Magnetism in Pd: Magnetoconductance and transport spectroscopy of atomic contacts

NASA Astrophysics Data System (ADS)

Strigl, F.; Keller, M.; Weber, D.; Pietsch, T.; Scheer, E.

2016-10-01

Since the rapid technological progress demands for ever smaller storage units, the emergence of stable magnetic order in nanomaterials down to the single-atom regime has attracted huge scientific attention to date. Electronic transport spectroscopy has been proven to be a versatile tool for the investigation of electronic, magnetic, and mechanical properties of atomic contacts. Here we report a comprehensive experimental study of the magnetoconductance and electronic properties of Pd atomic contacts at low temperature. The analysis of electronic transport (d I /d V ) spectra and the magnetoconductance curves yields a diverse behavior of Pd single-atom contacts, which is attributed to different contact configurations. The magnetoconductance shows a nonmonotonous but mostly continuous behavior, comparable to those found in atomic contacts of band ferromagnets. In the d I /d V spectra, frequently, a pronounced zero-bias anomaly (ZBA) as well as an aperiodic and nonsymmetric fluctuation pattern are observed. While the ZBA can be interpreted as a sign of the Kondo effect, suggesting the presence of magnetic impurity, the fluctuations are evaluated in the framework of conductance fluctuations in relation to the magnetoconductance traces and to previous findings in Au atomic contacts. This thorough analysis reveals that the magnetoconductance and transport spectrum of Au atomic contacts can completely be accounted for by conductance fluctuations, while in Pd contacts the presence of local magnetic order is required.

Dynamics of quantum correlation and coherence for two atoms coupled with a bath of fluctuating massless scalar field

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

Huang, Zhiming, E-mail: 465609785@qq.com; Situ, Haozhen, E-mail: situhaozhen@gmail.com

In this article, the dynamics of quantum correlation and coherence for two atoms interacting with a bath of fluctuating massless scalar field in the Minkowski vacuum is investigated. We firstly derive the master equation that describes the system evolution with initial Bell-diagonal state. Then we discuss the system evolution for three cases of different initial states: non-zero correlation separable state, maximally entangled state and zero correlation state. For non-zero correlation initial separable state, quantum correlation and coherence can be protected from vacuum fluctuations during long time evolution when the separation between the two atoms is relatively small. For maximally entangledmore » initial state, quantum correlation and coherence overall decrease with evolution time. However, for the zero correlation initial state, quantum correlation and coherence are firstly generated and then drop with evolution time; when separation is sufficiently small, they can survive from vacuum fluctuations. For three cases, quantum correlation and coherence first undergo decline and then fluctuate to relatively stable values with the increasing distance between the two atoms. Specially, for the case of zero correlation initial state, quantum correlation and coherence occur periodically revival at fixed zero points and revival amplitude declines gradually with increasing separation of two atoms.« less

Direct evidence of atomic-scale structural fluctuations in catalyst nanoparticles.

PubMed

Lin, Pin Ann; Gomez-Ballesteros, Jose L; Burgos, Juan C; Balbuena, Perla B; Natarajan, Bharath; Sharma, Renu

2017-05-01

Rational catalyst design requires an atomic scale mechanistic understanding of the chemical pathways involved in the catalytic process. A heterogeneous catalyst typically works by adsorbing reactants onto its surface, where the energies for specific bonds to dissociate and/or combine with other species (to form desired intermediate or final products) are lower. Here, using the catalytic growth of single-walled carbon nanotubes (SWCNTs) as a prototype reaction, we show that the chemical pathway may in-fact involve the entire catalyst particle, and can proceed via the fluctuations in the formation and decomposition of metastable phases in the particle interior. We record in situ and at atomic resolution, the dynamic phase transformations occurring in a Cobalt catalyst nanoparticle during SWCNT growth, using a state-of-the-art environmental transmission electron microscope (ETEM). The fluctuations in catalyst carbon content are quantified by the automated, atomic-scale structural analysis of the time-resolved ETEM images and correlated with the SWCNT growth rate. We find the fluctuations in the carbon concentration in the catalyst nanoparticle and the fluctuations in nanotube growth rates to be of complementary character. These findings are successfully explained by reactive molecular dynamics (RMD) simulations that track the spatial and temporal evolution of the distribution of carbon atoms within and on the surface of the catalyst particle. We anticipate that our approach combining real-time, atomic-resolution image analysis and molecular dynamics simulations will facilitate catalyst design, improving reaction efficiencies and selectivity towards the growth of desired structure.

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.

Arrays of strongly coupled atoms in a one-dimensional waveguide

NASA Astrophysics Data System (ADS)

Ruostekoski, Janne; Javanainen, Juha

2017-09-01

We study the cooperative optical coupling between regularly spaced atoms in a one-dimensional waveguide using decompositions to subradiant and super-radiant collective excitation eigenmodes, direct numerical solutions, and analytical transfer-matrix methods. We illustrate how the spectrum of transmitted light through the waveguide, including the emergence of narrow Fano resonances, can be understood by the resonance features of the eigenmodes. We describe a method based on super-radiant and subradiant modes to engineer the optical response of the waveguide and to store light. The stopping of light is obtained by transferring an atomic excitation to a subradiant collective mode with the zero radiative resonance linewidth by controlling the level shift of an atom in the waveguide. Moreover, we obtain an exact analytic solution for the transmitted light through the waveguide for the case of a regular lattice of atoms and provide a simple description of how the light transmission may present large resonance shifts when the lattice spacing is close, but not exactly equal, to half of the wavelength of the light. Experimental imperfections such as fluctuations of the positions of the atoms and loss of light from the waveguide are easily quantified in the numerical simulations, which produce the natural result that the optical response of the atomic array tends toward the response of a gas with random atomic positions.

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

Kira, M., E-mail: mackillo.kira@physik.uni-marburg.de

Atomic Bose–Einstein condensates (BECs) can be viewed as macroscopic objects where atoms form correlated atom clusters to all orders. Therefore, the presence of a BEC makes the direct use of the cluster-expansion approach–lucrative e.g. in semiconductor quantum optics–inefficient when solving the many-body kinetics of a strongly interacting Bose. An excitation picture is introduced with a nonunitary transformation that describes the system in terms of atom clusters within the normal component alone. The nontrivial properties of this transformation are systematically studied, which yields a cluster-expansion friendly formalism for a strongly interacting Bose gas. Its connections and corrections to the standard Hartree–Fock–Bogoliubov approachmore » are discussed and the role of the order parameter and the Bogoliubov excitations are identified. The resulting interaction effects are shown to visibly modify number fluctuations of the BEC. Even when the BEC has a nearly perfect second-order coherence, the BEC number fluctuations can still resolve interaction-generated non-Poissonian fluctuations. - Highlights: • Excitation picture expresses interacting Bose gas with few atom clusters. • Semiconductor and BEC many-body investigations are connected with cluster expansion. • Quantum statistics of BEC is identified in terms of atom clusters. • BEC number fluctuations show extreme sensitivity to many-body correlations. • Cluster-expansion friendly framework is established for an interacting Bose gas.« less

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

Hyper-Ramsey spectroscopy with probe-laser-intensity fluctuations

NASA Astrophysics Data System (ADS)

Beloy, K.

2018-03-01

We examine the influence of probe-laser-intensity fluctuations on hyper-Ramsey spectroscopy. We assume, as is appropriate for relevant cases of interest, that the probe-laser intensity I determines both the Rabi frequency (∝√{I } ) and the frequency shift to the atomic transition (∝I ) during probe-laser interactions with the atom. The spectroscopic signal depends on these two quantities that covary with fluctuations in the probe-laser intensity. Introducing a simple model for the fluctuations, we find that the signature robustness of the hyper-Ramsey method can be compromised. Taking the Yb+ electric octupole clock transition as an example, we quantify the clock error under different levels of probe-laser-intensity fluctuations.

Beyond Point Charges: Dynamic Polarization from Neural Net Predicted Multipole Moments.

PubMed

Darley, Michael G; Handley, Chris M; Popelier, Paul L A

2008-09-09

Intramolecular polarization is the change to the electron density of a given atom upon variation in the positions of the neighboring atoms. We express the electron density in terms of multipole moments. Using glycine and N-methylacetamide (NMA) as pilot systems, we show that neural networks can capture the change in electron density due to polarization. After training, modestly sized neural networks successfully predict the atomic multipole moments from the nuclear positions of all atoms in the molecule. Accurate electrostatic energies between two atoms can be then obtained via a multipole expansion, inclusive of polarization effects. As a result polarization is successfully modeled at short-range and without an explicit polarizability tensor. This approach puts charge transfer and multipolar polarization on a common footing. The polarization procedure is formulated within the context of quantum chemical topology (QCT). Nonbonded atom-atom interactions in glycine cover an energy range of 948 kJ mol(-1), with an average energy difference between true and predicted energy of 0.2 kJ mol(-1), the largest difference being just under 1 kJ mol(-1). Very similar energy differences are found for NMA, which spans a range of 281 kJ mol(-1). The current proof-of-concept enables the construction of a new protein force field that incorporates electron density fragments that dynamically respond to their fluctuating environment.

Observations of density fluctuations in an elongated Bose gas: ideal gas and quasicondensate regimes.

PubMed

Esteve, J; Trebbia, J-B; Schumm, T; Aspect, A; Westbrook, C I; Bouchoule, I

2006-04-07

We report in situ measurements of density fluctuations in a quasi-one-dimensional 87Rb Bose gas at thermal equilibrium in an elongated harmonic trap. We observe an excess of fluctuations compared to the shot-noise level expected for uncorrelated atoms. At low atomic density, the measured excess is in good agreement with the expected "bunching" for an ideal Bose gas. At high density, the measured fluctuations are strongly reduced compared to the ideal gas case. We attribute this reduction to repulsive interatomic interactions. The data are compared with a calculation for an interacting Bose gas in the quasicondensate regime.

Real-time observation of fluctuations at the driven-dissipative Dicke phase transition

PubMed Central

Brennecke, Ferdinand; Mottl, Rafael; Baumann, Kristian; Landig, Renate; Donner, Tobias; Esslinger, Tilman

2013-01-01

We experimentally study the influence of dissipation on the driven Dicke quantum phase transition, realized by coupling external degrees of freedom of a Bose–Einstein condensate to the light field of a high-finesse optical cavity. The cavity provides a natural dissipation channel, which gives rise to vacuum-induced fluctuations and allows us to observe density fluctuations of the gas in real-time. We monitor the divergence of these fluctuations over two orders of magnitude while approaching the phase transition, and observe a behavior that deviates significantly from that expected for a closed system. A correlation analysis of the fluctuations reveals the diverging time scale of the atomic dynamics and allows us to extract a damping rate for the external degree of freedom of the atoms. We find good agreement with our theoretical model including dissipation via both the cavity field and the atomic field. Using a dissipation channel to nondestructively gain information about a quantum many-body system provides a unique path to study the physics of driven-dissipative systems. PMID:23818599

Experimental nonlinear dynamical studies in cesium magneto-optical trap using time-series analysis

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

Anwar, M., E-mail: mamalik2000@gmail.com; Islam, R.; Faisal, M.

2015-03-30

A magneto-optical trap of neutral atoms is essentially a dissipative quantum system. The fast thermal atoms continuously dissipate their energy to the environment via spontaneous emissions during the cooling. The atoms are, therefore, strongly coupled with the vacuum reservoir and the laser field. The vacuum fluctuations as well as the field fluctuations are imparted to the atoms as random photon recoils. Consequently, the external and internal dynamics of atoms becomes stochastic. In this paper, we have investigated the stochastic dynamics of the atoms in a magneto-optical trap during the loading process. The time series analysis of the fluorescence signal showsmore » that the dynamics of the atoms evolves, like all dissipative systems, from deterministic to the chaotic regime. The subsequent disappearance and revival of chaos was attributed to chaos synchronization between spatially different atoms in the magneto-optical trap.« less

Engineering the Eigenstates of Coupled Spin-1/2 Atoms on a Surface.

PubMed

Yang, Kai; Bae, Yujeong; Paul, William; Natterer, Fabian D; Willke, Philip; Lado, Jose L; Ferrón, Alejandro; Choi, Taeyoung; Fernández-Rossier, Joaquín; Heinrich, Andreas J; Lutz, Christopher P

2017-12-01

Quantum spin networks having engineered geometries and interactions are eagerly pursued for quantum simulation and access to emergent quantum phenomena such as spin liquids. Spin-1/2 centers are particularly desirable, because they readily manifest coherent quantum fluctuations. Here we introduce a controllable spin-1/2 architecture consisting of titanium atoms on a magnesium oxide surface. We tailor the spin interactions by atomic-precision positioning using a scanning tunneling microscope (STM) and subsequently perform electron spin resonance on individual atoms to drive transitions into and out of quantum eigenstates of the coupled-spin system. Interactions between the atoms are mapped over a range of distances extending from highly anisotropic dipole coupling to strong exchange coupling. The local magnetic field of the magnetic STM tip serves to precisely tune the superposition states of a pair of spins. The precise control of the spin-spin interactions and ability to probe the states of the coupled-spin network by addressing individual spins will enable the exploration of quantum many-body systems based on networks of spin-1/2 atoms on surfaces.

Engineering the Eigenstates of Coupled Spin-1 /2 Atoms on a Surface

NASA Astrophysics Data System (ADS)

Yang, Kai; Bae, Yujeong; Paul, William; Natterer, Fabian D.; Willke, Philip; Lado, Jose L.; Ferrón, Alejandro; Choi, Taeyoung; Fernández-Rossier, Joaquín; Heinrich, Andreas J.; Lutz, Christopher P.

2017-12-01

Quantum spin networks having engineered geometries and interactions are eagerly pursued for quantum simulation and access to emergent quantum phenomena such as spin liquids. Spin-1 /2 centers are particularly desirable, because they readily manifest coherent quantum fluctuations. Here we introduce a controllable spin-1 /2 architecture consisting of titanium atoms on a magnesium oxide surface. We tailor the spin interactions by atomic-precision positioning using a scanning tunneling microscope (STM) and subsequently perform electron spin resonance on individual atoms to drive transitions into and out of quantum eigenstates of the coupled-spin system. Interactions between the atoms are mapped over a range of distances extending from highly anisotropic dipole coupling to strong exchange coupling. The local magnetic field of the magnetic STM tip serves to precisely tune the superposition states of a pair of spins. The precise control of the spin-spin interactions and ability to probe the states of the coupled-spin network by addressing individual spins will enable the exploration of quantum many-body systems based on networks of spin-1 /2 atoms on surfaces.

Higher-order spin-noise spectroscopy of atomic spins in fluctuating external fields

DOE PAGES

Li, Fuxiang; Crooker, S. A.; Sinitsyn, N. A.

2016-03-09

Here, we discuss the effect of external noisy magnetic fields on mesoscopic spin fluctuations that can be probed in semiconductors and atomic vapors by means of optical spin-noise spectroscopy. We also show that conventional arguments of the law of large numbers do not apply to spin correlations induced by external fields, namely, the magnitude of the 4th-order spin cumulant grows as ~N 2 with the number N of observed spins, i.e., it is not suppressed in comparison to the 2nd-order cumulant. Moreover, this allows us to design a simple experiment to measure the 4th-order cumulant of spin fluctuations in anmore » atomic system near thermodynamic equilibrium and develop a quantitative theory that explains all observations.« less

Effect of Elastic Strain Fluctuation on Atomic Layer Growth of Epitaxial Silicide in Si Nanowires by Point Contact Reactions.

PubMed

Chou, Yi-Chia; Tang, Wei; Chiou, Chien-Jyun; Chen, Kai; Minor, Andrew M; Tu, K N

2015-06-10

Effects of strain impact a range of applications involving mobility change in field-effect-transistors. We report the effect of strain fluctuation on epitaxial growth of NiSi2 in a Si nanowire via point contact and atomic layer reactions, and we discuss the thermodynamic, kinetic, and mechanical implications. The generation and relaxation of strain shown by in situ TEM is periodic and in synchronization with the atomic layer reaction. The Si lattice at the epitaxial interface is under tensile strain, which enables a high solubility of supersaturated interstitial Ni atoms for homogeneous nucleation of an epitaxial atomic layer of the disilicide phase. The tensile strain is reduced locally during the incubation period of nucleation by the dissolution of supersaturated Ni atoms in the Si lattice but the strained-Si state returns once the atomic layer epitaxial growth of NiSi2 occurs by consuming the supersaturated Ni.

Single atoms in a MOT

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

Meschede, Dieter; Ueberholz, Bernd; Gomer, Victor

1999-06-11

We are experimenting with individual neutral cesium atoms stored in a magneto-optical trap. The atoms are detected by their resonance fluorescence, and fluorescence fluctuations contain signatures of the atomic internal and external degrees of freedom. This noninvasive probe provides a rich source of information about atomic dynamics at all relevant time scales.

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.

Crystal structure of the sweet-tasting protein thaumatin II at 1.27 A

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

Masuda, Tetsuya, E-mail: t2masuda@kais.kyoto-u.ac.jp; Department Natural Resources, Graduate School of Global Environmental Studies, Kyoto University, Uji, Kyoto 611-0011; Ohta, Keisuke

2011-07-08

Highlights: {yields} X-ray crystallographic structure of sweet-tasting protein, thaumatin II, was determined at a resolution of 1.27 A. {yields} The overall structure of thaumatin II is similar to that of thaumatin I, but a slight shift of the C{alpha} atom of G96 in thaumatin II was observed. {yields} The side chain of two critical residues, 67 and 82, for sweetness was modeled in two alternative conformations. {yields} The flexibility and fluctuation of side chains at 67 and 82 seems to be suitable for interaction of thaumatin molecules with sweet receptors. -- Abstract: Thaumatin, an intensely sweet-tasting protein, elicits a sweetmore » taste sensation at 50 nM. Here the X-ray crystallographic structure of one of its variants, thaumatin II, was determined at a resolution of 1.27 A. Overall structure of thaumatin II is similar to thaumatin I, but a slight shift of the C{alpha} atom of G96 in thaumatin II was observed. Furthermore, the side chain of residue 67 in thaumatin II is highly disordered. Since residue 67 is one of two residues critical to the sweetness of thaumatin, the present results suggested that the critical positive charges at positions 67 and 82 are disordered and the flexibility and fluctuation of these side chains would be suitable for interaction of thaumatin molecules with sweet receptors.« less

In Situ Three-Dimensional Reciprocal-Space Mapping of Diffuse Scattering Intensity Distribution and Data Analysis for Precursor Phenomenon in Shape-Memory Alloy

NASA Astrophysics Data System (ADS)

Cheng, Tian-Le; Ma, Fengde D.; Zhou, Jie E.; Jennings, Guy; Ren, Yang; Jin, Yongmei M.; Wang, Yu U.

2012-01-01

Diffuse scattering contains rich information on various structural disorders, thus providing a useful means to study the nanoscale structural deviations from the average crystal structures determined by Bragg peak analysis. Extraction of maximal information from diffuse scattering requires concerted efforts in high-quality three-dimensional (3D) data measurement, quantitative data analysis and visualization, theoretical interpretation, and computer simulations. Such an endeavor is undertaken to study the correlated dynamic atomic position fluctuations caused by thermal vibrations (phonons) in precursor state of shape-memory alloys. High-quality 3D diffuse scattering intensity data around representative Bragg peaks are collected by using in situ high-energy synchrotron x-ray diffraction and two-dimensional digital x-ray detector (image plate). Computational algorithms and codes are developed to construct the 3D reciprocal-space map of diffuse scattering intensity distribution from the measured data, which are further visualized and quantitatively analyzed to reveal in situ physical behaviors. Diffuse scattering intensity distribution is explicitly formulated in terms of atomic position fluctuations to interpret the experimental observations and identify the most relevant physical mechanisms, which help set up reduced structural models with minimal parameters to be efficiently determined by computer simulations. Such combined procedures are demonstrated by a study of phonon softening phenomenon in precursor state and premartensitic transformation of Ni-Mn-Ga shape-memory alloy.

[Hydrogen exchange and proteolytic degradation of ribonuclease A. Similarities and distinctions of the kinetic mechanisms].

PubMed

Abaturov, L V; Nosova, N G

2007-01-01

The studies by IR spectroscopy of the temperature dependence of the H-D exchange rate of the RNase A peptide NH atoms permit one to characterize two types of conformation fluctuations, local and global. A comparison with the temperature dependence of the proteolytic degradation rate of RNase A shows that similar in nature fluctuations allow for the H-D exchange of NH atoms and the splitting of peptide bonds of the native protein. In the low temperature region, both processes occur through local fluctuations, by way of the EX2 mechanism, and in the high temperature region, they occur through global fluctuations with the overall denaturation desorganization of the native structure, by way of the EX1 mechanism. The biphasic dependence of the rate of H-D exchange and proteolytic degradation of RNase A on urea concentration is also explained by the combination of local and global fluctuations.

Temperature and radiation effects at the fluorine K-edge in LiF

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

Schwartz, Craig P.; Ponce, Francisco; Friedrich, Stephan

Here, the fluorine K-edge of LiF is studied both experimentally and theoretically as a function of temperature. Instantaneous thermal fluctuations in atomic positions are shown in molecular dynamics simulations to increase in amplitude from 0.029 to 0.064 nm in the temperature range from 40 to 298 K. This is sufficient to cause instantaneous deviations from local octahedral atomic symmetry in this rock-salt crystal, resulting in altered electronic structure. The lowered symmetry of the lowest core-excited states of fluorine atoms is evident in X-ray absorption spectra at the F K-edge. In addition, sufficient radiation exposure produces a new X-ray absorption peak,more » below the F K-edge of LiF, which is assigned to defects in LiF based on both calculations and comparison to previous experiments.« less

Temperature and radiation effects at the fluorine K-edge in LiF

DOE PAGES

Schwartz, Craig P.; Ponce, Francisco; Friedrich, Stephan; ...

