponential factors for the categories of anti-social behavior and burglary indicating that local variations in crime reports can be assessed using fluctuation scaling methods. At regional and countrywide scales, all categories exhibited scaling behavior indicative of temporal clustering evidenced by Taylor’s law exponents from 1.43±0.12 (Drugs) to 2.094±0081 (Other Crimes). Investigating crime behavior via fluctuation scaling gives insight beyond that of raw numbers and is unique in reporting on all processes contributing to the observed variance and is either robust to or exhibits signs of many types of data manipulation. PMID:25271781

Characterization of traffic-related PM concentration distribution and fluctuation patterns in near-highway urban residential street canyons.

PubMed

Hahn, Intaek; Brixey, Laurie A; Wiener, Russell W; Henkle, Stacy W; Baldauf, Richard

2009-12-01

Analyses of outdoor traffic-related particulate matter (PM) concentration distribution and fluctuation patterns in urban street canyons within a microscale distance of less than 500 m from a highway source are presented as part of the results from the Brooklyn Traffic Real-Time Ambient Pollutant Penetration and Environmental Dispersion (B-TRAPPED) study. Various patterns of spatial and temporal changes in the street canyon PM concentrations were investigated using time-series data of real-time PM concentrations measured during multiple monitoring periods. Concurrent time-series data of local street canyon wind conditions and wind data from the John F. Kennedy (JFK) International Airport National Weather Service (NWS) were used to characterize the effects of various wind conditions on the behavior of street canyon PM concentrations.Our results suggest that wind direction may strongly influence time-averaged mean PM concentration distribution patterns in near-highway urban street canyons. The rooftop-level wind speeds were found to be strongly correlated with the PM concentration fluctuation intensities in the middle sections of the street blocks. The ambient turbulence generated by shifting local wind directions (angles) showed a good correlation with the PM concentration fluctuation intensities along the entire distance of the first and second street blocks only when the wind angle standard deviations were larger than 30 degrees. Within-canyon turbulent shearing, caused by fluctuating local street canyon wind speeds, showed no correlation with PM concentration fluctuation intensities. The time-averaged mean PM concentration distribution along the longitudinal distances of the street blocks when wind direction was mostly constantly parallel to the street was found to be similar to the distribution pattern for the entire monitoring period when wind direction fluctuated wildly. Finally, we showed that two different PM concentration metrics-time-averaged mean concentration and number of concentration peaks above a certain threshold level-can possibly lead to different assessments of spatial concentration distribution patterns.

Linear and quadratic static response functions and structure functions in Yukawa liquids.

PubMed

Magyar, Péter; Donkó, Zoltán; Kalman, Gabor J; Golden, Kenneth I

2014-08-01

We compute linear and quadratic static density response functions of three-dimensional Yukawa liquids by applying an external perturbation potential in molecular dynamics simulations. The response functions are also obtained from the equilibrium fluctuations (static structure factors) in the system via the fluctuation-dissipation theorems. The good agreement of the quadratic response functions, obtained in the two different ways, confirms the quadratic fluctuation-dissipation theorem. We also find that the three-point structure function may be factorizable into two-point structure functions, leading to a cluster representation of the equilibrium triplet correlation function.

Heterogeneous activation in 2D colloidal glass-forming liquids classified by machine learning

NASA Astrophysics Data System (ADS)

Ma, Xiaoguang; Davidson, Zoey; Still, Tim; Ivancic, Robert; Schoenholz, Sam S.; Sussman, Daniel M.; Liu, A. J.; Yodh, A. G.

The trajectories of particles in colloidal glass-forming liquids are often characterized by long periods of ``in-cage'' fluctuations and rapid ``cage-breaking'' rearrangements. We study the rate of such rearrangements and its connection with local cage structures in a 2D binary mixture of poly(N-isopropyl acrylamide) spheres. We use the hopping function, Phop (t) , to identify rearrangements within particle trajectories. Then we obtain distributions of the residence time tR between consecutive rearrangements. The mean residence time tR (S) is found to correlate with the local configurations for the rearranging particles, characterized by 70 radial structural features and softness S, which ranks the structural similarities with respect to rearranging particles. Furthermore, tR (S) for particles with similar softness decays monotonically with increasing softness, indicating correlation between rearrangement rates and softness S. Finally we find that the conditional and full probability distribution functions, P (tR | S) and P (tR) , are well explained by a thermal activation model. We acknowledge financial supports from NSF-MRSEC DMR11-20901, NSF DMR16-07378, and NASA NNX08AO0G.

Entanglement contour perspective for "strong area-law violation" in a disordered long-range hopping model

NASA Astrophysics Data System (ADS)

Roy, Nilanjan; Sharma, Auditya

2018-03-01

We numerically investigate the link between the delocalization-localization transition and entanglement in a disordered long-range hopping model of spinless fermions by studying various static and dynamical quantities. This includes the inverse participation ratio, level statistics, entanglement entropy, and number fluctuations in the subsystem along with quench and wave-packet dynamics. Finite systems show delocalized, quasilocalized, and localized phases. The delocalized phase shows strong area-law violation, whereas the (quasi)localized phase adheres to (for large subsystems) the strict area law. The idea of "entanglement contour" nicely explains the violation of area law and its relationship with "fluctuation contour" reveals a signature at the transition point. The relationship between entanglement entropy and number fluctuations in the subsystem also carries signatures for the transition in the model. Results from the Aubry-Andre-Harper model are compared in this context. The propagation of charge and entanglement are contrasted by studying quench and wave-packet dynamics at the single-particle and many-particle levels.

Effect of wave localization on plasma instabilities. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Levedahl, William Kirk

1987-01-01

The Anderson model of wave localization in random media is involved to study the effect of solar wind density turbulence on plasma processes associated with the solar type III radio burst. ISEE-3 satellite data indicate that a possible model for the type III process is the parametric decay of Langmuir waves excited by solar flare electron streams into daughter electromagnetic and ion acoustic waves. The threshold for this instability, however, is much higher than observed Langmuir wave levels because of rapid wave convection of the transverse electromagnetic daughter wave in the case where the solar wind is assumed homogeneous. Langmuir and transverse waves near critical density satisfy the Ioffe-Reigel criteria for wave localization in the solar wind with observed density fluctuations -1 percent. Numerical simulations of wave propagation in random media confirm the localization length predictions of Escande and Souillard for stationary density fluctations. For mobile density fluctuations localized wave packets spread at the propagation velocity of the density fluctuations rather than the group velocity of the waves. Computer simulations using a linearized hybrid code show that an electron beam will excite localized Langmuir waves in a plasma with density turbulence. An action principle approach is used to develop a theory of non-linear wave processes when waves are localized. A theory of resonant particles diffusion by localized waves is developed to explain the saturation of the beam-plasma instability. It is argued that localization of electromagnetic waves will allow the instability threshold to be exceeded for the parametric decay discussed above.

Spherical harmonics analysis of surface density fluctuations of spherical ionic SDS and nonionic C12E8 micelles: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Yoshii, Noriyuki; Nimura, Yuki; Fujimoto, Kazushi; Okazaki, Susumu

2017-07-01

The surface structure and its fluctuation of spherical micelles were investigated using a series of density correlation functions newly defined by spherical harmonics and Legendre polynomials based on the molecular dynamics calculations. To investigate the influence of head-group charges on the micelle surface structure, ionic sodium dodecyl sulfate and nonionic octaethyleneglycol monododecylether (C12E8) micelles were investigated as model systems. Large-scale density fluctuations were observed for both micelles in the calculated surface static structure factor. The area compressibility of the micelle surface evaluated by the surface static structure factor was tens-of-times larger than a typical value of a lipid membrane surface. The structural relaxation time, which was evaluated from the surface intermediate scattering function, indicates that the relaxation mechanism of the long-range surface structure can be well described by the hydrostatic approximation. The density fluctuation on the two-dimensional micelle surface has similar characteristics to that of three-dimensional fluids near the critical point.

Spherical harmonics analysis of surface density fluctuations of spherical ionic SDS and nonionic C12E8 micelles: A molecular dynamics study.

PubMed

Yoshii, Noriyuki; Nimura, Yuki; Fujimoto, Kazushi; Okazaki, Susumu

2017-07-21

The surface structure and its fluctuation of spherical micelles were investigated using a series of density correlation functions newly defined by spherical harmonics and Legendre polynomials based on the molecular dynamics calculations. To investigate the influence of head-group charges on the micelle surface structure, ionic sodium dodecyl sulfate and nonionic octaethyleneglycol monododecylether (C 12 E 8 ) micelles were investigated as model systems. Large-scale density fluctuations were observed for both micelles in the calculated surface static structure factor. The area compressibility of the micelle surface evaluated by the surface static structure factor was tens-of-times larger than a typical value of a lipid membrane surface. The structural relaxation time, which was evaluated from the surface intermediate scattering function, indicates that the relaxation mechanism of the long-range surface structure can be well described by the hydrostatic approximation. The density fluctuation on the two-dimensional micelle surface has similar characteristics to that of three-dimensional fluids near the critical point.

Dynamical properties of α-amylase in the folded and unfolded state: the role of thermal equilibrium fluctuations for conformational entropy and protein stabilisation

NASA Astrophysics Data System (ADS)

Fitter, J.; Herrmann, R.; Hauß, T.; Lechner, R. E.; Dencher, N. A.

2001-07-01

A comparative analysis of thermal equilibrium fluctuations occurring in a mesophilic and in a thermophilic α-amylase was performed to study the effect of structural fluctuations on thermostability. The thermal fluctuations determining the conformational entropy of both enzymes have been characterised for the folded (at 30°C and 60°C) and for the unfolded state by applying neutron spectroscopy (at 30°C). The folded state shows a higher structural flexibility for the thermophilic protein as compared to the mesophilic homologue. In contrast, the unfolded state of both enzymes is rather similar with respect to the structural fluctuations. On the basis of this result, a mechanism characterised by entropic stabilisation (i.e., smaller Δ S for the unfolding transition of thermophilic α-amylase) can be assumed to be responsible for the higher thermostability of the thermophilic enzyme.

Spatial fluctuations in transient creep deformation

NASA Astrophysics Data System (ADS)

Laurson, Lasse; Rosti, Jari; Koivisto, Juha; Miksic, Amandine; Alava, Mikko J.

2011-07-01

We study the spatial fluctuations of transient creep deformation of materials as a function of time, both by digital image correlation (DIC) measurements of paper samples and by numerical simulations of a crystal plasticity or discrete dislocation dynamics model. This model has a jamming or yielding phase transition, around which power law or Andrade creep is found. During primary creep, the relative strength of the strain rate fluctuations increases with time in both cases—the spatially averaged creep rate obeys the Andrade law epsilont ~ t - 0.7, while the time dependence of the spatial fluctuations of the local creep rates is given by Δepsilont ~ t - 0.5. A similar scaling for the fluctuations is found in the logarithmic creep regime that is typically observed for lower applied stresses. We review briefly some classical theories of Andrade creep from the point of view of such spatial fluctuations. We consider these phenomenological, time-dependent creep laws in terms of a description based on a non-equilibrium phase transition separating evolving and frozen states of the system when the externally applied load is varied. Such an interpretation is discussed further by the data collapse of the local deformations in the spirit of absorbing state/depinning phase transitions, as well as deformation-deformation correlations and the width of the cumulative strain distributions. The results are also compared with the order parameter fluctuations observed close to the depinning transition of the 2d linear interface model or the quenched Edwards-Wilkinson equation.

SGO: A fast engine for ab initio atomic structure global optimization by differential evolution

NASA Astrophysics Data System (ADS)

Chen, Zhanghui; Jia, Weile; Jiang, Xiangwei; Li, Shu-Shen; Wang, Lin-Wang

2017-10-01

As the high throughout calculations and material genome approaches become more and more popular in material science, the search for optimal ways to predict atomic global minimum structure is a high research priority. This paper presents a fast method for global search of atomic structures at ab initio level. The structures global optimization (SGO) engine consists of a high-efficiency differential evolution algorithm, accelerated local relaxation methods and a plane-wave density functional theory code running on GPU machines. The purpose is to show what can be achieved by combining the superior algorithms at the different levels of the searching scheme. SGO can search the global-minimum configurations of crystals, two-dimensional materials and quantum clusters without prior symmetry restriction in a relatively short time (half or several hours for systems with less than 25 atoms), thus making such a task a routine calculation. Comparisons with other existing methods such as minima hopping and genetic algorithm are provided. One motivation of our study is to investigate the properties of magnetic systems in different phases. The SGO engine is capable of surveying the local minima surrounding the global minimum, which provides the information for the overall energy landscape of a given system. Using this capability we have found several new configurations for testing systems, explored their energy landscape, and demonstrated that the magnetic moment of metal clusters fluctuates strongly in different local minima.

Ionization balance of impurities in turbulent scrape-off layer plasmas I: local ionization-recombination equilibrium

NASA Astrophysics Data System (ADS)

Guzman, F.; Marandet, Y.; Tamain, P.; Bufferand, H.; Ciraolo, G.; Ghendrih, Ph; Guirlet, R.; Rosato, J.; Valentinuzzi, M.

2015-12-01

In magnetized fusion devices, cross field impurity transport is often dominated by turbulence, in particular in the scrape-off layer. In these outer regions of the plasma, fluctuations of plasma parameters can be comparable to mean values, and the way ionization and recombination sources are treated in transport codes becomes questionnable. In fact, sources are calculated using the mean density and temperature values, with no account of fluctuations. In this work we investigate the modeling uncertainties introduced by this approximation, both qualitatively and quantitatively for the local ionization equilibrium. As a first step transport effects are neglected, and their role will be discussed in a companion paper. We show that temperature fluctuations shift the ionization balance towards lower temperatures, essentially because of the very steep temperature dependence of the ionization rate coefficients near the threshold. To reach this conclusion, a thorough analysis of the time scales involved is carried out, in order to devise a proper way of averaging over fluctuations. The effects are found to be substantial only for fairly large relative fluctuation levels for temperature, that is of the order of a few tens of percents.

Development of TEC fluctuations in northern and southern hemispheres on the base of GPS observations

NASA Astrophysics Data System (ADS)

Shagimuratov, Irk; Krankowski, Andrzej; Sieradzki, Rafal; Ephishov, I. I.

GPS technique is widely used to study the global structure and dynamics of the ionosphere. In this paper GPS observations carried out at Arctic and Antarctic stations belonging to the IGS network were used to study TEC fluctuations in the high-latitude ionosphere during the ionospheric storms. Dual-frequency GPS phase measurements along individual satellite passes served as raw data. It was shown that ionospheric irregularities of a different scale were devel-oped in the auroral and polar ionosphere. It is a common phenomenon caused phase fluctuations of GPS signals. In November 2009, West Department of IZMIRAN in Kaliningrad (Russia) and University of Warmia and Mazury in Olsztyn (Poland) established computer server for automatic monitoring of these irregularities. The rate of TEC index (ROTI) expressed in TECU/min was used as a measure of TEC fluctuations. During its operation TEC variations related to ionospheric structures of a spatial scale more than 200-300 km were detected. Large-scale ionospheric structures cause an increase in horizontal gradients and difficulties with the carrier phase ambiguity resolution in GPS positioning. In turn, the phase fluctuations can cause cycle-slip effects. At the polar stations, ionospheric structures with TEC enhanced by a factor of 3-5 relative to the background were detected, whereas TEC increased to 5-8 TECU in about 10-15 min. These structures were observed during a storm, as well as during a moderate geomagnetic activity. It can be probably attributed to the polar cap patches. In this study are presented the extended and more detailed analyses of TEC fluctuations in both the northern and southern hemispheres and compare the winter and summer events (November and July 2004 storms). A special attention is given to the features related to TEC fluctuations occur-rence in both hemispheres for conjugated GPS stations. The temporal development of both storms was rather similar. During storms the intensity of irregularities essentially increases and its location expands to equator. Maximal activity of TEC fluctuations took place when IMF Bz component was negative. Storm-time development of TEC fluctuations caused by ionospheric irregularities was controlled by UT. At polar stations TEC fluctuations were more expressed at southern (winter) hemisphere. Over auroral stations the difference of TEC fluctuations oc-currence was less expressed. During storm the strong TEC fluctuations can be registered at subauroral ionosphere (on latitudes lower than 55 CGL). The seasonal effect in this area also took place. Differences and similarities of these storms occurrence of TEC fluctuations with dependence on season are discussed.

A doping dependent study of interplay between magnetic and superconducting properties in BaFe2-x Co x As2 single crystals

NASA Astrophysics Data System (ADS)

Bag, Biplab; Shaw, Gorky; Banerjee, S. S.; Vinod, K.; Bharathi, A.

2018-03-01

We show strong interplay between magnetic and superconducting order in three BaFe2-xCoxAs2 single crystals with different x. Our study reveals the presence of magnetic fluctuations with superconducting order in our samples and the strength of the magnetic fluctuations as well as the pinning properties are found to be the strongest for the optimally doped sample and weakest for the overdoped sample. Using local magnetization measurements, we show that application of an external magnetic field in our samples suppresses the magnetic fluctuations and enhances the diamagnetic response. Further, we show presence of unusual superconducting fluctuations above T c in our samples which we find strongly depends on the strength of the magnetic fluctuations. We believe that our data suggest the possible role of magnetic fluctuations in mediating superconducting fluctuations above Tc in our samples.

Stochasticity in materials structure, properties, and processing—A review

NASA Astrophysics Data System (ADS)

Hull, Robert; Keblinski, Pawel; Lewis, Dan; Maniatty, Antoinette; Meunier, Vincent; Oberai, Assad A.; Picu, Catalin R.; Samuel, Johnson; Shephard, Mark S.; Tomozawa, Minoru; Vashishth, Deepak; Zhang, Shengbai

2018-03-01

We review the concept of stochasticity—i.e., unpredictable or uncontrolled fluctuations in structure, chemistry, or kinetic processes—in materials. We first define six broad classes of stochasticity: equilibrium (thermodynamic) fluctuations; structural/compositional fluctuations; kinetic fluctuations; frustration and degeneracy; imprecision in measurements; and stochasticity in modeling and simulation. In this review, we focus on the first four classes that are inherent to materials phenomena. We next develop a mathematical framework for describing materials stochasticity and then show how it can be broadly applied to these four materials-related stochastic classes. In subsequent sections, we describe structural and compositional fluctuations at small length scales that modify material properties and behavior at larger length scales; systems with engineered fluctuations, concentrating primarily on composite materials; systems in which stochasticity is developed through nucleation and kinetic phenomena; and configurations in which constraints in a given system prevent it from attaining its ground state and cause it to attain several, equally likely (degenerate) states. We next describe how stochasticity in these processes results in variations in physical properties and how these variations are then accentuated by—or amplify—stochasticity in processing and manufacturing procedures. In summary, the origins of materials stochasticity, the degree to which it can be predicted and/or controlled, and the possibility of using stochastic descriptions of materials structure, properties, and processing as a new degree of freedom in materials design are described.

Anisotropy of Spin Fluctuations in a Tetragonal Heavy Fermion Antiferromagnet CeRhAl 4 Si 2

DOE PAGES

Sakai, H.; Hattori, T.; Tokunaga, Y.; ...

2017-06-01

An antiferromagnetic (AFM) Kondo lattice compound CeRhAl 4Si 2, which exhibits successive AFM transitions at T N1=14 K and T N2=9 K in zero external field, has been microscopically investigated by means of 27Al nuclear magnetic resonance (NMR) technique. In the high temperature range, magnetic excitations of 4f electrons can be well explained by isotropic localized spin fluctuations. Below ~50 K, it begins to show a characteristic anisotropy of spin fluctuations, which suggests a competition between spin fluctuations and nesting instability in this system.

Dynamical, structural and chemical heterogeneities in a binary metallic glass-forming liquid

NASA Astrophysics Data System (ADS)

Puosi, F.; Jakse, N.; Pasturel, A.

2018-04-01

As it approaches the glass transition, particle motion in liquids becomes highly heterogeneous and regions with virtually no mobility coexist with liquid-like domains. This complex dynamic is believed to be responsible for different phenomena including non-exponential relaxation and the breakdown of the Stokes-Einstein relation. Understanding the relationships between dynamical heterogeneities and local structure in metallic liquids and glasses is a major scientific challenge. Here we use classical molecular dynamics simulations to study the atomic dynamics and microscopic structure of Cu50Zr50 alloy in the supercooling regime. Dynamical heterogeneities are identified via an isoconfigurational analysis. We demonstrate the transition from isolated to clustering low mobility with decreasing temperature. These slow clusters, whose sizes grow upon cooling, are also associated with concentration fluctuations, characterized by a Zr-enriched phase, with a composition CuZr2 . In addition, a structural analysis of slow clusters based on Voronoi tessellation evidences an increase with respect of the bulk system of the fraction of Cu atoms having a local icosahedral order. These results are in agreement with the consolidated scenario of the relevant role played by icosahedral order in the dynamic slowing-down in supercooled metal alloys.

Complex Dynamics of Equatorial Scintillation

NASA Astrophysics Data System (ADS)

Piersanti, Mirko; Materassi, Massimo; Forte, Biagio; Cicone, Antonio

2017-04-01

Radio power scintillation, namely highly irregular fluctuations of the power of trans-ionospheric GNSS signals, is the effect of ionospheric plasma turbulence. The scintillation patterns on radio signals crossing the medium inherit the ionospheric turbulence characteristics of inter-scale coupling, local randomness and large time variability. On this basis, the remote sensing of local features of the turbulent plasma is feasible by studying radio scintillation induced by the ionosphere. The distinctive character of intermittent turbulent media depends on the fluctuations on the space- and time-scale statistical properties of the medium. Hence, assessing how the signal fluctuation properties vary under different Helio-Geophysical conditions will help to understand the corresponding dynamics of the turbulent medium crossed by the signal. Data analysis tools, provided by complex system science, appear to be best fitting to study the response of a turbulent medium, as the Earth's equatorial ionosphere, to the non-linear forcing exerted by the Solar Wind (SW). In particular we used the Adaptive Local Iterative Filtering, the Wavelet analysis and the Information theory data analysis tool. We have analysed the radio scintillation and ionospheric fluctuation data at low latitude focusing on the time and space multi-scale variability and on the causal relationship between forcing factors from the SW environment and the ionospheric response.

Evidence of a forward energy cascade and Kolmogorov self-similarity in submesoscale ocean surface drifter observations

NASA Astrophysics Data System (ADS)

Poje, Andrew C.; Ã-zgökmen, Tamay M.; Bogucki, Darek J.; Kirwan, A. D.

2017-02-01

Using two-point velocity and position data from the near-simultaneous release of O(100) GPS-tracked surface drifters in the northern Gulf of Mexico, we examine the applicability of classical turbulent scaling laws to upper ocean velocity fields. The dataset allows direct estimates of both velocity structure functions and the temporal evolution of the distribution of particle pair separations. On 100 m-10 km spatial scales, and time scales of order 1-10 days, all metrics of the observed surface fluctuations are consistent with standard Kolmogorov turbulence theory in an energy cascade inertial-range regime. The sign of the third-order structure function is negative and proportional to the separation distance for scales ≲10 km where local, fluctuating Rossby numbers are found to be larger than 0.1. The scale-independent energy dissipation rate, or downscale spectral flux, estimated from Kolmogorov's 4/5th law in this regime closely matches nearby microscale dissipation measurements in the near-surface. In contrast, similar statistics derived from a like-sized set of synthetic drifters advected by purely geostrophic altimetric AVISO data agree well with Kolmogorov-Kraichnan scaling for 2D turbulence in the forward enstrophy cascade range.

Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00980a Click here for additional data file.

PubMed Central

Aguayo-Ortiz, Rodrigo; Chávez-García, Cecilia; Straub, John E.

2017-01-01

γ-Secretase is an intramembrane-cleaving aspartyl protease that plays an essential role in the processing of a variety of integral membrane proteins. Its role in the ultimate cleavage step in the processing of amyloid precursor protein to form amyloid-β (Aβ) peptide makes it an important therapeutic target in Alzheimer's disease research. Significant recent advances have been made in structural studies of this critical membrane protein complex. However, details of the mechanism of activation of the enzyme complex remain unclear. Using a multiscale computational modeling approach, combining multiple coarse-grained microsecond dynamic trajectories with all-atom models, the structure and two conformational states of the γ-secretase complex were evaluated. The transition between enzymatic state 1 and state 2 is shown to critically depend on the protonation states of the key catalytic residues Asp257 and Asp385 in the active site domain. The active site formation, related to our γ-secretase state 2, is observed to involve a concerted movement of four transmembrane helices from the catalytic subunit, resulting in the required localization of the catalytic residues. Global analysis of the structural ensemble of the enzyme complex was used to identify collective fluctuations important to the mechanism of substrate recognition and demonstrate that the corresponding fluctuations observed were uncorrelated with structural changes associated with enzyme activation. Overall, this computational study provides essential insight into the role of structure and dynamics in the activation and function of γ-secretase. PMID:28970936

Isolating long-wavelength fluctuation from structural relaxation in two-dimensional glass: cage-relative displacement

NASA Astrophysics Data System (ADS)

Shiba, Hayato; Keim, Peter; Kawasaki, Takeshi

2018-03-01

It has recently been revealed that long-wavelength fluctuation exists in two-dimensional (2D) glassy systems, having the same origin as that given by the Mermin-Wagner theorem for 2D crystalline solids. In this paper, we discuss how to characterise quantitatively the long-wavelength fluctuation in a molecular dynamics simulation of a lightly supercooled liquid. We employ the cage-relative mean-square displacement (MSD), defined on relative displacement to its cage, to quantitatively separate the long-wavelength fluctuation from the original MSD. For increasing system size the amplitude of acoustic long wavelength fluctuations not only increases but shifts to later times causing a crossover with structural relaxation of caging particles. We further analyse the dynamic correlation length using the cage-relative quantities. It grows as the structural relaxation becomes slower with decreasing temperature, uncovering an overestimation by the four-point correlation function due to the long-wavelength fluctuation. These findings motivate the usage of cage-relative MSD as a starting point for analysis of 2D glassy dynamics.

Nonlinear decoding of a complex movie from the mammalian retina

PubMed Central

Deny, Stéphane; Martius, Georg

2018-01-01

Retina is a paradigmatic system for studying sensory encoding: the transformation of light into spiking activity of ganglion cells. The inverse problem, where stimulus is reconstructed from spikes, has received less attention, especially for complex stimuli that should be reconstructed “pixel-by-pixel”. We recorded around a hundred neurons from a dense patch in a rat retina and decoded movies of multiple small randomly-moving discs. We constructed nonlinear (kernelized and neural network) decoders that improved significantly over linear results. An important contribution to this was the ability of nonlinear decoders to reliably separate between neural responses driven by locally fluctuating light signals, and responses at locally constant light driven by spontaneous-like activity. This improvement crucially depended on the precise, non-Poisson temporal structure of individual spike trains, which originated in the spike-history dependence of neural responses. We propose a general principle by which downstream circuitry could discriminate between spontaneous and stimulus-driven activity based solely on higher-order statistical structure in the incoming spike trains. PMID:29746463

The effects of temperature and magnetic flux on electron transport through a four-channel DNA model

NASA Astrophysics Data System (ADS)

Lee, Sunhee; Hedin, Eric; Joe, Yong

2010-03-01

The temperature dependence of the conductivity of lambda phage DNA has been measured by Tran et al [1] experimentally, where the conductivity displayed strong (weak) temperature dependence above (below) a threshold temperature. In order to understand the temperature effects of electron transport theoretically, we study a two-dimensional and four-channel DNA model using a tight-binding (TB) Hamiltonian. The thermal effects within a TB model are incorporated into the hopping integral and the relative twist angle from its equilibrium value between base-pairs. Since these thermal structural fluctuations localize the electronic wave functions in DNA, we examine a temperature-dependent localization length, a temperature-driven transmission, and current-voltage characteristics in this system. In addition, we incorporate magnetic field effects into the analysis of the transmission through DNA in order to modulate the quantum interference between the electron paths that comprise the 4-channel structure. [1] P. Tran, B. Alavi, and G. Gruner, PRL 85, 1564 (2000).

Chloride ions induce order-disorder transition at water-oxide interfaces

NASA Astrophysics Data System (ADS)

Deshmukh, Sanket; Kamath, Ganesh; Ramanathan, Shriram; Sankaranarayanan, Subramanian K. R. S.

2013-12-01

Water can form quasi-two-dimensional ordered layers near a solid interface. The solvation dynamics and ionic transport phenomena through this ordered water structure is of direct relevance to a variety of problems in interface science. Molecular dynamics simulations are used to study the impact of local fluctuation of the chloride ion density in the vicinity of an oxide surface on the structure and dynamics of water layers. We demonstrate that local increase in chloride ions beyond a threshold concentration near the water-MgO (100) interface introduces an order-disorder transition of this two-dimensional layered network into bulklike water, leading to increased diffusional characteristics and reduced hydrogen bonding lifetimes. We find that the extent of this order-disorder transition can be tuned by modifying the defect chemistry and nature of the underlying substrate. The kinetic fluidity resulting from order-disorder transition at high chloride ion concentration has significance for a broad range of phenomena, ranging from freezing point depression of brine to onset of aqueous corrosion.

Spin-reorientation transitions in the Cairo pentagonal magnet Bi 4 Fe 5 O 13 F

DOE PAGES

Tsirlin, Alexander A.; Rousochatzakis, Ioannis; Filimonov, Dmitry; ...