2017-05-30

Here, the fluorine K-edge of LiF is studied both experimentally and theoretically as a function of temperature. Instantaneous thermal fluctuations in atomic positions are shown in molecular dynamics simulations to increase in amplitude from 0.029 to 0.064 nm in the temperature range from 40 to 298 K. This is sufficient to cause instantaneous deviations from local octahedral atomic symmetry in this rock-salt crystal, resulting in altered electronic structure. The lowered symmetry of the lowest core-excited states of fluorine atoms is evident in X-ray absorption spectra at the F K-edge. In addition, sufficient radiation exposure produces a new X-ray absorption peak,more » below the F K-edge of LiF, which is assigned to defects in LiF based on both calculations and comparison to previous experiments.« less

Vacuum fluctuations and radiation reaction contributions to the resonance dipole-dipole interaction between two atoms near a reflecting boundary

NASA Astrophysics Data System (ADS)

Zhou, Wenting; Rizzuto, Lucia; Passante, Roberto

2018-04-01

We investigate the resonance dipole-dipole interaction energy between two identical atoms, one in the ground state and the other in the excited state, interacting with the electromagnetic field in the presence of a perfectly reflecting plane boundary. The atoms are prepared in a correlated (symmetric or antisymmetric) Bell-type state. Following a procedure due to Dalibard et al. [J. Dalibard et al., J. Phys. (Paris) 43, 1617 (1982);, 10.1051/jphys:0198200430110161700 J. Phys. (Paris) 45, 637 (1984), 10.1051/jphys:01984004504063700], we separate the contributions of vacuum fluctuations and radiation reaction (source) field to the resonance interaction energy between the two atoms and show that only the source field contributes to the interatomic interaction, while vacuum field fluctuations do not. By considering specific geometric configurations of the two-atom system with respect to the mirror and specific choices of dipole orientations, we show that the presence of the mirror significantly affects the resonance interaction energy and that different features appear with respect to the case of atoms in free space, for example, a change in the spatial dependence of the interaction. Our findings also suggest that the presence of a boundary can be exploited to tailor and control the resonance interaction between two atoms, as well as the related energy transfer process. The possibility of observing these phenomena is also discussed.

Protecting quantum coherence of two-level atoms from vacuum fluctuations of electromagnetic field

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

Liu, Xiaobao; Tian, Zehua; Wang, Jieci

In the framework of open quantum systems, we study the dynamics of a static polarizable two-level atom interacting with a bath of fluctuating vacuum electromagnetic field and explore under which conditions the coherence of the open quantum system is unaffected by the environment. For both a single-qubit and two-qubit systems, we find that the quantum coherence cannot be protected from noise when the atom interacts with a non-boundary electromagnetic field. However, with the presence of a boundary, the dynamical conditions for the insusceptible of quantum coherence are fulfilled only when the atom is close to the boundary and is transverselymore » polarizable. Otherwise, the quantum coherence can only be protected in some degree in other polarizable direction. -- Highlights: •We study the dynamics of a two-level atom interacting with a bath of fluctuating vacuum electromagnetic field. •For both a single and two-qubit systems, the quantum coherence cannot be protected from noise without a boundary. •The insusceptible of the quantum coherence can be fulfilled only when the atom is close to the boundary and is transversely polarizable. •Otherwise, the quantum coherence can only be protected in some degree in other polarizable direction.« less

Normal Mode Analysis of Polytheonamide B

NASA Astrophysics Data System (ADS)

Mori, Takaharu; Kokubo, Hironori; Shimizu, Hirofumi; Iwamoto, Masayuki; Oiki, Shigetoshi; Okamoto, Yuko

2007-09-01

Polytheonamide B is a linear 48-residue peptide which forms a single β-helix structure with alternating d- and l-amino acids and contains methylated and hydroxy variants of proteinogenic amino acids. To investigate the dynamical properties of polytheonamide B we perform the normal mode analysis. Root-mean-square displacements of all backbone atoms, root-mean-square fluctuations of the backbone dihedral angles (φ,\\psi), and correlation factors for the Cα atom fluctuations and for the dihedral angle fluctuations are calculated. The normal mode analysis reveals that polytheonamide B shows the elastic rod behavior in the very low-frequency regions and that librational motions of backbone amide planes have the modes with relatively low frequencies, which is relevant to the function of polytheonamide B. In addition, these librational motions occur almost independently and weakly anticorrelate with those of the hydrogen-bonded neighboring amide planes. Calculations of the backbone fluctuations show that the flexibility of polytheonamide B is roughly uniform over the entire helix. We compare our results with those of gramicidin A, the analogue of polytheonamide B, to discuss the structures and functions, and obtain some common features in the flexibilities and dynamics of the backbone atoms. These results present important clues for clarifying the function of polytheonamide B at the atomic level.

Numerical Study on the Partitioning of the Molecular Polarizability into Fluctuating Charge and Induced Atomic Dipole Contributions

PubMed Central

Mei, Ye; Simmonett, Andrew C.; Pickard, Frank C.; DiStasio, Robert A.; Brooks, Bernard R.; Shao, Yihan

2015-01-01

In order to carry out a detailed analysis of the molecular static polarizability, which is the response of the molecule to a uniform external electric field, the molecular polarizability was computed using the finite-difference method for 21 small molecules, using density functional theory. Within nine charge population schemes (Löwdin, Mulliken, Becke, Hirshfeld, CM5, Hirshfeld-I, NPA, CHELPG, MK-ESP) in common use, the charge fluctuation contribution is found to dominate the molecular polarizability, with its ratio ranging from 59.9% with the Hirshfeld or CM5 scheme to 96.2% with the Mulliken scheme. The Hirshfeld-I scheme is also used to compute the other contribution to the molecular polarizability coming from the induced atomic dipoles, and the atomic polarizabilities in 8 small molecules and water pentamer are found to be highly anisotropic for most atoms. Overall, the results suggest that (a) more emphasis probably should be placed on the charge fluctuation terms in future polarizable force field development; (b) an anisotropic polarizability might be more suitable than an isotropic one in polarizable force fields based entirely or partially on the induced atomic dipoles. PMID:25945749

Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions

DOE PAGES

Mei, Ye; Simmonett, Andrew C.; Pickard, IV, Frank C.; ...

2015-05-06

In order to carry out a detailed analysis of the molecular static polarizability, which is the response of the molecule to a uniform external electric field, the molecular polarizability was computed in this study using the finite-difference method for 21 small molecules, using density functional theory. Within nine charge population schemes (Lowdin, Mulliken, Becke, Hirshfeld, CM5, Hirshfeld-I, NPA, CHELPG, MK-ESP) in common use, the charge fluctuation contribution is found to dominate the molecular polarizability, with its ratio ranging from 59.9% with the Hirshfeld or CM5 scheme to 96.2% with the Mulliken scheme. The Hirshfeld-I scheme is also used to computemore » the other contribution to the molecular polarizability coming from the induced atomic dipoles, and the atomic polarizabilities in eight small molecules and water pentamer are found to be highly anisotropic for most atoms. In conclusion, the overall results suggest that (a) more emphasis probably should be placed on the charge fluctuation terms in future polarizable force field development and (b) an anisotropic polarizability might be more suitable than an isotropic one in polarizable force fields based entirely or partially on the induced atomic dipoles.« less

An analytic technique for statistically modeling random atomic clock errors in estimation

NASA Technical Reports Server (NTRS)

Fell, P. J.

1981-01-01

Minimum variance estimation requires that the statistics of random observation errors be modeled properly. If measurements are derived through the use of atomic frequency standards, then one source of error affecting the observable is random fluctuation in frequency. This is the case, for example, with range and integrated Doppler measurements from satellites of the Global Positioning and baseline determination for geodynamic applications. An analytic method is presented which approximates the statistics of this random process. The procedure starts with a model of the Allan variance for a particular oscillator and develops the statistics of range and integrated Doppler measurements. A series of five first order Markov processes is used to approximate the power spectral density obtained from the Allan variance.

Direct comparison of Fe-Cr unmixing characterization by atom probe tomography and small angle scattering

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

Couturier, Laurent, E-mail: laurent.couturier55@ho

The fine microstructure obtained by unmixing of a solid solution either by classical precipitation or spinodal decomposition is often characterized either by small angle scattering or atom probe tomography. This article shows that a common data analysis framework can be used to analyze data obtained from these two techniques. An example of the application of this common analysis is given for characterization of the unmixing of the Fe-Cr matrix of a 15-5 PH stainless steel during long-term ageing at 350 °C and 400 °C. A direct comparison of the Cr composition fluctuations amplitudes and characteristic lengths obtained with both techniquesmore » is made showing a quantitative agreement for the fluctuation amplitudes. The origin of the discrepancy remaining for the characteristic lengths is discussed. - Highlights: •Common analysis framework for atom probe tomography and small angle scattering •Comparison of same microstructural characteristics obtained using both techniques •Good correlation of Cr composition fluctuations amplitudes from both techniques •Good correlation of Cr composition fluctuations amplitudes with classic V parameter.« less

Modeling the nanoscale viscoelasticity of fluids by bridging non-Markovian fluctuating hydrodynamics and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Voulgarakis, Nikolaos K.; Satish, Siddarth; Chu, Jhih-Wei

2009-12-01

A multiscale computational method is developed to model the nanoscale viscoelasticity of fluids by bridging non-Markovian fluctuating hydrodynamics (FHD) and molecular dynamics (MD) simulations. To capture the elastic responses that emerge at small length scales, we attach an additional rheological model parallel to the macroscopic constitutive equation of a fluid. The widely used linear Maxwell model is employed as a working choice; other models can be used as well. For a fluid that is Newtonian in the macroscopic limit, this approach results in a parallel Newtonian-Maxwell model. For water, argon, and an ionic liquid, the power spectrum of momentum field autocorrelation functions of the parallel Newtonian-Maxwell model agrees very well with those calculated from all-atom MD simulations. To incorporate thermal fluctuations, we generalize the equations of FHD to work with non-Markovian rheological models and colored noise. The fluctuating stress tensor (white noise) is integrated in time in the same manner as its dissipative counterpart and numerical simulations indicate that this approach accurately preserves the set temperature in a FHD simulation. By mapping position and velocity vectors in the molecular representation onto field variables, we bridge the non-Markovian FHD with atomistic MD simulations. Through this mapping, we quantitatively determine the transport coefficients of the parallel Newtonian-Maxwell model for water and argon from all-atom MD simulations. For both fluids, a significant enhancement in elastic responses is observed as the wave number of hydrodynamic modes is reduced to a few nanometers. The mapping from particle to field representations and the perturbative strategy of developing constitutive equations provide a useful framework for modeling the nanoscale viscoelasticity of fluids.

Quantum principle of sensing gravitational waves: From the zero-point fluctuations to the cosmological stochastic background of spacetime

NASA Astrophysics Data System (ADS)

Quiñones, Diego A.; Oniga, Teodora; Varcoe, Benjamin T. H.; Wang, Charles H.-T.

2017-08-01

We carry out a theoretical investigation on the collective dynamics of an ensemble of correlated atoms, subject to both vacuum fluctuations of spacetime and stochastic gravitational waves. A general approach is taken with the derivation of a quantum master equation capable of describing arbitrary confined nonrelativistic matter systems in an open quantum gravitational environment. It enables us to relate the spectral function for gravitational waves and the distribution function for quantum gravitational fluctuations and to indeed introduce a new spectral function for the zero-point fluctuations of spacetime. The formulation is applied to two-level identical bosonic atoms in an off-resonant high-Q cavity that effectively inhibits undesirable electromagnetic delays, leading to a gravitational transition mechanism through certain quadrupole moment operators. The overall relaxation rate before reaching equilibrium is found to generally scale collectively with the number N of atoms. However, we are also able to identify certain states of which the decay and excitation rates with stochastic gravitational waves and vacuum spacetime fluctuations amplify more significantly with a factor of N2. Using such favorable states as a means of measuring both conventional stochastic gravitational waves and novel zero-point spacetime fluctuations, we determine the theoretical lower bounds for the respective spectral functions. Finally, we discuss the implications of our findings on future observations of gravitational waves of a wider spectral window than currently accessible. Especially, the possible sensing of the zero-point fluctuations of spacetime could provide an opportunity to generate initial evidence and further guidance of quantum gravity.

Test-area surface tension calculation of the graphene-methane interface: Fluctuations and commensurability

NASA Astrophysics Data System (ADS)

d'Oliveira, H. D.; Davoy, X.; Arche, E.; Malfreyt, P.; Ghoufi, A.

2017-06-01

The surface tension (γ) of methane on a graphene monolayer is calculated by using the test-area approach. By using a united atom model to describe methane molecules, strong fluctuations of surface tension as a function of the surface area of the graphene are evidenced. In contrast with the liquid-vapor interfaces, the use of a larger cutoff does not fully erase the fluctuations in the surface tension. Counterintuitively, the description of methane and graphene from the Optimized Potentials for Liquid Simulations all-atom model and a flexible model, respectively, led to a lessening in the surface tension fluctuations. This result suggests that the origin of fluctuations in γ is due to a model-effect rather than size-effects. We show that the molecular origin of these fluctuations is the result of a commensurable organization between both graphene and methane. This commensurable structure can be avoided by describing methane and graphene from a flexible force field. Although differences in γ with respect to the model have been often reported, it is the first time that the model drastically affects the physics of a system.

Filling-Fraction Fluctuation Leading to Glasslike Ultralow Thermal Conductivity in Caged Skutterudites

NASA Astrophysics Data System (ADS)

Ren, Wei; Geng, Huiyuan; Zhang, Zihao; Zhang, Lixia

2017-06-01

It is generally believed that filling atoms randomly and uniformly distribute in caged crystals, such as skutterudite compounds. Here, we report first-principles and experimental discovery of a multiscale filling-fraction fluctuation in the R Fe4Sb12 system. La0.8Ti0.1Ga0.1Fe4Sb12 spontaneously separates into La-rich and La-poor skutterudite phases, leading to multiscale strain field fluctuations. As a result, glasslike ultralow lattice thermal conductivity approaching the theoretical minimum is achieved, mainly due to strain field scattering of high-energy phonons. These findings reveal that an uneven distribution of filling atoms is efficient to further reduce the lattice thermal conductivity of caged crystals.

Thermal Noise Reduction of Mechanical Oscillators by Actively Controlled External Dissipative Forces

NASA Technical Reports Server (NTRS)

Liang, Shoudan; Medich, David; Czajkowsky, Daniel M.; Sheng, Sitong; Yuan, Jian-Yang; Shao, Zhifeng

1999-01-01

We show that the thermal fluctuations of very soft mechanical oscillators, such as the cantilever in an atomic force microscope (AFM), can be reduced without changing the stiffness of the spring or having to lower the environment temperature. We derive a theoretical relationship between the thermal fluctuations of an oscillator and an actively external-dissipative force. This relationship is verified by experiments with an AFM cantilever where the external active force is coupled through a magnetic field. With simple instrumentation, we have reduced the thermal noise amplitude of the cantilever by a factor of 3.4, achieving an apparent temperature of 25 K with the environment at 295K. This active noise reduction approach can significantly improve the accuracy of static position or static force measurements in a number of practical applications.

Site-controlled quantum dots fabricated using an atomic-force microscope assisted technique

PubMed Central

Usuki, T; Ohshima, T; Sakuma, Y; Kawabe, M; Okada, Y; Takemoto, K; Miyazawa, T; Hirose, S; Nakata, Y; Takatsu, M; Yokoyama, N

2006-01-01

An atomic-force microscope assisted technique is developed to control the position and size of self-assembled semiconductor quantum dots (QDs). Presently, the site precision is as good as ± 1.5 nm and the size fluctuation is within ± 5% with the minimum controllable lateral diameter of 20 nm. With the ability of producing tightly packed and differently sized QDs, sophisticated QD arrays can be controllably fabricated for the application in quantum computing. The optical quality of such site-controlled QDs is found comparable to some conventionally self-assembled semiconductor QDs. The single dot photoluminescence of site-controlled InAs/InP QDs is studied in detail, presenting the prospect to utilize them in quantum communication as precisely controlled single photon emitters working at telecommunication bands.

Dynamics of entropic uncertainty for atoms immersed in thermal fluctuating massless scalar field

NASA Astrophysics Data System (ADS)

Huang, Zhiming

2018-04-01

In this article, the dynamics of quantum memory-assisted entropic uncertainty relation for two atoms immersed in a thermal bath of fluctuating massless scalar field is investigated. The master equation that governs the system evolution process is derived. It is found that the mixedness is closely associated with entropic uncertainty. For equilibrium state, the tightness of uncertainty vanishes. For the initial maximum entangled state, the tightness of uncertainty undergoes a slight increase and then declines to zero with evolution time. It is found that temperature can increase the uncertainty, but two-atom separation does not always increase the uncertainty. The uncertainty evolves to different relatively stable values for different temperatures and converges to a fixed value for different two-atom distances with evolution time. Furthermore, weak measurement reversal is employed to control the entropic uncertainty.

Stabilizing Rabi oscillation of a charge qubit via the atomic clock technique

NASA Astrophysics Data System (ADS)

Yu, Deshui; Landra, Alessandro; Kwek, Leong Chuan; Amico, Luigi; Dumke, Rainer

2018-02-01

We propose a superconducting circuit-atom hybrid, where the Rabi oscillation of single excess Cooper pair in the island is stabilized via the common atomic clock technique. The noise in the superconducting circuit is mapped onto the voltage source which biases the Cooper-pair box via an inductor and a gate capacitor. The fast fluctuations of the gate charge are significantly suppressed by an inductor-capacitor resonator, leading to a long-relaxation-time Rabi oscillation. More importantly, the residual low-frequency fluctuations are further reduced by using the general feedback-control method, in which the voltage bias is stabilized via continuously measuring the dc-Stark-shift-induced atomic Ramsey signal. The stability and coherence time of the resulting charge-qubit Rabi oscillation are both enhanced. The principal structure of this Cooper-pair-box oscillator is studied in detail.

Enhanced quantum spin fluctuations in a binary Bose-Einstein condensate

NASA Astrophysics Data System (ADS)

Bisset, R. N.; Kevrekidis, P. G.; Ticknor, C.

2018-02-01

For quantum fluids, the role of quantum fluctuations may be significant in several regimes such as when the dimensionality is low, the density is high, the interactions are strong, or for low particle numbers. In this paper, we propose a fundamentally different regime for enhanced quantum fluctuations without being restricted by any of the above conditions. Instead, our scheme relies on the engineering of an effective attractive interaction in a dilute, two-component Bose-Einstein condensate (BEC) consisting of thousands of atoms. In such a regime, the quantum spin fluctuations are significantly enhanced (atom bunching with respect to the noninteracting limit) since they act to reduce the interaction energy, a remarkable property given that spin fluctuations are normally suppressed (antibunching) at zero temperature. In contrast to the case of true attractive interactions, our approach is not vulnerable to BEC collapse. We numerically demonstrate that these quantum fluctuations are experimentally accessible by either spin or single-component Bragg spectroscopy, offering a useful platform on which to test beyond-mean-field theories. We also develop a variational model and use it to analytically predict the shift of the immiscibility critical point, finding good agreement with our numerics.

Statistical properties and condensate fluctuation of attractive Bose gas with finite number of particles

NASA Astrophysics Data System (ADS)

Bera, Sangita; Lekala, Mantile Leslie; Chakrabarti, Barnali; Bhattacharyya, Satadal; Rampho, Gaotsiwe Joel

2017-09-01

'We study the condensate fluctuation and several statistics of weakly interacting attractive Bose gas of 7 Li atoms in harmonic trap. Using exact recursion relation we calculate canonical ensemble partition function and study the thermal evolution of the condensate. As 7 Li condensate is associated with collapse, the number of condensate atom is truly finite and it facilitates to study the condensate in mesoscopic region. Being highly correlated, we utilize the two-body correlated basis function to get the many-body effective potential which is further used to calculate the energy levels. Taking van der Waals interaction as interatomic interaction we calculate several quantities like condensate fraction N, root-mean-square fluctuation δn0 and different orders of central moments. We observe the effect of finite size on the calculation of condensate fluctuations and the effect of attractive interaction over the noninteracting limit. We observe the depletion of the condensate with increase in temperature. The calculated moments nicely exhibit the mesoscopic effect. The sharp fall in the root-mean-square fluctuation near the critical point signifies the possibility of phase transition.

Polar fluctuations in Mn substituted KTaO{sub 3} ceramics

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

Axelsson, Anna-Karin; Pan Yuya; Valant, Matjaz

2010-09-15

Polar fluctuations were found in KTaO{sub 3} when K{sup +} was substituted with Mn{sup 2+} on the A-site. The temperature dependence of the real part of the dielectric permittivity of (K{sub 1-2x}Mn{sub x{open_square}x})TaO{sub 3} ceramics (x=0-0.05) shows a diffuse maximum between 50-100 K in the frequency range 10{sup 2}-10{sup 6} Hz, shifting to higher temperature with increasing frequency and Mn content. The results are analyzed using a modified Curie-Weiss law, the Cole-Cole equation and the Arrhenius law. Here it is suggested that the observed relaxor-type dielectric behavior is attributed to the formation of electric dipoles originating from two distinct sources;more » one from an atomic off-center position when Mn{sup 2+} substitutes for K{sup +} and one from the anion deficiencies formed by these aliovalent substitutions.« less

Ubiquity of quantum zero-point fluctuations in dislocation glide

NASA Astrophysics Data System (ADS)

Landeiro Dos Reis, Marie; Choudhury, Anshuman; Proville, Laurent

2017-03-01

Modeling the dislocation glide through atomic scale simulations in Al, Cu, and Ni and in solid solution alloys Al(Mg) and Cu(Ag), we show that in the course of the plastic deformation the variation of the crystal zero-point energy (ZPE) and the dislocation potential energy barriers are of opposite sign. The multiplicity of situations where we have observed the same trend allows us to conclude that quantum fluctuations, giving rise to the crystal ZPE, make easier the dislocation glide in most materials, even those constituted of atoms heavier than H and He.

Fluctuating hydrodynamics for multiscale modeling and simulation: energy and heat transfer in molecular fluids.

PubMed

Shang, Barry Z; Voulgarakis, Nikolaos K; Chu, Jhih-Wei

2012-07-28

This work illustrates that fluctuating hydrodynamics (FHD) simulations can be used to capture the thermodynamic and hydrodynamic responses of molecular fluids at the nanoscale, including those associated with energy and heat transfer. Using all-atom molecular dynamics (MD) trajectories as the reference data, the atomistic coordinates of each snapshot are mapped onto mass, momentum, and energy density fields on Eulerian grids to generate a corresponding field trajectory. The molecular length-scale associated with finite molecule size is explicitly imposed during this coarse-graining by requiring that the variances of density fields scale inversely with the grid volume. From the fluctuations of field variables, the response functions and transport coefficients encoded in the all-atom MD trajectory are computed. By using the extracted fluid properties in FHD simulations, we show that the fluctuations and relaxation of hydrodynamic fields quantitatively match with those observed in the reference all-atom MD trajectory, hence establishing compatibility between the atomistic and field representations. We also show that inclusion of energy transfer in the FHD equations can more accurately capture the thermodynamic and hydrodynamic responses of molecular fluids. The results indicate that the proposed MD-to-FHD mapping with explicit consideration of finite molecule size provides a robust framework for coarse-graining the solution phase of complex molecular systems.

Atomistic observation and simulation analysis of spatio-temporal fluctuations during radiation-induced amorphization.

PubMed

Watanabe, Seiichi; Hoshino, Misaki; Koike, Takuto; Suda, Takanori; Ohnuki, Soumei; Takahashi, Heishichirou; Lam, Nighi Q

2003-01-01

We performed a dynamical-atomistic study of radiation-induced amorphization in the NiTi intermetallic compound using in situ high-resolution high-voltage electron microscopy and molecular dynamics simulations in connection with image simulation. Spatio-temporal fluctuations as non-equilibrium fluctuations in an energy-dissipative system, due to transient atom-cluster formation during amorphization, were revealed by the present spatial autocorrelation analysis.

Detection of atomic force microscopy cantilever displacement with a transmitted electron beam

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

Wagner, R.; Woehl, T. J.; Keller, R. R.

2016-07-25

The response time of an atomic force microscopy (AFM) cantilever can be decreased by reducing cantilever size; however, the fastest AFM cantilevers are currently nearing the smallest size that can be detected with the conventional optical lever approach. Here, we demonstrate an electron beam detection scheme for measuring AFM cantilever oscillations. The oscillating AFM tip is positioned perpendicular to and in the path of a stationary focused nanometer sized electron beam. As the tip oscillates, the thickness of the material under the electron beam changes, causing a fluctuation in the number of scattered transmitted electrons that are detected. We demonstratemore » detection of sub-nanometer vibration amplitudes with an electron beam, providing a pathway for dynamic AFM with cantilevers that are orders of magnitude smaller and faster than the current state of the art.« less

Feedback control of persistent-current oscillation based on the atomic-clock technique

NASA Astrophysics Data System (ADS)

Yu, Deshui; Dumke, Rainer

2018-05-01

We propose a scheme of stabilizing the persistent-current Rabi oscillation based on the flux qubit-resonator-atom hybrid structure. The low-Q L C resonator weakly interacts with the flux qubit and maps the persistent-current Rabi oscillation of the flux qubit onto the intraresonator electric field. This oscillating electric field is further coupled to a Rydberg-Rydberg transition of the 87Rb atoms. The Rabi-frequency fluctuation of the flux qubit is deduced from measuring the atomic population via the fluorescence detection and stabilized by feedback controlling the external flux bias. Our numerical simulation indicates that the feedback-control method can efficiently suppress the background fluctuations in the flux qubit, especially in the low-frequency limit. This technique may be extensively applicable to different types of superconducting circuits, paving a way to long-term-coherence superconducting quantum information processing.

Self-regulated Gd atom trapping in open Fe nanocorrals

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

Cao, R. X.; Liu, Z.; Miao, B. F.

2014-07-01

Utilizing open Fe nanocorrals built by atom manipulation, we demonstrate self-regulated Gd atom trapping in open quantum corrals. The number of Gd atoms trapped is exactly determined by the diameter of the corral. The quantization can be understood as a self-regulating process, arising from the long-range interaction between Gd atoms and the open corral. We illustrate with arrays of open corrals that such atom trapping can suppress unwanted statistical fluctuations. Our approach opens a potential pathway for nanomaterial design and fabrication with atomic-level precision.

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

Engineering Matter Interactions Using Squeezed Vacuum

NASA Astrophysics Data System (ADS)

Zeytinoǧlu, Sina; Imamoǧlu, Ataç; Huber, Sebastian

2017-04-01

Virtually all interactions that are relevant for atomic and condensed matter physics are mediated by quantum fluctuations of the electromagnetic field vacuum. Consequently, controlling the vacuum fluctuations can be used to engineer the strength and the range of interactions. Recent experiments have used this premise to demonstrate novel quantum phases or entangling gates by embedding electric dipoles in photonic cavities or wave guides, which modify the electromagnetic fluctuations. Here, we show theoretically that the enhanced fluctuations in the antisqueezed quadrature of a squeezed vacuum state allow for engineering interactions between electric dipoles without the need for a photonic structure. Thus, the strength and range of the interactions can be engineered in a time-dependent way by changing the spatial profile of the squeezed vacuum in a traveling-wave geometry, which also allows the implementation of chiral dissipative interactions. Using experimentally realized squeezing parameters and including realistic losses, we predict single-atom cooperativities C of up to 10 for the squeezed-vacuum-enhanced interactions.

Harmonic Dynamics of Proteins: Normal Modes and Fluctuations in Bovine Pancreatic Trypsin Inhibitor

NASA Astrophysics Data System (ADS)

Brooks, Bernard; Karplus, Martin

1983-11-01

A normal mode analysis making use of an empirical potential function including local and nonlocal (nonbonded) interactions is performed for the bovine pancreatic trypsin inhibitor in the full conformational space of the molecule (1,740 degrees of freedom); that is, all bond lengths and angles, as well as dihedral angles, are included for the 580-atom system consisting of all heavy atoms and polar hydrogens. The heavy-atom frequency spectrum shows a dense distribution between 3 and 1,800 cm-1, with 350 modes below 216 cm-1. Most of the low-frequency modes, of which many have significant anharmonic character, are found to be delocalized over the protein. The root-mean-square amplitudes of the atomic fluctuations are calculated at 300 K from the normal modes and compared with those obtained from a solution molecular dynamics simulation based on the same potential function; very good agreement is obtained for the variation in the main-chain fluctuations as a function of residue number, though larger differences occur for the side chains. The fluctuations are generally, though not always, dominated by frequencies below 30 cm-1, in accord with the results of the dynamics simulation. The vibrational contributions to the thermodynamic properties of the protein are calculated as a function of temperature; the effects of perturbations on the spectrum, suggested for ligand or substrate binding, are examined. The analysis demonstrates that, in spite of the anharmonic contributions to the potential, a normal mode description can provide useful results concerning the internal motions of proteins.

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

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

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

2016-05-06

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

[The conformational dynamics of the tetramer hemoglobin molecule as revealed by hydrogen exchange. III. Influence of the heme removal].

PubMed

Abaturov, L V; Nosova, N G; Shliapnikova, S V

2006-01-01

Two main types of conformational fluctuations--local and global are characteristic of the native protein structure and revealed by hydrogen exchange. The probability of those fluctuations changes to a different extent upon hemoglobin oxygenation, changing of pH, splitting of the intersubunit contacts. To compare with the influence of the heme removal the rate of the H-D exchange of the peptide NH atoms of the human apoHb was studied at the pH range 5.5-9.0 and temperature 10-38 degrees C by the IR spectroscopy. The removal of the heme increases the rate of the H-D exchange of the 80% peptide NH atoms with the factor retardation of the exchange rate (P) in the range approximately 10(2)-10(8). For the most of the peptide NH atoms the probability of the local fluctuations weakly depends on the temperature, the enthalpy changes upon all such local conformational transitions deltaH(op) degrees are 0-15 kcal/M. Characterized by the stronger temperature dependence the global fluctuations are not arised upon the temperature increases up to 38 degrees C at pH 7.0 inspite of in these conditions the slow denaturation and aggregation of apoHb begin to occur. Upon the destabilization of the apoHb structure by the simultaneous decreasing of pH to 5.5 and temperature to 10 degrees C the global fluctuations of the apoHb native structure described by deltaH(op)o < 0 begin to intensify. The mechanism of the overall intensification of the local fluctuations upon the heme removal, the peculiarity of the heat denaturation of apoHb in conditions, close to that existing upon the selfassembly of Hb in vivo, and analogy between low temperature global fluctuations and cold denaturation of globular proteins are discussed.

Apo adenylate kinase encodes its holo form: a principal component and varimax analysis.

PubMed

Cukier, Robert I

2009-02-12

Adenylate kinase undergoes large-scale motions of its LID and AMP-binding (AMPbd) domains when its apo, open form closes over its substrates, AMP and Mg2+-ATP. It may be an example of an enzyme that provides an ensemble of conformations in its apo state from which its substrates can select and bind to produce catalytically competent conformations. In this work, the fluctuations of the enzyme apo Escherichia coli adenylate kinase (AKE) are obtained with molecular dynamics. The resulting trajectory is analyzed with principal component analysis (PCA) that decomposes the atom motions into orthogonal modes ordered by their decreasing contributions to the total protein fluctuation. In apo AKE, a small set of the PCA modes describes the bulk of the fluctuations. Identification of the atom motions that are important contributors to these modes is improved with the use of a varimax rotation method that rotates the PCA modes to a new mode set that concentrates the atom contributions to a smaller set of atoms in these new modes. In this way, the nature of the important motions of the LID and AMPbd domains are clarified. The dominant PCA modes are used to investigate if apo AKE can fluctuate to conformations that are holo-like, even though the apo trajectory is mainly confined to a region around the initial apo structure. This is accomplished by expressing the difference between the protein coordinates, obtained from the holo and apo crystal structures, using as a basis the PCA modes from the apo AKE trajectory. The coherent motion described by a small set of the apo PCA modes is shown to be able to produce protein conformations that are quite similar to the holo conformation of the protein. In this sense, apo AKE does encode in its fluctuations information about holo-like conformations.

Covalent bond orders and atomic valences from correlated wavefunctions

NASA Astrophysics Data System (ADS)

Ángyán, János G.; Rosta, Edina; Surján, Péter R.

1999-01-01

A comparison is made between two alternative definitions for covalent bond orders: one derived from the exchange part of the two-particle density matrix and the other expressed as the correlation of fluctuations (covariance) of the number of electrons between the atomic centers. Although these definitions lead to identical formulae for mono-determinantal SCF wavefunctions, they predict different bond orders for correlated wavefunctions. It is shown that, in this case, the fluctuation-based definition leads to slightly lower values of the bond order than does the exchange-based definition, provided one uses an appropriate space-partitioning technique like that of Bader's topological theory of atoms in a molecule; however, use of Mulliken partitioning in this context leads to unphysical behaviour. The example of H 2 is discussed in detail.

A novel Cs-(129)Xe atomic spin gyroscope with closed-loop Faraday modulation.

PubMed

Fang, Jiancheng; Wan, Shuangai; Qin, Jie; Zhang, Chen; Quan, Wei; Yuan, Heng; Dong, Haifeng

2013-08-01

We report a novel Cs-(129)Xe atomic spin gyroscope (ASG) with closed-loop Faraday modulation method. This ASG requires approximately 30 min to start-up and 110 °C to operate. A closed-loop Faraday modulation method for measurement of the optical rotation was used in this ASG. This method uses an additional Faraday modulator to suppress the laser intensity fluctuation and Faraday modulator thermal induced fluctuation. We theoretically and experimentally validate this method in the Cs-(129)Xe ASG and achieved a bias stability of approximately 3.25 °∕h.

Radiative transfer in scattering stochastic atmospheres

NASA Astrophysics Data System (ADS)

Silant'ev, N. A.; Alekseeva, G. A.; Novikov, V. V.

2017-12-01

Many stars, active galactic nuclei, accretion discs etc. are affected by the stochastic variations of temperature, turbulent gas motions, magnetic fields, number densities of atoms and dust grains. These stochastic variations influence on the extinction factors, Doppler widths of lines and so on. The presence of many reasons for fluctuations gives rise to Gaussian distribution of fluctuations. The usual models leave out of account the fluctuations. In many cases the consideration of fluctuations improves the coincidence of theoretical values with the observed data. The objective of this paper is the investigation of the influence of the number density fluctuations on the form of radiative transfer equations. We consider non-magnetized atmosphere in continuum.

Locating the quantum critical point of the Bose-Hubbard model through singularities of simple observables.

PubMed

Łącki, Mateusz; Damski, Bogdan; Zakrzewski, Jakub

2016-12-02

We show that the critical point of the two-dimensional Bose-Hubbard model can be easily found through studies of either on-site atom number fluctuations or the nearest-neighbor two-point correlation function (the expectation value of the tunnelling operator). Our strategy to locate the critical point is based on the observation that the derivatives of these observables with respect to the parameter that drives the superfluid-Mott insulator transition are singular at the critical point in the thermodynamic limit. Performing the quantum Monte Carlo simulations of the two-dimensional Bose-Hubbard model, we show that this technique leads to the accurate determination of the position of its critical point. Our results can be easily extended to the three-dimensional Bose-Hubbard model and different Hubbard-like models. They provide a simple experimentally-relevant way of locating critical points in various cold atomic lattice systems.

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).

Quantifying Nanoscale Order in Amorphous Materials via Fluctuation Electron Microscopy

ERIC Educational Resources Information Center

Bogle, Stephanie Nicole

2009-01-01

Fluctuation electron microscopy (FEM) has been used to study the nanoscale order in various amorphous materials. The method is explicitly sensitive to 3- and 4-body atomic correlation functions in amorphous materials; this is sufficient to establish the existence of structural order on the nanoscale, even when the radial distribution function…

Large Fluctuations for Spatial Diffusion of Cold Atoms

NASA Astrophysics Data System (ADS)

Aghion, Erez; Kessler, David A.; Barkai, Eli

2017-06-01

We use a new approach to study the large fluctuations of a heavy-tailed system, where the standard large-deviations principle does not apply. Large-deviations theory deals with tails of probability distributions and the rare events of random processes, for example, spreading packets of particles. Mathematically, it concerns the exponential falloff of the density of thin-tailed systems. Here we investigate the spatial density Pt(x ) of laser-cooled atoms, where at intermediate length scales the shape is fat tailed. We focus on the rare events beyond this range, which dominate important statistical properties of the system. Through a novel friction mechanism induced by the laser fields, the density is explored with the recently proposed non-normalized infinite-covariant density approach. The small and large fluctuations give rise to a bifractal nature of the spreading packet. We derive general relations which extend our theory to a class of systems with multifractal moments.

Hanle effect in nonmonochromatic laser light

NASA Astrophysics Data System (ADS)

Ryan, R. E.; Bergeman, T. H.

1991-06-01

We report results of calculations on the Hanle effect in a J=0⇆J=1 atomic transition with three types of model fluctuating light fields: (a) the Brownian-motion phase-diffusion field, as produced in recent experiments by Arnett et al. [Phys. Rev. A 41, 2580 (1990)]; (b) Gaussian amplitude fluctuations; and (c) the chaotic field model, in which real and imaginary parts of the electric-field amplitude fluctuate. For the stochastic density-matrix equations, we use methods developed by Zoller and co-workers [e.g., Dixit, Zoller, and Lambropoulos, Phys. Rev. A 21, 1289 (1980)] employing the Fokker-Planck operator and leading to matrix continued-fraction expansions. The Hanle effect is of interest as a prototype for multisublevel atomic transitions. The width of the Hanle dip at zero magnetic field reflects the tendency of the light field to preserve the coherence between excited-state sublevels. For monochromatic light, the Hanle dip width increases as the square root of light intensity. When the laser bandwidth increases, power broadening of the coherence dip normally decreases. However, with the Brownian-motion phase-diffusion model, if the laser spectral profile is nearly Gaussian, broadening the laser up to several times the natural width of the atomic line does not diminish the Hanle dip width. With amplitude fluctuations, even in the limit of monochromatic light, power broadening of the Hanle dip with intensity is reduced by one-third to one-half depending on the particular model.

A quantum diffusion law

NASA Astrophysics Data System (ADS)

Satpathi, Urbashi; Sinha, Supurna; Sorkin, Rafael D.

2017-12-01

We analyse diffusion at low temperature by bringing the fluctuation-dissipation theorem (FDT) to bear on a physically natural, viscous response-function R(t) . The resulting diffusion-law exhibits several distinct regimes of time and temperature, each with its own characteristic rate of spreading. As with earlier analyses, we find logarithmic spreading in the quantum regime, indicating that this behavior is robust. A consistent R(t) must satisfy the key physical requirements of Wightman positivity and passivity, and we prove that ours does so. We also prove in general that these two conditions are equivalent when the FDT holds. Given current technology, our diffusion law can be tested in a laboratory with ultra cold atoms.

Anharmonic Normal Mode Analysis of Elastic Network Model Improves the Modeling of Atomic Fluctuations in Protein Crystal Structures

PubMed Central

Zheng, Wenjun

2010-01-01

Abstract Protein conformational dynamics, despite its significant anharmonicity, has been widely explored by normal mode analysis (NMA) based on atomic or coarse-grained potential functions. To account for the anharmonic aspects of protein dynamics, this study proposes, and has performed, an anharmonic NMA (ANMA) based on the Cα-only elastic network models, which assume elastic interactions between pairs of residues whose Cα atoms or heavy atoms are within a cutoff distance. The key step of ANMA is to sample an anharmonic potential function along the directions of eigenvectors of the lowest normal modes to determine the mean-squared fluctuations along these directions. ANMA was evaluated based on the modeling of anisotropic displacement parameters (ADPs) from a list of 83 high-resolution protein crystal structures. Significant improvement was found in the modeling of ADPs by ANMA compared with standard NMA. Further improvement in the modeling of ADPs is attained if the interactions between a protein and its crystalline environment are taken into account. In addition, this study has determined the optimal cutoff distances for ADP modeling based on elastic network models, and these agree well with the peaks of the statistical distributions of distances between Cα atoms or heavy atoms derived from a large set of protein crystal structures. PMID:20550915

Investigations into the impact of various substrates and ZnO ultra thin seed layers prepared by atomic layer deposition on growth of ZnO nanowire array

PubMed Central

2012-01-01

The impact of various substrates and zinc oxide (ZnO) ultra thin seed layers prepared by atomic layer deposition on the geometric morphology of subsequent ZnO nanowire arrays (NWs) fabricated by the hydrothermal method was investigated. The investigated substrates included B-doped ZnO films, indium tin oxide films, single crystal silicon (111), and glass sheets. Scanning electron microscopy and X-ray diffraction measurements revealed that the geometry and aligment of the NWs were controlled by surface topography of the substrates and thickness of the ZnO seed layers, respectively. According to atomic force microscopy data, we suggest that the substrate, fluctuate amplitude and fluctuate frequency of roughness on ZnO seed layers have a great impact on the alignment of the resulting NWs, whereas the influence of the seed layers' texture was negligible. PMID:22759838

AFD: an application for bi-molecular interaction using axial frequency distribution.

PubMed

Raza, Saad; Azam, Syed Sikander

2018-03-06

Conformational flexibility and generalized structural features are responsible for specific phenomena existing in biological pathways. With advancements in computational chemistry, novel approaches and new methods are required to compare the dynamic nature of biomolecules, which are crucial not only to address dynamic functional relationships but also to gain detailed insights into the disturbance and positional fluctuation responsible for functional shifts. Keeping this in mind, axial frequency distribution (AFD) has been developed, designed, and implemented. AFD can profoundly represent distribution and density of ligand atom around a particular atom or set of atoms. It enabled us to obtain an explanation of local movements and rotations, which are not significantly highlighted by any other structural and dynamical parameters. AFD can be implemented on biological models representing ligand and protein interactions. It shows a comprehensive view of the binding pattern of ligand by exploring the distribution of atoms relative to the x-y plane of the system. By taking a relative centroid on protein or ligand, molecular interactions like hydrogen bonds, van der Waals, polar or ionic interaction can be analyzed to cater the ligand movement, stabilization or flexibility with respect to the protein. The AFD graph resulted in the residual depiction of bi-molecular interaction in gradient form which can yield specific information depending upon the system of interest.

Spin noise spectroscopy beyond thermal equilibrium and linear response.

PubMed

Glasenapp, P; Sinitsyn, N A; Yang, Luyi; Rickel, D G; Roy, D; Greilich, A; Bayer, M; Crooker, S A

2014-10-10

Per the fluctuation-dissipation theorem, the information obtained from spin fluctuation studies in thermal equilibrium is necessarily constrained by the system's linear response functions. However, by including weak radio frequency magnetic fields, we demonstrate that intrinsic and random spin fluctuations even in strictly unpolarized ensembles can reveal underlying patterns of correlation and coupling beyond linear response, and can be used to study nonequilibrium and even multiphoton coherent spin phenomena. We demonstrate this capability in a classical vapor of (41)K alkali atoms, where spin fluctuations alone directly reveal Rabi splittings, the formation of Mollow triplets and Autler-Townes doublets, ac Zeeman shifts, and even nonlinear multiphoton coherences.

Detection of individual atoms in helium buffer gas and observation of their real-time motion

NASA Technical Reports Server (NTRS)

Pan, C. L.; Prodan, J. V.; Fairbank, W. M., Jr.; She, C. Y.

1980-01-01

Single atoms are detected and their motion measured for the first time to our knowledge by the fluorescence photon-burst method in the presence of large quantities of buffer gas. A single-clipped digital correlator records the photon burst in real time and displays the atom's transit time across the laser beam. A comparison is made of the special requirements for single-atom detection in vacuum and in a buffer gas. Finally, the probability distribution of the bursts from many atoms is measured. It further proves that the bursts observed on resonance are due to single atoms and not simply to noise fluctuations.

Edge resonant fluctuations and particle transport in a reversed-field pinch

NASA Astrophysics Data System (ADS)

Möller, A.

1998-12-01

Electrostatic fluctuations are measured in the Extrap T2 reversed-field pinch [J. R. Drake et al., in Plasma Physics and Controlled Nuclear Fusion Research 1996 (International Atomic Energy Agency, Vienna, 1997), Vol. 2, pp. 193-199] using a Langmuir probe array. The electrostatic fluctuation, driven particle transport ΓnΦ is derived and found to constitute a large fraction of the total particle transport. The spectral density of all measured quantities exhibits a peak in the frequency range 100-250 kHz, which originates from fluctuations that are resonant close to the edge [n=-(40-80)]. This peak contains only about 10-20% of the total fluctuation power, but is shown to dominate ΓnΦ. The main reason for this is the high toroidal mode number as compared with internally resonant magnetohydrodynamic fluctuations. The edge resonant fluctuations also features a higher coherence (γ=0.5) and close to 90° phase shift between density and potential fluctuations.

Adiabatic transfer of energy fluctuations between membranes inside an optical cavity

NASA Astrophysics Data System (ADS)

Garg, Devender; Chauhan, Anil K.; Biswas, Asoka

2017-08-01

A scheme is presented for the adiabatic transfer of average fluctuations in the phonon number between two membranes in an optical cavity. We show that by driving the cavity modes with external time-delayed pulses, one can obtain an effect analogous to stimulated Raman adiabatic passage in the atomic systems. The adiabatic transfer of fluctuations from one membrane to the other is attained through a "dark" mode, which is robust against decay of the mediating cavity mode. The results are supported with analytical and numerical calculations with experimentally feasible parameters.