2017-09-19

Here, we show that interlayer spins play a dual role in the Cairo pentagonal magnet Bi 4Fe 5O 13F, on one hand mediating the three-dimensional magnetic order, and on the other driving spin-reorientation transitions both within and between the planes. The corresponding sequence of magnetic orders unraveled by neutron diffraction and Mössbauer spectroscopy features two orthogonal magnetic structures described by opposite local vector chiralities, and an intermediate, partly disordered phase with nearly collinear spins. A similar collinear phase has been predicted theoretically to be stabilized by quantum fluctuations, but Bi 4Fe 5O 13F is very far from the relevant parametermore » regime. While the observed in-plane reorientation cannot be explained by any standard frustration mechanism, our ab initio band-structure calculations reveal strong single-ion anisotropy of the interlayer Fe 3+ spins that turns out to be instrumental in controlling the local vector chirality and the associated interlayer order.« less

Spin-reorientation transitions in the Cairo pentagonal magnet Bi4Fe5O13F

NASA Astrophysics Data System (ADS)

Tsirlin, Alexander A.; Rousochatzakis, Ioannis; Filimonov, Dmitry; Batuk, Dmitry; Frontzek, Matthias; Abakumov, Artem M.

2017-09-01

We show that interlayer spins play a dual role in the Cairo pentagonal magnet Bi4Fe5O13F , on one hand mediating the three-dimensional magnetic order, and on the other driving spin-reorientation transitions both within and between the planes. The corresponding sequence of magnetic orders unraveled by neutron diffraction and Mössbauer spectroscopy features two orthogonal magnetic structures described by opposite local vector chiralities, and an intermediate, partly disordered phase with nearly collinear spins. A similar collinear phase has been predicted theoretically to be stabilized by quantum fluctuations, but Bi4Fe5O13F is very far from the relevant parameter regime. While the observed in-plane reorientation cannot be explained by any standard frustration mechanism, our ab initio band-structure calculations reveal strong single-ion anisotropy of the interlayer Fe3 + spins that turns out to be instrumental in controlling the local vector chirality and the associated interlayer order.

Hotspots of Community Change: Temporal Dynamics Are Spatially Variable in Understory Plant Composition of a California Oak Woodland

PubMed Central

Spotswood, Erica N.; Bartolome, James W.; Allen-Diaz, Barbara

2015-01-01

Community response to external drivers such climate and disturbance can lead to fluctuations in community composition, or to directional change. Temporal dynamics can be influenced by a combination of drivers operating at multiple spatial scales, including external landscape scale drivers, local abiotic conditions, and local species pools. We hypothesized that spatial variation in these factors can create heterogeneity in temporal dynamics within landscapes. We used understory plant species composition from an 11 year dataset from a California oak woodland to compare plots where disturbance was experimentally manipulated with the removal of livestock grazing and a prescribed burn. We quantified three properties of temporal variation: compositional change (reflecting the appearance and disappearance of species), temporal fluctuation, and directional change. Directional change was related most strongly to disturbance type, and was highest at plots where grazing was removed during the study. Temporal fluctuations, compositional change, and directional change were all related to intrinsic abiotic factors, suggesting that some locations are more responsive to external drivers than others. Temporal fluctuations and compositional change were linked to local functional composition, indicating that environmental filters can create subsets of the local species pool that do not respond in the same way to external drivers. Temporal dynamics are often assumed to be relatively static at the landscape scale, provided disturbance and climate are continuous. This study shows that local and landscape scale factors jointly influence temporal dynamics creating hotspots that are particularly responsive to climate and disturbance. Thus, adequate predictions of response to disturbance or to changing climate will only be achieved by considering how factors at multiple spatial scales influence community resilience and recovery. PMID:26222069

Hotspots of Community Change: Temporal Dynamics Are Spatially Variable in Understory Plant Composition of a California Oak Woodland.

PubMed

Spotswood, Erica N; Bartolome, James W; Allen-Diaz, Barbara

2015-01-01

Community response to external drivers such climate and disturbance can lead to fluctuations in community composition, or to directional change. Temporal dynamics can be influenced by a combination of drivers operating at multiple spatial scales, including external landscape scale drivers, local abiotic conditions, and local species pools. We hypothesized that spatial variation in these factors can create heterogeneity in temporal dynamics within landscapes. We used understory plant species composition from an 11 year dataset from a California oak woodland to compare plots where disturbance was experimentally manipulated with the removal of livestock grazing and a prescribed burn. We quantified three properties of temporal variation: compositional change (reflecting the appearance and disappearance of species), temporal fluctuation, and directional change. Directional change was related most strongly to disturbance type, and was highest at plots where grazing was removed during the study. Temporal fluctuations, compositional change, and directional change were all related to intrinsic abiotic factors, suggesting that some locations are more responsive to external drivers than others. Temporal fluctuations and compositional change were linked to local functional composition, indicating that environmental filters can create subsets of the local species pool that do not respond in the same way to external drivers. Temporal dynamics are often assumed to be relatively static at the landscape scale, provided disturbance and climate are continuous. This study shows that local and landscape scale factors jointly influence temporal dynamics creating hotspots that are particularly responsive to climate and disturbance. Thus, adequate predictions of response to disturbance or to changing climate will only be achieved by considering how factors at multiple spatial scales influence community resilience and recovery.

Calculation of the Curie temperature of Ni using first principles based Wang-Landau Monte-Carlo

NASA Astrophysics Data System (ADS)

Eisenbach, Markus; Yin, Junqi; Li, Ying Wai; Nicholson, Don

2015-03-01

We combine constrained first principles density functional with a Wang-Landau Monte Carlo algorithm to calculate the Curie temperature of Ni. Mapping the magnetic interactions in Ni onto a Heisenberg like model to underestimates the Curie temperature. Using a model we show that the addition of the magnitude of the local magnetic moments can account for the difference in the calculated Curie temperature. For ab initio calculations, we have extended our Locally Selfconsistent Multiple Scattering (LSMS) code to constrain the magnitude of the local moments in addition to their direction and apply the Replica Exchange Wang-Landau method to sample the larger phase space efficiently to investigate Ni where the fluctuation in the magnitude of the local magnetic moments is of importance equal to their directional fluctuations. We will present our results for Ni where we compare calculations that consider only the moment directions and those including fluctuations of the magnetic moment magnitude on the Curie temperature. This research was sponsored by the Department of Energy, Offices of Basic Energy Science and Advanced Computing. We used Oak Ridge Leadership Computing Facility resources at Oak Ridge National Laboratory, supported by US DOE under contract DE-AC05-00OR22725.

Pressure response of protein backbone structure. Pressure-induced amide 15N chemical shifts in BPTI.

PubMed Central

Akasaka, K.; Li, H.; Yamada, H.; Li, R.; Thoresen, T.; Woodward, C. K.

1999-01-01

The effect of pressure on amide 15N chemical shifts was studied in uniformly 15N-labeled basic pancreatic trypsin inhibitor (BPTI) in 90%1H2O/10%2H2O, pH 4.6, by 1H-15N heteronuclear correlation spectroscopy between 1 and 2,000 bar. Most 15N signals were low field shifted linearly and reversibly with pressure (0.468 +/- 0.285 ppm/2 kbar), indicating that the entire polypeptide backbone structure is sensitive to pressure. A significant variation of shifts among different amide groups (0-1.5 ppm/2 kbar) indicates a heterogeneous response throughout within the three-dimensional structure of the protein. A tendency toward low field shifts is correlated with a decrease in hydrogen bond distance on the order of 0.03 A/2 kbar for the bond between the amide nitrogen atom and the oxygen atom of either carbonyl or water. The variation of 15N shifts is considered to reflect site-specific changes in phi, psi angles. For beta-sheet residues, a decrease in psi angles by 1-2 degrees/2 kbar is estimated. On average, shifts are larger for helical and loop regions (0.553 +/- 0.343 and 0.519 +/- 0.261 ppm/2 kbar, respectively) than for beta-sheet (0.295 +/- 0.195 ppm/2 kbar), suggesting that the pressure-induced structural changes (local compressibilities) are larger in helical and loop regions than in beta-sheet. Because compressibility is correlated with volume fluctuation, the result is taken to indicate that the volume fluctuation is larger in helical and loop regions than in beta-sheet. An important aspect of the volume fluctuation inferred from pressure shifts is that they include motions in slower time ranges (less than milliseconds) in which many biological processes may take place. PMID:10548039

Impact of Alloy Fluctuations on Radiative and Auger Recombination in InGaN Quantum Wells

NASA Astrophysics Data System (ADS)

Jones, Christina; Teng, Chu-Hsiang; Yan, Qimin; Ku, Pei-Cheng; Kioupakis, Emmanouil

Light-emitting diodes (LEDs) based on indium gallium nitride (InGaN) are important for efficient solid-state lighting (2014 Nobel Prize in Physics). Despite its many successes, InGaN suffers from issues that reduce the efficiency of devices at high power, such as the green gap and efficiency droop. The origin of the droop has been attributed to Auger recombination, mediated by carrier scattering due to phonons and alloy disorder. Additionally, InGaN exhibits atomic-scale composition fluctuations that localize carriers and may affect the efficiency. In this work, we study the effect of local composition fluctuations on the radiative recombination rate, Auger recombination rate, and efficiency of InGaN/GaN quantum wells. We apply k.p calculations to simulate band edges and wave functions of quantum wells with fluctuating alloy distributions based on atom probe tomography data, and we evaluate double and triple overlaps of electron and hole wave functions. We compare results for quantum wells with fluctuating alloy distributions to those with uniform alloy compositions and to published work. Our results demonstrate that alloy-composition fluctuations aggravate the efficiency-droop and green-gap problems and further reduce LED efficiency at high power. We acknowledge the NSF CAREER award DMR-1254314, the NSF Graduate Research Fellowship Program DGE-1256260, and the DOE NERSC facility (DE-AC02-05CH11231).

Highly localized, fully 3-D disruptions of the reconnection layer in the Magnetic Reconnection Experiment

NASA Astrophysics Data System (ADS)

Dorfman, Seth

2011-10-01

Magnetic reconnection is a fundamental process in plasmas which converts magnetic energy to plasma kinetic and thermal energy through topological changes. One of the important goals in magnetic reconnection research is to explain the fast reconnection rate observed in real three-dimensional laboratory and astrophysical systems. In the Magnetic Reconnection Experiment (MRX), an enhancement of the reconnection electric field is often associated with a wholesale disruption of the reconnection current layer, an intrinsically 3-D phenomena observed in the presence of out-of-plane gradients of local quantities such as reconnection layer current and density. During a disruption, the out-of-plane current decreases as current carrying electrons are redirected in the outflow direction. Observed ``O-point'' signatures and density striations suggest that this redirection often occurs though the ejection of 3-D flux rope structures. Large fluctuations in the lower hybrid frequency range are also routinely seen, but the ratio of the phase speed to the diamagnetic drift speed does not match what is predicted by 3-D kinetic simulations without disruptions. A 2-D Hall MHD analysis of the out-of-plane gradients is consistent with the buildup of magnetic energy leading to the event, but variation in all three spacial dimensions is required in order to obtain results in agreement with the disruptive behavior observed. Analysis and comparison with 3-D simulations is ongoing to determine if the fluctuations and/or disruptive behavior are responsible for the corresponding discrepancies in the layer structure between the experiments and 2-D kinetic simulations,,. Supported by DOE, NASA, and NSF.

Computing physical properties with quantum Monte Carlo methods with statistical fluctuations independent of system size.

PubMed

Assaraf, Roland

2014-12-01

We show that the recently proposed correlated sampling without reweighting procedure extends the locality (asymptotic independence of the system size) of a physical property to the statistical fluctuations of its estimator. This makes the approach potentially vastly more efficient for computing space-localized properties in large systems compared with standard correlated methods. A proof is given for a large collection of noninteracting fragments. Calculations on hydrogen chains suggest that this behavior holds not only for systems displaying short-range correlations, but also for systems with long-range correlations.

Synchronisation and stability in river metapopulation networks.

PubMed

Yeakel, J D; Moore, J W; Guimarães, P R; de Aguiar, M A M

2014-03-01

Spatial structure in landscapes impacts population stability. Two linked components of stability have large consequences for persistence: first, statistical stability as the lack of temporal fluctuations; second, synchronisation as an aspect of dynamic stability, which erodes metapopulation rescue effects. Here, we determine the influence of river network structure on the stability of riverine metapopulations. We introduce an approach that converts river networks to metapopulation networks, and analytically show how fluctuation magnitude is influenced by interaction structure. We show that river metapopulation complexity (in terms of branching prevalence) has nonlinear dampening effects on population fluctuations, and can also buffer against synchronisation. We conclude by showing that river transects generally increase synchronisation, while the spatial scale of interaction has nonlinear effects on synchronised dynamics. Our results indicate that this dual stability - conferred by fluctuation and synchronisation dampening - emerges from interaction structure in rivers, and this may strongly influence the persistence of river metapopulations. © 2013 John Wiley & Sons Ltd/CNRS.

Dynamic nuclear polarization methods in solids and solutions to explore membrane proteins and membrane systems.

PubMed

Cheng, Chi-Yuan; Han, Songi

2013-01-01

Membrane proteins regulate vital cellular processes, including signaling, ion transport, and vesicular trafficking. Obtaining experimental access to their structures, conformational fluctuations, orientations, locations, and hydration in membrane environments, as well as the lipid membrane properties, is critical to understanding their functions. Dynamic nuclear polarization (DNP) of frozen solids can dramatically boost the sensitivity of current solid-state nuclear magnetic resonance tools to enhance access to membrane protein structures in native membrane environments. Overhauser DNP in the solution state can map out the local and site-specific hydration dynamics landscape of membrane proteins and lipid membranes, critically complementing the structural and dynamics information obtained by electron paramagnetic resonance spectroscopy. Here, we provide an overview of how DNP methods in solids and solutions can significantly increase our understanding of membrane protein structures, dynamics, functions, and hydration in complex biological membrane environments.

Unmasking the masked Universe: the 2M++ catalogue through Bayesian eyes

NASA Astrophysics Data System (ADS)

Lavaux, Guilhem; Jasche, Jens

2016-01-01

This work describes a full Bayesian analysis of the Nearby Universe as traced by galaxies of the 2M++ survey. The analysis is run in two sequential steps. The first step self-consistently derives the luminosity-dependent galaxy biases, the power spectrum of matter fluctuations and matter density fields within a Gaussian statistic approximation. The second step makes a detailed analysis of the three-dimensional large-scale structures, assuming a fixed bias model and a fixed cosmology. This second step allows for the reconstruction of both the final density field and the initial conditions at z = 1000 assuming a fixed bias model. From these, we derive fields that self-consistently extrapolate the observed large-scale structures. We give two examples of these extrapolation and their utility for the detection of structures: the visibility of the Sloan Great Wall, and the detection and characterization of the Local Void using DIVA, a Lagrangian based technique to classify structures.

Large-scale fluctuations in the diffusive decomposition of solid solutions

NASA Astrophysics Data System (ADS)

Karpov, V. G.; Grimsditch, M.

1995-04-01

The concept of an instability in the classic Ostwald ripening theory with respect to compositional fluctuations is suggested. We show that small statistical fluctuations in the precipitate phase lead to gigantic Coulomb-like fluctuations in the solute concentration which in turn affect the ripening. As a result large-scale fluctuations in both the precipitate and solute concentrations appear. These fluctuations are characterized by amplitudes of the order of the average values of the corresponding quantities and by a space scale L~(na)-1/2 which is considerably greater than both the average nuclear radius and internuclear distance. The Lifshitz-Slyozov theory of ripening is shown to remain locally applicable, over length scales much less than L. The implications of these findings for elastic light scattering in solid solutions that have undergone Ostwald ripening are considered.

Traffic jams induced by fluctuation of a leading car.

PubMed

Nagatani, T

2000-04-01

We present a phase diagram of the different kinds of congested traffic triggered by fluctuation of a leading car in an open system without sources and sinks. Traffic states and density waves are investigated numerically by varying the amplitude of fluctuation using a car following model. The phase transitions among the free traffic, oscillatory congested traffic, and homogeneous congested traffic occur by fluctuation of a leading car. With increasing the amplitude of fluctuation, the transition between the free traffic and oscillatory traffic occurs at lower density and the transition between the homogeneous congested traffic and the oscillatory traffic occurs at higher density. The oscillatory congested traffic corresponds to the coexisting phase. Also, the moving localized clusters appear just above the transition lines.

High-mobility strained organic semiconductors (Conference Presentation)

NASA Astrophysics Data System (ADS)

Takeya, Jun; Matsui, H.; Kubo, T.; Hausermann, Roger

2016-11-01

Small molecular organic semiconductor crystals form interesting electronic systems of periodically arranged "charge clouds" whose mutual electronic coupling determines whether or not electronic states can be coherent over fluctuating molecules. This presentation focuses on two methods to reduce molecular fluctuation, which strongly restricts mobility of highly mobile charge in single-crystal organic transistors. The first example is to apply external hydrostatic pressure. Using Hall-effect measurement for pentacene FETs, which tells us the extent of the electronic coherence, we found a crossover from hopping-like transport of nearly localized charge to band transport of delocalized charge with full coherence. As the result of temperature dependence measurement, it turned out that reduced molecular fluctuation is mainly responsible for the crossover. The second is to apply uniaxial strain to single-crystal organic FETs. We applied stain by bending thin films of newly synthesized decyldinaphthobenzodithiophene (C10-DNBDT) on plastic substrate so that 3% strain is uniaxially applied. As the result, the room-temperature mobility increased by the factor of 1.7. In-depth analysis using X-ray diffraction (XRD) measurements and density functional theory (DFT) calculations reveal the origin to be the suppression of the thermal fluctuation of the individual molecules, which is confirmed by temperature dependent measurements. Our findings show that compressing the crystal structure directly restricts the vibration of the molecules, thus suppressing dynamic disorder, a unique mechanism in organic semiconductors. Since strain can easily be induced during the fabrication process, these findings can directly be exploited to build high performance organic devices.

Brain hyperthermia and temperature fluctuations during sexual interaction in female rats.

PubMed

Mitchum, Robert D; Kiyatkin, Eugene A

2004-03-12

Since the metabolic activity of neural cells is accompanied by heat release, brain temperature monitoring provides insight into behavior-associated changes in neural activity. In the present study, local temperatures were continuously recorded in several brain structures (nucleus accumbens, medial-preoptic hypothalamus and hippocampus) and a non-locomotor head muscle (musculus temporalis) in a receptive female rat during sexually arousing stimulation and subsequent copulatory behavior with an experienced male. Placement of the male into a neighboring compartment increased the female's temperature (approximately 0.8 degrees C) and additional, transient increases (approximately 0.2 degrees C) occurred when the rats were allowed to see and smell each other through a transparent barrier. Temperatures gradually increased further as the male repeatedly mounted and achieved intromissions, peaked 2-3 min after male's ejaculation (0.2-0.4 degrees C), and abruptly dropped until the male initiated a new copulatory cycle. Similar biphasic fluctuations accompanied subsequent copulatory cycles. Although both arousal-related temperature increases and biphasic fluctuations associated with copulatory cycles were evident in each recording location, brain sites showed consistently faster and stronger increases than the muscle, suggesting metabolic brain activation as the primary source of brain temperature fluctuations and a force behind associated changes in brain temperature. Robust brain hyperthermia and the generally similar pattern of phasic temperature fluctuations associated with individual events of sexual interaction found in males and females suggest widespread neural activation (motivational arousal) as a driving force underlying this cooperative motivated behavior in animals of both sexes. Females, however, showed different temperature changes in association with the initial (first mount or intromission) and final (ejaculation) events of each copulatory cycle, suggesting sex-specific differences in neural activity associated with the initiation and regulation of sexual behavior.

NMR structural and dynamic characterization of the acid-unfolded state of apomyoglobin provides insights into the early events in protein folding.

PubMed

Yao, J; Chung, J; Eliezer, D; Wright, P E; Dyson, H J

2001-03-27

Apomyoglobin forms a denatured state under low-salt conditions at pH 2.3. The conformational propensities and polypeptide backbone dynamics of this state have been characterized by NMR. Nearly complete backbone and some side chain resonance assignments have been obtained, using a triple-resonance assignment strategy tailored to low protein concentration (0.2 mM) and poor chemical shift dispersion. An estimate of the population and location of residual secondary structure has been made by examining deviations of (13)C(alpha), (13)CO, and (1)H(alpha) chemical shifts from random coil values, scalar (3)J(HN,H)(alpha) coupling constants and (1)H-(1)H NOEs. Chemical shifts constitute a highly reliable indicator of secondary structural preferences, provided the appropriate random coil chemical shift references are used, but in the case of acid-unfolded apomyoglobin, (3)J(HN,H)(alpha) coupling constants are poor diagnostics of secondary structure formation. Substantial populations of helical structure, in dynamic equilibrium with unfolded states, are formed in regions corresponding to the A and H helices of the folded protein. In addition, the deviation of the chemical shifts from random coil values indicates the presence of helical structure encompassing the D helix and extending into the first turn of the E helix. The polypeptide backbone dynamics of acid-unfolded apomyoglobin have been investigated using reduced spectral density function analysis of (15)N relaxation data. The spectral density J(omega(N)) is particularly sensitive to variations in backbone fluctuations on the picosecond to nanosecond time scale. The central region of the polypeptide spanning the C-terminal half of the E helix, the EF turn, and the F helix behaves as a free-flight random coil chain, but there is evidence from J(omega(N)) of restricted motions on the picosecond to nanosecond time scale in the A and H helix regions where there is a propensity to populate helical secondary structure in the acid-unfolded state. Backbone fluctuations are also restricted in parts of the B and G helices due to formation of local hydrophobic clusters. Regions of restricted backbone flexibility are generally associated with large buried surface area. A significant increase in J(0) is observed for the NH resonances of some residues located in the A and G helices of the folded protein and is associated with fluctuations on a microsecond to millisecond time scale that probably arise from transient contacts between these distant regions of the polypeptide chain. Our results indicate that the equilibrium unfolded state of apomyoglobin formed at pH 2.3 is an excellent model for the events that are expected to occur in the earliest stages of protein folding, providing insights into the regions of the polypeptide that spontaneously undergo local hydrophobic collapse and sample nativelike secondary structure.

Data processing in neutron protein crystallography using positron-sensitive detectors

NASA Astrophysics Data System (ADS)

Schoenborn, B. P.

Neutrons provide a unique probe for localizing hydrogen atoms and for distinguishing hydrogen from deuterons. Hydrogen atoms largely determine the three dimensional structure of proteins and are responsible for many catalytic reactions. The study of hydrogen bonding and hydrogen exchange will therefore give insight into reaction mechanisms and conformational fluctuations. In addition, neutrons provide the ability to distinguish N from C and O and to allow correct orientation of groups such as histidine and glutamine. To take advantage of these unique features of neutron crystallography, one needs accurate Fourier maps depicting atomic structure to a high precision. Special attention is given to subtraction of the high background associated with hydrogen containing molecules, which produces a disproportionately large statistical error.

Optimized unconventional superconductivity in a molecular Jahn-Teller metal

PubMed Central

Zadik, Ruth H.; Takabayashi, Yasuhiro; Klupp, Gyöngyi; Colman, Ross H.; Ganin, Alexey Y.; Potočnik, Anton; Jeglič, Peter; Arčon, Denis; Matus, Péter; Kamarás, Katalin; Kasahara, Yuichi; Iwasa, Yoshihiro; Fitch, Andrew N.; Ohishi, Yasuo; Garbarino, Gaston; Kato, Kenichi; Rosseinsky, Matthew J.; Prassides, Kosmas

2015-01-01

Understanding the relationship between the superconducting, the neighboring insulating, and the normal metallic state above Tc is a major challenge for all unconventional superconductors. The molecular A3C60 fulleride superconductors have a parent antiferromagnetic insulator in common with the atom-based cuprates, but here, the C603– electronic structure controls the geometry and spin state of the structural building unit via the on-molecule Jahn-Teller effect. We identify the Jahn-Teller metal as a fluctuating microscopically heterogeneous coexistence of both localized Jahn-Teller–active and itinerant electrons that connects the insulating and superconducting states of fullerides. The balance between these molecular and extended lattice features of the electrons at the Fermi level gives a dome-shaped variation of Tc with interfulleride separation, demonstrating molecular electronic structure control of superconductivity. PMID:26601168

Stress-stress fluctuation formula for elastic constants in the NPT ensemble

NASA Astrophysics Data System (ADS)

Lips, Dominik; Maass, Philipp

2018-05-01

Several fluctuation formulas are available for calculating elastic constants from equilibrium correlation functions in computer simulations, but the ones available for simulations at constant pressure exhibit slow convergence properties and cannot be used for the determination of local elastic constants. To overcome these drawbacks, we derive a stress-stress fluctuation formula in the NPT ensemble based on known expressions in the NVT ensemble. We validate the formula in the NPT ensemble by calculating elastic constants for the simple nearest-neighbor Lennard-Jones crystal and by comparing the results with those obtained in the NVT ensemble. For both local and bulk elastic constants we find an excellent agreement between the simulated data in the two ensembles. To demonstrate the usefulness of the formula, we apply it to determine the elastic constants of a simulated lipid bilayer.

Meteor localization via statistical analysis of spatially temporal fluctuations in image sequences

NASA Astrophysics Data System (ADS)

Kukal, Jaromír.; Klimt, Martin; Šihlík, Jan; Fliegel, Karel

2015-09-01

Meteor detection is one of the most important procedures in astronomical imaging. Meteor path in Earth's atmosphere is traditionally reconstructed from double station video observation system generating 2D image sequences. However, the atmospheric turbulence and other factors cause spatially-temporal fluctuations of image background, which makes the localization of meteor path more difficult. Our approach is based on nonlinear preprocessing of image intensity using Box-Cox and logarithmic transform as its particular case. The transformed image sequences are then differentiated along discrete coordinates to obtain statistical description of sky background fluctuations, which can be modeled by multivariate normal distribution. After verification and hypothesis testing, we use the statistical model for outlier detection. Meanwhile the isolated outlier points are ignored, the compact cluster of outliers indicates the presence of meteoroids after ignition.

Extreme concentration fluctuations due to local reversibility of mixing in turbulent flows

NASA Astrophysics Data System (ADS)

Xia, Hua; Francois, Nicolas; Punzmann, Horst; Szewc, Kamil; Shats, Michael

2018-05-01

Mixing of a passive scalar in a fluid (e.g. a radioactive spill in the ocean) is the irreversible process towards homogeneous distribution of a substance. In a moving fluid, due to the chaotic advection [H. Aref, J. Fluid Mech. 143 (1984) 1; J. M. Ottino, The Kinematics of Mixing: Stretching,Chaos and Transport (Cambridge University Press, Cambridge, 1989)] mixing is much faster than if driven by molecular diffusion only. Turbulence is known as the most efficient mixing flow [B. I. Shraiman and E. D. Siggia, Nature 405 (2000) 639]. We show that in contrast to spatially periodic flows, two-dimensional turbulence exhibits local reversibility in mixing, which leads to the generation of unpredictable strong fluctuations in the scalar concentration. These fluctuations can also be detected from the analysis of the fluid particle trajectories of the underlying flow.

Functional connectivity arises from a slow rhythmic mechanism

PubMed Central

Li, Jingfeng M.; Bentley, William J.; Snyder, Lawrence H.

2015-01-01

The mechanism underlying temporal correlations among blood oxygen level-dependent signals is unclear. We used oxygen polarography to better characterize oxygen fluctuations and their correlation and to gain insight into the driving mechanism. The power spectrum of local oxygen fluctuations is inversely proportional to frequency raised to a power (1/f) raised to the beta, with an additional positive band-limited component centered at 0.06 Hz. In contrast, the power of the correlated oxygen signal is band limited from ∼0.01 Hz to 0.4 Hz with a peak at 0.06 Hz. These results suggest that there is a band-limited mechanism (or mechanisms) driving interregional oxygen correlation that is distinct from the mechanism(s) driving local (1/f) oxygen fluctuations. Candidates for driving interregional oxygen correlation include rhythmic or pseudo-oscillatory mechanisms. PMID:25918427

Effect of Oxide Interface Roughness on the Threshold Voltage Fluctuations in Decanano MOSFETs with Ultrathin Gate Oxides

NASA Technical Reports Server (NTRS)

Asenov, Asen; Kaya, S.

2000-01-01

In this paper we use the Density Gradient (DG) simulation approach to study, in 3-D, the effect of local oxide thickness fluctuations on the threshold voltage of decanano MOSFETs on a statistical scale. The random 2-D surfaces used to represent the interface are constructed using the standard assumptions for the auto-correlation function of the interface. The importance of the Quantum Mechanical effects when studying oxide thickness fluctuations are illustrated in several simulation examples.

Superconductivity in disordered thin films: giant mesoscopic fluctuations.

PubMed

Skvortsov, M A; Feigel'man, M V

2005-07-29

We discuss the intrinsic inhomogeneities of superconductive properties of uniformly disordered thin films with a large dimensionless conductance g. It is shown that mesoscopic fluctuations, which usually contain a small factor 1/g, are crucially enhanced near the critical conductance g(cF) > 1 where superconductivity is destroyed at T = 0 due to Coulomb suppression of the Cooper attraction. This leads to strong spatial fluctuations of the local transition temperature and thus to the percolative nature of the thermal superconductive transition.

Large-Scale Structure and Hyperuniformity of Amorphous Ices

NASA Astrophysics Data System (ADS)

Martelli, Fausto; Torquato, Salvatore; Giovambattista, Nicolas; Car, Roberto

2017-09-01

We investigate the large-scale structure of amorphous ices and transitions between their different forms by quantifying their large-scale density fluctuations. Specifically, we simulate the isothermal compression of low-density amorphous ice (LDA) and hexagonal ice to produce high-density amorphous ice (HDA). Both HDA and LDA are nearly hyperuniform; i.e., they are characterized by an anomalous suppression of large-scale density fluctuations. By contrast, in correspondence with the nonequilibrium phase transitions to HDA, the presence of structural heterogeneities strongly suppresses the hyperuniformity and the system becomes hyposurficial (devoid of "surface-area fluctuations"). Our investigation challenges the largely accepted "frozen-liquid" picture, which views glasses as structurally arrested liquids. Beyond implications for water, our findings enrich our understanding of pressure-induced structural transformations in glasses.