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

Exploring cavity-mediated long-range interactions in a dilute quantum gas

NASA Astrophysics Data System (ADS)

Landig, Renate; Mottl, Rafael; Brennecke, Ferdinand; Baumann, Kristian; Donner, Tobias; Esslinger, Tilman

2013-05-01

We report on the observation of a characteristic change in the excitation spectrum of a Bose-Einstein condensate and increased density fluctuations due to cavity-mediated atom-atom interactions. Increasing the strength of the interaction leads to a softening of an excitation mode at finite momentum, preceding a superfluid to supersolid phase transition. The observed behavior is reminiscent of a roton minimum, as predicted for quantum gases with long-range interactions. We create long-range interactions in the BEC using a non-resonant transverse pump beam which induces virtual photon exchange via the vacuum field of an optical cavity. The mode softening is spectroscopically studied across the phase transition using a variant of Bragg spectroscopy. At the phase transition a diverging density response is observed which is linked to increased density fluctuations. Using the cavity dissipation channel we monitor these fluctuations in real-time and identify the influence of measurement backaction onto the critical behavior of the system.

Analysis of decoherence mechanisms in a single-atom quantum memory

NASA Astrophysics Data System (ADS)

Koerber, Matthias; Langenfeld, Stefan; Morin, Olivier; Neuzner, Andreas; Ritter, Stephan; Rempe, Gerhard

2017-04-01

While photons are ideal for the transmission of quantum information, they require dedicated memories for long-term storage. The challenge for such a photonic quantum memory is the combination of an efficient light-matter interface with a low-decoherence encoding. To increase the time before the quantum information is lost, a thorough analysis of the relevant decoherence mechanisms is indispensable. Our optical quantum memory consists of a single rubidium atom trapped in a two dimensional optical lattice in a high-finesse Fabry-Perot-type optical resonator. The qubit is initially stored in a superposition of Zeeman states, making magnetic field fluctuations the dominant source of decoherence. The impact to this type of noise is greatly reduced by transferring the qubit into a subspace less susceptible to magnetic field fluctuations. In this configuration, the achievable coherence times are no longer limited by those fluctuations, but decoherence mechanisms induced by the trapping beams pose a new limit. We will discuss the origin and magnitude of the relevant effects and strategies for possible resolutions.

Modular injector integrated linear apparatus with motion profile optimization for spatial atomic layer deposition.

PubMed

Wang, Xiaolei; Li, Yun; Lin, Jilong; Shan, Bin; Chen, Rong

2017-11-01

A spatial atomic layer deposition apparatus integrated with a modular injector and a linear motor has been designed. It consists of four parts: a precursor delivery manifold, a modular injector, a reaction zone, and a driving unit. An injector with multi-layer structured channels is designed to help improve precursor distribution homogeneity. During the back and forth movement of the substrate at high speed, the inertial impact caused by jerk and sudden changes of acceleration will degrade the film deposition quality. Such residual vibration caused by inertial impact will aggravate the fluctuation of the gap distance between the injector and the substrate in the deposition process. Thus, an S-curve motion profile is implemented to reduce the large inertial impact, and the maximum position error could be reduced by 84%. The microstructure of the film under the S-curve motion profile shows smaller root-mean-square and scanning voltage amplitude under an atomic force microscope, which verifies the effectiveness of the S-curve motion profile in reducing the residual vibration and stabilizing the gap distance between the injector and the substrate. The film deposition rate could reach 100 nm/min while maintaining good uniformity without obvious periodic patterns on the surface.

Modular injector integrated linear apparatus with motion profile optimization for spatial atomic layer deposition

NASA Astrophysics Data System (ADS)

Wang, Xiaolei; Li, Yun; Lin, Jilong; Shan, Bin; Chen, Rong

2017-11-01

A spatial atomic layer deposition apparatus integrated with a modular injector and a linear motor has been designed. It consists of four parts: a precursor delivery manifold, a modular injector, a reaction zone, and a driving unit. An injector with multi-layer structured channels is designed to help improve precursor distribution homogeneity. During the back and forth movement of the substrate at high speed, the inertial impact caused by jerk and sudden changes of acceleration will degrade the film deposition quality. Such residual vibration caused by inertial impact will aggravate the fluctuation of the gap distance between the injector and the substrate in the deposition process. Thus, an S-curve motion profile is implemented to reduce the large inertial impact, and the maximum position error could be reduced by 84%. The microstructure of the film under the S-curve motion profile shows smaller root-mean-square and scanning voltage amplitude under an atomic force microscope, which verifies the effectiveness of the S-curve motion profile in reducing the residual vibration and stabilizing the gap distance between the injector and the substrate. The film deposition rate could reach 100 nm/min while maintaining good uniformity without obvious periodic patterns on the surface.

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.

Vibrational properties of the amide group in acetanilide: A molecular-dynamics study

NASA Astrophysics Data System (ADS)

Campa, Alessandro; Giansanti, Andrea; Tenenbaum, Alexander

1987-09-01

A simplified classical model of acetanilide crystal is built in order to study the mechanisms of vibrational energy transduction in a hydrogen-bonded solid. The intermolecular hydrogen bond is modeled by an electrostatic interaction between neighboring excess charges on hydrogen and oxygen atoms. The intramolecular interaction in the peptide group is provided by a dipole-charge interaction. Forces are calculated up to second-order terms in the atomic displacements from equilibrium positions; the model is thus a chain of nonlinear coupled oscillators. Numerical molecular-dynamics experiments are performed on chain segments of five molecules. The dynamics is ordered, at all temperatures. Energy is widely exchanged between the stretching and the bending of the N-H bond, with characteristic times of the order of 0.2 ps. Energy transduction through the H bond is somewhat slower and of smaller amplitude, and is strongly reduced when the energies of the two bound molecules are very different: This could reduce the dissipation of localized energy fluctuations.

Transport spectroscopy of coupled donors in silicon nano-transistors

PubMed Central

Moraru, Daniel; Samanta, Arup; Anh, Le The; Mizuno, Takeshi; Mizuta, Hiroshi; Tabe, Michiharu

2014-01-01

The impact of dopant atoms in transistor functionality has significantly changed over the past few decades. In downscaled transistors, discrete dopants with uncontrolled positions and number induce fluctuations in device operation. On the other hand, by gaining access to tunneling through individual dopants, a new type of devices is developed: dopant-atom-based transistors. So far, most studies report transport through dopants randomly located in the channel. However, for practical applications, it is critical to control the location of the donors with simple techniques. Here, we fabricate silicon transistors with selectively nanoscale-doped channels using nano-lithography and thermal-diffusion doping processes. Coupled phosphorus donors form a quantum dot with the ground state split into a number of levels practically equal to the number of coupled donors, when the number of donors is small. Tunneling-transport spectroscopy reveals fine features which can be correlated with the different numbers of donors inside the quantum dot, as also suggested by first-principles simulation results. PMID:25164032

Electronic structure of ruthenium-doped iron chalcogenides

NASA Astrophysics Data System (ADS)

Winiarski, M. J.; Samsel-Czekała, M.; Ciechan, A.

2014-12-01

The structural and electronic properties of hypothetical RuxFe1-xSe and RuxFe1-xTe systems have been investigated from first principles within the density functional theory (DFT). Reasonable values of lattice parameters and chalcogen atomic positions in the tetragonal unit cell of iron chalcogenides have been obtained with the use of norm-conserving pseudopotentials. The well known discrepancies between experimental data and DFT-calculated results for structural parameters of iron chalcogenides are related to the semicore atomic states which were frozen in the used here approach. Such an approach yields valid results of the electronic structures of the investigated compounds. The Ru-based chalcogenides exhibit the same topology of the Fermi surface (FS) as that of FeSe, differing only in subtle FS nesting features. Our calculations predict that the ground states of RuSe and RuTe are nonmagnetic, whereas those of the solid solutions RuxFe1-xSe and RuxFe1-xTe become the single- and double-stripe antiferromagnetic, respectively. However, the calculated stabilization energy values are comparable for each system. The phase transitions between these magnetic arrangements may be induced by slight changes of the chalcogen atom positions and the lattice parameters a in the unit cell of iron selenides and tellurides. Since the superconductivity in iron chalcogenides is believed to be mediated by the spin fluctuations in single-stripe magnetic phase, the RuxFe1-xSe and RuxFe1-xTe systems are good candidates for new superconducting iron-based materials.

Energy shift and Casimir-Polder force for an atom out of thermal equilibrium near a dielectric substrate

NASA Astrophysics Data System (ADS)

Zhou, Wenting; Yu, Hongwei

2014-09-01

We study the energy shift and the Casimir-Polder force of an atom out of thermal equilibrium near the surface of a dielectric substrate. We first generalize, adopting the local source hypothesis, the formalism proposed by Dalibard, Dupont-Roc, and Cohen-Tannoudji [J. Phys. (Paris) 43, 1617 (1982), 10.1051/jphys:0198200430110161700; J. Phys. (Paris) 45, 637 (1984), 10.1051/jphys:01984004504063700], which separates the contributions of thermal fluctuations and radiation reaction to the energy shift and allows a distinct treatment of atoms in the ground and excited states, to the case out of thermal equilibrium, and then we use the generalized formalism to calculate the energy shift and the Casimir-Polder force of an isotropically polarizable neutral atom. We identify the effects of the thermal fluctuations that originate from the substrate and the environment and discuss in detail how the Casimir-Polder force out of thermal equilibrium behaves in three different distance regions in both the low-temperature limit and the high-temperature limit for both the ground-state and excited-state atoms, with special attention devoted to the distinctive features as opposed to thermal equilibrium. In particular, we recover the distinctive behavior of the atom-wall force out of thermal equilibrium at large distances in the low-temperature limit recently found in a different theoretical framework, and furthermore we give a concrete region where this behavior holds.

Influence of ball milling on atomic structure and magnetic properties of Co{sub 40}Fe{sub 22}Ta{sub 8}B{sub 30} glassy alloy

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

Taghvaei, Amir Hossein, E-mail: Amirtaghvaei@gmail.com; Department of Materials Science and Engineering, Shiraz University of Technology, Shiraz; Stoica, Mihai

2014-06-01

The influence of ball milling on the atomic structure and magnetic properties of the Co{sub 40}Fe{sub 22}Ta{sub 8}B{sub 30} metallic glass with a high thermal stability and excellent soft magnetic properties has been investigated. After 14 h of milling, the obtained powders were found to consist mainly of an amorphous phase and a small fraction of the (Co,Fe){sub 21}Ta{sub 2}B{sub 6} nanocrystals. The changes in the reduced pair correlation functions suggest noticeable changes in the atomic structure of the amorphous upon ball milling. Furthermore, it has been shown that milling is accompanied by introduction of compressive and dilatational sites inmore » the glassy phase and increasing the fluctuation of the atomic-level hydrostatic stress without affecting the coordination number of the nearest neighbors. Ball milling has decreased the thermal stability and significantly affected the magnetic properties through increasing the saturation magnetization, Curie temperature of the amorphous phase and coercivity. - Highlights: • Ball milling affected the atomic structure of Co{sub 40}Fe{sub 22}Ta{sub 8}B{sub 30} metallic glass. • Mechanically-induced crystallization started after 4 h milling. • Milling increased the fluctuation of the atomic-level hydrostatic stress in glass. • Ball milling influenced the thermal stability and magnetic properties.« less

Condensate fluctuations of interacting Bose gases within a microcanonical ensemble.

PubMed

Wang, Jianhui; He, Jizhou; Ma, Yongli

2011-05-01

Based on counting statistics and Bogoliubov theory, we present a recurrence relation for the microcanonical partition function for a weakly interacting Bose gas with a finite number of particles in a cubic box. According to this microcanonical partition function, we calculate numerically the distribution function, condensate fraction, and condensate fluctuations for a finite and isolated Bose-Einstein condensate. For ideal and weakly interacting Bose gases, we compare the condensate fluctuations with those in the canonical ensemble. The present approach yields an accurate account of the condensate fluctuations for temperatures close to the critical region. We emphasize that the interactions between excited atoms turn out to be important for moderate temperatures.

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

Zhai, Hua; Zhang, Jialin, E-mail: jialinzhang@hunnu.edu.cn; Yu, Hongwei, E-mail: hwyu@hunnu.edu.cn

We study the geometric phase of a uniformly accelerated two-level atom coupled with vacuum fluctuations of electromagnetic fields in the presence of a perfectly reflecting plane. We find that the geometric phase difference between the accelerated and inertial atoms which can be observed by atom interferometry crucially depends on the polarizability of the atom and the distance to the boundary and it can be dramatically manipulated with anisotropically polarizable atoms. In particular, extremely close to the boundary, the phase difference can be increased by two times as compared to the case without any boundary. So, the detectability of the effectsmore » associated with acceleration using an atom interferometer can be significantly increased by the presence of a boundary using atoms with anisotropic polarizability.« less

A Next-Generation Apparatus for Lithium Optical Lattice Experiments

NASA Astrophysics Data System (ADS)

Keshet, Aviv

Quantum simulation is emerging as an ambitious and active subfield of atomic physics. This thesis describes progress towards the goal of simulating condensed matter systems, in particular the physics of the Fermi-Hubbard model, using ultracold Lithium atoms in an optical lattice. A major goal of the quantum simulation program is to observe phase transitions of the Hubbard model, into Neal antiferromagnetic phases and d-wave superfluid phases. Phase transitions are generally accompanied by a change in an underlying correlation in a physical system. Such correlations may be most amenable to probing by looking at fluctuations in the system. Experimental techniques for probing density and magnetization fluctuations in a variety of atomic Fermi systems are developed. The suppression of density fluctuations (or atom "shot noise") in an ideal degenerate Fermi gas is observed by absorption imaging of time-of-flight expanded clouds. In-trap measurements of density and magnetization fluctuations are not easy to probe with absorption imaging, due to their extremely high attenuation. A method to probe these fluctuations based on speckle patterns, caused by fluctuations in the index of refraction for a detuned illumination beam, is developed and applied first to weakly interacting and then to strongly interacting in-trap gases. Fluctuation probes such as these will be a crucial tool in future quantum simulation of condensed matter systems. The quantum simulation experiments that we want to perform require a complex sequence of precisely timed computer controlled events. A distributed GUI-based control system designed with such experiments in mind, The Cicero Word Generator, is described. The system makes use of a client-server separation between a user interface for sequence design and a set of output hardware servers. Output hardware servers are designed to use standard National Instruments output cards, but the client-server nature allows this to be extended to other output hardware. Output sequences running on multiple servers and output cards can be synchronized using a shared clock. By using an FPGA-generated variable frequency clock, redundant buffers can be dramatically shortened, and a time resolution of 100ns achieved over effectively arbitrary sequence lengths. Experimental set-ups for producing, manipulating, and probing ultracold atomic gases can be quite complicated. To move forward with a quantum simulation program, it is necessary to have an apparatus that operates with a reliability that is not easily achieved in the face of this complexity. The design of a new apparatus is discussed. This Sodium-Lithium ultracold gas production machine has been engineered to incorporate as much experimental experience as possible to enhance its reliability. Particular attention has been paid to maximizing optical access and the utilization of this optical access, controlling the ambient temperature of the experiment, achieving a high vacuum, and simplifying subsystems where possible. The apparatus is now on the verge of producing degenerate gases, and should serve as a stable platform on which to perform future lattice quantum simulation experiments. (Copies available exclusively from MIT Libraries, libraries.mit.edu/docs - docs mit.edu)

Mechanism for pumping lasers with squeezed light

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

Haake, F.; Walls, D.F.; Collett, M.J.

1989-03-15

In this paper we demonstrate how the squeezed-pump-laser model of Marte and Walls (Phys. Rev. A 37, 1235 (1988)) may be realized in practice. We consider a three-level atomic medium interacting with two cavity modes pumped with squeezed light. We show that this pumping mechanism both achieves atomic inversion and squeezes the fluctuations on the lasing transition.

Sub-picosecond timing fluctuation suppression in laser-based atmospheric transfer of microwave signal using electronic phase compensation

NASA Astrophysics Data System (ADS)

Chen, Shijun; Sun, Fuyu; Bai, Qingsong; Chen, Dawei; Chen, Qiang; Hou, Dong

2017-10-01

We demonstrated a timing fluctuation suppression in outdoor laser-based atmospheric radio-frequency transfer over a 110 m one-way free-space link using an electronic phase compensation technique. Timing fluctuations and Allan Deviation are both measured to characterize the instability of transferred frequency incurred during the transfer process. With transferring a 1 GHz microwave signal over a timing fluctuation suppressed transmission link, the total root-mean-square (rms) timing fluctuation was measured to be 920 femtoseconds in 5000 s, with fractional frequency instability on the order of 1 × 10-12 at 1 s, and order of 2 × 10-16 at 1000 s. This atmospheric frequency transfer scheme with the timing fluctuation suppression technique can be used to fast build an atomic clock-based frequency free-space transmission link since its stability is superior to a commercial Cs and Rb clock.

Microcanonical fluctuations of the condensate in weakly interacting Bose gases

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

Idziaszek, Zbigniew

2005-05-15

We study fluctuations of the number of Bose condensed atoms in a weakly interacting homogeneous and trapped gases. For a homogeneous system we apply the particle-number-conserving formulation of the Bogoliubov theory and calculate the condensate fluctuations within the canonical and the microcanonical ensembles. We demonstrate that, at least in the low-temperature regime, predictions of the particle-number-conserving and traditional, nonconserving theory are identical, and lead to the anomalous scaling of fluctuations. Furthermore, the microcanonical fluctuations differ from the canonical ones by a quantity which scales normally in the number of particles, thus predictions of both ensembles are equivalent in the thermodynamicmore » limit. We observe a similar behavior for a weakly interacting gas in a harmonic trap. This is in contrast to the trapped, ideal gas, where microcanonical and canonical fluctuations are different in the thermodynamic limit.« less

Radiative processes of uniformly accelerated entangled atoms

NASA Astrophysics Data System (ADS)

Menezes, G.; Svaiter, N. F.

2016-05-01

We study radiative processes of uniformly accelerated entangled atoms, interacting with an electromagnetic field prepared in the Minkowski vacuum state. We discuss the structure of the rate of variation of the atomic energy for two atoms traveling in different hyperbolic world lines. We identify the contributions of vacuum fluctuations and radiation reaction to the generation of entanglement as well as to the decay of entangled states. Our results resemble the situation in which two inertial atoms are coupled individually to two spatially separated cavities at different temperatures. In addition, for equal accelerations we obtain that one of the maximally entangled antisymmetric Bell state is a decoherence-free state.

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.

Reduced equations of motion for quantum systems driven by diffusive Markov processes.

PubMed

Sarovar, Mohan; Grace, Matthew D

2012-09-28

The expansion of a stochastic Liouville equation for the coupled evolution of a quantum system and an Ornstein-Uhlenbeck process into a hierarchy of coupled differential equations is a useful technique that simplifies the simulation of stochastically driven quantum systems. We expand the applicability of this technique by completely characterizing the class of diffusive Markov processes for which a useful hierarchy of equations can be derived. The expansion of this technique enables the examination of quantum systems driven by non-Gaussian stochastic processes with bounded range. We present an application of this extended technique by simulating Stark-tuned Förster resonance transfer in Rydberg atoms with nonperturbative position fluctuations.

The atomic structure of polar and non-polar InGaN quantum wells and the green gap problem.

PubMed

Humphreys, C J; Griffiths, J T; Tang, F; Oehler, F; Findlay, S D; Zheng, C; Etheridge, J; Martin, T L; Bagot, P A J; Moody, M P; Sutherland, D; Dawson, P; Schulz, S; Zhang, S; Fu, W Y; Zhu, T; Kappers, M J; Oliver, R A

2017-05-01

We have used high resolution transmission electron microscopy (HRTEM), aberration-corrected quantitative scanning transmission electron microscopy (Q-STEM), atom probe tomography (APT) and X-ray diffraction (XRD) to study the atomic structure of (0001) polar and (11-20) non-polar InGaN quantum wells (QWs). This paper provides an overview of the results. Polar (0001) InGaN in QWs is a random alloy, with In replacing Ga randomly. The InGaN QWs have atomic height interface steps, resulting in QW width fluctuations. The electrons are localised at the top QW interface by the built-in electric field and the well-width fluctuations, with a localisation energy of typically 20meV. The holes are localised near the bottom QW interface, by indium fluctuations in the random alloy, with a localisation energy of typically 60meV. On the other hand, the non-polar (11-20) InGaN QWs contain nanometre-scale indium-rich clusters which we suggest localise the carriers and produce longer wavelength (lower energy) emission than from random alloy non-polar InGaN QWs of the same average composition. The reason for the indium-rich clusters in non-polar (11-20) InGaN QWs is not yet clear, but may be connected to the lower QW growth temperature for the (11-20) InGaN QWs compared to the (0001) polar InGaN QWs. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR

PubMed Central

Fenwick, R. Bryn; van den Bedem, Henry; Fraser, James S.; Wright, Peter E.

2014-01-01

Detailed descriptions of atomic coordinates and motions are required for an understanding of protein dynamics and their relation to molecular recognition, catalytic function, and allostery. Historically, NMR relaxation measurements have played a dominant role in the determination of the amplitudes and timescales (picosecond–nanosecond) of bond vector fluctuations, whereas high-resolution X-ray diffraction experiments can reveal the presence of and provide atomic coordinates for multiple, weakly populated substates in the protein conformational ensemble. Here we report a hybrid NMR and X-ray crystallography analysis that provides a more complete dynamic picture and a more quantitative description of the timescale and amplitude of fluctuations in atomic coordinates than is obtainable from the individual methods alone. Order parameters (S2) were calculated from single-conformer and multiconformer models fitted to room temperature and cryogenic X-ray diffraction data for dihydrofolate reductase. Backbone and side-chain order parameters derived from NMR relaxation experiments are in excellent agreement with those calculated from the room-temperature single-conformer and multiconformer models, showing that the picosecond timescale motions observed in solution occur also in the crystalline state. These motions are quenched in the crystal at cryogenic temperatures. The combination of NMR and X-ray crystallography in iterative refinement promises to provide an atomic resolution description of the alternate conformational substates that are sampled through picosecond to nanosecond timescale fluctuations of the protein structure. The method also provides insights into the structural heterogeneity of nonmethyl side chains, aromatic residues, and ligands, which are less commonly analyzed by NMR relaxation measurements. PMID:24474795

Relevance of Bose-Einstein condensation to the interference of two independent Bose gases

NASA Astrophysics Data System (ADS)

Iazzi, Mauro; Yuasa, Kazuya

2011-03-01

Interference of two independently prepared ideal Bose gases is discussed, on the basis of the idea of measurement-induced interference. It is known that, even if the number of atoms in each gas is individually fixed finite and the symmetry of the system is not broken, an interference pattern is observed on each single snapshot. The key role is played by the Hanbury Brown and Twiss effect, which leads to an oscillating pattern of the cloud of identical atoms. Then, how essential is the Bose-Einstein condensation to the interference? In this work, we describe two ideal Bose gases trapped in two separate three-dimensional harmonic traps at a finite temperature T, using the canonical ensembles (with fixed numbers of atoms). We compute the full statistics of the snapshot profiles of the expanding and overlapping gases released from the traps. We obtain a simple formula valid for finite T, which shows that the average fringe spectrum (average fringe contrast) is given by the purity of each gas. The purity is known to be a good measure of condensation, and the formula clarifies the relevance of the condensation to the interference. The results for T=0, previously known in the literature, can be recovered from our analysis. The fluctuation of the interference spectrum is also studied, and it is shown that the fluctuation is vanishingly small only below the critical temperature Tc, meaning that interference pattern is certainly observed on every snapshot below Tc. The fact that the number of atoms is fixed in the canonical ensemble is crucial to this vanishing fluctuation.