The Influence of Ca2+ Buffers on Free [Ca2+] Fluctuations and the Effective Volume of Ca2+ Microdomains

PubMed Central

Weinberg, Seth H.; Smith, Gregory D.

2014-01-01

Intracellular calcium (Ca2+) plays a significant role in many cell signaling pathways, some of which are localized to spatially restricted microdomains. Ca2+ binding proteins (Ca2+ buffers) play an important role in regulating Ca2+ concentration ([Ca2+]). Buffers typically slow [Ca2+] temporal dynamics and increase the effective volume of Ca2+ domains. Because fluctuations in [Ca2+] decrease in proportion to the square-root of a domain’s physical volume, one might conjecture that buffers decrease [Ca2+] fluctuations and, consequently, mitigate the significance of small domain volume concerning Ca2+ signaling. We test this hypothesis through mathematical and computational analysis of idealized buffer-containing domains and their stochastic dynamics during free Ca2+ influx with passive exchange of both Ca2+ and buffer with bulk concentrations. We derive Langevin equations for the fluctuating dynamics of Ca2+ and buffer and use these stochastic differential equations to determine the magnitude of [Ca2+] fluctuations for different buffer parameters (e.g., dissociation constant and concentration). In marked contrast to expectations based on a naive application of the principle of effective volume as employed in deterministic models of Ca2+ signaling, we find that mobile and rapid buffers typically increase the magnitude of domain [Ca2+] fluctuations during periods of Ca2+ influx, whereas stationary (immobile) Ca2+ buffers do not. Also contrary to expectations, we find that in the absence of Ca2+ influx, buffers influence the temporal characteristics, but not the magnitude, of [Ca2+] fluctuations. We derive an analytical formula describing the influence of rapid Ca2+ buffers on [Ca2+] fluctuations and, importantly, identify the stochastic analog of (deterministic) effective domain volume. Our results demonstrate that Ca2+ buffers alter the dynamics of [Ca2+] fluctuations in a nonintuitive manner. The finding that Ca2+ buffers do not suppress intrinsic domain [Ca2+] fluctuations raises the intriguing question of whether or not [Ca2+] fluctuations are a physiologically significant aspect of local Ca2+ signaling. PMID:24940787

The influence of Ca²⁺ buffers on free [Ca²⁺] fluctuations and the effective volume of Ca²⁺ microdomains.

PubMed

Weinberg, Seth H; Smith, Gregory D

2014-06-17

Intracellular calcium (Ca(2+)) plays a significant role in many cell signaling pathways, some of which are localized to spatially restricted microdomains. Ca(2+) binding proteins (Ca(2+) buffers) play an important role in regulating Ca(2+) concentration ([Ca(2+)]). Buffers typically slow [Ca(2+)] temporal dynamics and increase the effective volume of Ca(2+) domains. Because fluctuations in [Ca(2+)] decrease in proportion to the square-root of a domain's physical volume, one might conjecture that buffers decrease [Ca(2+)] fluctuations and, consequently, mitigate the significance of small domain volume concerning Ca(2+) signaling. We test this hypothesis through mathematical and computational analysis of idealized buffer-containing domains and their stochastic dynamics during free Ca(2+) influx with passive exchange of both Ca(2+) and buffer with bulk concentrations. We derive Langevin equations for the fluctuating dynamics of Ca(2+) and buffer and use these stochastic differential equations to determine the magnitude of [Ca(2+)] fluctuations for different buffer parameters (e.g., dissociation constant and concentration). In marked contrast to expectations based on a naive application of the principle of effective volume as employed in deterministic models of Ca(2+) signaling, we find that mobile and rapid buffers typically increase the magnitude of domain [Ca(2+)] fluctuations during periods of Ca(2+) influx, whereas stationary (immobile) Ca(2+) buffers do not. Also contrary to expectations, we find that in the absence of Ca(2+) influx, buffers influence the temporal characteristics, but not the magnitude, of [Ca(2+)] fluctuations. We derive an analytical formula describing the influence of rapid Ca(2+) buffers on [Ca(2+)] fluctuations and, importantly, identify the stochastic analog of (deterministic) effective domain volume. Our results demonstrate that Ca(2+) buffers alter the dynamics of [Ca(2+)] fluctuations in a nonintuitive manner. The finding that Ca(2+) buffers do not suppress intrinsic domain [Ca(2+)] fluctuations raises the intriguing question of whether or not [Ca(2+)] fluctuations are a physiologically significant aspect of local Ca(2+) signaling. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Global financial crisis making a V-shaped fluctuation in NO2 pollution over the Yangtze River Delta

NASA Astrophysics Data System (ADS)

Du, Yin; Xie, Zhiqing

2017-04-01

The Yangtze River Delta (YRD), China's main cultural and economic center, has become one of the most seriously polluted areas in the world with respect to nitrogen oxides (NOx), owing to its rapid industrialization and urbanization, as well as substantial coal consumption. On the basis of nitrogen dioxide (NO2) density data from ozone monitoring instrument (OMI) and ground-based observations, the effects of industrial fluctuations due to the financial crisis on local NO2 pollution were quantitatively assessed. The results were as follows. (1) A distinct V-shaped fluctuation of major industrial products, thermal generating capacity, electricity consumption, and tropospheric NO2 densities was associated with the global financial crisis from May 2007 to December 2009, with the largest anomalies 1.5 times more than standard deviations at the height of the crisis period from November 2008 to February 2009. (2) Among all industrial sectors, thermal power plants were mainly responsible for fluctuations in local NO2 pollution during the crisis period. Thermal generating capacity had its greatest decrease of 12.10% at the height of the crisis compared with that during November 2007-February 2008, leading to local tropospheric NO2 density decreasing by 16.97%. As the crisis appeased, thermal generating capacity increased by 29.63% from November 2009 to February 2010, and tropospheric NO2 densities correspondingly increased by 30.07%. (3) Among all industrial sectors in the YRD, the thermal power sector has the greatest coal consumption of about 65.96%. A decline in thermal power of about 10% can induce a decrease of about 30% in NOx emissions and NO2 densities, meaning that a relative small fluctuation in industrial production can lead to a large decrease in tropospheric NO2 densities over industrially developed areas like the YRD region. Since electricity is mainly obtained from local coal-burning thermal plants without NOx-processing equipment, installing NOx-removal devices for all thermal power plants is an important and feasible way of controlling local NOx pollution at present.

Analysis of Tide and Offshore Storm-Induced Water Table Fluctuations for Structural Characterization of a Coastal Island Aquifer

NASA Astrophysics Data System (ADS)

Trglavcnik, Victoria; Morrow, Dean; Weber, Kela P.; Li, Ling; Robinson, Clare E.

2018-04-01

Analysis of water table fluctuations can provide important insight into the hydraulic properties and structure of a coastal aquifer system including the connectivity between the aquifer and ocean. This study presents an improved approach for characterizing a permeable heterogeneous coastal aquifer system through analysis of the propagation of the tidal signal, as well as offshore storm pulse signals through a coastal aquifer. Offshore storms produce high wave activity, but are not necessarily linked to significant onshore precipitation. In this study, we focused on offshore storm events during which no onshore precipitation occurred. Extensive groundwater level data collected on a sand barrier island (Sable Island, NS, Canada) show nonuniform discontinuous propagation of the tide and offshore storm pulse signals through the aquifer with isolated inland areas showing enhanced response to both oceanic forcing signals. Propagation analysis suggests that isolated inland water table fluctuations may be caused by localized leakage from a confined aquifer that is connected to the ocean offshore but within the wave setup zone. Two-dimensional groundwater flow simulations were conducted to test the leaky confined-unconfined aquifer conceptualization and to identify the effect of key parameters on tidal signal propagation in leaky confined-unconfined coastal aquifers. This study illustrates that analysis of offshore storm signal propagation, in addition to tidal signal propagation, provides a valuable and low resource approach for large-scale characterization of permeable heterogeneous coastal aquifers. Such an approach is needed for the effective management of coastal environments where water resources are threatened by human activities and the changing climate.

A Bayesian Estimate of the CMB-Large-scale Structure Cross-correlation

NASA Astrophysics Data System (ADS)

Moura-Santos, E.; Carvalho, F. C.; Penna-Lima, M.; Novaes, C. P.; Wuensche, C. A.

2016-08-01

Evidences for late-time acceleration of the universe are provided by multiple probes, such as Type Ia supernovae, the cosmic microwave background (CMB), and large-scale structure (LSS). In this work, we focus on the integrated Sachs-Wolfe (ISW) effect, I.e., secondary CMB fluctuations generated by evolving gravitational potentials due to the transition between, e.g., the matter and dark energy (DE) dominated phases. Therefore, assuming a flat universe, DE properties can be inferred from ISW detections. We present a Bayesian approach to compute the CMB-LSS cross-correlation signal. The method is based on the estimate of the likelihood for measuring a combined set consisting of a CMB temperature and galaxy contrast maps, provided that we have some information on the statistical properties of the fluctuations affecting these maps. The likelihood is estimated by a sampling algorithm, therefore avoiding the computationally demanding techniques of direct evaluation in either pixel or harmonic space. As local tracers of the matter distribution at large scales, we used the Two Micron All Sky Survey galaxy catalog and, for the CMB temperature fluctuations, the ninth-year data release of the Wilkinson Microwave Anisotropy Probe (WMAP9). The results show a dominance of cosmic variance over the weak recovered signal, due mainly to the shallowness of the catalog used, with systematics associated with the sampling algorithm playing a secondary role as sources of uncertainty. When combined with other complementary probes, the method presented in this paper is expected to be a useful tool to late-time acceleration studies in cosmology.

Predicting Real-Valued Protein Residue Fluctuation Using FlexPred.

PubMed

Peterson, Lenna; Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2017-01-01

The conventional view of a protein structure as static provides only a limited picture. There is increasing evidence that protein dynamics are often vital to protein function including interaction with partners such as other proteins, nucleic acids, and small molecules. Considering flexibility is also important in applications such as computational protein docking and protein design. While residue flexibility is partially indicated by experimental measures such as the B-factor from X-ray crystallography and ensemble fluctuation from nuclear magnetic resonance (NMR) spectroscopy as well as computational molecular dynamics (MD) simulation, these techniques are resource-intensive. In this chapter, we describe the web server and stand-alone version of FlexPred, which rapidly predicts absolute per-residue fluctuation from a three-dimensional protein structure. On a set of 592 nonredundant structures, comparing the fluctuations predicted by FlexPred to the observed fluctuations in MD simulations showed an average correlation coefficient of 0.669 and an average root mean square error of 1.07 Å. FlexPred is available at http://kiharalab.org/flexPred/ .

Electronic structure and magnetic properties of dilute U impurities in metals

NASA Astrophysics Data System (ADS)

Mohanta, S. K.; Cottenier, S.; Mishra, S. N.

2016-05-01

The electronic structure and magnetic moment of dilute U impurity in metallic hosts have been calculated from first principles. The calculations have been performed within local density approximation of the density functional theory using Augmented plane wave+local orbital (APW+lo) technique, taking account of spin-orbit coupling and Coulomb correlation through LDA+U approach. We present here our results for the local density of states, magnetic moment and hyperfine field calculated for an isolated U impurity embedded in hosts with sp-, d- and f-type conduction electrons. The results of our systematic study provide a comprehensive insight on the pressure dependence of 5f local magnetism in metallic systems. The unpolarized local density of states (LDOS), analyzed within the frame work of Stoner model suggest the occurrence of local moment for U in sp-elements, noble metals and f-block hosts like La, Ce, Lu and Th. In contrast, U is predicted to be nonmagnetic in most transition metal hosts except in Sc, Ti, Y, Zr, and Hf consistent with the results obtained from spin polarized calculation. The spin and orbital magnetic moments of U computed within the frame of LDA+U formalism show a scaling behavior with lattice compression. We have also computed the spin and orbital hyperfine fields and a detail analysis has been carried out. The host dependent trends for the magnetic moment, hyperfine field and 5f occupation reflect pressure induced change of electronic structure with U valency changing from 3+ to 4+ under lattice compression. In addition, we have made a detailed analysis of the impurity induced host spin polarization suggesting qualitatively different roles of f-band electrons on moment stability. The results presented in this work would be helpful towards understanding magnetism and spin fluctuation in U based alloys.

Development of a cross-polarization scattering system for the measurement of internal magnetic fluctuations in the DIII-D tokamak

DOE PAGES

Rhodes, Terry L.; Peebles, William A.; Crocker, Neal A.; ...

2014-08-05

The design and performance of a new cross-polarization scattering (CPS) system for the localized measurement of internal magnetic fluctuations is presented. CPS is a process whereby magnetic fluctuations scatter incident electromagnetic radiation into a perpendicular polarization which is subsequently detected. A new CPS design that incorporates a unique scattering geometry was laboratory tested, optimized, and installed on the DIII-D tokamak. Plasma tests of signal-to-noise, polarization purity, and frequency response indicate proper functioning of the system. Lastly, CPS data show interesting features related to internal MHD perturbations known as sawteeth that are not observed on density fluctuations.

Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly.

PubMed

Hanski, Ilkka A

2011-08-30

Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time.

Spectral structure and linear mechanisms in a 'rapidly' distorted boundary layer

NASA Astrophysics Data System (ADS)

Diwan, Sourabh; Morrison, Jonathan

2016-11-01

A characteristic feature of a turbulent boundary layer (TBL) at high Reynolds numbers is the presence of coherent motions such as the 'large scale motions' and 'superstructures'. In this work we attempt to mimic such coherent motions and their spectral structure using a simplified experimental arrangement of a boundary layer flow over a flat plate subjected to grid-generated turbulence and/or localized patch of surface roughness. The velocity measurements done downstream of a grit roughness patch (in absence of grid turbulence) show that over a certain distance the energy spectrum of streamwise velocity fluctuations shows a bi-modal shape which resembles that found in a high-Re TBL. We also carry out experiments with both grid turbulence and grit roughness present and show that it is possible to 'synthesize' the structure of a TBL in the wall-normal direction, in the limited context of streamwise coherent motions, using the present experimental design. These results indicate that the predictions of the Rapid Distortion Theory (RDT) can be applied to the present case in a region close to the plate leading edge, and we examine the linearized effects of 'blocking' and 'shear' on turbulent fluctuations near the edge of the boundary layer and close to the wall in the framework of the RDT. We acknowledge financial support from EPSRC (Grant No. EP/1037938).

Effects of energetic coherent motions on the power and wake of an axial-flow turbine

NASA Astrophysics Data System (ADS)

Chamorro, L. P.; Hill, C.; Neary, V. S.; Gunawan, B.; Arndt, R. E. A.; Sotiropoulos, F.

2015-05-01

A laboratory experiment examined the effects of energetic coherent motions on the structure of the wake and power fluctuations generated by a model axial-flow hydrokinetic turbine. The model turbine was placed in an open-channel flow and operated under subcritical conditions. The incoming flow was locally perturbed with vertically oriented cylinders of various diameters. An array of three acoustic Doppler velocimeters aligned in the cross-stream direction and a torque transducer were used to collect high-resolution and synchronous measurements of the three-velocity components of the incoming and wake flow as well as the turbine power. A strong scale-to-scale interaction between the large-scale and broadband turbulence shed by the cylinders and the turbine power revealed how the turbulence structure modulates the turbine behavior. In particular, the response of the turbine to the distinctive von Kármán-type vortices shed from the cylinders highlighted this phenomenon. The mean and fluctuating characteristics of the turbine wake are shown to be very sensitive to the energetic motions present in the flow. Tip vortices were substantially dampened and the near-field mean wake recovery accelerated in the presence of energetic motions in the flow. Strong coherent motions are shown to be more effective than turbulence levels for triggering the break-up of the spiral structure of the tip-vortices.

Vibrational spectroscopic determination of local solvent electric field, solute-solvent electrostatic interaction energy, and their fluctuation amplitudes.

PubMed

Lee, Hochan; Lee, Gayeon; Jeon, Jonggu; Cho, Minhaeng

2012-01-12

IR probes have been extensively used to monitor local electrostatic and solvation dynamics. Particularly, their vibrational frequencies are highly sensitive to local solvent electric field around an IR probe. Here, we show that the experimentally measured vibrational frequency shifts can be inversely used to determine local electric potential distribution and solute-solvent electrostatic interaction energy. In addition, the upper limits of their fluctuation amplitudes are estimated by using the vibrational bandwidths. Applying this method to fully deuterated N-methylacetamide (NMA) in D(2)O and examining the solvatochromic effects on the amide I' and II' mode frequencies, we found that the solvent electric potential difference between O(═C) and D(-N) atoms of the peptide bond is about 5.4 V, and thus, the approximate solvent electric field produced by surrounding water molecules on the NMA is 172 MV/cm on average if the molecular geometry is taken into account. The solute-solvent electrostatic interaction energy is estimated to be -137 kJ/mol, by considering electric dipole-electric field interaction. Furthermore, their root-mean-square fluctuation amplitudes are as large as 1.6 V, 52 MV/cm, and 41 kJ/mol, respectively. We found that the water electric potential on a peptide bond is spatially nonhomogeneous and that the fluctuation in the electrostatic peptide-water interaction energy is about 10 times larger than the thermal energy at room temperature. This indicates that the peptide-solvent interactions are indeed important for the activation of chemical reactions in aqueous solution.

Protein stability and dynamics influenced by ligands in extremophilic complexes - a molecular dynamics investigation.

PubMed

Khan, Sara; Farooq, Umar; Kurnikova, Maria

2017-08-22

In this study, we explore the structural and dynamic adaptations of the Tryptophan synthase α-subunit in a ligand bound state in psychrophilic, mesophilic and hyperthermophilic organisms at different temperatures by MD simulations. We quantify the global and local fluctuations in the 40 ns time scale by analyzing the root mean square deviation/fluctuations. The distinct behavior of the active site and loop 6 is observed with the elevation of temperature. Protein stability relies more on electrostatic interactions, and these interactions might be responsible for the stability of varying temperature evolved proteins. The paper also focuses on the effect of temperature on protein dynamics and stability governed by the distinct behavior of the ligand associated with its retention, binding and dissociation over the course of time. The integration of principle component analysis and a free energy landscape was useful in identifying the conformational space accessible to ligand bound homologues and how the presence of the ligand alters the conformational and dynamic properties of the protein.

Dynamically fluctuating electric dipole moments in fullerene-based magnets.

PubMed

Kambe, Takashi; Oshima, Kokichi

2014-09-19

We report here the direct evidence of the existence of a permanent electric dipole moment in both crystal phases of a fullerene-based magnet--the ferromagnetic α-phase and the antiferromagnetic α'-phase of tetra-kis-(dimethylamino)-ethylene-C60 (TDAE-C60)--as determined by dielectric measurements. We propose that the permanent electric dipole originates from the pairing of a TDAE molecule with surrounding C60 molecules. The two polymorphs exhibit clear differences in their dielectric responses at room temperature and during the freezing process with dynamically fluctuating electric dipole moments, although no difference in their room-temperature structures has been previously observed. This result implies that two polymorphs have different local environment around the molecules. In particular, the ferromagnetism of the α-phase is founded on the homogeneous molecule displacement and orientational ordering. The formation of the different phases with respect to the different rotational states in the Jahn-Teller distorted C60s is also discussed.

Dynamically fluctuating electric dipole moments in fullerene-based magnets

PubMed Central

Kambe, Takashi; Oshima, Kokichi

2014-01-01

We report here the direct evidence of the existence of a permanent electric dipole moment in both crystal phases of a fullerene-based magnet—the ferromagnetic α-phase and the antiferromagnetic α′-phase of tetra-kis-(dimethylamino)-ethylene-C60 (TDAE-C60)—as determined by dielectric measurements. We propose that the permanent electric dipole originates from the pairing of a TDAE molecule with surrounding C60 molecules. The two polymorphs exhibit clear differences in their dielectric responses at room temperature and during the freezing process with dynamically fluctuating electric dipole moments, although no difference in their room-temperature structures has been previously observed. This result implies that two polymorphs have different local environment around the molecules. In particular, the ferromagnetism of the α-phase is founded on the homogeneous molecule displacement and orientational ordering. The formation of the different phases with respect to the different rotational states in the Jahn–Teller distorted C60s is also discussed. PMID:25236361

Thermal fluctuations and elastic relaxation in the compressed exponential dynamics of colloidal gels

NASA Astrophysics Data System (ADS)

Bouzid, Mehdi; Colombo, Jader; Del Gado, Emanuela

Colloidal gels belong to the class of amorphous systems, they are disordered elastic solids that can form at very low volume fraction, via aggregation into a rich variety of networks. They exhibit a slow relaxation process in the aging regime similar to the glassy dynamics. A wide range of experiments on colloidal gels show unusual compressed exponential of the relaxation dynamical properties. We use molecular dynamics simulation to investigate how the dynamic change with the age of the system. Upon breaking and reorganization of the network structure, the system may display stretched or compressed exponential relaxation. We show that the transition between these two regimes is associated to the interplay between thermally activated rearrangements and the elastic relaxation of internal stresses. In particular, ballistic-like displacements emerge from the non local relaxation of internal stresses mediated by a series of ''micro-collapses''. When thermal fluctuations dominate, the gel restructuring involves instead more homogeneous displacements across the heterogeneous gel network, leading to a stretched exponential type of relaxation.

Dissipation of Turbulence in the Solar Wind as Measured by Cluster

NASA Technical Reports Server (NTRS)

Goldstein, Melvyn

2012-01-01

Turbulence in fluids and plasmas is a scale-dependent process that generates fluctuations towards ever-smaller scales until dissipation occurs. Recent Cluster observations in the solar wind demonstrate the existence of a cascade of magnetic energy from the scale of the proton Larmor radius, where kinetic properties of ions invalidate fluid approximations, down to the electron Larmor radius, where electrons become demagnetized. The cascade is quasi-two-dimensional and has been interpreted as consisting of highly oblique kinetic Alfvenic fluctuations that dissipate near at the electron gyroradius scale via proton and electron Landau damping. Here we investigate for the first time the spatial properties of the turbulence at these scales. We report the presence of thin current sheets and discontinuities with spatial sizes greater than or approximately equal to the proton Larmor radius. These isolated structures may be manifestations of intermittency, and such would localize sites of turbulent dissipation. Studying the relationship between turbulent dissipation, reconnection and intermittency is crucial for understanding the dynamics of laboratory and astrophysical plasmas.

Measuring and comparing structural fluctuation patterns in large protein datasets.

PubMed

Fuglebakk, Edvin; Echave, Julián; Reuter, Nathalie

2012-10-01

The function of a protein depends not only on its structure but also on its dynamics. This is at the basis of a large body of experimental and theoretical work on protein dynamics. Further insight into the dynamics-function relationship can be gained by studying the evolutionary divergence of protein motions. To investigate this, we need appropriate comparative dynamics methods. The most used dynamical similarity score is the correlation between the root mean square fluctuations (RMSF) of aligned residues. Despite its usefulness, RMSF is in general less evolutionarily conserved than the native structure. A fundamental issue is whether RMSF is not as conserved as structure because dynamics is less conserved or because RMSF is not the best property to use to study its conservation. We performed a systematic assessment of several scores that quantify the (dis)similarity between protein fluctuation patterns. We show that the best scores perform as well as or better than structural dissimilarity, as assessed by their consistency with the SCOP classification. We conclude that to uncover the full extent of the evolutionary conservation of protein fluctuation patterns, it is important to measure the directions of fluctuations and their correlations between sites. Nathalie.Reuter@mbi.uib.no Supplementary data are available at Bioinformatics Online.

Small Modifications to Network Topology Can Induce Stochastic Bistable Spiking Dynamics in a Balanced Cortical Model

PubMed Central

McDonnell, Mark D.; Ward, Lawrence M.

2014-01-01

Abstract Directed random graph models frequently are used successfully in modeling the population dynamics of networks of cortical neurons connected by chemical synapses. Experimental results consistently reveal that neuronal network topology is complex, however, in the sense that it differs statistically from a random network, and differs for classes of neurons that are physiologically different. This suggests that complex network models whose subnetworks have distinct topological structure may be a useful, and more biologically realistic, alternative to random networks. Here we demonstrate that the balanced excitation and inhibition frequently observed in small cortical regions can transiently disappear in otherwise standard neuronal-scale models of fluctuation-driven dynamics, solely because the random network topology was replaced by a complex clustered one, whilst not changing the in-degree of any neurons. In this network, a small subset of cells whose inhibition comes only from outside their local cluster are the cause of bistable population dynamics, where different clusters of these cells irregularly switch back and forth from a sparsely firing state to a highly active state. Transitions to the highly active state occur when a cluster of these cells spikes sufficiently often to cause strong unbalanced positive feedback to each other. Transitions back to the sparsely firing state rely on occasional large fluctuations in the amount of non-local inhibition received. Neurons in the model are homogeneous in their intrinsic dynamics and in-degrees, but differ in the abundance of various directed feedback motifs in which they participate. Our findings suggest that (i) models and simulations should take into account complex structure that varies for neuron and synapse classes; (ii) differences in the dynamics of neurons with similar intrinsic properties may be caused by their membership in distinctive local networks; (iii) it is important to identify neurons that share physiological properties and location, but differ in their connectivity. PMID:24743633

Influence of a depletion interaction on dynamical heterogeneity in a dense quasi-two-dimensional colloid liquid.

PubMed

Ho, Hau My; Cui, Bianxiao; Repel, Stephen; Lin, Binhua; Rice, Stuart A

2004-11-01

We report the results of digital video microscopy studies of the large particle displacements in a quasi-two-dimensional binary mixture of large (L) and small (S) colloid particles with diameter ratio sigma(L)/sigma(S)=4.65, as a function of the large and small colloid particle densities. As in the case of the one-component quasi-two-dimensional colloid system, the binary mixtures exhibit structural and dynamical heterogeneity. The distribution of large particle displacements over the time scale examined provides evidence for (at least) two different mechanisms of motion, one associated with particles in locally ordered regions and the other associated with particles in locally disordered regions. When rhoL*=Npisigma(L) (2)/4A< or =0.35, the addition of small colloid particles leads to a monotonic decrease in the large particle diffusion coefficient with increasing small particle volume fraction. When rhoL* > or =0.35 the addition of small colloid particles to a dense system of large colloid particles at first leads to an increase in the large particle diffusion coefficient, which is then followed by the expected decrease of the large particle diffusion coefficient with increasing small colloid particle volume fraction. The mode coupling theory of the ideal glass transition in three-dimensional systems makes a qualitative prediction that agrees with the initial increase in the large particle diffusion coefficient with increasing small particle density. Nevertheless, because the structural and dynamical heterogeneities of the quasi-two-dimensional colloid liquid occur within the field of equilibrium states, and the fluctuations generate locally ordered domains rather than just disordered regions of higher and lower density, it is suggested that mode coupling theory does not account for all classes of relevant fluctuations in a quasi-two-dimensional liquid. (c) 2004 American Institute of Physics.

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.

EUCLIA—Exploring the UV/Optical Continuum Lag in Active Galactic Nuclei. I. A Model without Light Echoing

NASA Astrophysics Data System (ADS)

Cai, Zhen-Yi; Wang, Jun-Xian; Zhu, Fei-Fan; Sun, Mou-Yuan; Gu, Wei-Min; Cao, Xin-Wu; Yuan, Feng

2018-03-01

The tight interband correlation and the lag–wavelength relation among UV/optical continua of active galactic nuclei have been firmly established. They are usually understood within the widespread reprocessing scenario; however, the implied interband lags are generally too small. Furthermore, it is challenged by new evidence, such as that the X-ray reprocessing yields too much high-frequency UV/optical variation and that it fails to reproduce the observed timescale-dependent color variations among the Swift light curves of NGC 5548. In a different manner, we demonstrate that an upgraded inhomogeneous accretion disk model, whose local independent temperature fluctuations are subject to a speculated common large-scale temperature fluctuation, can intrinsically generate the tight interband correlation and lag across the UV/optical and be in nice agreement with several observational properties of NGC 5548, including the timescale-dependent color variation. The emergent lag is a result of the differential regression capability of local temperature fluctuations when responding to the large-scale fluctuation. An average speed of propagations as large as ≳15% of the speed of light may be required by this common fluctuation. Several potential physical mechanisms for such propagations are discussed. Our interesting phenomenological scenario may shed new light on comprehending the UV/optical continuum variations of active galactic nuclei.

Bridging stylized facts in finance and data non-stationarities

NASA Astrophysics Data System (ADS)

Camargo, Sabrina; Duarte Queirós, Sílvio M.; Anteneodo, Celia

2013-04-01

Employing a recent technique which allows the representation of nonstationary data by means of a juxtaposition of locally stationary paths of different length, we introduce a comprehensive analysis of the key observables in a financial market: the trading volume and the price fluctuations. From the segmentation procedure we are able to introduce a quantitative description of statistical features of these two quantities, which are often named stylized facts, namely the tails of the distribution of trading volume and price fluctuations and a dynamics compatible with the U-shaped profile of the volume in a trading section and the slow decay of the autocorrelation function. The segmentation of the trading volume series provides evidence of slow evolution of the fluctuating parameters of each patch, pointing to the mixing scenario. Assuming that long-term features are the outcome of a statistical mixture of simple local forms, we test and compare different probability density functions to provide the long-term distribution of the trading volume, concluding that the log-normal gives the best agreement with the empirical distribution. Moreover, the segmentation of the magnitude price fluctuations are quite different from the results for the trading volume, indicating that changes in the statistics of price fluctuations occur at a faster scale than in the case of trading volume.

Noise and degradation of amorphous silicon devices

NASA Astrophysics Data System (ADS)

Bakker, J. P. R.

2003-10-01

Electrical noise measurements are reported on two devices of the disordered semiconductor hydrogenated amorphous silicon (a-Si:H). The material is applied in sandwich structures and in thin-film transistors (TFTs). In a sandwich configuration of an intrinsic layer and two thin doped layers, the observed 1/f resistance noise can be attributed to a distribution of energy levels in the system. Two candidates which eventually could explain the origin of the energy distribution are investigated: generation-recombination noise and long-range potential fluctuations. A simulation program was applied to fit the current-voltage characteristics and resolves the defect density, the energy position and width of the Gaussian distributions of deep defects. Generation-recombination (g-r) is calculated for a one-dimensional semiconductor device with traps, taking the transport of local fluctuations into account. Although the times characterizing capture and emission for deep defects are in the right (ms) range, the calculated noise intensity is five to six orders of magnitude below the measured noise level. Another noise source must cause the 1/f noise in a-Si:H. The alternative is provided by the theory of long-range potential fluctuations. The timescale of the fluctuations is again the capture or emission time for deep defects. When an electron is emitted or captured, the charge state of a deep defect fluctuates. As a result, the potential around that defect will fluctuate, being screened by the surrounding defects. Free electrons will instantaneously adjust to the local potential. The adjustment causes a resistance fluctuation, which is measured as a voltage fluctuation in presence of a constant current. The theory predicts the noise intensity accurately, without any adjustable parameters. Unlike the intensity, the spectral shape is fitted by adjustment of two parameters of the potential landscape. The complete temperature dependence of the noise spectra is consistently described by a Gaussian distribution of potential barriers, located 0.27 eV above the conduction band edge, with a halfwidth of 0.09 eV. A large number of experiments is explained by the theory of long-range potential fluctuations: the thickness dependence, the absence of an isotope effect and the analogous results for oppositely doped devices. From these experiments, it is concluded that a universal potential landscape exists in undoped a-Si:H. Further, the relation between degradation upon prolonged light-soaking and noise is studied. After degradation, the curvature of noise spectra is unaffected, while the intensity increases slightly. These observations are consistent with the theoretical predictions using the observed increase of the defect density. It seems that the potential landscape does not change significantly upon degradation. Noise measurements in the sub-threshold regime of a-Si:H TFTs turn out to yield diffusion noise. Diffusion of electrons through the one-dimensional channel is identified as the source of the noise. The drift mobility extracted from the combined noise and conduction data is below the value that characterizes the on-state. The number of free electrons as determined from combined noise and conduction measurements are in quantitative agreement with an alternative determination from conduction measurements only.

Local, global, and nonlinear screening in twisted double-layer graphene

DOE PAGES

Lu, Chih -Pin; Rodriguez-Vega, Martin; Li, Guohong; ...

2016-06-02

One-atom-thick crystalline layers and their vertical heterostructures carry the promise of designer electronic materials that are unattainable by standard growth techniques. To realize their potential it is necessary to isolate them from environmental disturbances, in particular those introduced by the substrate. However, finding and characterizing suitable substrates, and minimizing the random potential fluctuations they introduce, has been a persistent challenge in this emerging field. In this paper, we show that Landau-level (LL) spectroscopy offers the unique capability to quantify both the reduction of the quasiparticles’ lifetime and the long-range inhomogeneity due to random potential fluctuations. Harnessing this technique together withmore » direct scanning tunneling microscopy and numerical simulations we demonstrate that the insertion of a graphene buffer layer with a large twist angle is a very effective method to shield a 2D system from substrate interference that has the additional desirable property of preserving the electronic structure of the system under study. Finally, we further show that owing to its remarkable nonlinear screening capability a single graphene buffer layer provides better shielding than either increasing the distance to the substrate or doubling the carrier density and reduces the amplitude of the potential fluctuations in graphene to values even lower than the ones in AB-stacked bilayer graphene.« less

Local, global, and nonlinear screening in twisted double-layer graphene

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

Lu, Chih -Pin; Rodriguez-Vega, Martin; Li, Guohong

One-atom-thick crystalline layers and their vertical heterostructures carry the promise of designer electronic materials that are unattainable by standard growth techniques. To realize their potential it is necessary to isolate them from environmental disturbances, in particular those introduced by the substrate. However, finding and characterizing suitable substrates, and minimizing the random potential fluctuations they introduce, has been a persistent challenge in this emerging field. In this paper, we show that Landau-level (LL) spectroscopy offers the unique capability to quantify both the reduction of the quasiparticles’ lifetime and the long-range inhomogeneity due to random potential fluctuations. Harnessing this technique together withmore » direct scanning tunneling microscopy and numerical simulations we demonstrate that the insertion of a graphene buffer layer with a large twist angle is a very effective method to shield a 2D system from substrate interference that has the additional desirable property of preserving the electronic structure of the system under study. Finally, we further show that owing to its remarkable nonlinear screening capability a single graphene buffer layer provides better shielding than either increasing the distance to the substrate or doubling the carrier density and reduces the amplitude of the potential fluctuations in graphene to values even lower than the ones in AB-stacked bilayer graphene.« less

Resolving the fine-scale structure in turbulent Rayleigh-Bénard convection

NASA Astrophysics Data System (ADS)

Scheel, Janet D.; Emran, Mohammad S.; Schumacher, Jörg

2013-11-01

We present high-resolution direct numerical simulation studies of turbulent Rayleigh-Bénard convection in a closed cylindrical cell with an aspect ratio of one. The focus of our analysis is on the finest scales of convective turbulence, in particular the statistics of the kinetic energy and thermal dissipation rates in the bulk and the whole cell. The fluctuations of the energy dissipation field can directly be translated into a fluctuating local dissipation scale which is found to develop ever finer fluctuations with increasing Rayleigh number. The range of these scales as well as the probability of high-amplitude dissipation events decreases with increasing Prandtl number. In addition, we examine the joint statistics of the two dissipation fields and the consequences of high-amplitude events. We have also investigated the convergence properties of our spectral element method and have found that both dissipation fields are very sensitive to insufficient resolution. We demonstrate that global transport properties, such as the Nusselt number, and the energy balances are partly insensitive to insufficient resolution and yield correct results even when the dissipation fields are under-resolved. Our present numerical framework is also compared with high-resolution simulations which use a finite difference method. For most of the compared quantities the agreement is found to be satisfactory.

Proteins with similar architecture exhibit similar large-scale dynamic behavior.

PubMed Central

Keskin, O; Jernigan, R L; Bahar, I

2000-01-01

We have investigated the similarities and differences in the computed dynamic fluctuations exhibited by six members of a protein fold family with a coarse-grained Gaussian network model. Specifically, we consider the cofactor binding fragment of CysB; the lysine/arginine/ornithine-binding protein (LAO); the enzyme porphobilinogen deaminase (PBGD); the ribose-binding protein (RBP); the N-terminal lobe of ovotransferrin in apo-form (apo-OVOT); and the leucine/isoleucine/valine-binding protein (LIVBP). All have domains that resemble a Rossmann fold, but there are also some significant differences. Results indicate that similar global dynamic behavior is preserved for the members of a fold family, and that differences usually occur in regions only where specific function is localized. The present work is a computational demonstration that the scaffold of a protein fold may be utilized for diverse purposes. LAO requires a bound ligand before it conforms to the large-scale fluctuation behavior of the three other members of the family, CysB, PBGD, and RBP, all of which contain a substrate (cofactor) at the active site cleft. The dynamics of the ligand-free enzymes LIVBP and apo-OVOT, on the other hand, concur with that of unliganded LAO. The present results suggest that it is possible to construct structure alignments based on dynamic fluctuation behavior. PMID:10733987

Empirical Modeling of the Statistical Structure of Radio Signals from Satellites Moving over Mid- and High-Latitude Trajectories in the Southern Hemisphere

NASA Astrophysics Data System (ADS)

Fatkullin, M. N.; Solodovnikov, G. K.; Trubitsyn, V. M.

2004-01-01

The results of developing the empirical model of parameters of radio signals propagating in the inhomogeneous ionosphere at middle and high latitudes are presented. As the initial data we took the homogeneous data obtained as a result of observations carried out at the Antarctic ``Molodezhnaya'' station by the method of continuous transmission probing of the ionosphere by signals of the satellite radionavigation ``Transit'' system at coherent frequencies of 150 and 400 MHz. The data relate to the summer season period in the Southern hemisphere of the Earth in 1988-1989 during high (F > 160) activity of the Sun. The behavior of the following statistical characteristics of radio signal parameters was analyzed: (a) the interval of correlation of fluctuations of amplitudes at a frequency of 150 MHz (τkA) (b) the interval of correlation of fluctuations of the difference phase (τkϕ) and (c) the parameter characterizing frequency spectra of amplitude (PA) and phase (Pϕ) fluctuations. A third-degree polynomial was used for modeling of propagation parameters. For all above indicated propagation parameters, the coefficients of the third-degree polynomial were calculated as a function of local time and magnetic activity. The results of calculations are tabulated.

Evaluation of the local homogeneity fluctuation of sinter of the small chip size MLCCs by means of mid-infrared spectroscopy

NASA Astrophysics Data System (ADS)

Tsuzuku, Koichiro; Hagiwara, Tomoya; Takeoka, Shunsuke; Ikemoto, Yuka

2008-05-01

Vibration bands of dielectric ceramics appear at a mid-infrared (MIR) and those position and shape are changed owing to change environment of crystal lattice. Therefore, micro-focus MIR spectroscopy is a one of useful tool to evaluate very small size capacitor (e.g. smaller than 0.5 mm in chip size). Very small size multi-layer capacitor: MLCC are one of very important device to produce high quality electrical products such as cell phone, etc. Quality and reliability of MLCC are corresponding to not only average dielectric properties but also local fluctuation of them. Furthermore, local fluctuation of dielectric properties of MLCC could evaluate with MIR spectroscopy. It is possible to obtain a satisfied MIR spectrum from small size samples performed by a micro-focus spectrometer combined with synchrotron radiation as a high luminance light source at beam line BL43IR of SPring-8. From the above result, it is possible to evaluate the degree of homogeneity by comparing the shape change of Ti-O peak on IR spectra.

Edge localized mode characteristics during edge localized mode mitigation by supersonic molecular beam injection in Korea Superconducting Tokamak Advanced Research

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

Lee, H. Y.; Hong, J. H.; Jang, J. H.

It has been reported that supersonic molecular beam injection (SMBI) is an effective means of edge localized mode (ELM) mitigation. This paper newly reports the changes in the ELM, plasma profiles, and fluctuation characteristics during ELM mitigation by SMBI in Korea Superconducting Tokamak Advanced Research. During the mitigated ELM phase, the ELM frequency increased by a factor of 2–3 and the ELM size, which was estimated from the D{sub α} amplitude, the fractional changes in the plasma-stored energy and the line-averaged electron density, and divertor heat flux during an ELM burst, decreased by a factor of 0.34–0.43. Reductions in themore » electron and ion temperatures rather than in the electron density were observed during the mitigated ELM phase. In the natural ELM phase, frequency chirping of the plasma fluctuations was observed before the ELM bursts; however, the ELM bursts occurred without changes in the plasma fluctuation frequency in the mitigated ELM phase.« less

Units of analysis and kinetic structure of behavioral repertoires

PubMed Central

Thompson, Travis; Lubinski, David

1986-01-01

It is suggested that molar streams of behavior are constructed of various arrangements of three elementary constituents (elicited, evoked, and emitted response classes). An eight-cell taxonomy is elaborated as a framework for analyzing and synthesizing complex behavioral repertoires based on these functional units. It is proposed that the local force binding functional units into a smoothly articulated kinetic sequence arises from temporally arranged relative response probability relationships. Behavioral integration is thought to reflect the joint influence of the organism's hierarchy of relative response probabilities, fluctuating biological states, and the arrangement of environmental and behavioral events in time. PMID:16812461

The statistics of primordial density fluctuations

NASA Astrophysics Data System (ADS)

Barrow, John D.; Coles, Peter

1990-05-01

The statistical properties of the density fluctuations produced by power-law inflation are investigated. It is found that, even the fluctuations present in the scalar field driving the inflation are Gaussian, the resulting density perturbations need not be, due to stochastic variations in the Hubble parameter. All the moments of the density fluctuations are calculated, and is is argued that, for realistic parameter choices, the departures from Gaussian statistics are small and would have a negligible effect on the large-scale structure produced in the model. On the other hand, the model predicts a power spectrum with n not equal to 1, and this could be good news for large-scale structure.

Evidence for pressure-tuned quantum structural fluctuations in KCuF3

NASA Astrophysics Data System (ADS)

Yuan, S.; Kim, M.; Seeley, J.; Lal, S.; Abbamonte, P.; Cooper, S. L.

2012-02-01

Frustrated magnetic systems are currently of great interest because of the possibility that these materials exhibit novel ground states such as orbital and spin liquids. We provide evidence in the orbital-ordering material KCuF3 for pressure-tuned quantum melting of a static structural phase to a phase that dynamically fluctuates even near T ˜ 0K.[1] Pressure-dependent Raman scattering measurements show that applied pressure above P* ˜ 7kbar reverses a low temperature structural distortion in KCuF3, resulting in the development of a φ ˜ 0 fluctuational (quasielastic) response near T ˜ 0K. This pressure-induced fluctuational response is temperature independent and exhibits a characteristic fluctuation rate that is much larger than the temperature, γ >> KBT, consistent with quantum fluctuations of the CuF6 octahedra. We show that a previous developed model of pseudospin-phonon coupling qualitatively describes both the temperature- and pressure-dependent evolution of the Raman spectra of KCuF3. Work supported by the U.S. Department of Energy under Award No. DE-FG02-07ER46453 and by the National Science Foundation under Grant NSF DMR 08-56321. [4pt] [1] S. Yuan et al., arXiv:1107.1433 (2011).

Ion heating and short wavelength fluctuations in a helicon plasma source

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

Scime, E. E.; Carr, J. Jr.; Galante, M.

2013-03-15

For typical helicon source parameters, the driving antenna can couple to two plasma modes; the weakly damped 'helicon' wave, and the strongly damped, short wavelength, slow wave. Here, we present direct measurements, obtained with two different techniques, of few hundred kHz, short wavelength fluctuations that are parametrically driven by the primary antenna and localized to the edge of the plasma. The short wavelength fluctuations appear for plasma source parameters such that the driving frequency is approximately equal to the lower hybrid frequency. Measurements of the steady-state ion temperature and fluctuation amplitude radial profiles suggest that the anomalously high ion temperaturesmore » observed at the edge of helicon sources result from damping of the short wavelength fluctuations. Additional measurements of the time evolution of the ion temperature and fluctuation profiles in pulsed helicon source plasmas support the same conclusion.« less

Sensitivity of polarization fluctuations to the nature of protein-water interactions: Study of biological water in four different protein-water systems

NASA Astrophysics Data System (ADS)

Ghosh, Rikhia; Banerjee, Saikat; Hazra, Milan; Roy, Susmita; Bagchi, Biman

2014-12-01

Since the time of Kirkwood, observed deviations in magnitude of the dielectric constant of aqueous protein solution from that of neat water (˜80) and slower decay of polarization have been subjects of enormous interest, controversy, and debate. Most of the common proteins have large permanent dipole moments (often more than 100 D) that can influence structure and dynamics of even distant water molecules, thereby affecting collective polarization fluctuation of the solution, which in turn can significantly alter solution's dielectric constant. Therefore, distance dependence of polarization fluctuation can provide important insight into the nature of biological water. We explore these aspects by studying aqueous solutions of four different proteins of different characteristics and varying sizes, chicken villin headpiece subdomain (HP-36), immunoglobulin binding domain protein G (GB1), hen-egg white lysozyme (LYS), and Myoglobin (MYO). We simulate fairly large systems consisting of single protein molecule and 20000-30000 water molecules (varied according to the protein size), providing a concentration in the range of ˜2-3 mM. We find that the calculated dielectric constant of the system shows a noticeable increment in all the cases compared to that of neat water. Total dipole moment auto time correlation function of water ⟨δMW(0)δMW(t)⟩ is found to be sensitive to the nature of the protein. Surprisingly, dipole moment of the protein and total dipole moment of the water molecules are found to be only weakly coupled. Shellwise decomposition of water molecules around protein reveals higher density of first layer compared to the succeeding ones. We also calculate heuristic effective dielectric constant of successive layers and find that the layer adjacent to protein has much lower value (˜50). However, progressive layers exhibit successive increment of dielectric constant, finally reaching a value close to that of bulk 4-5 layers away. We also calculate shellwise orientational correlation function and tetrahedral order parameter to understand the local dynamics and structural re-arrangement of water. Theoretical analysis providing simple method for calculation of shellwise local dielectric constant and implication of these findings are elaborately discussed in the present work.

CXB surface brightness fluctuations: A new frontier of ICM structure and outskirts studies of (un)resolved galaxy clusters?

NASA Astrophysics Data System (ADS)

Kolodzig, A.; Gilfanov, M.; Hutsi, G.; Sunyaev, R.

2017-10-01

Surface brightness fluctuations of the cosmic X-ray background (CXB) carry unique information about the intracluster-medium (ICM) structure of galaxy clusters and groups up to the virial radius, which is inaccessible by conventional observations of selected nearby resolved clusters. We present results of our CXB fluctuation analysis of the ˜5ks-deep, ˜9deg^2-large Chandra survey XBOOTES. We find that our fluctuation signal of resolved clusters is dominated by nearby, high-luminosity sources. The shape of its power spectrum suggests that for the brightest cluster we are sensitive to the ICM structure up to ˜2× R_{500};(˜2 Mpc/h). The energy spectrum of the fluctuation signal from resolved and unresolved clusters follows a typical ICM spectrum, where redshifts and temperatures are consistent with expectations. It also demonstrates that fluctuations of our unresolved CXB are dominated by unresolved clusters with an average z˜0.4 and T˜1.3keV, suggesting an average L_{0.5-2keV}˜3×10^{42} erg/s and M_{500}˜4×10^{13} M_{Sun}/h. Comparison with modeling suggests, that our fluctuation signal can be described with the one-halo-term of clusters and that it might be sensitive to the presence of substructures. Discrepancies between model and measurement could be utilized to improve our understanding of the ICM structure in a statistical manner. We briefly discuss the potential of larger surveys (e.g. Stripe82, XXL, SRG/eRosita).

Local aspects of disentanglement induced by spontaneous emission

NASA Astrophysics Data System (ADS)

Jamróz, Anna

2006-06-01

We consider spontaneous emission of two two-level atoms interacting with vacuum fluctuations. We study the process of disentanglement in this system and show the possibility of changing disentanglement time by local unitary operations.

Instability-driven frequency decoupling between structure dynamics and wake fluctuations

NASA Astrophysics Data System (ADS)

Jin, Yaqing; Kim, Jin-Tae; Chamorro, Leonardo P.

2018-04-01

Flow-induced dynamics of flexible structures is, in general, significantly modulated by periodic vortex shedding. Experiments and numerical simulations suggest that the frequencies associated with the dominant motions of structures are highly coupled with those of the wake under low-turbulence uniform flow. Here we present experimental evidence that demonstrates a significant decoupling between the dynamics of simple structures and wake fluctuations for various geometries, Reynolds numbers, and mass ratios. High-resolution particle tracking velocimetry and hot-wire anemometry are used to quantitatively characterize the dynamics of the structures and wake fluctuations; a complementary planar particle image velocimetry measurement is conducted to illustrate distinctive flow patterns. Results show that for structures with directional stiffness, von Kármán vortex shedding might dominate the wake of bodies governed by natural-frequency motion. This phenomenon can be a consequence of Kelvin-Helmholtz instability, where the structural characteristics of the body dominate the oscillations.

Local regulation of interchange turbulence in a dipole-confined plasma torus using current-collection feedback

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

Roberts, T. M., E-mail: tmr2122@columbia.edu; Mauel, M. E., E-mail: mauel@columbia.edu; Worstell, M. W.

2015-05-15

Turbulence in plasma confined by a magnetic dipole is dominated by interchange fluctuations with complex dynamics and short spatial coherence. We report the first use of local current-collection feedback to modify, amplify, and suppress these fluctuations. The spatial extent of turbulence regulation is limited to a correlation length near the collector. Changing the gain and phase of collection results in power either extracted from or injected into the turbulence. The measured plasma response shows some agreement with calculations of the linear response of global interchange-like MHD and entropy modes to current-collection feedback.

Fatigue Analysis of the Piston Rod in a Kaplan Turbine Based on Crack Propagation under Unsteady Hydraulic Loads

NASA Astrophysics Data System (ADS)

Liu, X.; Y Luo, Y.; Wang, Z. W.

2014-03-01

As an important component of the blade-control system in Kaplan turbines, piston rods are subjected to fluctuating forces transferred by the turbines blades from hydraulic pressure oscillations. Damage due to unsteady hydraulic loads might generate unexpected down time and high repair cost. In one running hydropower plant, the fracture failure of the piston rod was found twice at the same location. With the transient dynamic analysis, the retainer ring structure of the piston rod existed a relative high stress concentration. This predicted position of the stress concentration agreed well with the actual fracture position in the plant. However, the local strain approach was not able to explain why this position broke frequently. Since traditional structural fatigue analyses use a local stress strain approach to assess structural integrity, do not consider the effect of flaws which can significantly degrade structural life. Using linear elastic fracture mechanism (LEFM) approaches that include the effect of flaws is becoming common practice in many industries. In this research, a case involving a small semi-ellipse crack was taken into account at the stress concentration area, crack growth progress was calculated by FEM. The relationship between crack length and remaining life was obtained. The crack propagation path approximately agreed with the actual fracture section. The results showed that presence of the crack had significantly changed the local stress and strain distributions of the piston rod compared with non-flaw assumption.

A correlation between the cosmic microwave background and large-scale structure in the Universe.

PubMed

Boughn, Stephen; Crittenden, Robert

2004-01-01

Observations of distant supernovae and the fluctuations in the cosmic microwave background (CMB) indicate that the expansion of the Universe may be accelerating under the action of a 'cosmological constant' or some other form of 'dark energy'. This dark energy now appears to dominate the Universe and not only alters its expansion rate, but also affects the evolution of fluctuations in the density of matter, slowing down the gravitational collapse of material (into, for example, clusters of galaxies) in recent times. Additional fluctuations in the temperature of CMB photons are induced as they pass through large-scale structures and these fluctuations are necessarily correlated with the distribution of relatively nearby matter. Here we report the detection of correlations between recent CMB data and two probes of large-scale structure: the X-ray background and the distribution of radio galaxies. These correlations are consistent with those predicted by dark energy, indicating that we are seeing the imprint of dark energy on the growth of structure in the Universe.

Simulation Analysis of Zero Mean Flow Edge Turbulence in LAPD

NASA Astrophysics Data System (ADS)

Friedman, Brett Cory

I model, simulate, and analyze the turbulence in a particular experiment on the Large Plasma Device (LAPD) at UCLA. The experiment, conducted by Schaffner et al. [D. Schaffner et al., Phys. Rev. Lett. 109, 135002 (2012)], nulls out the intrinsic mean flow in LAPD by limiter biasing. The model that I use in the simulation is an electrostatic reduced Braginskii two-fluid model that describes the time evolution of density, electron temperature, electrostatic potential, and parallel electron velocity fluctuations in the edge region of LAPD. The spatial domain is annular, encompassing the radial coordinates over which a significant equilibrium density gradient exists. My model breaks the independent variables in the equations into time-independent equilibrium parts and time-dependent fluctuating parts, and I use experimentally obtained values as input for the equilibrium parts. After an initial exponential growth period due to a linear drift wave instability, the fluctuations saturate and the frequency and azimuthal wavenumber spectra become broadband with no visible coherent peaks, at which point the fluctuations become turbulent. The turbulence develops intermittent pressure and flow filamentary structures that grow and dissipate, but look much different than the unstable linear drift waves, primarily in the extremely long axial wavelengths that the filaments possess. An energy dynamics analysis that I derive reveals the mechanism that drives these structures. The long k|| ˜ 0 intermittent potential filaments convect equilibrium density across the equilibrium density gradient, setting up local density filaments. These density filaments, also with k || ˜ 0, produce azimuthal density gradients, which drive radially propagating secondary drift waves. These finite k|| drift waves nonlinearly couple to one another and reinforce the original convective filament, allowing the process to bootstrap itself. The growth of these structures is by nonlinear instability because they require a finite amplitude to start, and they require nonlinear terms in the equations to sustain their growth. The reason why k|| ˜ 0 structures can grow and support themselves in a dynamical system with no k|| = 0 linear instability is because the linear eigenmodes of the system are nonorthogonal. Nonorthogonal eigenmodes that individually decay under linear dynamics can transiently inject energy into the system, allowing for instability. The instability, however, can only occur when the fluctuations have a finite starting amplitude, and nonlinearities are available to mix energy among eigenmodes. Finally, I attempt to figure out how many effective degrees of freedom control the turbulence to determine whether it is stochastic or deterministic. Using two different methods - permutation entropy analysis by means of time delay trajectory reconstruction and Proper Orthogonal Decomposition - I determine that more than a few degrees of freedom, possibly even dozens or hundreds, are all active. The turbulence, while not stochastic, is not a manifestation of low-dimensional chaos - it is high-dimensional.

Electron-cyclotron wave scattering by edge density fluctuations in ITER

NASA Astrophysics Data System (ADS)

Tsironis, Christos; Peeters, Arthur G.; Isliker, Heinz; Strintzi, Dafni; Chatziantonaki, Ioanna; Vlahos, Loukas

2009-11-01

The effect of edge turbulence on the electron-cyclotron wave propagation in ITER is investigated with emphasis on wave scattering, beam broadening, and its influence on localized heating and current drive. A wave used for electron-cyclotron current drive (ECCD) must cross the edge of the plasma, where density fluctuations can be large enough to bring on wave scattering. The scattering angle due to the density fluctuations is small, but the beam propagates over a distance of several meters up to the resonance layer and even small angle scattering leads to a deviation of several centimeters at the deposition location. Since the localization of ECCD is crucial for the control of neoclassical tearing modes, this issue is of great importance to the ITER design. The wave scattering process is described on the basis of a Fokker-Planck equation, where the diffusion coefficient is calculated analytically as well as computed numerically using a ray tracing code.

Itinerancy enhanced quantum fluctuation of magnetic moments in iron-based superconductors

DOE PAGES

Tam, Yu -T.; Ku, W.; Yao, D. -X.

2015-09-10

We investigate the influence of itinerant carriers on dynamics and fluctuation of local moments in Fe-based superconductors, via linear spin-wave analysis of a spin-fermion model containing both itinerant and local degrees of freedom. Surprisingly against the common lore, instead of enhancing the (π,0) order, itinerant carriers with well nested Fermi surfaces is found to induce significant amount of spatial and temporal quantum fluctuation that leads to the observed small ordered moment. Interestingly, the underlying mechanism is shown to be intra-pocket nesting-associated long-range coupling, rather than the previously believed ferromagnetic double-exchange effect. This challenges the validity of ferromagnetically compensated first-neighbor couplingmore » reported from short-range fitting to the experimental dispersion, which turns out to result instead from the ferro-orbital order that is also found instrumental in stabilizing the magnetic order.« less

Identification of local myocardial repolarization time by bipolar electrode potential.

PubMed

Namba, Tsunetoyo; Todo, Takahiro; Yao, Takenori; Ashihara, Takashi; Haraguchi, Ryo; Nakazawa, Kazuo; Ikeda, Takanori; Ohe, Tohru

2007-01-01

The aim of this study was to investigate whether bipolar electrode potentials (BEPs) reflect local myocardial repolarization dynamics, using computer simulation. Simulated action potential and BEP mapping of myocardial tissue during fibrillation was performed. The BEP was modified to make all the fluctuations have the same polarity. Then, the modified BEP (mBEP) was transformed to "dynamic relative amplitude" (DRA) designed to make all the fluctuations have the similar amplitude. The repolarization end point corresponded to the end of the repolarization-related small fluctuation that clearly appeared in the DRA of mBEP. Using the DRA of mBEP, we could reproduce the repolarization dynamics in the myocardial tissue during fibrillation. The BEP may facilitate identifying the repolarization time. Furthermore, BEP mapping has the possibility that it would be available for evaluating repolarization behavior in myocardial tissue even during fibrillation. The accuracy of activation-recovery interval was also reconfirmed.

Weak correlations between hemodynamic signals and ongoing neural activity during the resting state

PubMed Central

Winder, Aaron T.; Echagarruga, Christina; Zhang, Qingguang; Drew, Patrick J.

2017-01-01

Spontaneous fluctuations in hemodynamic signals in the absence of a task or overt stimulation are used to infer neural activity. We tested this coupling by simultaneously measuring neural activity and changes in cerebral blood volume (CBV) in the somatosensory cortex of awake, head-fixed mice during periods of true rest, and during whisker stimulation and volitional whisking. Here we show that neurovascular coupling was similar across states, and large spontaneous CBV changes in the absence of sensory input were driven by volitional whisker and body movements. Hemodynamic signals during periods of rest were weakly correlated with neural activity. Spontaneous fluctuations in CBV and vessel diameter persisted when local neural spiking and glutamatergic input was blocked, and during blockade of noradrenergic receptors, suggesting a non-neuronal origin for spontaneous CBV fluctuations. Spontaneous hemodynamic signals reflect a combination of behavior, local neural activity, and putatively non-neural processes. PMID:29184204

Weak correlations between hemodynamic signals and ongoing neural activity during the resting state.