Quantum chaos in ultracold collisions of gas-phase erbium atoms.

PubMed

Frisch, Albert; Mark, Michael; Aikawa, Kiyotaka; Ferlaino, Francesca; Bohn, John L; Makrides, Constantinos; Petrov, Alexander; Kotochigova, Svetlana

2014-03-27

Atomic and molecular samples reduced to temperatures below one microkelvin, yet still in the gas phase, afford unprecedented energy resolution in probing and manipulating the interactions between their constituent particles. As a result of this resolution, atoms can be made to scatter resonantly on demand, through the precise control of a magnetic field. For simple atoms, such as alkalis, scattering resonances are extremely well characterized. However, ultracold physics is now poised to enter a new regime, where much more complex species can be cooled and studied, including magnetic lanthanide atoms and even molecules. For molecules, it has been speculated that a dense set of resonances in ultracold collision cross-sections will probably exhibit essentially random fluctuations, much as the observed energy spectra of nuclear scattering do. According to the Bohigas-Giannoni-Schmit conjecture, such fluctuations would imply chaotic dynamics of the underlying classical motion driving the collision. This would necessitate new ways of looking at the fundamental interactions in ultracold atomic and molecular systems, as well as perhaps new chaos-driven states of ultracold matter. Here we describe the experimental demonstration that random spectra are indeed found at ultralow temperatures. In the experiment, an ultracold gas of erbium atoms is shown to exhibit many Fano-Feshbach resonances, of the order of three per gauss for bosons. Analysis of their statistics verifies that their distribution of nearest-neighbour spacings is what one would expect from random matrix theory. The density and statistics of these resonances are explained by fully quantum mechanical scattering calculations that locate their origin in the anisotropy of the atoms' potential energy surface. Our results therefore reveal chaotic behaviour in the native interaction between ultracold atoms.

Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models

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

Kouza, Maksim, E-mail: mkouza@chem.uw.edu.pl; Kolinski, Andrzej; Co, Nguyen Truong

2015-04-14

Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleusmore » size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in slowing down fibril elongation in vivo.« less

A triple point in 3-level systems

NASA Astrophysics Data System (ADS)

Nahmad-Achar, E.; Cordero, S.; López-Peña, R.; Castaños, O.

2014-11-01

The energy spectrum of a 3-level atomic system in the Ξ-configuration is studied. This configuration presents a triple point independently of the number of atoms, which remains in the thermodynamic limit. This means that in a vicinity of this point any quantum fluctuation will drastically change the composition of the ground state of the system. We study the expectation values of the atomic population of each level, the number of photons, and the probability distribution of photons at the triple point.

Stresses and elastic constants of crystalline sodium, from molecular dynamics

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

Schiferl, S.K.

1985-02-01

The stresses and the elastic constants of bcc sodium are calculated by molecular dynamics (MD) for temperatures to T = 340K. The total adiabatic potential of a system of sodium atoms is represented by pseudopotential model. The resulting expression has two terms: a large, strictly volume-dependent potential, plus a sum over ion pairs of a small, volume-dependent two-body potential. The stresses and the elastic constants are given as strain derivatives of the Helmholtz free energy. The resulting expressions involve canonical ensemble averages (and fluctuation averages) of the position and volume derivatives of the potential. An ensemble correction relates the resultsmore » to MD equilibrium averages. Evaluation of the potential and its derivatives requires the calculation of integrals with infinite upper limits of integration, and integrand singularities. Methods for calculating these integrals and estimating the effects of integration errors are developed. A method is given for choosing initial conditions that relax quickly to a desired equilibrium state. Statistical methods developed earlier for MD data are extended to evaluate uncertainties in fluctuation averages, and to test for symmetry. 45 refs., 10 figs., 4 tabs.« less

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

Dayeh, M. A.; Fuselier, S. A.; Funsten, H. O.

We present remote, continuous observations from the Interstellar Boundary Explorer of the terrestrial plasma sheet location back to -16 Earth radii (R E) in the magnetospheric tail using energetic neutral atom emissions. The time period studied includes two orbits near the winter and summer solstices, thus associated with large negative and positive dipole tilt, respectively. Continuous side-view images reveal a complex shape that is dominated mainly by large-scale warping due to the diurnal motion of the dipole axis. Superposed on the global warped geometry are short-time fluctuations in plasma sheet location that appear to be consistent with plasma sheet flappingmore » and possibly twisting due to changes in the interplanetary conditions. We conclude that the plasma sheet warping due to the diurnal motion dominates the average shape of the plasma sheet. Over short times, the position of the plasma sheet can be dominated by twisting and flapping.« less

Fluctuation-exchange study of antiferromagnetism in disordered electron-doped cuprate superconductors.

PubMed

Yan, Xin-Zhong; Ting, C S

2006-08-11

On the basis of the Hubbard model, we extend the fluctuation-exchange (FLEX) approach to investigating the properties of the antiferromagnetic (AF) phase in electron-doped cuprate superconductors. Furthermore, by incorporating the effect of scatterings due to the disordered dopant atoms into the FLEX formalism, our numerical results show that the antiferromagnetic transition temperature, the onset temperature of pseudogap due to spin fluctuations, the spectral density of the single particle near the Fermi surface, and the staggered magnetization in the AF phase as a function of electron doping can consistently account for the experimental measurements.

Study on structures and properties of ammonia clusters (NH3)n (n=1-5) and liquid ammonia in terms of ab initio method and atom-bond electronegativity equalization method ammonia-8P fluctuating charge potential model.

PubMed

Yu, Ling; Yang, Zhong-Zhi

2010-05-07

Structures, binding energies, and vibrational frequencies of (NH(3))(n) (n=2-5) isomers and dynamical properties of liquid ammonia have been explored using a transferable intermolecular potential eight point model including fluctuating charges and flexible body based on a combination of the atom-bond electronegativity equalization and molecular (ABEEM) mechanics (ABEEM ammonia-8P) in this paper. The important feature of this model is to divide the charge sites of one ammonia molecule into eight points region containing four atoms, three sigma bonds, and a lone pair, and allows the charges in system to fluctuate responding to the ambient environment. Due to the explicit descriptions of charges and special treatment of hydrogen bonds, the results of equilibrium geometries, dipole moments, cluster interaction energies, vibrational frequencies for the gas phase of small ammonia clusters, and radial distribution function for liquid ammonia calculated with the ABEEM ammonia-8P potential model are in good agreement with those measured by available experiments and those obtained from high level ab initio calculations. The properties of ammonia dimer are studied in detail involving the structure and one-dimensional, two-dimensional potential energy surface. As for interaction energies, the root mean square deviation is 0.27 kcal/mol, and the linear correlation coefficient reaches 0.994.

Kinetic Roughening and Energetics of Tetragonal Lysozyme Crystal Growth: A Preliminary Atomic Force Microscopy Investigation

NASA Technical Reports Server (NTRS)

Gorti, Sridhar; Forsythe, Elizabeth L.; Pusey, Marc L.

2004-01-01

We examined particulars of crystal growth from measurements obtained at both microscopic and molecular levels. The crystal growth measurements performed at the microscopic level are well characterized by a model that balances the flux of macromolecules towards the crystal surface with the flux of the crystal surface. Numerical evaluation of model with measurements of crystal growth, in time, provided accurate estimates for the average growth velocities. Growth velocities thus obtained were also interpreted using well-established phenomenological theories. Moreover, we find that microscopic measurements of growth velocity measurements obtained as a function of temperature best characterizes changes in crystal growth modes, when present. We also examined the possibility of detecting a change in crystal growth modes at the molecular level using atomic force microscopy, AFM. From preliminary AFM measurements performed at various supersaturations, we find that magnitude of surface height fluctuations, h(x), increases with supersaturation. Further examination of surface height fluctuations using methods established for fluctuation spectroscopy also enabled the discovery of the existence of a characteristic length, c, which may possibly determine the mode of crystal growth. Although the results are preliminary, we establish the non- critical divergence of 5 and the root-mean-square (rms) magnitude of height-height fluctuations as the kinetic roughening transition temperatures are approached. Moreover, we also examine approximate models for interpreting the non-critical behavior of both 6 and rms magnitude of height-height fluctuations, as the solution supersaturation is increased towards the kinetic roughening supersaturation.

Birth order and fluctuating asymmetry: a first look.

PubMed Central

Lalumière, M L; Harris, G T; Rice, M E

1999-01-01

We investigated the hypothesis that maternal immunoreactivity to male-specific features of the foetus can increase developmental instability. We predicted that the participants' number of older brothers would be positively related to the fluctuating asymmetry of ten bilateral morphological traits. The participants were 40 adult male psychiatric patients and 31 adult male hospital employees. Consistent with the hypothesis, the participants' number of older brothers--but not number of older sisters, younger brothers or younger sisters--was positively associated with fluctuating asymmetry. The patients had significantly larger fluctuating asymmetry scores and tended to have more older brothers than the employees, but the positive relationship between the number of older brothers and fluctuating asymmetry was observed in both groups. PMID:10643079

Investigation of air-assisted sprays submitted to high frequency transverse acoustic fields: Droplet clustering

NASA Astrophysics Data System (ADS)

Ficuciello, A.; Blaisot, J. B.; Richard, C.; Baillot, F.

2017-06-01

An experimental investigation of the effects of a high amplitude transverse acoustic field on coaxial jets is presented in this paper. Water and air are used as working fluids at ambient pressure. The coaxial injectors are placed on the top of a semi-open resonant cavity where the acoustic pressure fluctuations of the standing wave can reach a maximum peak-to-peak amplitude of 12 kPa at the forcing frequency of 1 kHz. Several test conditions are considered in order to quantify the influence of injection conditions, acoustic field amplitude, and injector position with respect to the standing wave acoustic field. A high speed back-light visualization technique is used to characterize the jet response. Image processing is used to obtain valuable information about the jet behavior. It is shown that the acoustic field drastically affects the atomization process for all atomization regimes. The position of the injector in the acoustic field determines the jet response, and a droplet-clustering phenomenon is highlighted in multi-point injection conditions and quantified by determining discrete droplet location distributions. A theoretical model based on nonlinear acoustics related to the spatial distribution of the radiation pressure exerted on an object explains the behavior observed.

Synthetic Unruh effect in cold atoms

NASA Astrophysics Data System (ADS)

Rodríguez-Laguna, Javier; Tarruell, Leticia; Lewenstein, Maciej; Celi, Alessio

2017-01-01

We propose to simulate a Dirac field near an event horizon using ultracold atoms in an optical lattice. Such a quantum simulator allows for the observation of the celebrated Unruh effect. Our proposal involves three stages: (1) preparation of the ground state of a massless two-dimensional Dirac field in Minkowski space-time; (2) quench of the optical lattice setup to simulate how an accelerated observer would view that state; (3) measurement of the local quantum fluctuation spectra by one-particle excitation spectroscopy in order to simulate a De Witt detector. According to Unruh's prediction, fluctuations measured in such a way must be thermal. Moreover, following Takagi's inversion theorem, they will obey the Bose-Einstein distribution, which will smoothly transform into the Fermi-Dirac as one of the dimensions of the lattice is reduced.

CABS-flex: server for fast simulation of protein structure fluctuations

PubMed Central

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2013-01-01

The CABS-flex server (http://biocomp.chem.uw.edu.pl/CABSflex) implements CABS-model–based protocol for the fast simulations of near-native dynamics of globular proteins. In this application, the CABS model was shown to be a computationally efficient alternative to all-atom molecular dynamics—a classical simulation approach. The simulation method has been validated on a large set of molecular dynamics simulation data. Using a single input (user-provided file in PDB format), the CABS-flex server outputs an ensemble of protein models (in all-atom PDB format) reflecting the flexibility of the input structure, together with the accompanying analysis (residue mean-square-fluctuation profile and others). The ensemble of predicted models can be used in structure-based studies of protein functions and interactions. PMID:23658222

CABS-flex: Server for fast simulation of protein structure fluctuations.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2013-07-01

The CABS-flex server (http://biocomp.chem.uw.edu.pl/CABSflex) implements CABS-model-based protocol for the fast simulations of near-native dynamics of globular proteins. In this application, the CABS model was shown to be a computationally efficient alternative to all-atom molecular dynamics--a classical simulation approach. The simulation method has been validated on a large set of molecular dynamics simulation data. Using a single input (user-provided file in PDB format), the CABS-flex server outputs an ensemble of protein models (in all-atom PDB format) reflecting the flexibility of the input structure, together with the accompanying analysis (residue mean-square-fluctuation profile and others). The ensemble of predicted models can be used in structure-based studies of protein functions and interactions.

Spontaneous breaking of time-reversal symmetry in strongly interacting two-dimensional electron layers in silicon and germanium.

PubMed

Shamim, S; Mahapatra, S; Scappucci, G; Klesse, W M; Simmons, M Y; Ghosh, A

2014-06-13

We report experimental evidence of a remarkable spontaneous time-reversal symmetry breaking in two-dimensional electron systems formed by atomically confined doping of phosphorus (P) atoms inside bulk crystalline silicon (Si) and germanium (Ge). Weak localization corrections to the conductivity and the universal conductance fluctuations were both found to decrease rapidly with decreasing doping in the Si:P and Ge:P delta layers, suggesting an effect driven by Coulomb interactions. In-plane magnetotransport measurements indicate the presence of intrinsic local spin fluctuations at low doping, providing a microscopic mechanism for spontaneous lifting of the time-reversal symmetry. Our experiments suggest the emergence of a new many-body quantum state when two-dimensional electrons are confined to narrow half-filled impurity bands.

Electrostatics of the protein-water interface and the dynamical transition in proteins.

PubMed

Matyushov, Dmitry V; Morozov, Alexander Y

2011-07-01

Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent experiments indicate a connection between the dynamical transition and the dielectric response of the hydrated protein. We analyze two mechanisms of the coupling between the protein atomic motions and the protein-water interface. The first mechanism considers viscoelastic changes in the global shape of the protein plasticized by its coupling to the hydration shell. The second mechanism involves modulations of the local motions of partial charges inside the protein by electrostatic fluctuations. The model is used to analyze mean-square displacements of iron of metmyoglobin reported by Mössbauer spectroscopy. We show that high displacement of heme iron at physiological temperatures is dominated by electrostatic fluctuations. Two onsets, one arising from the viscoelastic response and the second from electrostatic fluctuations, are seen in the temperature dependence of the mean-square displacements when the corresponding relaxation times enter the instrumental resolution window.

Electrostatics of the protein-water interface and the dynamical transition in proteins

NASA Astrophysics Data System (ADS)

Matyushov, Dmitry V.; Morozov, Alexander Y.

2011-07-01

Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent experiments indicate a connection between the dynamical transition and the dielectric response of the hydrated protein. We analyze two mechanisms of the coupling between the protein atomic motions and the protein-water interface. The first mechanism considers viscoelastic changes in the global shape of the protein plasticized by its coupling to the hydration shell. The second mechanism involves modulations of the local motions of partial charges inside the protein by electrostatic fluctuations. The model is used to analyze mean-square displacements of iron of metmyoglobin reported by Mössbauer spectroscopy. We show that high displacement of heme iron at physiological temperatures is dominated by electrostatic fluctuations. Two onsets, one arising from the viscoelastic response and the second from electrostatic fluctuations, are seen in the temperature dependence of the mean-square displacements when the corresponding relaxation times enter the instrumental resolution window.

The Langevin equation

NASA Astrophysics Data System (ADS)

Pomeau, Yves; Piasecki, Jarosław

2017-11-01

The existence of atoms has been long predicted by philosophers and scientists. The development of thermodynamics and of the statistical interpretation of its concepts at the end of the nineteenth century and in the early years of the twentieth century made it possible to bridge the gap of scales between the macroscopic world and the world of atoms. Einstein and Smoluchowski showed in 1905 and 1906 that the Brownian motion of particles of measurable size is a manifestation of the motion of atoms in fluids. Their derivation was completely different from each other. Langevin showed in 1908 how to put in a coherent framework the subtle effect of the randomness of the atomic world, responsible for the fluctuating force driving the motion of the Brownian particle and the viscosity of the "macroscopic" flow taking place around the same Brownian particle. Whereas viscous forces were already well understood at this time, the "Langevin" force appears there for the first time: it represents the fluctuating part of the interaction between the Brownian particle and the surrounding fluid. We discuss the derivation by Einstein and Smoluchowski as well as a previous paper by Sutherland on the diffusion coefficient of large spheres. Next we present Langevin's short note and explain the fundamental splitting into a random force and a macroscopic viscous force. This brings us to discuss various points, like the kind of constraints on Langevin-like equations. We insist in particular on the one arising from the time-reversal symmetry of the equilibrium fluctuations. Moreover, we discuss another constraint, raised first by Lorentz, which implies that, if the Brownian particle is not very heavy, the viscous force cannot be taken as the standard Stokes drag on an object moving at uniform speed. Lastly, we examine the so-called Langevin-Heisenberg and/or Langevin-Schrödinger equation used in quantum mechanics.

Atom-scale compositional distribution in InAlAsSb-based triple junction solar cells by atom probe tomography.

PubMed

Hernández-Saz, J; Herrera, M; Delgado, F J; Duguay, S; Philippe, T; Gonzalez, M; Abell, J; Walters, R J; Molina, S I

2016-07-29

The analysis by atom probe tomography (APT) of InAlAsSb layers with applications in triple junction solar cells (TJSCs) has shown the existence of In- and Sb-rich regions in the material. The composition variation found is not evident from the direct observation of the 3D atomic distribution and because of this a statistical analysis has been required. From previous analysis of these samples, it is shown that the small compositional fluctuations determined have a strong effect on the optical properties of the material and ultimately on the performance of TJSCs.

Relative Energy Shift of a Two-Level Atom in a Cylindrical Spacetime

NASA Astrophysics Data System (ADS)

Zhang, Jia-Lin

2012-11-01

We investigate the evolution dynamics of a two-level atom system interacting with the massless scalar field in a Cylindrical spacetime. We find that both the energy shifts of ground state and excited state can be separated into two parts due to the vacuum fluctuations. One is the corresponding energy shift for a rest atom in four-dimensional Minkowski space without spatial compactification, the other is just the modification of the spatial compactified periodic length. It will reveal that the influence of the presence of one spatial compactified dimension can not be neglected in Lamb shift as the relative energy level shift of an atom.

Adiabatic quantum computation with neutral atoms via the Rydberg blockade

NASA Astrophysics Data System (ADS)

Goyal, Krittika; Deutsch, Ivan

2011-05-01

We study a trapped-neutral-atom implementation of the adiabatic model of quantum computation whereby the Hamiltonian of a set of interacting qubits is changed adiabatically so that its ground state evolves to the desired output of the algorithm. We employ the ``Rydberg blockade interaction,'' which previously has been used to implement two-qubit entangling gates in the quantum circuit model. Here it is employed via off-resonant virtual dressing of the excited levels, so that atoms always remain in the ground state. The resulting dressed-Rydberg interaction is insensitive to the distance between the atoms within a certain blockade radius, making this process robust to temperature and vibrational fluctuations. Single qubit interactions are implemented with global microwaves and atoms are locally addressed with light shifts. With these ingredients, we study a protocol to implement the two-qubit Quadratic Unconstrained Binary Optimization (QUBO) problem. We model atom trapping, addressing, coherent evolution, and decoherence. We also explore collective control of the many-atom system and generalize the QUBO problem to multiple qubits. We study a trapped-neutral-atom implementation of the adiabatic model of quantum computation whereby the Hamiltonian of a set of interacting qubits is changed adiabatically so that its ground state evolves to the desired output of the algorithm. We employ the ``Rydberg blockade interaction,'' which previously has been used to implement two-qubit entangling gates in the quantum circuit model. Here it is employed via off-resonant virtual dressing of the excited levels, so that atoms always remain in the ground state. The resulting dressed-Rydberg interaction is insensitive to the distance between the atoms within a certain blockade radius, making this process robust to temperature and vibrational fluctuations. Single qubit interactions are implemented with global microwaves and atoms are locally addressed with light shifts. With these ingredients, we study a protocol to implement the two-qubit Quadratic Unconstrained Binary Optimization (QUBO) problem. We model atom trapping, addressing, coherent evolution, and decoherence. We also explore collective control of the many-atom system and generalize the QUBO problem to multiple qubits. We acknowledge funding from the AQUARIUS project, Sandia National Laboratories

Enhanced squeezing of a collective spin via control of its qudit subsystems.

PubMed

Norris, Leigh M; Trail, Collin M; Jessen, Poul S; Deutsch, Ivan H

2012-10-26

Unitary control of qudits can improve the collective spin squeezing of an atomic ensemble. Preparing the atoms in a state with large quantum fluctuations in magnetization strengthens the entangling Faraday interaction. The resulting increase in interatomic entanglement can be converted into metrologically useful spin squeezing. Further control can squeeze the internal atomic spin without compromising entanglement, providing an overall multiplicative factor in the collective squeezing. We model the effects of optical pumping and study the tradeoffs between enhanced entanglement and decoherence. For realistic parameters we see improvements of ~10 dB.

Detecting weak position fluctuations from encoder signal using singular spectrum analysis.