PubMed

Winder, Aaron T; Echagarruga, Christina; Zhang, Qingguang; Drew, Patrick J

2017-12-01

Spontaneous fluctuations in hemodynamic signals in the absence of a task or overt stimulation are used to infer neural activity. We tested this coupling by simultaneously measuring neural activity and changes in cerebral blood volume (CBV) in the somatosensory cortex of awake, head-fixed mice during periods of true rest and during whisker stimulation and volitional whisking. We found that neurovascular coupling was similar across states and that large, spontaneous CBV changes in the absence of sensory input were driven by volitional whisker and body movements. Hemodynamic signals during periods of rest were weakly correlated with neural activity. Spontaneous fluctuations in CBV and vessel diameter persisted when local neural spiking and glutamatergic input were blocked, as well as during blockade of noradrenergic receptors, suggesting a non-neuronal origin for spontaneous CBV fluctuations. Spontaneous hemodynamic signals reflect a combination of behavior, local neural activity, and putatively non-neural processes.

Comparison of large-scale structures and velocities in the local universe

NASA Technical Reports Server (NTRS)

Yahil, Amos

1994-01-01

Comparison of the large-scale density and velocity fields in the local universe shows detailed agreement, strengthening the standard paradigm of the gravitational origin of these structures. Quantitative analysis can determine the cosmological density parameter, Omega, and biasing factor, b; there is virtually no sensitivity in any local analyses to the cosmologial constant, lambda. Comparison of the dipole anisotropy of the cosmic microwave background with the acceleration due to the Infrared Astronomy Satellite (IRAS) galaxies puts the linear growth factor in the range beta approximately equals Omega (exp 0.6)/b = 0.6(+0.7/-0.3) (95% confidence). A direct comparison of the density and velocity fields of nearby galaxies gives beta = 1.3 (+0.7/-0.6), and from nonlinear analysis the weaker limit (Omega greater than 0.45 for b greater than 0.5 (again 95% confidence). A tighter limit (Omega greater than 0.3 (4-6 sigma)), is obtained by a reconstruction of the probability distribution function of the initial fluctuations from which the structures observed today arose. The last two methods depend critically on the smooth velocity field determined from the observed velocities of nearby galaxies by the POTENT method. A new analysis of these velocities, with more than three times the data used to obtain the above quoted results, is now underway and promises to tighten the uncertainties considerably, as well as reduce systematic bias.

Dispersion in Fractures with Ramified Dissolution Patterns

NASA Astrophysics Data System (ADS)

Xu, Le; Marks, Benjy; Toussaint, Renaud; Flekkøy, Eirik G.; Måløy, Knut J.

2018-04-01

The injection of a reactive fluid into an open fracture may modify the fracture surface locally and create a ramified structure around the injection point. This structure will have a significant impact on the dispersion of the injected fluid due to increased permeability, which will introduce large velocity fluctuations into the fluid. Here, we have injected a fluorescent tracer fluid into a transparent artificial fracture with such a ramified structure. The transparency of the model makes it possible to follow the detailed dispersion of the tracer concentration. The experiments have been compared to two dimensional (2D) computer simulations which include both convective motion and molecular diffusion. A comparison was also performed between the dispersion from an initially ramified dissolution structure and the dispersion from an initially circular region. A significant difference was seen both at small and large length scales. At large length scales, the persistence of the anisotropy of the concentration distribution far from the ramified structure is discussed with reference to some theoretical considerations and comparison with simulations.

Evaluation of interlayer interfacial stiffness and layer wave velocity of multilayered structures by ultrasonic spectroscopy.

PubMed

Ishii, Yosuke; Biwa, Shiro

2014-07-01

An ultrasonic evaluation procedure for the interlayer interfacial normal stiffness and the intralayer longitudinal wave velocity of multilayered plate-like structures is proposed. Based on the characteristics of the amplitude reflection spectrum of ultrasonic wave at normal incidence to a layered structure with spring-type interlayer interfaces, it is shown that the interfacial normal stiffness and the longitudinal wave velocity in the layers can be simultaneously evaluated from the frequencies of local maxima and minima of the spectrum provided that all interfaces and layers have the same properties. The effectiveness of the proposed procedure is investigated from the perspective of the sensitivity of local extremal frequencies of the reflection spectrum. The feasibility of the proposed procedure is also investigated when the stiffness of each interface is subjected to small random fluctuations about a certain average value. The proposed procedure is applied to a 16-layered cross-ply carbon-fiber-reinforced composite laminate. The normal stiffness of resin-rich interfaces and the longitudinal wave velocity of plies in the thickness direction evaluated from the experimental reflection spectrum are shown to be consistent with simple theoretical estimations.

Sensors for Using Times of Flight to Measure Flow Velocities

NASA Technical Reports Server (NTRS)

Fralick, Gutave; Wrbanek, John D.; Hwang, Danny; Turso, James

2006-01-01

Thin-film sensors for measuring flow velocities in terms of times of flight are undergoing development. These sensors are very small and can be mounted flush with surfaces of airfoils, ducts, and other objects along which one might need to measure flows. Alternatively or in addition, these sensors can be mounted on small struts protruding from such surfaces for acquiring velocity measurements at various distances from the surfaces for the purpose of obtaining boundary-layer flow-velocity profiles. These sensors are related to, but not the same as, hot-wire anemometers. Each sensor includes a thin-film, electrically conductive loop, along which an electric current is made to flow to heat the loop to a temperature above that of the surrounding fluid. Instantaneous voltage fluctuations in segments of the loop are measured by means of electrical taps placed at intervals along the loop. These voltage fluctuations are caused by local fluctuations in electrical resistance that are, in turn, caused by local temperature fluctuations that are, in turn, caused by fluctuations in flow-induced cooling and, hence, in flow velocity. The differential voltage as a function of time, measured at each pair of taps, is subjected to cross-correlation processing with the corresponding quantities measured at other pairs of taps at different locations on the loop. The cross-correlations yield the times taken by elements of fluid to travel between the pairs of taps. Then the component of velocity along the line between any two pairs of taps is calculated simply as the distance between the pairs of taps divided by the travel time. Unlike in the case of hot-wire anemometers, there is no need to obtain calibration data on voltage fluctuations versus velocity fluctuations because, at least in principle, the correlation times are independent of the calibration data.

Hyperuniformity, quasi-long-range correlations, and void-space constraints in maximally random jammed particle packings. II. Anisotropy in particle shape.

PubMed

Zachary, Chase E; Jiao, Yang; Torquato, Salvatore

2011-05-01

We extend the results from the first part of this series of two papers by examining hyperuniformity in heterogeneous media composed of impenetrable anisotropic inclusions. Specifically, we consider maximally random jammed (MRJ) packings of hard ellipses and superdisks and show that these systems both possess vanishing infinite-wavelength local-volume-fraction fluctuations and quasi-long-range pair correlations scaling as r(-(d+1)) in d Euclidean dimensions. Our results suggest a strong generalization of a conjecture by Torquato and Stillinger [Phys. Rev. E 68, 041113 (2003)], namely, that all strictly jammed saturated packings of hard particles, including those with size and shape distributions, are hyperuniform with signature quasi-long-range correlations. We show that our arguments concerning the constrained distribution of the void space in MRJ packings directly extend to hard-ellipse and superdisk packings, thereby providing a direct structural explanation for the appearance of hyperuniformity and quasi-long-range correlations in these systems. Additionally, we examine general heterogeneous media with anisotropic inclusions and show unexpectedly that one can decorate a periodic point pattern to obtain a hard-particle system that is not hyperuniform with respect to local-volume-fraction fluctuations. This apparent discrepancy can also be rationalized by appealing to the irregular distribution of the void space arising from the anisotropic shapes of the particles. Our work suggests the intriguing possibility that the MRJ states of hard particles share certain universal features independent of the local properties of the packings, including the packing fraction and average contact number per particle.

Notes on phase transitions and the role of spin fluctuations

NASA Astrophysics Data System (ADS)

Stishov, S. M.

2016-09-01

The physical properties of two chiral systems with localized and delocalized magnetic moments, {\\text{Cu}}2{\\text{OSeO}}3 and MnSi, are reviewed. It is concluded that the longitudinal fluctuations of magnetic moments have no strong effect on the qualitative picture of phase transitions and the magnetic phase diagrams of chiral systems.

Disorder-Induced Topological State Transition in Photonic Metamaterials

NASA Astrophysics Data System (ADS)

Liu, Changxu; Gao, Wenlong; Yang, Biao; Zhang, Shuang

2017-11-01

The topological state transition has been widely studied based on the quantized topological band invariant such as the Chern number for the system without intense randomness that may break the band structures. We numerically demonstrate the disorder-induced state transition in the photonic topological systems for the first time. Instead of applying the ill-defined topological band invariant in a disordered system, we utilize an empirical parameter to unambiguously illustrate the state transition of the topological metamaterials. Before the state transition, we observe a robust surface state with well-confined electromagnetic waves propagating unidirectionally, immune to the disorder from permittivity fluctuation up to 60% of the original value. During the transition, a hybrid state composed of a quasiunidirectional surface mode and intensively localized hot spots is established, a result of the competition between the topological protection and Anderson localization.

Shape-designed frustration by local polymorphism in a near-equilibrium colloidal glass.

PubMed

Zhao, Kun; Mason, Thomas G

2015-09-29

We show that hard, convex, lithographic, prismatic kite platelets, each having three 72° vertices and one 144° vertex, preferentially form a disordered and arrested 2D glass when concentrated quasi-statically in a monolayer while experiencing thermal Brownian fluctuations. By contrast with 2D systems of other hard convex shapes, such as squares, rhombs, and pentagons, which readily form crystals at high densities, 72° kites retain a liquid-like disordered structure that becomes frozen-in as their long-time translational and rotational diffusion become highly bounded, yielding a 2D colloidal glass. This robust glass-forming propensity arises from competition between highly diverse few-particle local polymorphic configurations (LPCs) that have incommensurate features and symmetries. Thus, entropy maximization is consistent with the preservation of highly diverse LPCs en route to the arrested glass.

Transport and Quantum Coherence in Graphene Rings: Aharonov-Bohm Oscillations, Klein Tunneling, and Particle Localization

NASA Astrophysics Data System (ADS)

Filusch, Alexander; Wurl, Christian; Pieper, Andreas; Fehske, Holger

2018-06-01

Simulating quantum transport through mesoscopic, ring-shaped graphene structures, we address various quantum coherence and interference phenomena. First, a perpendicular magnetic field, penetrating the graphene ring, gives rise to Aharonov-Bohm oscillations in the conductance as a function of the magnetic flux, on top of the universal conductance fluctuations. At very high fluxes, the interference gets suppressed and quantum Hall edge channels develop. Second, applying an electrostatic potential to one of the ring arms, nn'n- or npn-junctions can be realized with particle transmission due to normal tunneling or Klein tunneling. In the latter case, the Aharonov-Bohm oscillations weaken for smooth barriers. Third, if potential disorder comes in to play, both Aharonov-Bohm and Klein tunneling effects rate down, up to the point where particle localization sets in.

Nonequilibrium fluctuations as a distinctive feature of weak localization

PubMed Central

Barone, C.; Romeo, F.; Pagano, S.; Attanasio, C.; Carapella, G.; Cirillo, C.; Galdi, A.; Grimaldi, G.; Guarino, A.; Leo, A.; Nigro, A.; Sabatino, P.

2015-01-01

Two-dimensional materials, such as graphene, topological insulators, and two-dimensional electron gases, represent a technological playground to develop coherent electronics. In these systems, quantum interference effects, and in particular weak localization, are likely to occur. These coherence effects are usually characterized by well-defined features in dc electrical transport, such as a resistivity increase and negative magnetoresistance below a crossover temperature. Recently, it has been shown that in magnetic and superconducting compounds, undergoing a weak-localization transition, a specific low-frequency 1/f noise occurs. An interpretation in terms of nonequilibrium universal conductance fluctuations has been given. The universality of this unusual electric noise mechanism has been here verified by detailed voltage-spectral density investigations on ultrathin copper films. The reported experimental results validate the proposed theoretical framework, and also provide an alternative methodology to detect weak-localization effects by using electric noise spectroscopy. PMID:26024506

Single-molecule spectromicroscopy: a route towards sub-wavelength refractometry.

PubMed

Anikushina, T A; Gladush, M G; Gorshelev, A A; Naumov, A V

2015-01-01

We suggest a novel approach for spatially resolved probing of local fluctuations of the refractive index n in solids by means of single-molecule (SM) spectroscopy. It is based on the dependence T1(n) of the effective radiative lifetime T1 of dye centres in solids on n due to the local-field effects. Detection of SM zero-phonon lines at low temperatures gives the values of the SM natural spectral linewidth (which is inversely proportional to T1) and makes it possible to reveal the distribution of the local n values in solids. Here we demonstrate this possibility on the example of amorphous polyethylene and polycrystalline naphthalene doped with terrylene. In particular, we show that the obtained distributions of lifetime limited spectral linewidths of terrylene molecules embedded into these matrices are due to the spatial fluctuations of the refractive index local values.

Distinct nature of orbital-selective Mott phases dominated by low-energy local spin fluctuations

NASA Astrophysics Data System (ADS)

Song, Ze-Yi; Jiang, Xiu-Cai; Lin, Hai-Qing; Zhang, Yu-Zhong

2017-12-01

Quantum orbital-selective Mott (OSM) transitions are investigated within dynamical mean-field theory based on a two-orbital Hubbard model with different bandwidth at half filling. We find two distinct OSM phases both showing coexistence of itinerant electrons and localized spins, dependent on whether the Hund's coupling is full or of Ising type. The critical values and the nature of the OSM transitions are efficiently determined by entanglement entropy. We reveal that vanishing of the Kondo energy scale evidenced by absence of local spin fluctuations at low frequency in local dynamical spin susceptibility is responsible for the appearance of non-Fermi-liquid OSM phase in Ising Hund's coupling case. We argue that this scenario can also be applied to account for emergent quantum non-Fermi liquid in the one-band Hubbard model when short-range antiferromagnetic order is considered.

Finding Statistically Significant Communities in Networks

PubMed Central

Lancichinetti, Andrea; Radicchi, Filippo; Ramasco, José J.; Fortunato, Santo

2011-01-01

Community structure is one of the main structural features of networks, revealing both their internal organization and the similarity of their elementary units. Despite the large variety of methods proposed to detect communities in graphs, there is a big need for multi-purpose techniques, able to handle different types of datasets and the subtleties of community structure. In this paper we present OSLOM (Order Statistics Local Optimization Method), the first method capable to detect clusters in networks accounting for edge directions, edge weights, overlapping communities, hierarchies and community dynamics. It is based on the local optimization of a fitness function expressing the statistical significance of clusters with respect to random fluctuations, which is estimated with tools of Extreme and Order Statistics. OSLOM can be used alone or as a refinement procedure of partitions/covers delivered by other techniques. We have also implemented sequential algorithms combining OSLOM with other fast techniques, so that the community structure of very large networks can be uncovered. Our method has a comparable performance as the best existing algorithms on artificial benchmark graphs. Several applications on real networks are shown as well. OSLOM is implemented in a freely available software (http://www.oslom.org), and we believe it will be a valuable tool in the analysis of networks. PMID:21559480

Interplay of superconductivity and magnetic fluctuations in single crystals of BaFe2-xCoxAs2

NASA Astrophysics Data System (ADS)

Bag, Biplab; Kumar, Ankit; Banerjee, S. S.; Vinod, K.; Bharathi, A.

2018-04-01

We report unusual pinning response in optimally doped and overdoped single crystals of BaFe2-xCoxAs2. Here we use magneto-optical imaging technique to measure the local magnetization response which shows an unusual transformation from low temperature diamagnetic state to high temperature positive magnetization response. Our data suggests coexistence of magnetic fluctuation along with superconductivity in the optimally doped crystal. The strength of magnetic fluctuations is the strongest in the optimally doped compound with the highest Tc.

IMPRINTS OF EXPANSION ON THE LOCAL ANISOTROPY OF SOLAR WIND TURBULENCE

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

Verdini, Andrea; Grappin, Roland

2015-08-01

We study the anisotropy of II-order structure functions (SFs) defined in a frame attached to the local mean field in three-dimensional (3D) direct numerical simulations of magnetohydrodynamic turbulence, with the solar wind expansion both included and not included. We simulate spacecraft flybys through the numerical domain by taking increments along the radial (wind) direction that form an angle of 45° with the ambient magnetic field. We find that only when expansion is taken into account do the synthetic observations match the 3D anisotropy observed in the solar wind, including the change of anisotropy with scale. Our simulations also show thatmore » the anisotropy changes dramatically when considering increments oblique to the radial directions. Both results can be understood by noting that expansion reduces the radial component of the magnetic field at all scales, thus confining fluctuations in the plane perpendicular to the radial. Expansion is thus shown to affect not only the (global) spectral anisotropy, but also the local anisotropy of second-order SF by influencing the distribution of the local mean field, which enters this higher-order statistics.« less

Influence of mode-beating pulse on laser-induced plasma

NASA Astrophysics Data System (ADS)

Nishihara, M.; Freund, J. B.; Glumac, N. G.; Elliott, G. S.

2018-04-01

This paper addresses the influence of mode-beating pulse on laser-induced plasma. The second harmonic of a Nd:YAG laser, operated either with the single mode or multimode, was used for non-resonant optical breakdown, and subsequent plasma development was visualized using a streak imaging system. The single mode lasing leads to a stable breakdown location and smooth envelopment of the plasma boundary, while the multimode lasing, with the dominant mode-beating frequency of 500-800 MHz, leads to fluctuations in the breakdown location, a globally modulated plasma surface, and growth of local microstructures at the plasma boundary. The distribution of the local inhomogeneity was measured from the elastic scattering signals on the streak image. The distance between the local structures agreed with the expected wavelength of hydrodynamic instability development due to the interference between the surface excited wave and transmitted wave. A numerical simulation, however, indicates that the local microstructure could also be directly generated at the peaks of the higher harmonic components if the multimode pulse contains up to the eighth harmonic of the fundamental cavity mode.

Statistical characteristics of locally generated ESF during equinoctial months over Sanya

NASA Astrophysics Data System (ADS)

Meng, Xing; Fang, Hanxian; Li, Guozhu; Weng, Libin

2018-05-01

Understanding the local generation rate of equatorial spread-F (ESF) is important for forecasting ionospheric scintillation. Using the GPS ionospheric scintillation/TEC and VHF radar data during March-April and September-October from 2010 to 2014, the occurrence of ionospheric scintillation, TEC fast fluctuation, and backscatter plume were studied. Through analyzing the simultaneous occurrence of ionospheric scintillation, TEC fast fluctuation and backscatter plume, the local generation rate of ESF over Sanya was investigated. The results show that the monthly generation rate varies between 0% and 68%. A significant equinoctial asymmetry of local generation rate of ESF can be found in 2010, 2013 and 2014. The local generation rate of ESF increases from 2010 to 2014 during March-April, while it does not have similar trend during September-October. The plasma vertical drift influenced by solar activity has a significant impact on the monthly generation rate. The equinoctial asymmetry of plasma vertical drift may contribute a lot to the equinoctial asymmetry of the generation rate of ESF.

Variation in sensitivity of large benthic Foraminifera to the combined effects of ocean warming and local impacts.

PubMed

Prazeres, Martina; Roberts, T Edward; Pandolfi, John M

2017-03-23

Large benthic foraminifera (LBF) are crucial marine calcifiers in coral reefs, and sensitive to environmental changes. Yet, many species successfully colonise a wide range of habitats including highly fluctuating environments. We tested the combined effects of ocean warming, local impacts and different light levels on populations of the common LBF Amphistegina lobifera collected along a cross-shelf gradient of temperature and nutrients fluctuations. We analysed survivorship, bleaching frequency, chlorophyll a content and fecundity. Elevated temperature and nitrate significantly reduced survivorship and fecundity of A. lobifera across populations studied. This pattern was exacerbated when combined with below optimum light levels. Inshore populations showed a consistent resistance to increased temperature and nitrate levels, but all populations studied were significantly affected by light reduction. These findings demonstrated the capacity of some populations of LBF to acclimate to local conditions; nonetheless improvements in local water quality can ultimately ameliorate effects of climate change in local LBF populations.

Temporal Genetic Dynamics of an Invasive Species, Frankliniella occidentalis (Pergande), in an Early Phase of Establishment.

PubMed

Yang, Xian-Ming; Lou, Heng; Sun, Jing-Tao; Zhu, Yi-Ming; Xue, Xiao-Feng; Hong, Xiao-Yue

2015-07-03

Many species can successfully colonize new areas despite their propagules having low genetic variation. We assessed whether the decreased genetic diversity could result in temporal fluctuations of genetic parameters of the new populations of an invasive species, western flower thrips, Frankliniella occidentalis, using mitochondrial and microsatellite markers. This study was conducted in eight localities from four climate regions in China, where F. occidentalis was introduced in the year 2000 and had lower genetic diversity than its native populations. We also tested the level of genetic differentiation in these introduced populations. The genetic diversity of the samples at different years in the same locality was not significantly different from each other in most localities. FST and STRUCTURE analysis also showed that most temporal population comparisons from the same sites were not significantly differentiated. Our results showed that the invasive populations of F. occidentalis in China can maintain temporal stability in genetic composition at an early phase of establishment despite having lower genetic diversity than in their native range.

Submesoscale dispersion in the vicinity of the Deepwater Horizon spill.

PubMed

Poje, Andrew C; Ozgökmen, Tamay M; Lipphardt, Bruce L; Haus, Brian K; Ryan, Edward H; Haza, Angelique C; Jacobs, Gregg A; Reniers, A J H M; Olascoaga, Maria Josefina; Novelli, Guillaume; Griffa, Annalisa; Beron-Vera, Francisco J; Chen, Shuyi S; Coelho, Emanuel; Hogan, Patrick J; Kirwan, Albert D; Huntley, Helga S; Mariano, Arthur J

2014-09-02

Reliable forecasts for the dispersion of oceanic contamination are important for coastal ecosystems, society, and the economy as evidenced by the Deepwater Horizon oil spill in the Gulf of Mexico in 2010 and the Fukushima nuclear plant incident in the Pacific Ocean in 2011. Accurate prediction of pollutant pathways and concentrations at the ocean surface requires understanding ocean dynamics over a broad range of spatial scales. Fundamental questions concerning the structure of the velocity field at the submesoscales (100 m to tens of kilometers, hours to days) remain unresolved due to a lack of synoptic measurements at these scales. Using high-frequency position data provided by the near-simultaneous release of hundreds of accurately tracked surface drifters, we study the structure of submesoscale surface velocity fluctuations in the Northern Gulf of Mexico. Observed two-point statistics confirm the accuracy of classic turbulence scaling laws at 200-m to 50-km scales and clearly indicate that dispersion at the submesoscales is local, driven predominantly by energetic submesoscale fluctuations. The results demonstrate the feasibility and utility of deploying large clusters of drifting instruments to provide synoptic observations of spatial variability of the ocean surface velocity field. Our findings allow quantification of the submesoscale-driven dispersion missing in current operational circulation models and satellite altimeter-derived velocity fields.

Submesoscale dispersion in the vicinity of the Deepwater Horizon spill

PubMed Central

Poje, Andrew C.; Özgökmen, Tamay M.; Lipphardt, Bruce L.; Haus, Brian K.; Ryan, Edward H.; Haza, Angelique C.; Jacobs, Gregg A.; Reniers, A. J. H. M.; Olascoaga, Maria Josefina; Novelli, Guillaume; Griffa, Annalisa; Beron-Vera, Francisco J.; Chen, Shuyi S.; Coelho, Emanuel; Hogan, Patrick J.; Kirwan, Albert D.; Huntley, Helga S.; Mariano, Arthur J.

2014-01-01

Reliable forecasts for the dispersion of oceanic contamination are important for coastal ecosystems, society, and the economy as evidenced by the Deepwater Horizon oil spill in the Gulf of Mexico in 2010 and the Fukushima nuclear plant incident in the Pacific Ocean in 2011. Accurate prediction of pollutant pathways and concentrations at the ocean surface requires understanding ocean dynamics over a broad range of spatial scales. Fundamental questions concerning the structure of the velocity field at the submesoscales (100 m to tens of kilometers, hours to days) remain unresolved due to a lack of synoptic measurements at these scales. Using high-frequency position data provided by the near-simultaneous release of hundreds of accurately tracked surface drifters, we study the structure of submesoscale surface velocity fluctuations in the Northern Gulf of Mexico. Observed two-point statistics confirm the accuracy of classic turbulence scaling laws at 200-m to 50-km scales and clearly indicate that dispersion at the submesoscales is local, driven predominantly by energetic submesoscale fluctuations. The results demonstrate the feasibility and utility of deploying large clusters of drifting instruments to provide synoptic observations of spatial variability of the ocean surface velocity field. Our findings allow quantification of the submesoscale-driven dispersion missing in current operational circulation models and satellite altimeter-derived velocity fields. PMID:25136097

Detection of urea-induced internal denaturation of dsDNA using solid-state nanopores.

PubMed

Singer, Alon; Kuhn, Heiko; Frank-Kamenetskii, Maxim; Meller, Amit

2010-11-17

The ability to detect and measure dsDNA thermal fluctuations is of immense importance in understanding the underlying mechanisms responsible for transcription and replication regulation. We describe here the ability of solid-state nanopores to detect sub-nanometer changes in DNA structure as a result of chemically enhanced thermal fluctuations. In this study, we investigate the subtle changes in the mean effective diameter of a dsDNA molecule with 3-5 nm solid-state nanopores as a function of urea concentration and the DNA's AT content. Our studies reveal an increase in the mean effective diameter of a DNA molecule of approximately 0.6 nm at 8.7 M urea. In agreement with the mechanism of DNA local denaturation, we observe a sigmoid dependence of these effects on urea concentration. We find that the translocation times in urea are markedly slower than would be expected if the dynamics were governed primarily by viscous effects. Furthermore, we find that the sensitivity of the nanopore is sufficient to statistically differentiate between DNA molecules of nearly identical lengths differing only in sequence and AT content when placed in 3.5 M urea. Our results demonstrate that nanopores can detect subtle structural changes and are thus a valuable tool for detecting differences in biomolecules' environment.

Adiabatic-connection fluctuation-dissipation DFT for the structural properties of solids—The renormalized ALDA and electron gas kernels

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

Patrick, Christopher E., E-mail: chripa@fysik.dtu.dk; Thygesen, Kristian S., E-mail: thygesen@fysik.dtu.dk

2015-09-14

We present calculations of the correlation energies of crystalline solids and isolated systems within the adiabatic-connection fluctuation-dissipation formulation of density-functional theory. We perform a quantitative comparison of a set of model exchange-correlation kernels originally derived for the homogeneous electron gas (HEG), including the recently introduced renormalized adiabatic local-density approximation (rALDA) and also kernels which (a) satisfy known exact limits of the HEG, (b) carry a frequency dependence, or (c) display a 1/k{sup 2} divergence for small wavevectors. After generalizing the kernels to inhomogeneous systems through a reciprocal-space averaging procedure, we calculate the lattice constants and bulk moduli of a testmore » set of 10 solids consisting of tetrahedrally bonded semiconductors (C, Si, SiC), ionic compounds (MgO, LiCl, LiF), and metals (Al, Na, Cu, Pd). We also consider the atomization energy of the H{sub 2} molecule. We compare the results calculated with different kernels to those obtained from the random-phase approximation (RPA) and to experimental measurements. We demonstrate that the model kernels correct the RPA’s tendency to overestimate the magnitude of the correlation energy whilst maintaining a high-accuracy description of structural properties.« less

Intermittency of solar system plasma turbulence near Venus and Earth

NASA Astrophysics Data System (ADS)

Teodorescu, Eliza; Echim, Marius; Chang, Tom

2016-04-01

We analyze magnetic field data from Venus Express (VEX) and CLUSTER to investigate the turbulent properties of the solar wind and the Earth's and Venus' magnetosheaths. A systematic study of the PDFs (Probability Distribution Functions) of the measured magnetic fluctuations and their fourth order moments (kurtosis) reveals numerous intermittent time series. The presence of intermittency is marked by non-Gaussian PDFs with heavy wings and a scale dependent kurtosis. Higher order analyses on the scale dependence of several moment orders of the PDFs, the structure functions, along with the scaling of the kurtosis allow for a selection of scales that pertain to different scaling regimes, governed by different physics. On such sub-ranges of scales we investigate the fractal structure of fluctuations through the Rank Ordered Multifractal Analysis - ROMA (Chang and Wu, 2008). ROMA is applied to a selection of intermittent magnetic field time series in the solar wind and planetary magnetosheaths and helps to quantify the turbulence properties through the estimation of a spectrum of local Hurst exponents. Research supported by the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement no 313038/STORM, and a grant of the Romanian Ministry of National Education, CNCS - UEFISCDI, project number PN-II-ID-PCE-2012-4-0418.

Competing spin density wave, collinear, and helical magnetism in Fe 1 + x Te

DOE PAGES

Stock, C.; Rodriguez, E. E.; Bourges, P.; ...

2017-04-07

The Fe 1+xTe phase diagram consists of two distinct magnetic structures with collinear order present at low interstitial iron concentrations and a helical phase at large values of x with these phases separated by a Lifshitz point. In this paper, we use unpolarized single-crystal diffraction to confirm the helical phase for large interstitial iron concentrations and polarized single-crystal diffraction to demonstrate the collinear order for the iron-deficient side of the Fe 1+xTe phase diagram. Polarized neutron inelastic scattering shows that the fluctuations associated with this collinear order are predominately transverse at low-energy transfers, consistent with a localized magnetic moment picture.more » We then apply neutron inelastic scattering and polarization analysis to investigate the dynamics and structure near the boundary between collinear and helical orders in the Fe 1+xTe phase diagram. We first show that the phase separating collinear and helical orders is characterized by a spin density wave with a single propagation wave vector of (~0.45, 0, 0.5). We do not observe harmonics or the presence of a charge density wave. The magnetic fluctuations associated with this wave vector are different from the collinear phase, being strongly longitudinal in nature and correlated anisotropically in the (H,K) plane. The excitations preserve the C 4 symmetry of the lattice but display different widths in momentum along the two tetragonal directions at low-energy transfers. Finally, while the low-energy excitations and minimal magnetic phase diagram can be understood in terms of localized interactions, we suggest that the presence of the density wave phase implies the importance of electronic and orbital properties.« less

Competing spin density wave, collinear, and helical magnetism in Fe 1 + x Te

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

Stock, C.; Rodriguez, E. E.; Bourges, P.

The Fe 1+xTe phase diagram consists of two distinct magnetic structures with collinear order present at low interstitial iron concentrations and a helical phase at large values of x with these phases separated by a Lifshitz point. In this paper, we use unpolarized single-crystal diffraction to confirm the helical phase for large interstitial iron concentrations and polarized single-crystal diffraction to demonstrate the collinear order for the iron-deficient side of the Fe 1+xTe phase diagram. Polarized neutron inelastic scattering shows that the fluctuations associated with this collinear order are predominately transverse at low-energy transfers, consistent with a localized magnetic moment picture.more » We then apply neutron inelastic scattering and polarization analysis to investigate the dynamics and structure near the boundary between collinear and helical orders in the Fe 1+xTe phase diagram. We first show that the phase separating collinear and helical orders is characterized by a spin density wave with a single propagation wave vector of (~0.45, 0, 0.5). We do not observe harmonics or the presence of a charge density wave. The magnetic fluctuations associated with this wave vector are different from the collinear phase, being strongly longitudinal in nature and correlated anisotropically in the (H,K) plane. The excitations preserve the C 4 symmetry of the lattice but display different widths in momentum along the two tetragonal directions at low-energy transfers. Finally, while the low-energy excitations and minimal magnetic phase diagram can be understood in terms of localized interactions, we suggest that the presence of the density wave phase implies the importance of electronic and orbital properties.« less

Competing spin density wave, collinear, and helical magnetism in Fe1 +xTe

NASA Astrophysics Data System (ADS)

Stock, C.; Rodriguez, E. E.; Bourges, P.; Ewings, R. A.; Cao, H.; Chi, S.; Rodriguez-Rivera, J. A.; Green, M. A.

2017-04-01

The Fe1 +xTe phase diagram consists of two distinct magnetic structures with collinear order present at low interstitial iron concentrations and a helical phase at large values of x with these phases separated by a Lifshitz point. We use unpolarized single-crystal diffraction to confirm the helical phase for large interstitial iron concentrations and polarized single-crystal diffraction to demonstrate the collinear order for the iron-deficient side of the Fe1 +xTe phase diagram. Polarized neutron inelastic scattering shows that the fluctuations associated with this collinear order are predominately transverse at low-energy transfers, consistent with a localized magnetic moment picture. We then apply neutron inelastic scattering and polarization analysis to investigate the dynamics and structure near the boundary between collinear and helical orders in the Fe1 +xTe phase diagram. We first show that the phase separating collinear and helical orders is characterized by a spin density wave with a single propagation wave vector of (˜0.45 , 0, 0.5). We do not observe harmonics or the presence of a charge density wave. The magnetic fluctuations associated with this wave vector are different from the collinear phase, being strongly longitudinal in nature and correlated anisotropically in the (H ,K ) plane. The excitations preserve the C4 symmetry of the lattice but display different widths in momentum along the two tetragonal directions at low-energy transfers. While the low-energy excitations and minimal magnetic phase diagram can be understood in terms of localized interactions, we suggest that the presence of the density wave phase implies the importance of electronic and orbital properties.

Relaxation mode analysis and Markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature

NASA Astrophysics Data System (ADS)

Mitsutake, Ayori; Takano, Hiroshi

2015-09-01

It is important to extract reaction coordinates or order parameters from protein simulations in order to investigate the local minimum-energy states and the transitions between them. The most popular method to obtain such data is principal component analysis, which extracts modes of large conformational fluctuations around an average structure. We recently applied relaxation mode analysis for protein systems, which approximately estimates the slow relaxation modes and times from a simulation and enables investigations of the dynamic properties underlying the structural fluctuations of proteins. In this study, we apply this relaxation mode analysis to extract reaction coordinates for a system in which there are large conformational changes such as those commonly observed in protein folding/unfolding. We performed a 750-ns simulation of chignolin protein near its folding transition temperature and observed many transitions between the most stable, misfolded, intermediate, and unfolded states. We then applied principal component analysis and relaxation mode analysis to the system. In the relaxation mode analysis, we could automatically extract good reaction coordinates. The free-energy surfaces provide a clearer understanding of the transitions not only between local minimum-energy states but also between the folded and unfolded states, even though the simulation involved large conformational changes. Moreover, we propose a new analysis method called Markov state relaxation mode analysis. We applied the new method to states with slow relaxation, which are defined by the free-energy surface obtained in the relaxation mode analysis. Finally, the relaxation times of the states obtained with a simple Markov state model and the proposed Markov state relaxation mode analysis are compared and discussed.

Towards uncovering the structure of power fluctuations of wind farms

NASA Astrophysics Data System (ADS)

Liu, Huiwen; Jin, Yaqing; Tobin, Nicolas; Chamorro, Leonardo P.

2017-12-01

The structure of the turbulence-driven power fluctuations in a wind farm is fundamentally described from basic concepts. A derived tuning-free model, supported with experiments, reveals the underlying spectral content of the power fluctuations of a wind farm. It contains two power-law trends and oscillations in the relatively low- and high-frequency ranges. The former is mostly due to the turbulent interaction between the flow and the turbine properties, whereas the latter is due to the advection between turbine pairs. The spectral wind-farm scale power fluctuations ΦP exhibit a power-law decay proportional to f-5 /3 -2 in the region corresponding to the turbulence inertial subrange and at relatively large scales, ΦP˜f-2 . Due to the advection and turbulent diffusion of large-scale structures, a spectral oscillation exists with the product of a sinusoidal behavior and an exponential decay in the frequency domain.

Towards uncovering the structure of power fluctuations of wind farms.

PubMed

Liu, Huiwen; Jin, Yaqing; Tobin, Nicolas; Chamorro, Leonardo P

2017-12-01

The structure of the turbulence-driven power fluctuations in a wind farm is fundamentally described from basic concepts. A derived tuning-free model, supported with experiments, reveals the underlying spectral content of the power fluctuations of a wind farm. It contains two power-law trends and oscillations in the relatively low- and high-frequency ranges. The former is mostly due to the turbulent interaction between the flow and the turbine properties, whereas the latter is due to the advection between turbine pairs. The spectral wind-farm scale power fluctuations Φ_{P} exhibit a power-law decay proportional to f^{-5/3-2} in the region corresponding to the turbulence inertial subrange and at relatively large scales, Φ_{P}∼f^{-2}. Due to the advection and turbulent diffusion of large-scale structures, a spectral oscillation exists with the product of a sinusoidal behavior and an exponential decay in the frequency domain.

Forbidden phonon: Dynamical signature of bond symmetry breaking in the iron chalcogenides

DOE PAGES

Fobes, David M.; Zaliznyak, Igor A.; Tranquada, John M.; ...

2016-09-01

Investigation of the inelastic neutron scattering spectra in Fe 1+yTe 1₋xSe x near a signature wave vector Q=(1,0,0) for the bond-order wave (BOW) formation of parent compound Fe 1+yTe reveals an acoustic-phonon-like dispersion present in all structural phases. While a structural Bragg peak accompanies the mode in the low-temperature phase of Fe 1+yTe, it is absent in the high-temperature tetragonal phase, where Bragg scattering at this Q is forbidden by symmetry. Notably, this mode is also observed in superconducting FeTe 0.55Se 0.45, where structural and magnetic transitions are suppressed, and no BOW has been observed. Lastly, the presence of thismore » “forbidden” phonon indicates that the lattice symmetry is dynamically or locally broken by magneto-orbital BOW fluctuations, which are strongly coupled to lattice in these materials.« less

Engineered control of enzyme structural dynamics and function.

PubMed

Boehr, David D; D'Amico, Rebecca N; O'Rourke, Kathleen F

2018-04-01

Enzymes undergo a range of internal motions from local, active site fluctuations to large-scale, global conformational changes. These motions are often important for enzyme function, including in ligand binding and dissociation and even preparing the active site for chemical catalysis. Protein engineering efforts have been directed towards manipulating enzyme structural dynamics and conformational changes, including targeting specific amino acid interactions and creation of chimeric enzymes with new regulatory functions. Post-translational covalent modification can provide an additional level of enzyme control. These studies have not only provided insights into the functional role of protein motions, but they offer opportunities to create stimulus-responsive enzymes. These enzymes can be engineered to respond to a number of external stimuli, including light, pH, and the presence of novel allosteric modulators. Altogether, the ability to engineer and control enzyme structural dynamics can provide new tools for biotechnology and medicine. © 2018 The Protein Society.

Two-peak structure in the K-edge RIXS spectra of a spatially frustrated Heisenberg antiferromagnet

NASA Astrophysics Data System (ADS)

Datta, Trinanjan; Luo, Cheng; Yao, Dao-Xin

2014-03-01

Quantum fluctuations due to spatial anisotropy and strong magnetic frustration lead to the formation of a two-peak structure in the K-edge bimagnon RIXS intensity spectra of a Jx-Jy-J2 Heisenberg model on a square lattice. We compute the RIXS intensity, including up to first order 1/S spin wave expansion correction, using the Bethe-Salpeter equation within the ladder approximation scheme. The two-peak feature occurs in both the antiferromagnetic phase and the collinear antiferromagnetic phase. A knowledge of the peak splitting energy from both magnetically ordered regime can provide experimentalists with an alternative means to measure and study the effects of local microscopic exchange constants. Cottrell Research Corporation, NSFC-11074310, NSFC-11275279, Specialized Research Fund for the Doctoral Program of Higher Education.

Quantum critical scaling and fluctuations in Kondo lattice materials

PubMed Central

Yang, Yi-feng; Pines, David; Lonzarich, Gilbert

2017-01-01

We propose a phenomenological framework for three classes of Kondo lattice materials that incorporates the interplay between the fluctuations associated with the antiferromagnetic quantum critical point and those produced by the hybridization quantum critical point that marks the end of local moment behavior. We show that these fluctuations give rise to two distinct regions of quantum critical scaling: Hybridization fluctuations are responsible for the logarithmic scaling in the density of states of the heavy electron Kondo liquid that emerges below the coherence temperature T∗, whereas the unconventional power law scaling in the resistivity that emerges at lower temperatures below TQC may reflect the combined effects of hybridization and antiferromagnetic quantum critical fluctuations. Our framework is supported by experimental measurements on CeCoIn5, CeRhIn5, and other heavy electron materials. PMID:28559308

Intermittent Anisotropic Turbulence Detected by THEMIS in the Magnetosheath

NASA Astrophysics Data System (ADS)

Macek, W. M.; Wawrzaszek, A.; Kucharuk, B.; Sibeck, D. G.

2017-12-01

Following our previous study of Time History of Events and Macroscale Interactions during Substorms (THEMIS) data, we consider intermittent turbulence in the magnetosheath depending on various conditions of the magnetized plasma behind the Earth’s bow shock and now also near the magnetopause. Namely, we look at the fluctuations of the components of the Elsässer variables in the plane perpendicular to the scale-dependent background magnetic fields and along the local average ambient magnetic fields. We have shown that Alfvén fluctuations often exhibit strong anisotropic non-gyrotropic turbulent intermittent behavior resulting in substantial deviations of the probability density functions from a normal Gaussian distribution with a large kurtosis. In particular, for very high Alfvénic Mach numbers and high plasma beta, we have clear anisotropy with non-Gaussian statistics in the transverse directions. However, along the magnetic field, the kurtosis is small and the plasma is close to equilibrium. On the other hand, intermittency becomes weaker for moderate Alfvén Mach numbers and lower values of the plasma parameter beta. It also seems that the degree of intermittency of turbulence for the outgoing fluctuations propagating relative to the ambient magnetic field is usually similar as for the ingoing fluctuations, which is in agreement with approximate equipartition of energy between these oppositely propagating Alfvén waves. We believe that the different characteristics of this intermittent anisotropic turbulent behavior in various regions of space and astrophysical plasmas can help identify nonlinear structures responsible for deviations of the plasma from equilibrium.

Stochastic and information-thermodynamic structures of population dynamics in a fluctuating environment

NASA Astrophysics Data System (ADS)

Kobayashi, Tetsuya J.; Sughiyama, Yuki

2017-07-01

Adaptation in a fluctuating environment is a process of fueling environmental information to gain fitness. Living systems have gradually developed strategies for adaptation from random and passive diversification of the phenotype to more proactive decision making, in which environmental information is sensed and exploited more actively and effectively. Understanding the fundamental relation between fitness and information is therefore crucial to clarify the limits and universal properties of adaptation. In this work, we elucidate the underlying stochastic and information-thermodynamic structure in this process, by deriving causal fluctuation relations (FRs) of fitness and information. Combined with a duality between phenotypic and environmental dynamics, the FRs reveal the limit of fitness gain, the relation of time reversibility with the achievability of the limit, and the possibility and condition for gaining excess fitness due to environmental fluctuation. The loss of fitness due to causal constraints and the limited capacity of real organisms is shown to be the difference between time-forward and time-backward path probabilities of phenotypic and environmental dynamics. Furthermore, the FRs generalize the concept of the evolutionary stable state (ESS) for fluctuating environment by giving the probability that the optimal strategy on average can be invaded by a suboptimal one owing to rare environmental fluctuation. These results clarify the information-thermodynamic structures in adaptation and evolution.

Phase Averaged Measurements of the Coherent Structure of a Mach Number 0.6 Jet. M.S. Thesis

NASA Technical Reports Server (NTRS)

Emami, S.

1983-01-01

The existence of a large scale structure in a Mach number 0.6, axisymmetric jet of cold air was proven. In order to further characterize the coherent structure, phase averaged measurements of the axial mass velocity, radial velocity, and the product of the two were made. These measurements yield information about the percent of the total fluctuations contained in the coherent structure. These measured values were compared to the total fluctuation levels for each quantity and the result expressed as a percent of the total fluctuation level contained in the organized structure at a given frequency. These measurements were performed for five frequencies (St=0.16, 0.32, 0.474, 0.95, and 1.26). All of the phase averaged measurements required that the jet be artificially excited.

Impact of neutral density fluctuations on gas puff imaging diagnostics

NASA Astrophysics Data System (ADS)

Wersal, C.; Ricci, P.

2017-11-01

A three-dimensional turbulence simulation of the SOL and edge regions of a toroidally limited tokamak is carried out. The simulation couples self-consistently the drift-reduced two-fluid Braginskii equations to a kinetic equation for neutral atoms. A diagnostic neutral gas puff on the low-field side midplane is included and the impact of neutral density fluctuations on D_α light emission investigated. We find that neutral density fluctuations affect the D_α emission. In particular, at a radial distance from the gas puff smaller than the neutral mean free path, neutral density fluctuations are anti-correlated with plasma density, electron temperature, and D_α fluctuations. It follows that the neutral fluctuations reduce the D_α emission in most of the observed region and, therefore, have to be taken into account when interpreting the amplitude of the D_α emission. On the other hand, higher order statistical moments (skewness, kurtosis) and turbulence characteristics (such as correlation length, or the autocorrelation time) are not significantly affected by the neutral fluctuations. At distances from the gas puff larger than the neutral mean free path, a non-local shadowing effect influences the neutral density fluctuations. There, the D_α fluctuations are correlated with the neutral density fluctuations, and the high-order statistical moments and measurements of other turbulence properties are strongly affected by the neutral density fluctuations.

Modeling of 3D magnetic equilibrium effects on edge turbulence stability during RMP ELM suppression in tokamaks

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

Wilcox, R. S.; Wingen, Andreas; Cianciosa, Mark R.

Some recent experimental observations have found turbulent fluctuation structures that are non-axisymmetric in a tokamak with applied 3D fields. Here, two fluid resistive effects are shown to produce changes relevant to turbulent transport in the modeled 3D magnetohydrodynamic (MHD) equilibrium of tokamak pedestals with these 3D fields applied. Ideal MHD models are insufficient to reproduce the relevant effects. By calculating the ideal 3D equilibrium using the VMEC code, the geometric shaping parameters that determine linear turbulence stability, including the normal curvature and local magnetic shear, are shown to be only weakly modified by applied 3D fields in the DIII-D tokamak.more » These ideal MHD effects are therefore not sufficient to explain the observed changes to fluctuations and transport. Using the M3D-C1 code to model the 3D equilibrium, density is shown to be redistributed on flux surfaces in the pedestal when resistive two fluid effects are included, while islands are screened by rotation in this region. Furthermore, the redistribution of density results in density and pressure gradient scale lengths that vary within pedestal flux surfaces between different helically localized flux tubes. This would produce different drive terms for trapped electron mode and kinetic ballooning mode turbulence, the latter of which is expected to be the limiting factor for pedestal pressure gradients in DIII-D.« less

Modeling of 3D magnetic equilibrium effects on edge turbulence stability during RMP ELM suppression in tokamaks

DOE PAGES

Wilcox, R. S.; Wingen, Andreas; Cianciosa, Mark R.; ...

2017-07-28

Some recent experimental observations have found turbulent fluctuation structures that are non-axisymmetric in a tokamak with applied 3D fields. Here, two fluid resistive effects are shown to produce changes relevant to turbulent transport in the modeled 3D magnetohydrodynamic (MHD) equilibrium of tokamak pedestals with these 3D fields applied. Ideal MHD models are insufficient to reproduce the relevant effects. By calculating the ideal 3D equilibrium using the VMEC code, the geometric shaping parameters that determine linear turbulence stability, including the normal curvature and local magnetic shear, are shown to be only weakly modified by applied 3D fields in the DIII-D tokamak.more » These ideal MHD effects are therefore not sufficient to explain the observed changes to fluctuations and transport. Using the M3D-C1 code to model the 3D equilibrium, density is shown to be redistributed on flux surfaces in the pedestal when resistive two fluid effects are included, while islands are screened by rotation in this region. Furthermore, the redistribution of density results in density and pressure gradient scale lengths that vary within pedestal flux surfaces between different helically localized flux tubes. This would produce different drive terms for trapped electron mode and kinetic ballooning mode turbulence, the latter of which is expected to be the limiting factor for pedestal pressure gradients in DIII-D.« less

Correlations Between the Cosmic X-Ray and Microwave Backgrounds: Constraints on a Cosmological Constant

NASA Technical Reports Server (NTRS)

Boughn, S. P.; Crittenden, R. G.; Turok, N. G.

1998-01-01

In universes with significant curvature or cosmological constant, cosmic microwave background (CMB) anisotropies are created very recently via the Rees-Sciama or integrated Sachs-Wolfe effects. This causes the CMB anisotropies to become partially correlated with the local matter density (z less than 4). We examine the prospects of using the hard (2- 10 keV) X-ray background as a probe of the local density and the measured correlation between the HEAO1 A2 X-ray survey and the 4-year COBE-DMR map to obtain a constraint on the cosmological constant. The 95% confidence level upper limit on the cosmological constant is OMega(sub Lambda) less than or equal to 0.5, assuming that the observed fluctuations in the X-ray map result entirely from large scale structure. (This would also imply that the X-rays trace matter with a bias factor of b(sub x) approx. = 5.6 Omega(sub m, sup 0.53)). This bound is weakened considerably if a large portion of the X-ray fluctuations arise from Poisson noise from unresolved sources. For example, if one assumes that the X-ray bias is b(sub x) = 2, then the 95% confidence level upper limit is weaker, Omega(sub Lambda) less than or equal to 0.7. More stringent limits should be attainable with data from the next generation of CMB and X-ray background maps.

Deformation analysis and prediction of bank protection structure with river level fluctuations

NASA Astrophysics Data System (ADS)

Hu, Rui; Xing, Yixuan

2017-04-01

Bank structure is an important barrier to maintain the safety of the embankment. The deformation of bank protection structure is not only affected by soil pressure caused by the excavation of the riverway, but also by the water pressure caused river water level fluctuations. Thus, it is necessary to establish a coupled soil-water model to analyze the deformation of bank structure. Based on Druck-Prager failure criteria and groundwater seepage theory, a numerical model of bank protection structure with consideration of the pore water pressure of soil mass is established. According to the measured river level data with seasonal fluctuating, numerical analysis of the deformation of bank protection structure is implemented. The simulation results show that the river water level fluctuation has clear influence on the maximum lateral displacement of the pile. Meanwhile, the distribution of plastic zone is related to the depth of groundwater level. Finally, according to the river water level data of the recent ten years, we analyze the deformation of the bank structure under extreme river level. The result shows that, compared with the scenario of extreme high river level, the horizontal displacement of bank protection structure is larger (up to 65mm) under extreme low river level, which is a potential risk to the embankment. Reference Schweiger H F. On the use of drucker-prager failure criteria for earth pressure problems[J]. Computers and Geotechnics, 1994, 16(3): 223-246. DING Yong-chun，CHENG Ze-kun. Numerical study on performance of waterfront excavation[J]. Chinese Journal of Geotechnical Engineering，2013，35(2):515-521. Wu L M, Wang Z Q. Three gorges reservoir water level fluctuation influents on the stability of the slope[J]. Advanced Materials Research. Trans Tech Publications, 2013, 739: 283-286.

p-exponent and p-leaders, Part II: Multifractal analysis. Relations to detrended fluctuation analysis

NASA Astrophysics Data System (ADS)

Leonarduzzi, R.; Wendt, H.; Abry, P.; Jaffard, S.; Melot, C.; Roux, S. G.; Torres, M. E.

2016-04-01

Multifractal analysis studies signals, functions, images or fields via the fluctuations of their local regularity along time or space, which capture crucial features of their temporal/spatial dynamics. It has become a standard signal and image processing tool and is commonly used in numerous applications of different natures. In its common formulation, it relies on the Hölder exponent as a measure of local regularity, which is by nature restricted to positive values and can hence be used for locally bounded functions only. In this contribution, it is proposed to replace the Hölder exponent with a collection of novel exponents for measuring local regularity, the p-exponents. One of the major virtues of p-exponents is that they can potentially take negative values. The corresponding wavelet-based multiscale quantities, the p-leaders, are constructed and shown to permit the definition of a new multifractal formalism, yielding an accurate practical estimation of the multifractal properties of real-world data. Moreover, theoretical and practical connections to and comparisons against another multifractal formalism, referred to as multifractal detrended fluctuation analysis, are achieved. The performance of the proposed p-leader multifractal formalism is studied and compared to previous formalisms using synthetic multifractal signals and images, illustrating its theoretical and practical benefits. The present contribution is complemented by a companion article studying in depth the theoretical properties of p-exponents and the rich classification of local singularities it permits.

Two-dimensional infrared spectroscopy of intermolecular hydrogen bonds in the condensed phase.

PubMed

Elsaesser, Thomas

2009-09-15

Hydrogen bonding plays a key role in the structural, physical, and chemical properties of liquids such as water and in macromolecular structures such as proteins. Vibrational spectroscopy is an important tool for understanding hydrogen bonding because it provides a way to observe local molecular geometries and their interaction with the environment. Linear vibrational spectroscopy has mapped characteristic changes of vibrational spectra and the occurrence of new bands that form upon hydrogen bonding. However, linear vibrational spectroscopy gives very limited insight into ultrafast dynamics of the underlying molecular interactions, such as the motions of hydrogen-bonded groups, energy dissipation and delocalization, and the fluctuations within hydrogen-bonded structures that occur in the ultrafast time domain. Nonlinear vibrational spectroscopy with its femtosecond time resolution can discern these dynamic processes in real time and has emerged as an important tool for unraveling molecular dynamics and for quantifying interactions that govern the vibrational and structural dynamics of hydrogen bonds. This Account reviews recent progress originating from third-order nonlinear methods of coherent multidimensional vibrational spectroscopy. Ultrafast dynamics of intermolecular hydrogen bonds are addressed for a number of prototype systems: hydrogen-bonded carboxylic acid dimers in an aprotic liquid environment, the disordered fluctuating hydrogen-bond network of liquid water, and DNA oligomers interacting with water. Cyclic carboxylic acid dimers display a rich scheme of vibrational couplings, resulting in OH stretching absorption bands with highly complex spectral envelopes. Two-dimensional spectroscopy of acetic acid dimers in a nonpolar liquid environment demonstrates that multiple Fermi resonances of the OH stretching mode with overtones and combination tones of fingerprint vibrations dominate both the 2D and linear absorption spectra. The coupling of the OH stretching mode with low-frequency hydrogen-bonding modes leads to additional progressions and coherent low-frequency hydrogen-bond motions in the subpicosecond time domain. In water, the 2D spectra reveal ultrafast spectral diffusion on a sub-100 fs time scale caused by the ultrafast structural fluctuations of the strongly coupled hydrogen-bond network. Librational motions play a key role for the ultrafast loss of structural memory. Spectral diffusion rates are enhanced by resonant transfer of OH stretching quanta between water molecules, typically occurring on a 100 fs time scale. In DNA oligomers, femtosecond nonlinear vibrational spectroscopy resolves NH and OH stretching bands in the highly congested infrared spectra of these molecules, which contain alternating adenine-thymine pairs. Studies at different levels of hydration reveal the spectral signatures of water molecules directly interacting with the phosphate groups of DNA and of a second water species forming a fluctuating environment around the DNA oligomers. We expect that the application of 2D infrared spectroscopy in an extended spectral range will reveal the intrinsic coupling between water and specific functional units of DNA.

Dynamical Vertex Approximation for the Hubbard Model

NASA Astrophysics Data System (ADS)

Toschi, Alessandro

A full understanding of correlated electron systems in the physically relevant situations of three and two dimensions represents a challenge for the contemporary condensed matter theory. However, in the last years considerable progress has been achieved by means of increasingly more powerful quantum many-body algorithms, applied to the basic model for correlated electrons, the Hubbard Hamiltonian. Here, I will review the physics emerging from studies performed with the dynamical vertex approximation, which includes diagrammatic corrections to the local description of the dynamical mean field theory (DMFT). In particular, I will first discuss the phase diagram in three dimensions with a special focus on the commensurate and incommensurate magnetic phases, their (quantum) critical properties, and the impact of fluctuations on electronic lifetimes and spectral functions. In two dimensions, the effects of non-local fluctuations beyond DMFT grow enormously, determining the appearance of a low-temperature insulating behavior for all values of the interaction in the unfrustrated model: Here the prototypical features of the Mott-Hubbard metal-insulator transition, as well as the existence of magnetically ordered phases, are completely overwhelmed by antiferromagnetic fluctuations of exponentially large extension, in accordance with the Mermin-Wagner theorem. Eventually, by a fluctuation diagnostics analysis of cluster DMFT self-energies, the same magnetic fluctuations are identified as responsible for the pseudogap regime in the holed-doped frustrated case, with important implications for the theoretical modeling of the cuprate physics.

Drude weight fluctuations in many-body localized systems

NASA Astrophysics Data System (ADS)

Filippone, Michele; Brouwer, Piet W.; Eisert, Jens; von Oppen, Felix

2016-11-01

We numerically investigate the distribution of Drude weights D of many-body states in disordered one-dimensional interacting electron systems across the transition to a many-body localized phase. Drude weights are proportional to the spectral curvatures induced by magnetic fluxes in mesoscopic rings. They offer a method to relate the transition to the many-body localized phase to transport properties. In the delocalized regime, we find that the Drude weight distribution at a fixed disorder configuration agrees well with the random-matrix-theory prediction P (D ) ∝(γ2+D2) -3 /2 , although the distribution width γ strongly fluctuates between disorder realizations. A crossover is observed towards a distribution with different large-D asymptotics deep in the many-body localized phase, which however differs from the commonly expected Cauchy distribution. We show that the average distribution width <γ >, rescaled by L Δ ,Δ being the average level spacing in the middle of the spectrum and L the systems size, is an efficient probe of the many-body localization transition, as it increases (vanishes) exponentially in the delocalized (localized) phase.

[Locally weighted least squares estimation of DPOAE evoked by continuously sweeping primaries].

PubMed

Han, Xiaoli; Fu, Xinxing; Cui, Jie; Xiao, Ling

2013-12-01

Distortion product otoacoustic emission (DPOAE) signal can be used for diagnosis of hearing loss so that it has an important clinical value. Continuously using sweeping primaries to measure DPOAE provides an efficient tool to record DPOAE data rapidly when DPOAE is measured in a large frequency range. In this paper, locally weighted least squares estimation (LWLSE) of 2f1-f2 DPOAE is presented based on least-squares-fit (LSF) algorithm, in which DPOAE is evoked by continuously sweeping tones. In our study, we used a weighted error function as the loss function and the weighting matrixes in the local sense to obtain a smaller estimated variance. Firstly, ordinary least squares estimation of the DPOAE parameters was obtained. Then the error vectors were grouped and the different local weighting matrixes were calculated in each group. And finally, the parameters of the DPOAE signal were estimated based on least squares estimation principle using the local weighting matrixes. The simulation results showed that the estimate variance and fluctuation errors were reduced, so the method estimates DPOAE and stimuli more accurately and stably, which facilitates extraction of clearer DPOAE fine structure.

Fluctuation relations between hierarchical kinetically equivalent networks with Arrhenius-type transitions and their roles in systems and structural biology.

PubMed

Deng, De-Ming; Lu, Yi-Ta; Chang, Cheng-Hung

2017-06-01

The legality of using simple kinetic schemes to determine the stochastic properties of a complex system depends on whether the fluctuations generated from hierarchical equivalent schemes are consistent with one another. To analyze this consistency, we perform lumping processes on the stochastic differential equations and the generalized fluctuation-dissipation theorem and apply them to networks with the frequently encountered Arrhenius-type transition rates. The explicit Langevin force derived from those networks enables us to calculate the state fluctuations caused by the intrinsic and extrinsic noises on the free energy surface and deduce their relations between kinetically equivalent networks. In addition to its applicability to wide classes of network related systems, such as those in structural and systems biology, the result sheds light on the fluctuation relations for general physical variables in Keizer's canonical theory.