PubMed

Xu, Xiaoqiang; Zhao, Ming; Lin, Jing

2017-11-01

Mechanical fault or defect will cause some weak fluctuations to the position signal. Detection of such fluctuations via encoders can help determine the health condition and performance of the machine, and offer a promising alternative to the vibration-based monitoring scheme. However, besides the interested fluctuations, encoder signal also contains a large trend and some measurement noise. In applications, the trend is normally several orders larger than the concerned fluctuations in magnitude, which makes it difficult to detect the weak fluctuations without signal distortion. In addition, the fluctuations can be complicated and amplitude modulated under non-stationary working condition. To overcome this issue, singular spectrum analysis (SSA) is proposed for detecting weak position fluctuations from encoder signal in this paper. It enables complicated encode signal to be reduced into several interpretable components including a trend, a set of periodic fluctuations and noise. A numerical simulation is given to demonstrate the performance of the method, it shows that SSA outperforms empirical mode decomposition (EMD) in terms of capability and accuracy. Moreover, linear encoder signals from a CNC machine tool are analyzed to determine the magnitudes and sources of fluctuations during feed motion. The proposed method is proven to be feasible and reliable for machinery condition monitoring. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Elastic interaction of hydrogen atoms on graphene: A multiscale approach from first principles to continuum elasticity

NASA Astrophysics Data System (ADS)

Branicio, Paulo S.; Vastola, Guglielmo; Jhon, Mark H.; Sullivan, Michael B.; Shenoy, Vivek B.; Srolovitz, David J.

2016-10-01

The deformation of graphene due to the chemisorption of hydrogen atoms on its surface and the long-range elastic interaction between hydrogen atoms induced by these deformations are investigated using a multiscale approach based on first principles, empirical interactions, and continuum modeling. Focus is given to the intrinsic low-temperature structure and interactions. Therefore, all calculations are performed at T =0 , neglecting possible temperature or thermal fluctuation effects. Results from different methods agree well and consistently describe the local deformation of graphene on multiple length scales reaching 500 Å . The results indicate that the elastic interaction mediated by this deformation is significant and depends on the deformation of the graphene sheet both in and out of plane. Surprisingly, despite the isotropic elasticity of graphene, within the linear elastic regime, atoms elastically attract or repel each other depending on (i) the specific site they are chemisorbed; (ii) the relative position of the sites; (iii) and if they are on the same or on opposite surface sides. The interaction energy sign and power-law decay calculated from molecular statics agree well with theoretical predictions from linear elasticity theory, considering in-plane or out-of-plane deformations as a superposition or in a coupled nonlinear approach. Deviations on the exact power law between molecular statics and the linear elastic analysis are evidence of the importance of nonlinear effects on the elasticity of monolayer graphene. These results have implications for the understanding of the generation of clusters and regular formations of hydrogen and other chemisorbed atoms on graphene.

Disorder in Protein Crystals.

NASA Astrophysics Data System (ADS)

Clarage, James Braun, II

1990-01-01

Methods have been developed for analyzing the diffuse x-ray scattering in the halos about a crystal's Bragg reflections as a means of determining correlations in atomic displacements in protein crystals. The diffuse intensity distribution for rhombohedral insulin, tetragonal lysozyme, and triclinic lysozyme crystals was best simulated in terms of exponential displacement correlation functions. About 90% of the disorder can be accounted for by internal movements correlated with a decay distance of about 6A; the remaining 10% corresponds to intermolecular movements that decay in a distance the order of size of the protein molecule. The results demonstrate that protein crystals fit into neither the Einstein nor the Debye paradigms for thermally fluctuating crystalline solids. Unlike the Einstein model, there are correlations in the atomic displacements, but these correlations decay more steeply with distance than predicted by the Debye-Waller model for an elastic solid. The observed displacement correlations are liquid -like in the sense that they decay exponentially with the distance between atoms, just as positional correlations in a liquid. This liquid-like disorder is similar to the disorder observed in 2-D crystals of polystyrene latex spheres, and similar systems where repulsive interactions dominate; hence, these colloidal crystals appear to provide a better analogy for the dynamics of protein crystals than perfectly elastic lattices.

Spontaneous fluctuation of the resting membrane potential in Paramecium: amplification caused by intracellular Ca2+.

PubMed

Nakaoka, Yasuo; Imaji, Takafumi; Hara, Masahiro; Hashimoto, Noboru

2009-01-01

The ciliated protozoan Paramecium spontaneously changes its swimming direction in the absence of external stimuli. Such behavior is based on resting potential fluctuations, the amplitudes of which reach a few mV. When the resting potential fluctuation is positive and large, a spike-like depolarization is frequently elicited that reverses the beating of the cilia associated with directional changes during swimming. We aimed to study how the resting potential fluctuation is amplified. Simultaneous measurements of the resting potential and intracellular Ca(2+) ([Ca(2+)](i)) from a deciliated cell showed that positive potential fluctuations were frequently accompanied by a small increase in [Ca(2+)](i). This result suggests that Ca(2+) influx through the somatic membrane occurs during the resting state. The mean amplitude of the resting potential fluctuation was largely decreased by either an intracellular injection of a calcium chelater (BAPTA) or by an extracellular addition of Ba(2+). Hence, a small increase in [Ca(2+)](i) amplifies the resting potential fluctuation. Simulation analysis of the potential fluctuation was made by assuming that Ca(2+) and K(+) channels of surface membrane are fluctuating between open and closed states. The simulated fluctuation increased to exhibit almost the same amplitude as the measured fluctuation using the assumption that a small Ca(2+) influx activates Ca(2+) channels in a positive feedback manner.

Removing Beam Current Artifacts in Helium Ion Microscopy: A Comparison of Image Processing Techniques.

PubMed

Barlow, Anders J; Portoles, Jose F; Sano, Naoko; Cumpson, Peter J

2016-10-01

The development of the helium ion microscope (HIM) enables the imaging of both hard, inorganic materials and soft, organic or biological materials. Advantages include outstanding topographical contrast, superior resolution down to <0.5 nm at high magnification, high depth of field, and no need for conductive coatings. The instrument relies on helium atom adsorption and ionization at a cryogenically cooled tip that is atomically sharp. Under ideal conditions this arrangement provides a beam of ions that is stable for days to weeks, with beam currents in the order of picoamperes. Over time, however, this stability is lost as gaseous contamination builds up in the source region, leading to adsorbed atoms of species other than helium, which ultimately results in beam current fluctuations. This manifests itself as horizontal stripe artifacts in HIM images. We investigate post-processing methods to remove these artifacts from HIM images, such as median filtering, Gaussian blurring, fast Fourier transforms, and principal component analysis. We arrive at a simple method for completely removing beam current fluctuation effects from HIM images while maintaining the full integrity of the information within the image.

Quantum Landau damping in dipolar Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Mendonça, J. T.; Terças, H.; Gammal, A.

2018-06-01

We consider Landau damping of elementary excitations in Bose-Einstein condensates (BECs) with dipolar interactions. We discuss quantum and quasiclassical regimes of Landau damping. We use a generalized wave-kinetic description of BECs which, apart from the long-range dipolar interactions, also takes into account the quantum fluctuations and the finite-energy corrections to short-range interactions. Such a description is therefore more general than the usual mean-field approximation. The present wave-kinetic approach is well suited for the study of kinetic effects in BECs, such as those associated with Landau damping, atom trapping, and turbulent diffusion. The inclusion of quantum fluctuations and energy corrections changes the dispersion relation and the damping rates, leading to possible experimental signatures of these effects. Quantum Landau damping is described with generality, and particular examples of dipolar condensates in two and three dimensions are studied. The occurrence of roton-maxon excitations, and their relevance to Landau damping, are also considered in detail. The present approach is mainly based on a linear perturbative procedure, but the nonlinear regime of Landau damping, which includes atom trapping and atom diffusion, is also briefly discussed.

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.

Role of Protein Flexibility in Ion Permeation: A Case Study in Gramicidin A

PubMed Central

Baştuğ, Turgut; Gray-Weale, Angus; Patra, Swarna M.; Kuyucak, Serdar

2006-01-01

Proteins have a flexible structure, and their atoms exhibit considerable fluctuations under normal operating conditions. However, apart from some enzyme reactions involving ligand binding, our understanding of the role of flexibility in protein function remains mostly incomplete. Here we investigate this question in the realm of membrane proteins that form ion channels. Specifically, we consider ion permeation in the gramicidin A channel, and study how the energetics of ion conduction changes as the channel structure is progressively changed from completely flexible to a fixed one. For each channel structure, the potential of mean force for a permeating potassium ion is determined from molecular dynamics (MD) simulations. Using the same molecular dynamics data for completely flexible gramicidin A, we also calculate the average densities and fluctuations of the peptide atoms and investigate the correlations between these fluctuations and the motion of a permeating ion. Our results show conclusively that peptide flexibility plays an important role in ion permeation in the gramicidin A channel, thus providing another reason—besides the well-known problem with the description of single file pore water—why this channel cannot be modeled using continuum electrostatics with a fixed structure. The new method developed here for studying the role of protein flexibility on its function clarifies the contributions of the fluctuations to energy and entropy, and places limits on the level of detail required in a coarse-grained model. PMID:16415054

Thermal Casimir-Polder forces on a V-type three-level atom

NASA Astrophysics Data System (ADS)

Xu, Chen-Ran; Xu, Jing-Ping; Al-amri, M.; Zhu, Cheng-Jie; Xie, Shuang-Yuan; Yang, Ya-Ping

2017-09-01

We study the thermal Casimir-Polder (CP) forces on a V-type three-level atom. The competition between the thermal effect and the quantum interference of the two transition dipoles on the force is investigated. To shed light onto the role of the quantum interference, we analyze two kinds of initial states of the atom, i.e., the superradiant state and the subradiant state. Considering the atom being in the thermal reservoir, the resonant CP force arising from the real photon emission dominates in the evolution of the CP force. Under the zero-temperature condition, the quantum interference can effectively modify the amplitude and the evolution of the force, leading to a long-time force or even the cancellation of the force. Our results reveal that in the finite-temperature case, the thermal photons can enhance the amplitude of all force elements, but have no influence on the net resonant CP force in the steady state, which means that the second law of thermodynamics still works. For the ideal degenerate V-type atom with parallel dipoles under the initial subradiant state, the robust destructive quantum interference overrides the thermal fluctuations, leading to the trapping of the atom in the subradiant state and the disappearance of the CP force. However, in terms of a realistic Zeeman atom, the thermal photons play a significant role during the evolution of the CP force. The thermal fluctuations can enhance the amplitude of the initial CP force by increasing the temperature, and weaken the influence of the quantum interference on the evolution of the CP force from the initial superradiant (subradiant) state to the steady state.

PHYSICAL MODEL FOR RECOGNITION TUNNELING

PubMed Central

Krstić, Predrag; Ashcroft, Brian; Lindsay, Stuart

2015-01-01

Recognition tunneling (RT) identifies target molecules trapped between tunneling electrodes functionalized with recognition molecules that serve as specific chemical linkages between the metal electrodes and the trapped target molecule. Possible applications include single molecule DNA and protein sequencing. This paper addresses several fundamental aspects of RT by multiscale theory, applying both all-atom and coarse-grained DNA models: (1) We show that the magnitude of the observed currents are consistent with the results of non-equilibrium Green's function calculations carried out on a solvated all-atom model. (2) Brownian fluctuations in hydrogen bond-lengths lead to current spikes that are similar to what is observed experimentally. (3) The frequency characteristics of these fluctuations can be used to identify the trapped molecules with a machine-learning algorithm, giving a theoretical underpinning to this new method of identifying single molecule signals. PMID:25650375

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

PubMed

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

2007-10-25

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

Observing random walks of atoms in buffer gas through resonant light absorption

NASA Astrophysics Data System (ADS)

Aoki, Kenichiro; Mitsui, Takahisa

2016-07-01

Using resonant light absorption, random-walk motions of rubidium atoms in nitrogen buffer gas are observed directly. The transmitted light intensity through atomic vapor is measured, and its spectrum is obtained, down to orders of magnitude below the shot-noise level to detect fluctuations caused by atomic motions. To understand the measured spectra, the spectrum for atoms performing random walks in a Gaussian light beam is computed, and its analytical form is obtained. The spectrum has 1 /f2 (f is frequency) behavior at higher frequencies, crossing over to a different, but well-defined, behavior at lower frequencies. The properties of this theoretical spectrum agree excellently with the measured spectrum. This understanding also enables us to obtain the diffusion constant, the photon cross section of atoms in buffer gas, and the atomic number density from a single spectral measurement. We further discuss other possible applications of our experimental method and analysis.

Dissipation induced asymmetric steering of distant atomic ensembles

NASA Astrophysics Data System (ADS)

Cheng, Guangling; Tan, Huatang; Chen, Aixi

2018-04-01

The asymmetric steering effects of separated atomic ensembles denoted by the effective bosonic modes have been explored by the means of quantum reservoir engineering in the setting of the cascaded cavities, in each of which an atomic ensemble is involved. It is shown that the steady-state asymmetric steering of the mesoscopic objects is unconditionally achieved via the dissipation of the cavities, by which the nonlocal interaction occurs between two atomic ensembles, and the direction of steering could be easily controlled through variation of certain tunable system parameters. One advantage of the present scheme is that it could be rather robust against parameter fluctuations, and does not require the accurate control of evolution time and the original state of the system. Furthermore, the double-channel Raman transitions between the long-lived atomic ground states are used and the atomic ensembles act as the quantum network nodes, which makes our scheme insensitive to the collective spontaneous emission of atoms.

Laser theory with finite atom-field interacting time

NASA Astrophysics Data System (ADS)

Yu, Deshui; Chen, Jingbiao

2008-07-01

We investigate the influence of atomic transit time τ on the laser linewidth by the quantum Langevin approach. With comparing the bandwidths of cavity mode κ , atomic polarization γab , and atomic transit broadening τ-1 , we study the laser linewidth in different limits. We also discuss the spectrum of fluctuations of output field and the influence of pumping statistics on the output field.The influence of atomic transit time τ on laser field has not been carefully discussed before, to our knowledge. In particular, a laser operating in the region of γab≪τ-1≪κ/2 appears not to have been analyzed in previous laser theories. Our work could be a useful complementarity to laser theory. It is also an important theoretical foundation for the recently proposed active optical atomic clock based on bad-cavity laser mechanism.

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.

The dynamic behavior of a liquid ethanol-water mixture: a perspective from quantum chemical topology.

PubMed

Mejía, Sol M; Mills, Matthew J L; Shaik, Majeed S; Mondragon, Fanor; Popelier, Paul L A

2011-05-07

Quantum Chemical Topology (QCT) is used to reveal the dynamics of atom-atom interactions in a liquid. A molecular dynamics simulation was carried out on an ethanol-water liquid mixture at its azeotropic concentration (X(ethanol)=0.899), using high-rank multipolar electrostatics. A thousand (ethanol)(9)-water heterodecamers, respecting the water-ethanol ratio of the azeotropic mixture, were extracted from the simulation. Ab initio electron densities were computed at the B3LYP/6-31+G(d) level for these molecular clusters. A video shows the dynamical behavior of a pattern of bond critical points and atomic interaction lines, fluctuating over 1 ns. A bond critical point distribution revealed the fluctuating behavior of water and ethanol molecules in terms of O-H···O, C-H···O and H···H interactions. Interestingly, the water molecule formed one to six C-H···O and one to four O-H···O interactions as a proton acceptor. We found that the more localized a dynamical bond critical point distribution, the higher the average electron density at its bond critical points. The formation of multiple C-H···O interactions affected the shape of the oxygen basin of the water molecule, which is shown in three dimensions. The hydrogen atoms of water strongly preferred to form H···H interactions with ethanol's alkyl hydrogen atoms over its hydroxyl hydrogen. This journal is © the Owner Societies 2011

Environmental Electrometry with Luminescent Carbon Nanotubes.

PubMed

Noé, Jonathan C; Nutz, Manuel; Reschauer, Jonathan; Morell, Nicolas; Tsioutsios, Ioannis; Reserbat-Plantey, Antoine; Watanabe, Kenji; Taniguchi, Takashi; Bachtold, Adrian; Högele, Alexander

2018-06-25

We demonstrate that localized excitons in luminescent carbon nanotubes can be utilized to study electrostatic fluctuations in the nanotube environment with sensitivity down to the elementary charge. By monitoring the temporal evolution of the cryogenic photoluminescence from individual carbon nanotubes grown on silicon oxide and hexagonal boron nitride, we characterize the dynamics of charge trap defects for both dielectric supports. We find a one order of magnitude reduction in the photoluminescence spectral wandering for nanotubes on extended atomically flat terraces of hexagonal boron nitride. For nanotubes on hexagonal boron nitride with pronounced spectral fluctuations, our analysis suggests proximity to terrace ridges where charge fluctuators agglomerate to exhibit areal densities exceeding those of silicon oxide. Our results establish carbon nanotubes as sensitive probes of environmental charge fluctuations and highlight their potential for applications in electrometric nanodevices with all-optical readout.

Femtosecond-level timing fluctuation suppression in atmospheric frequency transfer with passive phase conjunction correction.

PubMed

Sun, Fuyu; Hou, Dong; Zhang, Danian; Tian, Jie; Hu, Jianguo; Huang, Xianhe; Chen, Shijun

2017-09-04

We demonstrate femtosecond-level timing fluctuation suppression in indoor atmospheric comb-based frequency transfer with a passive phase conjunction correction technique. Timing fluctuations and Allan deviations are both measured to characterize the excess frequency instability incurred during the frequency transfer process. By transferring a 2 GHz microwave over a 52-m long free-space link in 5000 s, the total root-mean-square (RMS) timing fluctuation was measured to be about 280 fs with a fractional frequency instability on the order of 3 × 10 -13 at 1 s and 6 × 10 -17 at 1000 s. This atmospheric comb-based frequency transfer with passive phase conjunction correction can be used to build an atomic clock-based free-space frequency transmission link because its instability is less than that of a commercial Cs or H-master clock.

Self-organization in cold atomic gases: a synchronization perspective.

PubMed

Tesio, E; Robb, G R M; Oppo, G-L; Gomes, P M; Ackemann, T; Labeyrie, G; Kaiser, R; Firth, W J

2014-10-28

We study non-equilibrium spatial self-organization in cold atomic gases, where long-range spatial order spontaneously emerges from fluctuations in the plane transverse to the propagation axis of a single optical beam. The self-organization process can be interpreted as a synchronization transition in a fully connected network of fictitious oscillators, and described in terms of the Kuramoto model. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Diffusion of water and sodium counter-ions in nanopores of a β-lactoglobulin crystal: a molecular dynamics study

NASA Astrophysics Data System (ADS)

Malek, Kourosh; Odijk, Theo; Coppens, Marc-Olivier

2005-07-01

The dynamics of water and sodium counter-ions (Na+) in a C2221 orthorhombic β-lactoglobulin crystal is investigated by means of 5 ns molecular dynamics simulations. The effect of the fluctuation of the protein atoms on the motion of water and sodium ions is studied by comparing simulations in a rigid and in a flexible lattice. The electrostatic interactions of sodium ions with the positively charged LYS residues inside the crystal channels significantly influence the ionic motion. According to our results, water molecules close to the protein surface undergo an anomalous diffusive motion. On the other hand, the motion of water molecules further away from the protein surface is normal diffusive. Protein fluctuations affect the diffusion constant of water, which increases from 0.646 ± 0.108 to 0.887 ± 0.41 nm2 ns-1, when protein fluctuations are taken into account. The pore size (0.63-1.05 nm) and the water diffusivities are in good agreement with previous experimental results. The dynamics of sodium ions is disordered. LYS residues inside the pore are the main obstacles to the motion of sodium ions. However, the simulation time is still too short for providing a precise description of anomalous diffusion of sodium ions. The results are not only of interest for studying ion and water transport through biological nanopores, but may also elucidate water-protein and ion-protein interactions in protein crystals.

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

Yazdani, Ahmad, E-mail: Yazdania@modares.ac.ir; Shadrokh, Zohreh; Department of Physics, University of Shahrood, P.O. Box 316-36155, Shahrood

Highlights: • Opto-crystalline character of the composition of Cu{sub 2}S and S{sub 2}Sn was considered. • The formation Cu{sub 2}SnS{sub 3} is strongly related to phase separation at interface. • The entanglement of phases is strongly due to the chemical bond competition. • The suggested fluctuation region is approved by PL spectra. • Reconstruction and cluster formation is evident by formation of flat-spiral flowers. - Abstract: Optical character of crystal structure of the composition of two different semiconducting metallic sulfides, Cu{sub 2}S and S{sub 2}Sn, in pure phase formation of the ternary chalcogenide Cu{sub 2}SnS{sub 3} was considered. Because ofmore » the difficulties related to the phase separation at the definite Eutectic temperature for the composite formation, which is evident in optical absorption fluctuations, solvothermal synthesis in the intermediate temperature range 180–220 °C seems convenient where tetragonal crystal structure is investigated by XRD. Absorption fluctuations below E = E{sub g} were more pronounced for the lower limit case (180 °C) reflected in a sharp peak located at 1.48 eV on S1 as seen in UV-PL measurement. The characteristic behavior of the interface, resulting in the reconstruction and cluster formation due to the offset of bond rupturing displacement of atomic positions, is in favor of aggregation instead of agglomeration, which is evident by formation of small flat-spiral flowers in SEM images.« less

Effect of magnetic and density fluctuations on the propagation of lower hybrid waves in tokamaks

NASA Astrophysics Data System (ADS)

Vahala, George; Vahala, Linda; Bonoli, Paul T.

1992-12-01

Lower hybrid waves have been used extensively for plasma heating, current drive, and ramp-up as well as sawteeth stabilization. The wave kinetic equation for lower hybrid wave propagation is extended to include the effects of both magnetic and density fluctuations. This integral equation is then solved by Monte Carlo procedures for a toroidal plasma. It is shown that even for magnetic/density fluctuation levels on the order of 10-4, there are significant magnetic fluctuation effects on the wave power deposition into the plasma. This effect is quite pronounced if the magnetic fluctuation spectrum is peaked within the plasma. For Alcator-C-Mod [I. H. Hutchinson and the Alcator Group, Proceedings of the IEEE 13th Symposium on Fusion Engineering (IEEE, New York, 1990), Cat. No. 89CH 2820-9, p. 13] parameters, it seems possible to be able to infer information on internal magnetic fluctuations from hard x-ray data—especially since the effects of fluctuations on electron power density can explain the hard x-ray data from the JT-60 tokamak [H. Kishimoto and JT-60 Team, in Plasma Physics and Controlled Fusion (International Atomic Energy Agency, Vienna, 1989), Vol. I, p. 67].