Time scale defined by the fractal structure of the price fluctuations in foreign exchange markets

NASA Astrophysics Data System (ADS)

Kumagai, Yoshiaki

2010-04-01

In this contribution, a new time scale named C-fluctuation time is defined by price fluctuations observed at a given resolution. The intraday fractal structures and the relations of the three time scales: real time (physical time), tick time and C-fluctuation time, in foreign exchange markets are analyzed. The data set used is trading prices of foreign exchange rates; US dollar (USD)/Japanese yen (JPY), USD/Euro (EUR), and EUR/JPY. The accuracy of the data is one minute and data within a minute are recorded in order of transaction. The series of instantaneous velocity of C-fluctuation time flowing are exponentially distributed for small C when they are measured by real time and for tiny C when they are measured by tick time. When the market is volatile, for larger C, the series of instantaneous velocity are exponentially distributed.

Effect of pressure fluctuations on Richtmyer-Meshkov coherent structures

NASA Astrophysics Data System (ADS)

Bhowmick, Aklant K.; Abarzhi, Snezhana

2016-11-01

We investigate the formation and evolution of Richtmyer Meshkov bubbles after the passage of a shock wave across a two fluid interface in the presence of pressure fluctuations. The fluids are ideal and incompressible and the pressure fluctuations are scale invariant in space and time, and are modeled by a power law time dependent acceleration field with exponent -2. Solutions indicate sensitivity to pressure fluctuations. In the linear regime, the growth of curvature and bubble velocity is linear. The growth rate is dominated by the initial velocity for weak pressure fluctuations, and by the acceleration term for strong pressure fluctuations. In the non-linear regime, the bubble curvature is constant and the solutions form a one parameter family (parametrized by the bubble curvature). The solutions are shown to be convergent and asymptotically stable. The physical solution (stable fastest growing) is a flat bubble for small pressure fluctuations and a curved bubble for large pressure fluctuations. The velocity field (in the frame of references accounting for the background motion) involves intense motion of the fluids in a vicinity of the interface, effectively no motion of the fluids away from the interfaces, and formation of vortical structures at the interface. The work is supported by the US National Science Foundation.

Effect of pressure fluctuations on Richtmyer-Meshkov coherent structures

NASA Astrophysics Data System (ADS)

Bhowmick, Aklant K.; Abarzhi, Snezhana

2016-10-01

We investigate the formation and evolution of Richtmyer Meshkov bubbles after the passage of a shock wave across a two fluid interface in the presence of pressure fluctuations. The fluids are ideal and incompressible and the pressure fluctuations are scale invariant in space and time, and are modeled by a power law time dependent acceleration field with exponent -2. Solutions indicate sensitivity to pressure fluctuations. In the linear regime, the growth of curvature and bubble velocity is linear. The growth rate is dominated by the initial velocity for weak pressure fluctuations, and by the acceleration term for strong pressure fluctuations. In the non-linear regime, the bubble curvature is constant and the solutions form a one parameter family (parametrized by the bubble curvature). The solutions are shown to be convergent and asymptotically stable. The physical solution (stable fastest growing) is a flat bubble for small pressure fluctuations and a curved bubble for large pressure fluctuations. The velocity field (in the frame of references accounting for the background motion) involves intense motion of the fluids in a vicinity of the interface, effectively no motion of the fluids away from the interfaces, and formation of vortical structures at the interface. The work is supported by the US National Science Foundation.

Local oscillator induced degradation of medium-term stability in passive atomic frequency standards

NASA Technical Reports Server (NTRS)

Dick, G. John; Prestage, John D.; Greenhall, Charles A.; Maleki, Lute

1990-01-01

As the performance of passive atomic frequency standards improves, a new limitation is encountered due to frequency fluctuations in an ancillary local oscillator (L.O.). The effect is due to time variation in the gain of the feedback which compensates L.O. frequency fluctuations. The high performance promised by new microwave and optical trapped ion standards may be severely compromised by this effect. Researchers present an analysis of this performance limitation for the case of sequentially interrogated standards. The time dependence of the sensitivity of the interrogation process to L.O. frequency fluctuations is evaluated for single-pulse and double-pulse Ramsey RF interrogation and for amplitude modulated pulses. The effect of these various time dependencies on performance of the standard is calculated for an L.O. with frequency fluctuations showing a typical 1/f spectral density. A limiting 1/sq. root gamma dependent deviation of frequency fluctuations is calculated as a function of pulse lengths, dead time, and pulse overlap. Researchers also present conceptual and hardware-oriented solutions to this problem which achieve a much more nearly constant sensitivity to L.O. fluctuations. Solutions involve use of double-pulse interrogation; alternate interrogation of multiple traps so that the dead time of one trap can be covered by operation of the other; and the use of double-pulse interrogation for two traps, so that during the time of the RF pulses, the increasing sensitivity of one trap tends to compensate for the decreasing sensitivity of the other. A solution making use of amplified-modulated pulses is also presented which shows nominally zero time variation.

Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation

PubMed Central

Moritsugu, Kei; Koike, Ryotaro; Yamada, Kouki; Kato, Hiroaki; Kidera, Akinori

2015-01-01

Molecular dynamics (MD) simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely to be hidden behind their complicated motions with a wide range of spatial and temporal scales. A straightforward and intuitive analysis of protein dynamics observed in MD simulation trajectories is therefore of growing significance with the large increase in both the simulation time and system size. In this study, we propose a novel description of protein motions based on the hierarchical clustering of fluctuations in the inter-atomic distances calculated from an MD trajectory, which constructs a single tree diagram, named a “Motion Tree”, to determine a set of rigid-domain pairs hierarchically along with associated inter-domain fluctuations. The method was first applied to the MD trajectory of substrate-free adenylate kinase to clarify the usefulness of the Motion Tree, which illustrated a clear-cut dynamics picture of the inter-domain motions involving the ATP/AMP lid and the core domain together with the associated amplitudes and correlations. The comparison of two Motion Trees calculated from MD simulations of ligand-free and -bound glutamine binding proteins clarified changes in inherent dynamics upon ligand binding appeared in both large domains and a small loop that stabilized ligand molecule. Another application to a huge protein, a multidrug ATP binding cassette (ABC) transporter, captured significant increases of fluctuations upon binding a drug molecule observed in both large scale inter-subunit motions and a motion localized at a transmembrane helix, which may be a trigger to the subsequent structural change from inward-open to outward-open states to transport the drug molecule. These applications demonstrated the capabilities of Motion Trees to provide an at-a-glance view of various sizes of functional motions inherent in the complicated MD trajectory. PMID:26148295

The indispensable role of the transversal spin fluctuations mechanism in laser-induced demagnetization of Co/Pt multilayers with nanoscale magnetic domains.

PubMed

Zhang, Wei; He, Wei; Peng, Li-Cong; Zhang, Ying; Cai, Jian-Wang; Evans, Richard F L; Zhang, Xiang-Qun; Cheng, Zhao-Hua

2018-07-06

The switching of magnetic domains induced by an ultrashort laser pulse has been demonstrated in nanostructured ferromagnetic films. This leads to the dawn of a new era in breaking the ultimate physical limit for the speed of magnetic switching and manipulation, which is relevant to current and future information storage. However, our understanding of the interactions between light and spins in magnetic heterostructures with nanoscale domain structures is still lacking. Here, both time-resolved magneto-optical Kerr effect experiments and atomistic simulations are carried out to investigate the dominant mechanism of laser-induced ultrafast demagnetization in [Co/Pt] 20 multilayers with nanoscale magnetic domains. It is found that the ultrafast demagnetization time remains constant with various magnetic configurations, indicating that the domain structures play a minor role in laser-induced ultrafast demagnetization. In addition, both in experiment and atomistic simulations, we find a dependence of ultrafast demagnetization time τ M on the laser fluence, which is in contrast to the observations of spin transport within magnetic domains. The remarkable agreement between experiment and atomistic simulations indicates that the local dissipation of spin angular momentum is the dominant demagnetization mechanism in this system. More interestingly, we made a comparison between the atomistic spin dynamic simulation and the longitudinal spin flip model, highlighting that the transversal spin fluctuations mechanism is responsible for the ultrafast demagnetization in the case of inhomogeneous magnetic structures. This is a significant advance in clarifying the microscopic mechanism underlying the process of ultrafast demagnetization in inhomogeneous magnetic structures.

How amide hydrogens exchange in native proteins.

PubMed

Persson, Filip; Halle, Bertil

2015-08-18

Amide hydrogen exchange (HX) is widely used in protein biophysics even though our ignorance about the HX mechanism makes data interpretation imprecise. Notably, the open exchange-competent conformational state has not been identified. Based on analysis of an ultralong molecular dynamics trajectory of the protein BPTI, we propose that the open (O) states for amides that exchange by subglobal fluctuations are locally distorted conformations with two water molecules directly coordinated to the N-H group. The HX protection factors computed from the relative O-state populations agree well with experiment. The O states of different amides show little or no temporal correlation, even if adjacent residues unfold cooperatively. The mean residence time of the O state is ∼100 ps for all examined amides, so the large variation in measured HX rate must be attributed to the opening frequency. A few amides gain solvent access via tunnels or pores penetrated by water chains including native internal water molecules, but most amides access solvent by more local structural distortions. In either case, we argue that an overcoordinated N-H group is necessary for efficient proton transfer by Grotthuss-type structural diffusion.

How amide hydrogens exchange in native proteins

PubMed Central

Persson, Filip; Halle, Bertil

2015-01-01

Amide hydrogen exchange (HX) is widely used in protein biophysics even though our ignorance about the HX mechanism makes data interpretation imprecise. Notably, the open exchange-competent conformational state has not been identified. Based on analysis of an ultralong molecular dynamics trajectory of the protein BPTI, we propose that the open (O) states for amides that exchange by subglobal fluctuations are locally distorted conformations with two water molecules directly coordinated to the N–H group. The HX protection factors computed from the relative O-state populations agree well with experiment. The O states of different amides show little or no temporal correlation, even if adjacent residues unfold cooperatively. The mean residence time of the O state is ∼100 ps for all examined amides, so the large variation in measured HX rate must be attributed to the opening frequency. A few amides gain solvent access via tunnels or pores penetrated by water chains including native internal water molecules, but most amides access solvent by more local structural distortions. In either case, we argue that an overcoordinated N–H group is necessary for efficient proton transfer by Grotthuss-type structural diffusion. PMID:26195754

Observation of the electron density fluctuations by using the O-mode Microwave Imaging Reflectometry in LHD

NASA Astrophysics Data System (ADS)

Nagayama, Yoshio; Yamaguchi, Soichiro; Tsuchiya, Hayato; Kuwahara, Daisuke; LHD Experimental Team

2016-10-01

Visualization of local electron density fluctuations will be very useful to study the physics of confinement and instabilities in fusion plasma. In the Large Helical Device (LHD), the O-mode microwave imaging reflectometry (O-MIR) has been intensively developed in order to visualize the electron density fluctuations. The frequency is 26 - 34 GHz. This corresponds to the electron density of 0.8 - 1.5 × 1019 m-3. The plasma is illuminated by the Gaussian beam with four frequencies. The imaging optics make a plasma image onto the newly developed 2D (8 × 8) Horn-antenna Millimeter-wave Imaging Device (HMID). In HMID, the signal wave that is accumulated by the horn antenna is transduced to the micro-strip line by using the finline transducer. The signal wave is mixed by the double balanced mixer with the local wave that is delivered by cables. By using O-MIR, electron density fluctuations are measured at the H-mode edge and the ITB layer in LHD. This work is supported by NIFS/NINS under the project of Formation of International Scientific Base and Network, by the NIFS LHD project, by KAKENHI, and by IMS.

Local Energies and Energy Fluctuations — Applied to the High Entropy Alloy CrFeCoNi

NASA Astrophysics Data System (ADS)

Fukushima, Tetsuya; Katayama-Yoshida, Hiroshi; Sato, Kazunori; Ogura, Masako; Zeller, Rudolf; Dederichs, Peter H.

2017-11-01

High entropy alloys show a variety of fascinating properties like high hardness, wear resistance, corrosion resistance, etc. They are random solid solutions of many components with rather high concentrations. We perform ab-initio calculations for the high entropy alloy CrFeCoNi, which equal concentration of 25% for each element. By the KKRnano program package, which is based on an order-N screened Korringa-Kohn-Rostoker Green's function method, we consider a face-centered cubic (FCC) supercell with 1372 randomly distributed elements, and in addition also smaller supercells with 500 and 256 atoms. It is found from our calculations that the local moments of the Cr atoms show a large environmental variation, ranging from -1.70 μB to +1.01 μB with an average of about -0.51 μB. We present a new method to calculate "local energies" of all atoms. This is based on the partitioning of the whole space into Voronoi cells and allows to calculate the energetic contribution of each atomic cell to the total energy of the supercell. The supercell calculations show very large variations of the local energies, analogous to the variations of the local moments. This shows that the random solid solution is not stable and has a tendency to form an L12-structure with the Cr-atoms ordered at the corner of the cube and the elements Fe, Co, and Ni randomly distributed on the three other FCC sublattices. For this structure the variation of the local moments are much smaller.

Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly

PubMed Central

Hanski, Ilkka A.

2011-01-01

Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time. PMID:21788506

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

Sasakura, Naoki

The tensor model is discussed as theory of dynamical fuzzy spaces in order to formulate gravity on fuzzy spaces. The numerical analyses of the tensor models possessing Gaussian background solutions have shown that the low-lying long-wavelength fluctuations around the backgrounds are in remarkable agreement with the geometric fluctuations on flat spaces in the general relativity. It has also been shown that part of the orthogonal symmetry of the tensor model spontaneously broken by the backgrounds agrees with the local translation symmetry of the general relativity. Thus the tensor model provides an interesting model of simultaneous emergence of space, the generalmore » relativity, and its local translation symmetry.« less

Effective Lagrangian in de Sitter spacetime

NASA Astrophysics Data System (ADS)

Kitamoto, Hiroyuki; Kitazawa, Yoshihisa

2017-01-01

Scale invariant fluctuations of metric are a universal feature of quantum gravity in de Sitter spacetime. We construct an effective Lagrangian which summarizes their implications on local physics by integrating superhorizon metric fluctuations. It shows infrared quantum effects are local and render fundamental couplings time dependent. We impose Lorenz invariance on the effective Lagrangian as it is required by the principle of general covariance. We show that such a requirement leads to unique physical predictions by fixing the quantization ambiguities. We explain how the gauge parameter dependence of observables is canceled. In particular the relative evolution speed of the couplings are shown to be gauge invariant.

Environmental Noise Could Promote Stochastic Local Stability of Behavioral Diversity Evolution

NASA Astrophysics Data System (ADS)

Zheng, Xiu-Deng; Li, Cong; Lessard, Sabin; Tao, Yi

2018-05-01

In this Letter, we investigate stochastic stability in a two-phenotype evolutionary game model for an infinite, well-mixed population undergoing discrete, nonoverlapping generations. We assume that the fitness of a phenotype is an exponential function of its expected payoff following random pairwise interactions whose outcomes randomly fluctuate with time. We show that the stochastic local stability of a constant interior equilibrium can be promoted by the random environmental noise even if the system may display a complicated nonlinear dynamics. This result provides a new perspective for a better understanding of how environmental fluctuations may contribute to the evolution of behavioral diversity.

[Local fractal analysis of noise-like time series by all permutations method for 1-115 min periods].

PubMed

Panchelyuga, V A; Panchelyuga, M S

2015-01-01

Results of local fractal analysis of 329-per-day time series of 239Pu alpha-decay rate fluctuations by means of all permutations method (APM) are presented. The APM-analysis reveals in the time series some steady frequency set. The coincidence of the frequency set with the Earth natural oscillations was demonstrated. A short review of works by different authors who analyzed the time series of fluctuations in processes of different nature is given. We have shown that the periods observed in those works correspond to the periods revealed in our study. It points to a common mechanism of the phenomenon observed.

Charged particle dynamics in the presence of non-Gaussian Lévy electrostatic fluctuations

DOE PAGES

Del-Castillo-Negrete, Diego B.; Moradi, Sara; Anderson, Johan

2016-09-01

Full orbit dynamics of charged particles in a 3-dimensional helical magnetic field in the presence of -stable Levy electrostatic fluctuations and linear friction modeling collisional Coulomb drag is studied via Monte Carlo numerical simulations. The Levy fluctuations are introduced to model the effect of non-local transport due to fractional diffusion in velocity space resulting from intermittent electrostatic turbulence. The probability distribution functions of energy, particle displacements, and Larmor radii are computed and showed to exhibit a transition from exponential decay, in the case of Gaussian fluctuations, to power law decay in the case of Levy fluctuations. The absolute value ofmore » the power law decay exponents are linearly proportional to the Levy index. Furthermore, the observed anomalous non-Gaussian statistics of the particles' Larmor radii (resulting from outlier transport events) indicate that, when electrostatic turbulent fluctuations exhibit non-Gaussian Levy statistics, gyro-averaging and guiding centre approximations might face limitations and full particle orbit effects should be taken into account.« less

Charged particle dynamics in the presence of non-Gaussian Lévy electrostatic fluctuations

NASA Astrophysics Data System (ADS)

Moradi, Sara; del-Castillo-Negrete, Diego; Anderson, Johan

2016-09-01

Full orbit dynamics of charged particles in a 3-dimensional helical magnetic field in the presence of α-stable Lévy electrostatic fluctuations and linear friction modeling collisional Coulomb drag is studied via Monte Carlo numerical simulations. The Lévy fluctuations are introduced to model the effect of non-local transport due to fractional diffusion in velocity space resulting from intermittent electrostatic turbulence. The probability distribution functions of energy, particle displacements, and Larmor radii are computed and showed to exhibit a transition from exponential decay, in the case of Gaussian fluctuations, to power law decay in the case of Lévy fluctuations. The absolute value of the power law decay exponents is linearly proportional to the Lévy index α. The observed anomalous non-Gaussian statistics of the particles' Larmor radii (resulting from outlier transport events) indicate that, when electrostatic turbulent fluctuations exhibit non-Gaussian Lévy statistics, gyro-averaging and guiding centre approximations might face limitations and full particle orbit effects should be taken into account.

Correlations between quasi-coherent fluctuations and the pedestal evolution during the inter-edge localized modes phase on DIII-D

DOE PAGES

Diallo, A.; Groebner, R. J.; Rhodes, T. L.; ...

2015-05-15

Direct measurements of the pedestal recovery during an edge-localized mode cycle provide evidence that quasi-coherent fluctuations (QCFs) play a role in the inter-ELM pedestal dynamics. When using fast Thomson scattering measurements, we found that the pedestal density and temperature evolutions are probed on sub-millisecond time scales to show a fast recovery of the density gradient compared to the temperature gradient. The temperature gradient appears to provide a drive for the onset of quasi-coherent fluctuations (as measured with the magnetic probe and the density diagnostics) localized in the pedestal. The amplitude evolution of these QCFs tracks the temperature gradient evolution includingmore » its saturation. Such correlation suggests that these QCFs play a key role in limiting the pedestal temperature gradient. Moreover, the saturation of the QCFs coincides with the pressure gradient reaching the kinetic-ballooning mode (KBM) critical gradient as predicted by EPED1. Furthermore, linear microinstability analysis using GS2 indicates that the steep gradient is near the KBM threshold. Finally, the modeling and the observations together suggest that QCFs are consistent with dominant KBMs, although microtearing cannot be excluded as subdominant.« less

Quantum-gravity predictions for the fine-structure constant

NASA Astrophysics Data System (ADS)

Eichhorn, Astrid; Held, Aaron; Wetterich, Christof

2018-07-01

Asymptotically safe quantum fluctuations of gravity can uniquely determine the value of the gauge coupling for a large class of grand unified models. In turn, this makes the electromagnetic fine-structure constant calculable. The balance of gravity and matter fluctuations results in a fixed point for the running of the gauge coupling. It is approached as the momentum scale is lowered in the transplanckian regime, leading to a uniquely predicted value of the gauge coupling at the Planck scale. The precise value of the predicted fine-structure constant depends on the matter content of the grand unified model. It is proportional to the gravitational fluctuation effects for which computational uncertainties remain to be settled.

Geometric and energetic considerations of surface fluctuations during ion transfer across the water-immiscible organic liquid interface

NASA Astrophysics Data System (ADS)

Karnes, John J.; Benjamin, Ilan

2016-07-01

Molecular dynamics simulations and umbrella sampling free energy calculations are used to examine the thermodynamics, energetics, and structural fluctuations that accompany the transfer of a small hydrophilic ion (Cl-) across the water/nitrobenzene interface. By examining several constrained interface structures, we isolate the energetic costs of interfacial deformation and co-transfer of hydration waters during the ion transfer. The process is monitored using both energy-based solvation coordinates and a geometric coordinate recently introduced by Morita and co-workers to describe surface fluctuations. Our simulations show that these coordinates provide a complimentary description of the water surface fluctuations during the transfer and are necessary for elucidating the mechanism of the ion transfer.

2D microwave imaging reflectometer electronics.

PubMed

Spear, A G; Domier, C W; Hu, X; Muscatello, C M; Ren, X; Tobias, B J; Luhmann, N C

2014-11-01

A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program.

Structural fluctuation governed dynamic diradical character in pentacene.

PubMed

Yang, Hongfang; Chen, Mengzhen; Song, Xinyu; Bu, Yuxiang

2015-06-07

We unravel intriguing dynamical diradical behavior governed by structural fluctuation in pentacene using ab initio molecular dynamics simulation. In contrast to static equilibrium configuration of pentacene with a closed-shell ground state without diradical character, due to structural fluctuation, some of its dynamical snapshot configurations exhibit an open-shell broken-symmetry singlet ground state with diradical character, and such diradical character presents irregular pulsing behavior in time evolution. Not all structural changes can lead to diradical character, only those involving the shortening of cross-linking C-C bonds and variations of the C-C bonds in polyacetylene chains are the main contributors. This scenario about diradicalization is distinctly different from that in long acenes. The essence is that structural distortion cooperatively raises the HOMO and lowers the LUMO, efficiently reducing the HOMO-LUMO and singlet-triplet energy gaps, which facilitate the formation of a broken-symmetry open-shell singlet state. The irregular pulsing behavior originates from the mixing of normal vibrations in pentacene. This fascinating behavior suggests the potential application of pentacene as a suitable building block in the design of new electronic devices due to its magnetism-controllability through energy induction. This work provides new insight into inherent electronic property fluctuation in acenes.

Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations

PubMed Central

Im, Wonpil; Brooks, Charles L.

2005-01-01

The mechanism of interfacial folding and membrane insertion of designed peptides is explored by using an implicit membrane generalized Born model and replica-exchange molecular dynamics. Folding/insertion simulations initiated from fully extended peptide conformations in the aqueous phase, at least 28 Å away from the membrane interface, demonstrate a general mechanism for structure formation and insertion (when it occurs). The predominately hydrophobic peptides from the synthetic WALP and TMX series first become localized at the membrane-solvent interface where they form significant helical secondary structure via a helix–turn–helix motif that inserts the central hydrophobic residues into the membrane interior, and then fluctuations occur that provide a persistent helical structure throughout the peptide and it inserts with its N-terminal end moving across the membrane. More specifically, we observed that: (i) the WALP peptides (WALP16, WALP19, and WALP23) spontaneously insert in the membrane as just noted; (ii) TMX-1 also inserts spontaneously after a similar mechanism and forms a transmembrane helix with a population of ≈50% at 300 K; and (iii) TMX-3 does not insert, but exists in a fluctuating membrane interface-bound form. These findings are in excellent agreement with available experimental data and demonstrate the potential for new implicit solvent/membrane models together with advanced simulation protocols to guide experimental programs in exploring the nature and mechanism of membrane-associated folding and insertion of biologically important peptides. PMID:15860587

Compensatory Water Effects Link Yearly Global Land CO2 Sink Changes to Temperature

NASA Technical Reports Server (NTRS)

Jung, Martin; Reichstein, Markus; Tramontana, Gianluca; Viovy, Nicolas; Schwalm, Christopher R.; Wang, Ying-Ping; Weber, Ulrich; Weber, Ulrich; Zaehle, Soenke; Zeng, Ning;

Structural changes and fluctuations of proteins. I. A statistical thermodynamic model.

PubMed

Ikegami, A

1977-01-01

A general theory of the structural changes and fluctuations of proteins has been proposed based on statistical thermodynamic considerations at the chain level. The "structure" of protein was assumed to be characterized by the state of secondary bonds between unique pairs of specific sites on peptide chains. Every secondary bond changes between the bonded and unbonded states by thermal agitation and the "structure" is continuously fluctuating. The free energy of the "structural state" that is defined by the fraction of secondary bonds in the bonded state has been expressed by the bond energy, the cooperative interaction between bonds, the mixing entropy of bonds, and the entropy of polypeptide chains. The most probable "structural state" can be simply determined by graphical analysis and the effect of temperature or solvent composition on it is discussed. The temperature dependence of the free energy, the probability distribution of structural states and the specific heat have been calculted for two examples of structural change. The theory predicts two different types of structural changes from the ordered to disorderd state, a "structured transition" and a "gradual structural change" with rising temperature. In the "structural transition", the probability distribution has two maxima in the temperature range of transition. In the "gradual structural change", the probabilty distribution has only one maximum during the change. A considerable fraction of secondary bonds is in the unbounded state and is always fluctuating even in the ordered state at room temperature. Such structural flucutations in a single protein molecule have been discussed quantitatively. The theory is extended to include small molecules which bind to the protein molecule and affect the structural state. The changes of structural state caused by specific and non-specific binding and allosteric effects are explained in a unified manner.

Mosaic organization of DNA nucleotides

NASA Technical Reports Server (NTRS)

Peng, C. K.; Buldyrev, S. V.; Havlin, S.; Simons, M.; Stanley, H. E.; Goldberger, A. L.

1994-01-01

Long-range power-law correlations have been reported recently for DNA sequences containing noncoding regions. We address the question of whether such correlations may be a trivial consequence of the known mosaic structure ("patchiness") of DNA. We analyze two classes of controls consisting of patchy nucleotide sequences generated by different algorithms--one without and one with long-range power-law correlations. Although both types of sequences are highly heterogenous, they are quantitatively distinguishable by an alternative fluctuation analysis method that differentiates local patchiness from long-range correlations. Application of this analysis to selected DNA sequences demonstrates that patchiness is not sufficient to account for long-range correlation properties.

Motile bacteria in a critical fluid mixture

NASA Astrophysics Data System (ADS)

Koumakis, Nick; Devailly, Clémence; Poon, Wilson C. K.

2018-06-01

We studied the swimming of Escherichia coli bacteria in the vicinity of the critical point in a solution of the nonionic surfactant C12E5 in buffer solution. In phase-contrast microscopy, each swimming cell produces a transient trail behind itself lasting several seconds. Comparing quantitative image analysis with simulations show that these trails are due to local phase reorganization triggered by differential adsorption. This contrasts with similar trails seen in bacteria swimming in liquid crystals, which are due to shear effects. We show how our trails are controlled, and use them to probe the structure and dynamics of critical fluctuations in the fluid medium.

Role of magnetism in superconductivity of BaFe 2As 2: Study of 5d Au-doped crystals

DOE PAGES

Li, Li; Cao, Huibo; McGuire, Michael A.; ...

2015-09-09

We investigate properties of BaFe 2As 2 (122) single crystals upon gold doping, which is the transition metal with the highest atomic weight. The Au substitution into the FeAs-planes of 122 crystal structure (Au-122) is only possible up to a small amount of ~3%. We find that 5d is more effective in reducing magnetism in 122 than its counter 3d Cu, and this relates to superconductivity. We provide evidence of short-range magnetic fluctuations and local lattice inhomogeneities that may prevent strong percolative superconductivity in Ba(Fe 1-xAu x)2As 2.

Pseudogap temperature and effects of a harmonic trap in the BCS-BEC crossover regime of an ultracold Fermi gas

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

Tsuchiya, Shunji; Research and Education Center for Natural Sciences, Keio University, 4-1-1 Hiyoshi, Kanagawa 223-8521; CREST

2011-10-15

We theoretically investigate excitation properties in the pseudogap regime of a trapped Fermi gas. Using a combined T-matrix theory with the local density approximation, we calculate strong-coupling corrections to single-particle local density of states (LDOS), as well as the single-particle local spectral weight (LSW). Starting from the superfluid phase transition temperature T{sub c}, we clarify how the pseudogap structures in these quantities disappear with increasing the temperature. As in the case of a uniform Fermi gas, LDOS and LSW give different pseudogap temperatures T{sup *} and T{sup **} at which the pseudogap structures in these quantities completely disappear. Determining T{supmore » *} and T{sup **} over the entire BCS (Bardeen-Cooper-Schrieffer)-BEC (Bose-Einstein condensation) crossover region, we identify the pseudogap regime in the phase diagram with respect to the temperature and the interaction strength. We also show that the so-called back-bending peak recently observed in the photoemission spectra by the JILA group may be explained as an effect of pseudogap phenomenon in the trap center. Since strong pairing fluctuations, spatial inhomogeneity, and finite temperatures are important keys in considering real cold Fermi gases, our results would be useful for clarifying normal-state properties of this strongly interacting Fermi system.« less

Tracking Architecture Based on Dual-Filter with State Feedback and Its Application in Ultra-Tight GPS/INS Integration

PubMed Central

Zhang, Xi; Miao, Lingjuan; Shao, Haijun

2016-01-01

If a Kalman Filter (KF) is applied to Global Positioning System (GPS) baseband signal preprocessing, the estimates of signal phase and frequency can have low variance, even in highly dynamic situations. This paper presents a novel preprocessing scheme based on a dual-filter structure. Compared with the traditional model utilizing a single KF, this structure avoids carrier tracking being subjected to code tracking errors. Meanwhile, as the loop filters are completely removed, state feedback values are adopted to generate local carrier and code. Although local carrier frequency has a wide fluctuation, the accuracy of Doppler shift estimation is improved. In the ultra-tight GPS/Inertial Navigation System (INS) integration, the carrier frequency derived from the external navigation information is not viewed as the local carrier frequency directly. That facilitates retaining the design principle of state feedback. However, under harsh conditions, the GPS outputs may still bear large errors which can destroy the estimation of INS errors. Thus, an innovative integrated navigation filter is constructed by modeling the non-negligible errors in the estimated Doppler shifts, to ensure INS is properly calibrated. Finally, field test and semi-physical simulation based on telemetered missile trajectory validate the effectiveness of methods proposed in this paper. PMID:27144570

Tracking Architecture Based on Dual-Filter with State Feedback and Its Application in Ultra-Tight GPS/INS Integration.