Compressing the fluctuation of the magnetic field by dynamic compensation

NASA Astrophysics Data System (ADS)

Wang, Wenli; Dong, Richang; Wei, Rong; Chen, Tingting; Wang, Qian; Wang, Yuzhu

2018-03-01

We present a dynamic compensation method to compress the spatial fluctuation of the static magnetic field (C-field) that provides a quantization axis in the atomic fountain clock. The coil current of the C-field is point-by-point modulated in accordance with the atoms probing the magnetic field along the flight trajectory. A homogeneous field with a 0.2 nT inhomogeneity is produced compared to a 5 nT under the static magnetic field with a constant current during the Ramsey interrogation. The corresponding uncertainty associated with the second-order Zeeman shift that we calculate is improved by one order of magnitude. The technique provides an alternative method to improve the uniformity of the magnetic field, particularly for large-scale equipment that is difficult to construct with an effective magnetic shielding. Our method is simple, robust, and essentially important in frequency evaluations concerning the dominant uncertainty contribution due to the quadratic Zeeman shift.

Counting of fermions and spins in strongly correlated systems in and out of thermal equilibrium

NASA Astrophysics Data System (ADS)

Braungardt, Sibylle; Rodríguez, Mirta; Sen(de), Aditi; Sen, Ujjwal; Glauber, Roy J.; Lewenstein, Maciej

2011-01-01

Atom counting theory can be used to study the role of thermal noise in quantum phase transitions and to monitor the dynamics of a quantum system. We illustrate this for a strongly correlated fermionic system, which is equivalent to an anisotropic quantum XY chain in a transverse field and can be realized with cold fermionic atoms in an optical lattice. We analyze the counting statistics across the phase diagram in the presence of thermal fluctuations and during its thermalization when the system is coupled to a heat bath. At zero temperature, the quantum phase transition is reflected in the cumulants of the counting distribution. We find that the signatures of the crossover remain visible at low temperature and are obscured with increasing thermal fluctuations. We find that the same quantities may be used to scan the dynamics during the thermalization of the system.

Decarboxylation of furfural on Pd(111): Ab initio molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Xue, Wenhua; Dang, Hongli; Shields, Darwin; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

2013-03-01

Furfural conversion over metal catalysts plays an important role in the studies of biomass-derived feedstocks. We report ab initio molecular dynamics simulations for the decarboxylation process of furfural on the palladium surface at finite temperatures. We observed and analyzed the atomic-scale dynamics of furfural on the Pd(111) surface and the fluctuations of the bondlengths between the atoms in furfural. We found that the dominant bonding structure is the parallel structure in which the furfural plane, while slightly distorted, is parallel to the Pd surface. Analysis of the bondlength fluctuations indicates that the C-H bond is the aldehyde group of a furfural molecule is likely to be broken first, while the C =O bond has a tendency to be isolated as CO. Our results show that the reaction of decarbonylation dominates, consistent with the experimental measurements. Supported by DOE (DE-SC0004600). Simulations and calculations were performed on XSEDE's and NERSC's supercomputers.

Dissipation-Induced Anomalous Multicritical Phenomena

NASA Astrophysics Data System (ADS)

Soriente, M.; Donner, T.; Chitra, R.; Zilberberg, O.

2018-05-01

We explore the influence of dissipation on a paradigmatic driven-dissipative model where a collection of two level atoms interact with both quadratures of a quantum cavity mode. The closed system exhibits multiple phase transitions involving discrete and continuous symmetries breaking and all phases culminate in a multicritical point. In the open system, we show that infinitesimal dissipation erases the phase with broken continuous symmetry and radically alters the model's phase diagram. The multicritical point now becomes brittle and splits into two tricritical points where first- and second-order symmetry-breaking transitions meet. A quantum fluctuations analysis shows that, surprisingly, the tricritical points exhibit anomalous finite fluctuations, as opposed to standard tricritical points arising in He 3 -He 4 mixtures. Our work has direct implications for a variety of fields, including cold atoms and ions in optical cavities, circuit-quantum electrodynamics as well as optomechanical systems.

Quantum-Fluctuation-Driven Crossover from a Dilute Bose-Einstein Condensate to a Macrodroplet in a Dipolar Quantum Fluid

NASA Astrophysics Data System (ADS)

Chomaz, L.; Baier, S.; Petter, D.; Mark, M. J.; Wächtler, F.; Santos, L.; Ferlaino, F.

2016-10-01

In a joint experimental and theoretical effort, we report on the formation of a macrodroplet state in an ultracold bosonic gas of erbium atoms with strong dipolar interactions. By precise tuning of the s -wave scattering length below the so-called dipolar length, we observe a smooth crossover of the ground state from a dilute Bose-Einstein condensate to a dense macrodroplet state of more than 2 ×104 atoms . Based on the study of collective excitations and loss features, we prove that quantum fluctuations stabilize the ultracold gas far beyond the instability threshold imposed by mean-field interactions. Finally, we perform expansion measurements, showing that although self-bound solutions are prevented by losses, the interplay between quantum stabilization and losses results in a minimal time-of-flight expansion velocity at a finite scattering length.

Melting and Freezing of Metal Clusters

NASA Astrophysics Data System (ADS)

Aguado, Andrés; Jarrold, Martin F.

2011-05-01

Recent developments allow heat capacities to be measured for size-selected clusters isolated in the gas phase. For clusters with tens to hundreds of atoms, the heat capacities determined as a function of temperature usually have a single peak attributed to a melting transition. The melting temperatures and latent heats show large size-dependent fluctuations. In some cases, the melting temperatures change by hundreds of degrees with the addition of a single atom. Theory has played a critical role in understanding the origin of the size-dependent fluctuations, and in understanding the properties of the liquid-like and solid-like states. In some cases, the heat capacities have extra features (an additional peak or a dip) that reveal a more complex behavior than simple melting. In this article we provide a description of the methods used to measure the heat capacities and provide an overview of the experimental and theoretical results obtained for sodium and aluminum clusters.

Shape of the terrestrial plasma sheet in the near-Earth magnetospheric tail as imaged by the Interstellar Boundary Explorer

DOE PAGES

Dayeh, M. A.; Fuselier, S. A.; Funsten, H. O.; ...

2015-04-11

We present remote, continuous observations from the Interstellar Boundary Explorer of the terrestrial plasma sheet location back to -16 Earth radii (R E) in the magnetospheric tail using energetic neutral atom emissions. The time period studied includes two orbits near the winter and summer solstices, thus associated with large negative and positive dipole tilt, respectively. Continuous side-view images reveal a complex shape that is dominated mainly by large-scale warping due to the diurnal motion of the dipole axis. Superposed on the global warped geometry are short-time fluctuations in plasma sheet location that appear to be consistent with plasma sheet flappingmore » and possibly twisting due to changes in the interplanetary conditions. We conclude that the plasma sheet warping due to the diurnal motion dominates the average shape of the plasma sheet. Over short times, the position of the plasma sheet can be dominated by twisting and flapping.« less

Geometric decomposition of the conformation tensor in viscoelastic turbulence

NASA Astrophysics Data System (ADS)

Hameduddin, Ismail; Meneveau, Charles; Zaki, Tamer A.; Gayme, Dennice F.

2018-05-01

This work introduces a mathematical approach to analysing the polymer dynamics in turbulent viscoelastic flows that uses a new geometric decomposition of the conformation tensor, along with associated scalar measures of the polymer fluctuations. The approach circumvents an inherent difficulty in traditional Reynolds decompositions of the conformation tensor: the fluctuating tensor fields are not positive-definite and so do not retain the physical meaning of the tensor. The geometric decomposition of the conformation tensor yields both mean and fluctuating tensor fields that are positive-definite. The fluctuating tensor in the present decomposition has a clear physical interpretation as a polymer deformation relative to the mean configuration. Scalar measures of this fluctuating conformation tensor are developed based on the non-Euclidean geometry of the set of positive-definite tensors. Drag-reduced viscoelastic turbulent channel flow is then used an example case study. The conformation tensor field, obtained using direct numerical simulations, is analysed using the proposed framework.

Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations.

PubMed

Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

2015-06-15

In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and interpretations of hydrophobicity in terms of alternative but parallel signatures such as interfacial fluctuations, dewetting transitions, and enhanced fluctuation probabilities at interfaces. © 2015 Wiley Periodicals, Inc.

Respiratory sinus arrhythmia: opposite effects on systolic and mean arterial pressure in supine humans

NASA Technical Reports Server (NTRS)

Elstad, M.; Toska, K.; Chon, K. H.; Raeder, E. A.; Cohen, R. J.

2001-01-01

1. Are arterial blood pressure fluctuations buffered or reinforced by respiratory sinus arrhythmia (RSA)? There is still considerable debate about this simple question. Different results have been obtained, triggering a discussion as to whether or not the baroreflexes are responsible for RSA. We suspected that the measurements of different aspects of arterial pressure (mean arterial pressure (MAP) and systolic pressure (SP)) can explain the conflicting results. 2. Simultaneous recordings of beat-to-beat MAP, SP, left cardiac stroke volume (SV, pulsed ultrasound Doppler), heart rate (HR) and respiration (RE) were obtained in 10 healthy young adults during spontaneous respiration. In order to eliminate HR variations at respiratory frequency we used propranolol and atropine administration in the supine and tilted positions. Respiration-synchronous variation in the recorded variables was quantified by spectral analysis of the recordings of each of these variables, and the phase relations between them were determined by cross-spectral analysis. 3. MAP fluctuations increased after removing heart rate variations in both supine and tilted position, whereas SP fluctuations decreased in the supine position and increased in the head-up tilted position. 4. RSA buffers respiration-synchronous fluctuations in MAP in both positions. However, fluctuations in SP were reinforced by RSA in the supine and buffered in the tilted position.

Five-Year Wilkinson Microwave Anisotropy Probe (WMAP) Observations: Data Processing, Sky Maps, and Basic Results

NASA Technical Reports Server (NTRS)

Weiland, J.L.; Hill, R.S.; Odegard, 3.; Larson, D.; Bennett, C.L.; Dunkley, J.; Jarosik, N.; Page, L.; Spergel, D.N.; Halpern, M.;

Non-destructive Faraday imaging of dynamically controlled ultracold atoms

NASA Astrophysics Data System (ADS)

Gajdacz, Miroslav; Pedersen, Poul; Mørch, Troels; Hilliard, Andrew; Arlt, Jan; Sherson, Jacob

2013-05-01

We investigate non-destructive measurements of ultra-cold atomic clouds based on dark field imaging of spatially resolved Faraday rotation. In particular, we pursue applications to dynamically controlled ultracold atoms. The dependence of the Faraday signal on laser detuning, atomic density and temperature is characterized in a detailed comparison with theory. In particular the destructivity per measurement is extremely low and we illustrate this by imaging the same cloud up to 2000 times. The technique is applied to avoid the effect of shot-to-shot fluctuations in atom number calibration. Adding dynamic changes to system parameters, we demonstrate single-run vector magnetic field imaging and single-run spatial imaging of the system's dynamic behavior. The method can be implemented particularly easily in standard imaging systems by the insertion of an extra polarizing beam splitter. These results are steps towards quantum state engineering using feedback control of ultracold atoms.

Thermoelectricity in atom-sized junctions at room temperatures

PubMed Central

Tsutsui, Makusu; Morikawa, Takanori; Arima, Akihide; Taniguchi, Masateru

2013-01-01

Atomic and molecular junctions are an emerging class of thermoelectric materials that exploit quantum confinement effects to obtain an enhanced figure of merit. An important feature in such nanoscale systems is that the electron and heat transport become highly sensitive to the atomic configurations. Here we report the characterization of geometry-sensitive thermoelectricity in atom-sized junctions at room temperatures. We measured the electrical conductance and thermoelectric power of gold nanocontacts simultaneously down to the single atom size. We found junction conductance dependent thermoelectric voltage oscillations with period 2e2/h. We also observed quantum suppression of thermovoltage fluctuations in fully-transparent contacts. These quantum confinement effects appeared only statistically due to the geometry-sensitive nature of thermoelectricity in the atom-sized junctions. The present method can be applied to various nanomaterials including single-molecules or nanoparticles and thus may be used as a useful platform for developing low-dimensional thermoelectric building blocks. PMID:24270238

The physics of background discrimination in liquid xenon, and first results from Xenon10 in the hunt for WIMP dark matter

NASA Astrophysics Data System (ADS)

Dahl, Carl Eric

2009-06-01

The WIMP limit set by the Xenon10 experiment in 2007 signals a new era in direct detection of dark matter, with several large-scale liquid target detectors now under construction. A major challenge in these detectors will be to understand backgrounds at the level necessary to claim a positive WIMP signal. In liquid xenon, these backgrounds are dominated by electron recoils, which may be distinguished from the WIMP signal (nuclear recoils) by their higher charge-to-light ratio. During the construction and operation of Xenon10, the prototype detector Xed probed the physics of this discrimination. Particle interactions in liquid xenon both ionize and excite xenon atoms, giving charge and scintillation signals, respectively. Some fraction of ions recombine, reducing the charge signal and creating additional scintillation. The charge-to-light ratio, determined by the initial exciton-ion ratio and the ion recombination fraction, provides the basis for discrimination between electron and nuclear recoils. Intrinsic fluctuations in the recombination fraction limit discrimination. Changes in recombination induce an exact anti-correlation between charge and light, and when calibrated this anti-correlation distinguishes recombination fluctuations from uncorrelated fluctuations in the measured signals. We determine the mean recombination and recombination fluctuations as a function of energy and applied field for electron and nuclear recoils, finding that recombination fluctuations are already the limiting factor for discrimination above ~12 keVr (nuclear recoil energy). Below 12 keVr statistical fluctuations in the number of scintillation photons counted dominate, and we project a x6 improvement in background rejection with a x2 increase in light collection efficiency. We also build a simple recombination model that successfully reproduces the mean recombination in electron and nuclear recoils, including the surprising reversal of the expected trend for recombination with ionization density in low energy electron recoils. The model also reproduces the measured recombination fluctuations to within a factor of two at high energies. Surprisingly, the model suggests that recombination at low energies is independent of ionization density, and our observed discrimination is due not to the different stopping powers of electrons and nuclei as was thought, but rather to a different initial exciton-ion ratio. We suggest two possible physical models for this new result.

Additional evidence from x-ray powder diffraction patterns that icosahedral quasi-crystals of intermetallic compounds are twinned cubic crystals

PubMed Central

Pauling, Linus

1988-01-01

Analysis of the measured values of Q for the weak peaks (small maxima, usually considered to be background fluctuations, “noise”) on the x-ray powder diffraction curves for 17 rapidly quenched alloys leads directly to the conclusion that they are formed by an 820-atom or 1012-atom primitive cubic structure that by icosahedral twinning produces the so-called icosahedral quasi-crystals. PMID:16593948

Unconventional States of Matter with Cold Atoms and Dipolar Molecules

DTIC Science & Technology

2014-08-20

ferromagnetic state. For alkaline-earth fermions, the large SU(2N) symmetry greatly enhances quantum spin fluctuations, which give rises to novel...both bosons and fermions, novel quantum magnetism with large spin SU(2N) al- kaline fermions, novel topological states with synthetic gauge fields...presented in Sect. 1.1. The study of novel quantum magnetism with large spin alkaline earth atoms is presented in Sect. 1.2. In Sect. 1.3, we present our

Fluctuation Theorem for Many-Body Pure Quantum States.

PubMed

Iyoda, Eiki; Kaneko, Kazuya; Sagawa, Takahiro

2017-09-08

We prove the second law of thermodynamics and the nonequilibrium fluctuation theorem for pure quantum states. The entire system obeys reversible unitary dynamics, where the initial state of the heat bath is not the canonical distribution but is a single energy eigenstate that satisfies the eigenstate-thermalization hypothesis. Our result is mathematically rigorous and based on the Lieb-Robinson bound, which gives the upper bound of the velocity of information propagation in many-body quantum systems. The entanglement entropy of a subsystem is shown connected to thermodynamic heat, highlighting the foundation of the information-thermodynamics link. We confirmed our theory by numerical simulation of hard-core bosons, and observed dynamical crossover from thermal fluctuations to bare quantum fluctuations. Our result reveals a universal scenario that the second law emerges from quantum mechanics, and can be experimentally tested by artificial isolated quantum systems such as ultracold atoms.

Fluctuation Theorem for Many-Body Pure Quantum States

NASA Astrophysics Data System (ADS)

Iyoda, Eiki; Kaneko, Kazuya; Sagawa, Takahiro

2017-09-01

We prove the second law of thermodynamics and the nonequilibrium fluctuation theorem for pure quantum states. The entire system obeys reversible unitary dynamics, where the initial state of the heat bath is not the canonical distribution but is a single energy eigenstate that satisfies the eigenstate-thermalization hypothesis. Our result is mathematically rigorous and based on the Lieb-Robinson bound, which gives the upper bound of the velocity of information propagation in many-body quantum systems. The entanglement entropy of a subsystem is shown connected to thermodynamic heat, highlighting the foundation of the information-thermodynamics link. We confirmed our theory by numerical simulation of hard-core bosons, and observed dynamical crossover from thermal fluctuations to bare quantum fluctuations. Our result reveals a universal scenario that the second law emerges from quantum mechanics, and can be experimentally tested by artificial isolated quantum systems such as ultracold atoms.

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.

Global and system-specific resting-state fMRI fluctuations are uncorrelated: principal component analysis reveals anti-correlated networks.

PubMed

Carbonell, Felix; Bellec, Pierre; Shmuel, Amir

2011-01-01

The influence of the global average signal (GAS) on functional-magnetic resonance imaging (fMRI)-based resting-state functional connectivity is a matter of ongoing debate. The global average fluctuations increase the correlation between functional systems beyond the correlation that reflects their specific functional connectivity. Hence, removal of the GAS is a common practice for facilitating the observation of network-specific functional connectivity. This strategy relies on the implicit assumption of a linear-additive model according to which global fluctuations, irrespective of their origin, and network-specific fluctuations are super-positioned. However, removal of the GAS introduces spurious negative correlations between functional systems, bringing into question the validity of previous findings of negative correlations between fluctuations in the default-mode and the task-positive networks. Here we present an alternative method for estimating global fluctuations, immune to the complications associated with the GAS. Principal components analysis was applied to resting-state fMRI time-series. A global-signal effect estimator was defined as the principal component (PC) that correlated best with the GAS. The mean correlation coefficient between our proposed PC-based global effect estimator and the GAS was 0.97±0.05, demonstrating that our estimator successfully approximated the GAS. In 66 out of 68 runs, the PC that showed the highest correlation with the GAS was the first PC. Since PCs are orthogonal, our method provides an estimator of the global fluctuations, which is uncorrelated to the remaining, network-specific fluctuations. Moreover, unlike the regression of the GAS, the regression of the PC-based global effect estimator does not introduce spurious anti-correlations beyond the decrease in seed-based correlation values allowed by the assumed additive model. After regressing this PC-based estimator out of the original time-series, we observed robust anti-correlations between resting-state fluctuations in the default-mode and the task-positive networks. We conclude that resting-state global fluctuations and network-specific fluctuations are uncorrelated, supporting a Resting-State Linear-Additive Model. In addition, we conclude that the network-specific resting-state fluctuations of the default-mode and task-positive networks show artifact-free anti-correlations.

Effects of Mass Fluctuation on Thermal Transport Properties in Bulk Bi2Te3

NASA Astrophysics Data System (ADS)

Huang, Ben; Zhai, Pengcheng; Yang, Xuqiu; Li, Guodong

2017-05-01

In this paper, we applied large-scale molecular dynamics and lattice dynamics to study the influence of mass fluctuation on thermal transport properties in bulk Bi2Te3, namely thermal conductivity ( K), phonon density of state (PDOS), group velocity ( v g), and mean free path ( l). The results show that total atomic mass change can affect the relevant vibrational frequency on the micro level and heat transfer rate in the macro statistic, hence leading to the strength variation of the anharmonic phonon processes (Umklapp scattering) in the defect-free Bi2Te3 bulk. Moreover, it is interesting to find that the anharmonicity of Bi2Te3 can be also influenced by atomic differences of the structure such as the mass distribution in the primitive cell. Considering the asymmetry of the crystal structure and interatomic forces, it can be concluded by phonon frequency, lifetime, and velocity calculation that acoustic-optical phonon scattering shows the structure-sensitivity to the mass distribution and complicates the heat transfer mechanism, hence resulting in the low lattice thermal conductivity of Bi2Te3. This study is helpful for designing the material with tailored thermal conductivity via atomic substitution.

Probing nanocrystalline grain dynamics in nanodevices

PubMed Central

Yeh, Sheng-Shiuan; Chang, Wen-Yao; Lin, Juhn-Jong

2017-01-01

Dynamical structural defects exist naturally in a wide variety of solids. They fluctuate temporally and hence can deteriorate the performance of many electronic devices. Thus far, the entities of these dynamic objects have been identified to be individual atoms. On the other hand, it is a long-standing question whether a nanocrystalline grain constituted of a large number of atoms can switch, as a whole, reversibly like a dynamical atomic defect (that is, a two-level system). This is an emergent issue considering the current development of nanodevices with ultralow electrical noise, qubits with long quantum coherence time, and nanoelectromechanical system sensors with ultrahigh resolution. We demonstrate experimental observations of dynamic nanocrystalline grains that repeatedly switch between two or more metastable coordinate states. We study temporal resistance fluctuations in thin ruthenium dioxide (RuO2) metal nanowires and extract microscopic parameters, including relaxation time scales, mobile grain sizes, and the bonding strengths of nanograin boundaries. These material parameters are not obtainable by other experimental approaches. When combined with previous in situ high-resolution transmission electron microscopy, our electrical method can be used to infer rich information about the structural dynamics of a wide variety of nanodevices and new two-dimensional materials. PMID:28691094

C-Cr segregation at grain boundary before the carbide nucleation in Alloy 690

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

Li Hui, E-mail: huili@shu.edu.cn; Laboratory for Microstructures, Shanghai University, Shanghai, 200444; Xia Shuang

2012-04-15

The grain boundary segregation in Alloy 690 was investigated by atom probe tomography. B, C and Si segregated at the grain boundary. The high concentration regions for each segregation element form a set of straight arrays that are parallel to each other in the grain boundary plane. The concentration fluctuation has a periodicity of about 7 nm in the grain boundary plane. Before the Cr{sub 23}C{sub 6} nucleation at grain boundaries, the C-Cr co-segregate on one side of the grain boundaries while not the exact grain boundary core regions have been detected. The reasons why grain boundary carbides have coherentmore » orientation relationship only with one side of nearby grain which grain boundary is located at high index crystal plane were discussed. - Highlights: Black-Right-Pointing-Pointer Grain boundary segregation in Alloy 690 was investigated by atom probe tomography. Black-Right-Pointing-Pointer B, C and Si segregate at the grain boundary. Black-Right-Pointing-Pointer Concentration of segregated atoms periodicity fluctuated in the grain boundary plane. Black-Right-Pointing-Pointer C and Cr co-segregate on one side of the grain boundary before carbide nucleation.« less

Quantum noise in a transversely-pumped-cavity Bose-Hubbard model

NASA Astrophysics Data System (ADS)

Nagy, Dávid; Kónya, Gábor; Domokos, Peter; Szirmai, Gergely

2018-06-01

We investigate the quantum measurement noise effects on the dynamics of an atomic Bose lattice gas inside an optical resonator. We describe the dynamics by means of a hybrid model consisting of a Bose-Hubbard Hamiltonian for the atoms and a Heisenberg-Langevin equation for the lossy cavity-field mode. We assume that the atoms are prepared initially in the ground state of the lattice Hamiltonian and then start to interact with the cavity mode. We show that the cavity-field fluctuations originating from the dissipative outcoupling of photons from the resonator lead to vastly different effects in the different possible ground-state phases, i.e., the superfluid, the supersolid, the Mott and charge-density-wave phases. In the former two phases with the presence of a superfluid wavefunction, the quantum measurement noise appears as a driving term leading to depletion of the ground state. The timescale for the system to leave the ground state is presented in a simple analytical form. For the latter two incompressible phases, the quantum noise results in the fluctuation of the chemical potential. We derive an analytical expression for the corresponding broadening of the quasiparticle resonances.