PubMed

Zhang, Xi; Miao, Lingjuan; Shao, Haijun

2016-05-02

If a Kalman Filter (KF) is applied to Global Positioning System (GPS) baseband signal preprocessing, the estimates of signal phase and frequency can have low variance, even in highly dynamic situations. This paper presents a novel preprocessing scheme based on a dual-filter structure. Compared with the traditional model utilizing a single KF, this structure avoids carrier tracking being subjected to code tracking errors. Meanwhile, as the loop filters are completely removed, state feedback values are adopted to generate local carrier and code. Although local carrier frequency has a wide fluctuation, the accuracy of Doppler shift estimation is improved. In the ultra-tight GPS/Inertial Navigation System (INS) integration, the carrier frequency derived from the external navigation information is not viewed as the local carrier frequency directly. That facilitates retaining the design principle of state feedback. However, under harsh conditions, the GPS outputs may still bear large errors which can destroy the estimation of INS errors. Thus, an innovative integrated navigation filter is constructed by modeling the non-negligible errors in the estimated Doppler shifts, to ensure INS is properly calibrated. Finally, field test and semi-physical simulation based on telemetered missile trajectory validate the effectiveness of methods proposed in this paper.

Free energy landscape of a minimalist salt bridge model.

PubMed

Li, Xubin; Lv, Chao; Corbett, Karen M; Zheng, Lianqing; Wu, Dongsheng; Yang, Wei

2016-01-01

Salt bridges are essential to protein stability and dynamics. Despite the importance, there has been scarce of detailed discussion on how salt bridge partners interact with each other in distinct solvent exposed environments. In this study, employing a recent generalized orthogonal space tempering (gOST) method, we enabled efficient molecular dynamics simulation of repetitive breaking and reforming of salt bridge structures within a minimalist salt-bridge model, the Asp-Arg dipeptide and thereby were able to map its detailed free energy landscape in aqueous solution. Free energy surface analysis shows that although individually-solvated states are more favorable, salt-bridge states still occupy a noticeable portion of the overall population. Notably, the competing forces, e.g. intercharge attractions that drive the formation of salt bridges and solvation forces that pull the charged groups away from each other, are energetically comparable. As the result, the salt bridge stability is highly tunable by local environments; for instance when local water molecules are perturbed to interact more strongly with each other, the population of the salt-bridge states is likely to increase. Our results reveal the critical role of local solvent structures in modulating salt-bridge partner interactions and imply the importance of water fluctuations on conformational dynamics that involves solvent accessible salt bridge formations. © 2015 The Protein Society.

Enhanced emission of fluorophores on shrink-induced wrinkled composite structures.

PubMed

Sharma, Himanshu; Digman, Michelle A; Felsinger, Natasha; Gratton, Enrico; Khine, Michelle

2014-01-01

We introduce a manufacturable and scalable method for creating tunable wrinkled ferromagnetic-metallic structures to enhance fluorescence signals. Thin layers of nickel (Ni) and gold (Au) were deposited onto a pre-stressed thermoplastic (shrink wrap film) polymer. Heating briefly forced the metal films to buckle when the thermoplastic retracted, resulting in multi-scale composite 'wrinkles'. This is the first demonstration of leveraging the plasmons in such hybrid nanostructures by metal enhanced fluorescence (MEF) in the near-infrared wavelengths. We observed more than three orders of magnitude enhancement in the fluorescence signal of a single molecule of goat anti-mouse immunoglobulin G (IgG) antibody conjugated to fluorescein isothiocyanate, FITC, (FITC-IgG) by two-photon excitation with these structures. These large enhancements in the fluorescence signal at the nanoscale gaps between the composite wrinkles corresponded to shortened lifetimes due to localized surface plasmons. To characterize these structures, we combined fluctuation correlation spectroscopy (FCS), fluorescence lifetime imaging microscopy (FLIM), and two-photon microscopy to spatially and temporally map the hot spots with high resolution.

Structural dynamics inside a functionalized metal–organic framework probed by ultrafast 2D IR spectroscopy

DOE PAGES

Nishida, Jun; Tamimi, Amr; Fei, Honghan; ...

2014-12-15

One key property of metal-organic frameworks (MOFs) are their structural elasticity. IHere we show that 2D IR spectroscopy with pulse-shaping techniques can probe the ultrafast structural fluctuations of MOFs. 2D IR data, obtained from a vibrational probe attached to the linkers of UiO-66 MOF in low concentration, revealed that the structural fluctuations have time constants of 7 and 670 ps with no solvent. Filling the MOF pores with dimethylformamide (DMF) slows the structural fluctuations by reducing the ability of the MOF to undergo deformations, and the dynamics of the DMF molecules are also greatly restricted. Finally, methodology advances were requiredmore » to remove the severe light scattering caused by the macroscopic-sized MOF particles, eliminate interfering oscillatory components from the 2D IR data, and address Förster vibrational excitation transfer.« less

Spin-density fluctuations and the fluctuation-dissipation theorem in 3 d ferromagnetic metals

DOE PAGES

Wysocki, Alex L.; Valmispild, V. N.; Kutepov, A.; ...

2017-11-15

Spatial and time scales of spin-density fluctuations (SDFs) were analyzed in 3d ferromagnets using ab initio linear-response calculations of complete wave-vector and energy dependence of the dynamic spin susceptibility tensor. We demonstrate that SDFs are spread continuously over the entire Brillouin zone and while the majority of them reside within the 3d bandwidth, a significant amount comes from much higher energies. A validity of the adiabatic approximation in spin dynamics is discussed. The SDF spectrum is shown to have two main constituents: a minor low-energy spin-wave contribution and a much larger high-energy component from more localized excitations. Furthermore, using themore » fluctuation-dissipation theorem, the on-site spin correlator and the related effective fluctuating moment were properly evaluated and their universal dependence on the 3d band population is further discussed.« less

Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins.

PubMed

Lebard, David N; Matyushov, Dmitry V

2008-12-01

Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of electrostatic fluctuations, expressed in terms of the reorganization energy of changing the redox state of the protein, is related to the formation of the hydrophobic protein-water interface, allowing large-amplitude collective fluctuations of the water density in the protein's first solvation shell. On top of the monotonic increase of the reorganization energy with increasing temperature, we have observed a spike at approximately 220 K also accompanied by a significant slowing of the exponential collective Stokes shift dynamics. In contrast to the local density fluctuations of the hydration-shell waters, these spikes might be related to the global property of the water solvent crossing the Widom line or undergoing a weak first-order transition.

Mechano-genetic DNA hydrogels as a simple, reconstituted model to probe the effect of active fluctuations on gene transcription

NASA Astrophysics Data System (ADS)

Nguyen, Dan; Saleh, Omar

Active fluctuations - non-directed fluctuations attributable, not to thermal energy, but to non-equilibrium processes - are thought to influence biology by increasing the diffusive motion of biomolecules. Dense DNA regions within cells (i.e. chromatin) are expected to exhibit such phenomena, as they are cross-linked networks that continually experience propagating forces arising from dynamic cellular activity. Additional agitation within these gene-encoding DNA networks could have potential genetic consequences. By changing the local mobility of transcriptional machinery and regulatory proteins towards/from their binding sites, and thereby influencing transcription rates, active fluctuations could prove to be a physical means of modulating gene expression. To begin probing this effect, we construct genetic DNA hydrogels, as a simple, reconstituted model of chromatin, and quantify transcriptional output from these hydrogels in the presence/absence of active fluctuations.

Association between magnetic field fluctuations and energetic particle bursts in the earth's magnetotail

NASA Technical Reports Server (NTRS)

Lui, A. T. Y.; Krimigis, S. M.; Armstrong, T. P.

1982-01-01

The association between energetic protons (0.29-0.50 MeV) and simultaneous local fluctuations of magnetic field at 35 to 45 earth radii in the magnetotail is examined statistically with data from APL/JHU particle telescopes aboard IMP 7 and IMP 8. About four satellite years of 5.5 min averaged measurements are used in this study. In addition to confirming that the level of magnetic field fluctuations generally increases with the presence of energetic protons and their streaming anisotropy, it is found that increases in occurrence frequency of streaming of energetic protons are ordered far better by magnetic field fluctuations than by proximity to the neutral sheet. However, the presence of large magnetic field fluctuations (delta B greater than 5 nT or delta B/B greater than 50%) is neither a necessary nor a sufficient condition for the detection of large streaming in energetic protons.

Spin-density fluctuations and the fluctuation-dissipation theorem in 3 d ferromagnetic metals

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

Wysocki, Alex L.; Valmispild, V. N.; Kutepov, A.

Spatial and time scales of spin-density fluctuations (SDFs) were analyzed in 3d ferromagnets using ab initio linear-response calculations of complete wave-vector and energy dependence of the dynamic spin susceptibility tensor. We demonstrate that SDFs are spread continuously over the entire Brillouin zone and while the majority of them reside within the 3d bandwidth, a significant amount comes from much higher energies. A validity of the adiabatic approximation in spin dynamics is discussed. The SDF spectrum is shown to have two main constituents: a minor low-energy spin-wave contribution and a much larger high-energy component from more localized excitations. Furthermore, using themore » fluctuation-dissipation theorem, the on-site spin correlator and the related effective fluctuating moment were properly evaluated and their universal dependence on the 3d band population is further discussed.« less

Microstructural analysis in the depth direction of a heteroepitaxial AlN thick film grown on a trench-patterned template by nanobeam X-ray diffraction

NASA Astrophysics Data System (ADS)

Shida, K.; Takeuchi, S.; Tohei, T.; Miyake, H.; Hiramatsu, K.; Sumitani, K.; Imai, Y.; Kimura, S.; Sakai, A.

2018-04-01

This work quantitatively assessed the three-dimensional distribution of crystal lattice distortions in an epitaxial AlN thick film grown on a trench-patterned template, using nanobeam X-ray diffraction. Position-dependent ω-2θ-φ mapping clearly demonstrated local tilting, spacing and twisting of lattice planes as well as fluctuations in these phenomena on a sub-micrometer scale comparable to the pitch of the trench-and-terrace patterning. Analysis of the crystal lattice distortion in the depth direction was performed using a newly developed method in which the X-ray nanobeam diffracted from the sample surface to specific depths can be selectively detected by employing a Pt wire profiler. This technique generated depth-resolved ω-2θ-φ maps confirming that fluctuations in lattice plane tilting and spacing greatly depend on the dislocation distribution and the history of the AlN epitaxial growth on the trench-patterned structure. It was also found that both fluctuations were reduced on approaching the AlN surface and, in particular, were sharply reduced at specific depths in the terrace regions. These sharp reductions are attributed to the formation of sacrificial zones with degraded crystal quality around the trenches and possibly lead to raising the crystal quality near the surface of the AlN film.

Spontaneous Fluctuations can Guide Drug Design Strategies for Structurally Disordered Proteins.

PubMed

Maity, Barun Kumar; Vishvakarma, Vicky; Surendran, Dayana; Rawat, Anoop; Das, Anirban; Pramanik, Shreya; Arfin, Najmul; Maiti, Sudipta

2018-06-21

Structure-based 'rational' drug-design strategies fail for diseases associated with intrinsically disordered proteins (IDPs). However, structural disorder allows large amplitude spontaneous intramolecular dynamics in a protein. We demonstrate a method that exploits this dynamics to provide quantitative information about the degree of interaction of an IDP with other molecules. A candidate ligand molecule may not bind strongly, but even momentary interactions can be expected to perturb the fluctuations. We measure the amplitude and frequency of the equilibrium fluctuations of fluorescently labeled small oligomers of hIAPP (an IDP associated with Type II diabetes) in a physiological solution, using nanosecond fluorescence cross-correlation spectroscopy. We show that the inter-terminal distance fluctuates at a characteristic timescale of 134 ± 10 ns, and 6.4 ± 0.2 % of the population is in the 'closed' (quenched) state at equilibrium. These fluctuations are affected in a dose-dependent manner by a series of small molecules known to reduce the toxicity of various amyloid peptides. The degree of interaction shows the following order: resveratrol < epicatechin ~ quercetin < congo red < epigallocatechin-3-gallate. Such ordering can provide a direction for exploring the chemical space for finding stronger-binding ligands. We test the biological relevance of these measurements by measuring the effect of these molecules on the affinity of hIAPP for lipid vesicles and cell membranes. We find that the ability of a molecule to modulate intramolecular fluctuations correlates well with its ability to lower membrane affinity. We conclude that structural disorder may provide new avenues for rational drug design for IDPs.

Electron Pitch-Angle Distribution in Pressure Balance Structures Measured by Ulysses/SWOOPS

NASA Technical Reports Server (NTRS)

Yamauchi, Yohei; Suess, Steven T.; Sakurai, Takashi; Six, N. Frank (Technical Monitor)

2002-01-01

Pressure balance structures (PBSs) are a common feature in the high-latitude solar wind near solar minimum. From previous studies, PBSs are believed to be remnants of coronal plumes. Yamauchi et al [2002] investigated the magnetic structures of the PBSs, applying a minimum variance analysis to Ulysses/Magnetometer data. They found that PBSs contain structures like current sheets or plasmoids, and suggested that PBSs are associated with network activity such as magnetic reconnection in the photosphere at the base of polar plumes. We have investigated energetic electron data from Ulysses/SWOOPS to see whether bi-directional electron flow exists and we have found evidence supporting the earlier conclusions. We find that 45 ot of 53 PBSs show local bi-directional or isotopic electron flux or flux associated with current-sheet structure. Only five events show the pitch-angle distribution expected for Alfvenic fluctuations. We conclude that PBSs do contain magnetic structures such as current sheets or plasmoids that are expected as a result of network activity at the base of polar plumes.

Local isotropy and refractive index fluctuations in the surface layer of the atmosphere

NASA Technical Reports Server (NTRS)

Portman, D. J.

1969-01-01

Theoretical and experimental evidence for the existence of local isotropy is briefly examined and conflicting results are found. Recent measurements of temperature spectra support earlier hot wire anemometer and optical scintillation measurements that show little evidence of local isotropy at 1 to 1.5 meters over an extensive uniform and level grass covered field.

INTERPRETATION OF THE STRUCTURE FUNCTION OF ROTATION MEASURE IN THE INTERSTELLAR MEDIUM

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

Xu, Siyao; Zhang, Bing, E-mail: syxu@pku.edu.cn, E-mail: zhang@physics.unlv.edu

2016-06-20

The observed structure function (SF) of rotation measure (RM) varies as a broken power-law function of angular scales. The systematic shallowness of its spectral slope is inconsistent with the standard Kolmogorov scaling. This motivates us to examine the statistical analysis on RM fluctuations. The correlations of RM constructed by Lazarian and Pogosyan are demonstrated to be adequate in explaining the observed features of RM SFs through a direct comparison between the theoretically obtained and observationally measured SF results. By segregating the density and magnetic field fluctuations and adopting arbitrary indices for their respective power spectra, we find that when themore » SFs of RM and emission measure have a similar form over the same range of angular scales, the statistics of the RM fluctuations reflect the properties of density fluctuations. RM SFs can be used to evaluate the mean magnetic field along the line of sight, but cannot serve as an informative source on the properties of turbulent magnetic field in the interstellar medium. We identify the spectral break of RM SFs as the inner scale of a shallow spectrum of electron density fluctuations, which characterizes the typical size of discrete electron density structures in the observed region.« less

Speed hysteresis and noise shaping of traveling fronts in neural fields: role of local circuitry and nonlocal connectivity

NASA Astrophysics Data System (ADS)

Capone, Cristiano; Mattia, Maurizio

2017-01-01

Neural field models are powerful tools to investigate the richness of spatiotemporal activity patterns like waves and bumps, emerging from the cerebral cortex. Understanding how spontaneous and evoked activity is related to the structure of underlying networks is of central interest to unfold how information is processed by these systems. Here we focus on the interplay between local properties like input-output gain function and recurrent synaptic self-excitation of cortical modules, and nonlocal intermodular synaptic couplings yielding to define a multiscale neural field. In this framework, we work out analytic expressions for the wave speed and the stochastic diffusion of propagating fronts uncovering the existence of an optimal balance between local and nonlocal connectivity which minimizes the fluctuations of the activation front propagation. Incorporating an activity-dependent adaptation of local excitability further highlights the independent role that local and nonlocal connectivity play in modulating the speed of propagation of the activation and silencing wavefronts, respectively. Inhomogeneities in space of local excitability give raise to a novel hysteresis phenomenon such that the speed of waves traveling in opposite directions display different velocities in the same location. Taken together these results provide insights on the multiscale organization of brain slow-waves measured during deep sleep and anesthesia.

The fast reciprocating magnetic probe system on the J-TEXT tokamak

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

Li, Fuming; Chen, Zhipeng, E-mail: zpchen@hust.edu.cn; Zhuang, Ge

The fast reciprocating magnetic probe (FRMP) system is newly developed on the Joint Texas Experimental Tokamak (J-TEXT) to measure the local magnetic fluctuations at the plasma edge. The magnetic probe array in the FRMP consists of four 2-dimensional magnetic probes arranged at different radial locations to detect local poloidal and radial magnetic fields. These probes are protected by a graphite and boron nitride casing to improve the frequency response of each probe; they are mounted on the head of a movable rod, which is oriented along radial direction at the top of the torus. In the experiments, multiple core diagnosticsmore » show that the insertion of the FRMP has little impact on the equilibrium of the plasma. Local magnetic fluctuations inside the last closed flux surface are successfully measured by the FRMP.« less

High-energy anomalies in covalent high-Tc cuprates with large Hubbard Ud on copper

NASA Astrophysics Data System (ADS)

Barišić, O. S.; Barišić, S.

2015-03-01

A large Ud theory is constructed for the metallic state of high-Tc cuprates. The Emery three-band model, extended with Ox-Oy hopping tpp, and with Ud → ∞, is mapped on slave fermions. The Dyson time-dependent diagrammatic theory in terms of the Cu-O hopping tpd, starting from the nondegenerate unperturbed ground state, is translationally and asymptotically locally gauge invariant. The small parameter of the theory is the average hole occupation of Cu sites nd. The lowest order of the theory generates the single particle propagators of the hybridized pdp- and dpd-fermions with the exact covalent three band structure. The leading many-body effect is band narrowing, accompanied by Landau-like damping of the single particle propagation, due to incoherent local charge Cu-O fluctuations. The corresponding continuum is found below and above the Fermi level.

Landauer’s formula with finite-time relaxation: Kramers’ crossover in electronic transport

DOE PAGES

Gruss, Daniel; Velizhanin, Kirill A.; Zwolak, Michael

2016-04-20

Landauer’s formula is the standard theoretical tool to examine ballistic transport in nano- and meso-scale junctions, but it necessitates that any variation of the junction with time must be slow compared to characteristic times of the system, e.g., the relaxation time of local excitations. Transport through structurally dynamic junctions is, however, increasingly of interest for sensing, harnessing fluctuations, and real-time control. Here, we calculate the steady-state current when relaxation of electrons in the reservoirs is present and demonstrate that it gives rise to three regimes of behavior: weak relaxation gives a contact-limited current; strong relaxation localizes electrons, distorting their naturalmore » dynamics and reducing the current; and in an intermediate regime the Landauer view of the system only is recovered. Lastly, we also demonstrate that a simple equation of motion emerges, which is suitable for efficiently simulating time-dependent transport.« less

Antiferromagnetic Ordering in Quasi-Triangular Localized Spin System, β'-Et2Me2P[Pd(dmit)2]2, Studied by 13C NMR

NASA Astrophysics Data System (ADS)

Otsuka, Kei; Iikubo, Hideaki; Kogure, Takayuki; Takano, Yoshiki; Hiraki, Ko-ichi; Takahashi, Toshihiro; Cui, Hengbo; Kato, Reizo

2014-05-01

We performed 13C NMR measurements of a selectively 13C isotope-labeled single-crystal sample of a frustrated spin system, β'-Et2Me2P[Pd(dmit)2]2. A long-range antiferromagnetic (AF) ordering below 17 K was confirmed by the observation of NMR spectrum broadening and well split resonance lines at lower temperatures. NMR spectra in the AF state can be well explained by a two sublattice model. From the analysis of the angular dependence of the NMR spectrum, we clarified the magnetic structure in the AF state, where the easy and hard axes are the crystallographic c*- and b-axes, respectively, and the effective localized moments are quite small, ˜0.28 μB/dimer. This suggests a strong quantum fluctuation effect due to magnetic frustrations in a quasi-triangular spin-1/2 system.

Decrease in electrical resistivity on depletion of islands of mobility during aging of a bulk metal glass

NASA Astrophysics Data System (ADS)

Aji, Daisman P. B.; Johari, G. P.

2018-04-01

The effect of structural relaxation on electrical resistivity, ρglass, of strain-free Zr46.75Ti8.25Cu7.5Ni10Be27.5 bulk metallic glass was studied during isothermal aging at several temperatures, Tas. Since cooling of a liquid metal increases its resistivity ρliq, one expects ρglass to increase on aging toward ρliq at T = Ta. Instead, ρglass decreased non-exponentially with the aging time. The activation energy of aging kinetics is 189 kJ mol-1, which is higher than the activation energy of the Johari-Goldstein (JG) relaxation. After considering the sample's contraction, phase separation, and crystallization as possible causes of the decrease in ρglass, we attribute the decrease to depletion of islands of atomic mobility, soft spots, or static heterogeneity. Vibrations of the atoms in these local (loosely packed) regions and in the region's interfacial area contribute to electron scattering. As these deplete on aging, the contribution decreases and ρglass decreases, with a concomitant decrease in macroscopic volume, enthalpy, and entropy (V, H, and S). Local regions of faster mobility also decrease on cooling as V, H, and S of a liquid decrease, but structure fluctuations dominate electron scattering of a liquid metal and ρliq increases effectively according to the Ziman-Nagel theory for a homogenously disordered structure. Whether depletion of such local regions initiates the structural relaxation of a glass, or vice versa, may be resolved by finding a glass that physically ages but shows no JG relaxation.

Local activity determines functional connectivity in the resting human brain: a simultaneous FDG-PET/fMRI study.

PubMed

Riedl, Valentin; Bienkowska, Katarzyna; Strobel, Carola; Tahmasian, Masoud; Grimmer, Timo; Förster, Stefan; Friston, Karl J; Sorg, Christian; Drzezga, Alexander

2014-04-30

Over the last decade, synchronized resting-state fluctuations of blood oxygenation level-dependent (BOLD) signals between remote brain areas [so-called BOLD resting-state functional connectivity (rs-FC)] have gained enormous relevance in systems and clinical neuroscience. However, the neural underpinnings of rs-FC are still incompletely understood. Using simultaneous positron emission tomography/magnetic resonance imaging we here directly investigated the relationship between rs-FC and local neuronal activity in humans. Computational models suggest a mechanistic link between the dynamics of local neuronal activity and the functional coupling among distributed brain regions. Therefore, we hypothesized that the local activity (LA) of a region at rest determines its rs-FC. To test this hypothesis, we simultaneously measured both LA (glucose metabolism) and rs-FC (via synchronized BOLD fluctuations) during conditions of eyes closed or eyes open. During eyes open, LA increased in the visual system, and the salience network (i.e., cingulate and insular cortices) and the pattern of elevated LA coincided almost exactly with the spatial pattern of increased rs-FC. Specifically, the voxelwise regional profile of LA in these areas strongly correlated with the regional pattern of rs-FC among the same regions (e.g., LA in primary visual cortex accounts for ∼ 50%, and LA in anterior cingulate accounts for ∼ 20% of rs-FC with the visual system). These data provide the first direct evidence in humans that local neuronal activity determines BOLD FC at rest. Beyond its relevance for the neuronal basis of coherent BOLD signal fluctuations, our procedure may translate into clinical research particularly to investigate potentially aberrant links between local dynamics and remote functional coupling in patients with neuropsychiatric disorders.

An experimental study of the velocity-forced flame response of a lean-premixed multi-nozzle can combustor for gas turbines

NASA Astrophysics Data System (ADS)

Szedlmayer, Michael Thomas

The velocity forced flame response of a multi-nozzle, lean-premixed, swirl-stabilized, turbulent combustor was investigated at atmospheric pressure. The purpose of this study was to analyze the mechanisms that allowed velocity fluctuations to cause fluctuations in the rate of heat release in a gas turbine combustor experiencing combustion instability. Controlled velocity fluctuations were introduced to the combustor by a rotating siren device which periodically allowed the air-natural gas mixture to flow. The velocity fluctuation entering the combustor was measured using the two-microphone method. The resulting heat release rate fluctuation was measured using CH* chemiluminescence. The global response of the flame was quantified using the flame transfer function with the velocity fluctuation as the input and the heat release rate fluctuation as the output. Velocity fluctuation amplitude was initially maintained at 5% of the inlet velocity in order to remain in the linear response regime. Flame transfer function measurements were acquired at a wide range of operating conditions and forcing frequencies. The selected range corresponds to the conditions and instability frequencies typical of real gas turbine combustors. Multi-nozzle flame transfer functions were found to bear a qualitative similarity to the single-nozzle flame transfer functions in the literature. The flame transfer function gain exhibited alternating minima and maxima while the phase decreased linearly with increasing forcing frequency. Several normalization techniques were applied to all flame transfer function data in an attempt to collapse the data into a single curve. The best collapse was found to occur using a Strouhal number which was the ratio of the characteristic flame length to the wavelength of the forced disturbance. Critical values of Strouhal number are used to predict the shedding of vortical structures in shear layers. Because of the collapse observed when the flame transfer functions are plotted versus Strouhal number, vortical structures are thought to have a strong influence on the response of this multi-nozzle configuration. The structure of heat release rate fluctuations throughout the flame is analyzed using CH* chemiluminescence acquired with a high speed camera. Flames with a similar level of flame transfer function gain are found to exhibit similarity in the spatial distribution of their heat release rate fluctuations, regardless of the operating condition. Flames with high gain are found to have high amplitude fluctuations near the downstream end of the flame, with weak fluctuations near the flame base. The phase of the downstream fluctuations changes minimally across the downstream region, indicating that they occur inphase. Flames with low gain exhibit stronger fluctuations near the flame base, but weak fluctuations in the downstream region. The phase of the fluctuations near the flame base changes continuously along the flame axis, indicating that parts of the flame will fluctuate out-of-phase. Accordingly, from a global perspective, destructive interference between heat release rate fluctuations in different parts of the flame can be expected. The behavior observed in the flame is ascribed to the interaction of acoustic velocity fluctuations, vortical disturbances and swirl fluctuations. The response of the multi-nozzle flame to high amplitude velocity fluctuations was tested for a single operating condition. Based on the global flame response, most frequencies responded linearly over the tested range of amplitudes. Nonlinear effects were found to occur at three frequencies. The behaviors observed at these frequencies matched those observed in the literature and included flame response saturation and mode triggering. For conditions which responded linearly at all amplitudes, the structure of heat release rate fluctuations was found to remain nearly constant. For conditions with nonlinear behavior, the structure of the fluctuations was a function of the forcing amplitude, particularly in the downstream region. The behavior of the multi-nozzle flame was compared directly to that of a single-nozzle flame of the same nozzle design. The multi-nozzle characteristic flame length was found to be on average 10% longer than for the single-nozzle flame. The flame transfer functions from the two cases were found to exhibit qualitative similarity, where the frequencies at which the extrema occur are similar. The actual value of gain for the same operating condition and frequency does, however, vary by more than a factor of two in some cases. The phase value can also vary by as much as pi radians. These differences indicate that single-nozzle flame transfer functions should not be used directly to predict the instability driving force of real gas turbine combustors.

Triadic Closure in Configuration Models with Unbounded Degree Fluctuations

NASA Astrophysics Data System (ADS)

van der Hofstad, Remco; van Leeuwaarden, Johan S. H.; Stegehuis, Clara

2018-01-01

The configuration model generates random graphs with any given degree distribution, and thus serves as a null model for scale-free networks with power-law degrees and unbounded degree fluctuations. For this setting, we study the local clustering c(k), i.e., the probability that two neighbors of a degree-k node are neighbors themselves. We show that c(k) progressively falls off with k and the graph size n and eventually for k=Ω (√{n}) settles on a power law c(k)˜ n^{5-2τ }k^{-2(3-τ )} with τ \\in (2,3) the power-law exponent of the degree distribution. This fall-off has been observed in the majority of real-world networks and signals the presence of modular or hierarchical structure. Our results agree with recent results for the hidden-variable model and also give the expected number of triangles in the configuration model when counting triangles only once despite the presence of multi-edges. We show that only triangles consisting of triplets with uniquely specified degrees contribute to the triangle counting.