Adiabatic passage of radio-frequency-assisted Förster resonances in Rydberg atoms for two-qubit gates and the generation of Bell states

NASA Astrophysics Data System (ADS)

Beterov, I. I.; Hamzina, G. N.; Yakshina, E. A.; Tretyakov, D. B.; Entin, V. M.; Ryabtsev, I. I.

2018-03-01

High-fidelity entangled Bell states are of great interest in quantum physics. Entanglement of ultracold neutral atoms in two spatially separated optical dipole traps is promising for implementation of quantum computing and quantum simulation and for investigation of Bell states of material objects. We propose a method to entangle two atoms via long-range Rydberg-Rydberg interaction. Alternative to previous approaches, based on Rydberg blockade, we consider radio-frequency-assisted Stark-tuned Förster resonances in Rb Rydberg atoms. To reduce the sensitivity of the fidelity of Bell states to the fluctuations of interatomic distance, we propose to use the double adiabatic passage across the radio-frequency-assisted Stark-tuned Förster resonances, which results in a deterministic phase shift of the collective two-atom state.

In Situ Visualization of the Growth and Fluctuations of Nanoparticle Superlattice in Liquids

NASA Astrophysics Data System (ADS)

Ou, Zihao; Shen, Bonan; Chen, Qian

We use liquid phase transmission electron microscopy to image and understand the crystal growth front and interfacial fluctuation of a nanoparticle superlattice. With single particle resolution and hundreds of nanoscale building blocks in view, we are able to identify the interface between ordered lattice and disordered structure and visualize the kinetics of single building block attachment at the lattice growth front. The spatial interfacial fluctuation profiles support the capillary wave theory, from which we derive a surface stiffness value consistent with scaling analysis. Our experiments demonstrate the potential of extending model study on collective systems to nanoscale with single particle resolution and testing fundamental theories of condensed matter at a length scale linking atoms and micron-sized colloids.

Electrostatic attraction between neutral microdroplets by ion fluctuations

NASA Astrophysics Data System (ADS)

Sheng, Yu-Jane; Tsao, Heng-Kwong

2004-06-01

The interaction between two aqueous droplets containing ions is investigated. The ion-fluctuation correlation gives rise to attraction between two neutral microdroplets, similar to the van der Waals interaction between neutral atoms. Electrostatic attraction consists of contributions from various induced multipole-multipole interactions, including dipole-dipole < P2z >2 r-6 , dipole-quadrupole < P2z > < Q 2zz > r-8 , dipole-octupole < P2z > < O 2zzz > r-10 , and quadrupole-quadrupole interactions < Q 2zz >2 r-10 . The mean-square multipole moments are determined analytically by linear response theory. The fluctuation-driven attraction is so strong at short distance that it may dominate over the Coulomb repulsion between like-charged droplets. These theoretical results are confirmed by Monte Carlo simulations.

Electrostatic attraction between neutral microdroplets by ion fluctuations.

PubMed

Sheng, Yu-Jane; Tsao, Heng-Kwong

2004-06-01

The interaction between two aqueous droplets containing ions is investigated. The ion-fluctuation correlation gives rise to attraction between two neutral microdroplets, similar to the van der Waals interaction between neutral atoms. Electrostatic attraction consists of contributions from various induced multipole-multipole interactions, including dipole-dipole < P(2)(z) >(2) r(-6), dipole-quadrupole < P(2)(z) > < Q (2)(zz ) > r(-8), dipole-octupole < P(2)(z) > < O (2)(zzz ) > r(-10), and quadrupole-quadrupole interactions < Q (2)(zz ) >(2) r(-10). The mean-square multipole moments are determined analytically by linear response theory. The fluctuation-driven attraction is so strong at short distance that it may dominate over the Coulomb repulsion between like-charged droplets. These theoretical results are confirmed by Monte Carlo simulations.

Simultaneous dense coding affected by fluctuating massless scalar field

NASA Astrophysics Data System (ADS)

Huang, Zhiming; Ye, Yiyong; Luo, Darong

2018-04-01

In this paper, we investigate the simultaneous dense coding (SDC) protocol affected by fluctuating massless scalar field. The noisy model of SDC protocol is constructed and the master equation that governs the SDC evolution is deduced. The success probabilities of SDC protocol are discussed for different locking operators under the influence of vacuum fluctuations. We find that the joint success probability is independent of the locking operators, but other success probabilities are not. For quantum Fourier transform and double controlled-NOT operators, the success probabilities drop with increasing two-atom distance, but SWAP operator is not. Unlike the SWAP operator, the success probabilities of Bob and Charlie are different. For different noisy interval values, different locking operators have different robustness to noise.

Internal dynamics of F-actin and myosin subfragment-1 studied by quasielastic neutron scattering

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

Matsuo, Tatsuhito; Arata, Toshiaki; Oda, Toshiro

2015-04-10

Various biological functions related to cell motility are driven by the interaction between the partner proteins, actin and myosin. To obtain insights into how this interaction occurs, the internal dynamics of F-actin and myosin subfragment-1 (S1) were characterized by the quasielastic neutron scattering measurements on the solution samples of F-actin and S1. Contributions of the internal motions of the proteins to the scattering spectra were separated from those of the global macromolecular diffusion. Analysis of the spectra arising from the internal dynamics showed that the correlation times of the atomic motions were about two times shorter for F-actin than formore » S1, suggesting that F-actin fluctuates more rapidly than S1. It was also shown that the fraction of the immobile atoms is larger for S1 than for F-actin. These results suggest that F-actin actively facilitates the binding of myosin by utilizing the more frequent conformational fluctuations than those of S1. - Highlights: • We studied the internal dynamics of F-actin and myosin S1 by neutron scattering. • The correlation times of the atomic motions were smaller for F-actin than for S1. • The fraction of the immobile atoms was also smaller for F-actin than for S1. • Our results suggest that mobility of atoms in F-actin is higher than that in S1. • We propose that high flexibility of F-actin facilitates the binding of myosin.« less

Anomalous diffusion in a dynamical optical lattice

NASA Astrophysics Data System (ADS)

Zheng, Wei; Cooper, Nigel R.

2018-02-01

Motivated by experimental progress in strongly coupled atom-photon systems in optical cavities, we study theoretically the quantum dynamics of atoms coupled to a one-dimensional dynamical optical lattice. The dynamical lattice is chosen to have a period that is incommensurate with that of an underlying static lattice, leading to a dynamical version of the Aubry-André model which can cause localization of single-particle wave functions. We show that atomic wave packets in this dynamical lattice generically spread via anomalous diffusion, which can be tuned between superdiffusive and subdiffusive regimes. This anomalous diffusion arises from an interplay between Anderson localization and quantum fluctuations of the cavity field.

From cosmology to cold atoms: observation of Sakharov oscillations in a quenched atomic superfluid.

PubMed

Hung, Chen-Lung; Gurarie, Victor; Chin, Cheng

2013-09-13

Predicting the dynamics of many-body systems far from equilibrium is a challenging theoretical problem. A long-predicted phenomenon in hydrodynamic nonequilibrium systems is the occurrence of Sakharov oscillations, which manifest in the anisotropy of the cosmic microwave background and the large-scale correlations of galaxies. Here, we report the observation of Sakharov oscillations in the density fluctuations of a quenched atomic superfluid through a systematic study in both space and time domains and with tunable interaction strengths. Our work suggests a different approach to the study of nonequilibrium dynamics of quantum many-body systems and the exploration of their analogs in cosmology and astrophysics.

Radiative process of two entanglement atoms in de Sitter spacetime

NASA Astrophysics Data System (ADS)

Liu, Xiaobao; Tian, Zehua; Wang, Jieci; Jing, Jiliang

2018-05-01

We investigate the radiative processes of a quantum system composed by two identical two-level atoms in the de Sitter spacetime, interacting with a conformally coupled massless scalar field prepared in the de Sitter-invariant vacuum. We discuss the structure of the rate of variations of the atomic energy for two static atoms. Following a procedure developed by Dalibard, Dupont-Roc, and Cohen-Tannoudji, our intention is to identify in a quantitative way the contributions of vacuum fluctuations and the radiation reaction to the generation of quantum entanglement and to the degradation of entangled states. We find that when the distance between two atoms larger than the characteristic length scale, the rate of variation of atomic energy in the de Sitter-invariant vacuum behaves differently compared with that in the thermal Minkowski spacetime. In particular, the generation and degradation of quantum entanglement can be enhanced or inhibited, which are dependent not only on the specific entangled state but also on the distance between the atoms.

Ionization equilibrium at the transition from valence-band to acceptor-band migration of holes in boron-doped diamond

NASA Astrophysics Data System (ADS)

Poklonski, N. A.; Vyrko, S. A.; Poklonskaya, O. N.; Kovalev, A. I.; Zabrodskii, A. G.

2016-06-01

A quasi-classical model of ionization equilibrium in the p-type diamond between hydrogen-like acceptors (boron atoms which substitute carbon atoms in the crystal lattice) and holes in the valence band (v-band) is proposed. The model is applicable on the insulator side of the insulator-metal concentration phase transition (Mott transition) in p-Dia:B crystals. The densities of the spatial distributions of impurity atoms (acceptors and donors) and of holes in the crystal are considered to be Poissonian, and the fluctuations of their electrostatic potential energy are considered to be Gaussian. The model accounts for the decrease in thermal ionization energy of boron atoms with increasing concentration, as well as for electrostatic fluctuations due to the Coulomb interaction limited to two nearest point charges (impurity ions and holes). The mobility edge of holes in the v-band is assumed to be equal to the sum of the threshold energy for diffusion percolation and the exchange energy of the holes. On the basis of the virial theorem, the temperature Tj is determined, in the vicinity of which the dc band-like conductivity of holes in the v-band is approximately equal to the hopping conductivity of holes via the boron atoms. For compensation ratio (hydrogen-like donor to acceptor concentration ratio) K ≈ 0.15 and temperature Tj, the concentration of "free" holes in the v-band and their jumping (turbulent) drift mobility are calculated. Dependence of the differential energy of thermal ionization of boron atoms (at the temperature 3Tj/2) as a function of their concentration N is calculated. The estimates of the extrapolated into the temperature region close to Tj hopping drift mobility of holes hopping from the boron atoms in the charge states (0) to the boron atoms in the charge states (-1) are given. Calculations based on the model show good agreement with electrical conductivity and Hall effect measurements for p-type diamond with boron atom concentrations in the range from 3 × 1017 to 3 × 1020 cm-3, i.e., up to the Mott transition. The model uses no fitting parameters.

Anisotropic polarization π -molecular skeleton coupled dynamics in proton-displacive organic ferroelectrics

NASA Astrophysics Data System (ADS)

Fujioka, J.; Horiuchi, S.; Kida, N.; Shimano, R.; Tokura, Y.

2009-09-01

We have investigated the polarization π -molecular skeleton coupled dynamics for the proton-displacive organic ferroelectrics, cocrystal of phenazine with the 2,5-dihalo-3,6-dihydroxy-p-benzoquinones by measurements of the terahertz/infrared spectroscopy. In the course of the ferroelectric-to-paraelectric transition, the ferroelectric soft phonon mode originating from the intermolecular dynamical displacement is observed in the imaginary part of dielectric spectra γ2 , when the electric field of the light (E) is parallel to the spontaneous polarization (P) . The soft phonon mode is isolated from the intramolecular vibrational mode and hence the intramolecular skeleton dynamics is almost decoupled from the polarization fluctuation. In the spectra for E parallel to the hydrogen-bonded supramolecular chain, by contrast, the vibrational mode mainly originating from the oxygen atom motion within the π -molecular plane is anomalously blurred and amalgamated into the polarization relaxation mode concomitantly with the dynamical proton disorder. This indicates that the dynamical disorder of the intramolecular skeleton structure, specifically that of oxygen atom, is strongly enhanced by the proton fluctuation and is significantly coupled to the polarization fluctuation along the hydrogen-bonded supramolecular chain. The results are discussed in terms of the proton-mediated anisotropic polarization π -molecular skeleton interaction, which characterizes these emerging proton-displacive ferroelectrics.

One-dimensional model of interacting-step fluctuations on vicinal surfaces: Analytical formulas and kinetic Monte Carlo simulations

NASA Astrophysics Data System (ADS)

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

2010-12-01

We study analytically and numerically a one-dimensional model of interacting line defects (steps) fluctuating on a vicinal crystal. Our goal is to formulate and validate analytical techniques for approximately solving systems of coupled nonlinear stochastic differential equations (SDEs) governing fluctuations in surface motion. In our analytical approach, the starting point is the Burton-Cabrera-Frank (BCF) model by which step motion is driven by diffusion of adsorbed atoms on terraces and atom attachment-detachment at steps. The step energy accounts for entropic and nearest-neighbor elastic-dipole interactions. By including Gaussian white noise to the equations of motion for terrace widths, we formulate large systems of SDEs under different choices of diffusion coefficients for the noise. We simplify this description via (i) perturbation theory and linearization of the step interactions and, alternatively, (ii) a mean-field (MF) approximation whereby widths of adjacent terraces are replaced by a self-consistent field but nonlinearities in step interactions are retained. We derive simplified formulas for the time-dependent terrace-width distribution (TWD) and its steady-state limit. Our MF analytical predictions for the TWD compare favorably with kinetic Monte Carlo simulations under the addition of a suitably conservative white noise in the BCF equations.

Mechanism study on pressure fluctuation of pump-turbine runner with large blade lean angle

NASA Astrophysics Data System (ADS)

Yulin, Fan; Xuhe, Wang; Baoshan, Zhu; Dongyue, Zhou; Xijun, Zhou

2016-11-01

Excessive pressure fluctuations in the vaneless space can cause mechanical vibration and even mechanical failures in pump-turbine operation. Mechanism studies on the pressure fluctuations and optimization design of blade geometry to reduce the pressure fluctuations have important significance in industrial production. In the present paper, two pump-turbine runners with big positive and negative blade lean angle were designed by using a multiobjective design strategy. Model test showed that the runner with negative blade lean angle not only had better power performance, but also had lower pressure fluctuation than the runner with positive blade lean angle. In order to figure out the mechanism of pressure fluctuation reduction in the vaneless;jik8space, full passage model for both runners were built and transient CFD computations were conducted to simulate the flow states inside the channel. Detailed flow field analyses indicated that the difference of low-pressure area in the trailing edge of blade pressure side were the main causes of pressure fluctuation reduction in the vaneless space.

Quantum Electronic Solids

DTIC Science & Technology

2013-03-07

surface (yellow circles) indicate presence of strong antiferromagnetic fluctuations 0 +π −π ky kx 0 +π +2π • Simple, archetypal structure of...It seamlessly connects to graphene to make atomically thin, gateable SGr-Gr junctions. • Digital electronics is feasible; • SGr is stable at

Mermin-Wagner fluctuations in 2D amorphous solids.

PubMed

Illing, Bernd; Fritschi, Sebastian; Kaiser, Herbert; Klix, Christian L; Maret, Georg; Keim, Peter

2017-02-21

In a recent commentary, J. M. Kosterlitz described how D. Thouless and he got motivated to investigate melting and suprafluidity in two dimensions [Kosterlitz JM (2016) J Phys Condens Matter 28:481001]. It was due to the lack of broken translational symmetry in two dimensions-doubting the existence of 2D crystals-and the first computer simulations foretelling 2D crystals (at least in tiny systems). The lack of broken symmetries proposed by D. Mermin and H. Wagner is caused by long wavelength density fluctuations. Those fluctuations do not only have structural impact, but additionally a dynamical one: They cause the Lindemann criterion to fail in 2D in the sense that the mean squared displacement of atoms is not limited. Comparing experimental data from 3D and 2D amorphous solids with 2D crystals, we disentangle Mermin-Wagner fluctuations from glassy structural relaxations. Furthermore, we demonstrate with computer simulations the logarithmic increase of displacements with system size: Periodicity is not a requirement for Mermin-Wagner fluctuations, which conserve the homogeneity of space on long scales.

Mermin-Wagner fluctuations in 2D amorphous solids

NASA Astrophysics Data System (ADS)

Illing, Bernd; Fritschi, Sebastian; Kaiser, Herbert; Klix, Christian L.; Maret, Georg; Keim, Peter

2017-02-01

In a recent commentary, J. M. Kosterlitz described how D. Thouless and he got motivated to investigate melting and suprafluidity in two dimensions [Kosterlitz JM (2016) J Phys Condens Matter 28:481001]. It was due to the lack of broken translational symmetry in two dimensions—doubting the existence of 2D crystals—and the first computer simulations foretelling 2D crystals (at least in tiny systems). The lack of broken symmetries proposed by D. Mermin and H. Wagner is caused by long wavelength density fluctuations. Those fluctuations do not only have structural impact, but additionally a dynamical one: They cause the Lindemann criterion to fail in 2D in the sense that the mean squared displacement of atoms is not limited. Comparing experimental data from 3D and 2D amorphous solids with 2D crystals, we disentangle Mermin-Wagner fluctuations from glassy structural relaxations. Furthermore, we demonstrate with computer simulations the logarithmic increase of displacements with system size: Periodicity is not a requirement for Mermin-Wagner fluctuations, which conserve the homogeneity of space on long scales.

Mermin–Wagner fluctuations in 2D amorphous solids

PubMed Central

Illing, Bernd; Fritschi, Sebastian; Kaiser, Herbert; Klix, Christian L.; Maret, Georg; Keim, Peter

2017-01-01

In a recent commentary, J. M. Kosterlitz described how D. Thouless and he got motivated to investigate melting and suprafluidity in two dimensions [Kosterlitz JM (2016) J Phys Condens Matter 28:481001]. It was due to the lack of broken translational symmetry in two dimensions—doubting the existence of 2D crystals—and the first computer simulations foretelling 2D crystals (at least in tiny systems). The lack of broken symmetries proposed by D. Mermin and H. Wagner is caused by long wavelength density fluctuations. Those fluctuations do not only have structural impact, but additionally a dynamical one: They cause the Lindemann criterion to fail in 2D in the sense that the mean squared displacement of atoms is not limited. Comparing experimental data from 3D and 2D amorphous solids with 2D crystals, we disentangle Mermin–Wagner fluctuations from glassy structural relaxations. Furthermore, we demonstrate with computer simulations the logarithmic increase of displacements with system size: Periodicity is not a requirement for Mermin–Wagner fluctuations, which conserve the homogeneity of space on long scales. PMID:28137872

Enhanced stochastic fluctuations to measure steep adhesive energy landscapes

PubMed Central

Haider, Ahmad; Potter, Daniel; Sulchek, Todd A.

2016-01-01

Free-energy landscapes govern the behavior of all interactions in the presence of thermal fluctuations in the fields of physical chemistry, materials sciences, and the biological sciences. From the energy landscape, critical information about an interaction, such as the reaction kinetic rates, bond lifetimes, and the presence of intermediate states, can be determined. Despite the importance of energy landscapes to understanding reaction mechanisms, most experiments do not directly measure energy landscapes, particularly for interactions with steep force gradients that lead to premature jump to contact of the probe and insufficient sampling of transition regions. Here we present an atomic force microscopy (AFM) approach for measuring energy landscapes that increases sampling of strongly adhesive interactions by using white-noise excitation to enhance the cantilever’s thermal fluctuations. The enhanced fluctuations enable the recording of subtle deviations from a harmonic potential to accurately reconstruct interfacial energy landscapes with steep gradients. Comparing the measured energy landscape with adhesive force measurements reveals the existence of an optimal excitation voltage that enables the cantilever fluctuations to fully sample the shape and depth of the energy surface. PMID:27911778

Killing to Fluctuate, or: How Death and Reproduction Drive a Fluctuation-Response Relation in Biofilms

NASA Astrophysics Data System (ADS)

Kalziqi, Arben; Yunker, Peter; Thomas, Jacob

Unlike equilibrium atomic solids, biofilms do not experience significant thermal fluctuations at the constituent level. However, cells inside the biofilm stochastically die and reproduce, provoking a mechanical response. We investigate the mechanical response of biofilms to the death and reproduction of cells by measuring surface-height fluctuations of biofilms with two mutual predator strains of Vibrio cholerae which kill one another on contact via the Type VI Secretion System. Biofilm surface topography is measured in the homeostatic limit, wherein cell division and death occur at roughly the same rate, via white light interferometry. Although biofilms are far from equilibrium systems, measured height correlation functions line up with expectations from a generalized fluctuation-response relation derived from replication and death events, as predicted by Risler et al. (PRL 2015). Using genetically modified strains of V. cholerae which cannot kill, we demonstrate that extracted effective temperatures increase with the amount of death and reproduction. Thus, high-precision measurement of surface topography reveals the physical consequences of death and reproduction within a biofilm, providing a new approach to studying interactions between bacteria and cells.

Precisely detecting atomic position of atomic intensity images.

PubMed

Wang, Zhijun; Guo, Yaolin; Tang, Sai; Li, Junjie; Wang, Jincheng; Zhou, Yaohe

2015-03-01

We proposed a quantitative method to detect atomic position in atomic intensity images from experiments such as high-resolution transmission electron microscopy, atomic force microscopy, and simulation such as phase field crystal modeling. The evaluation of detection accuracy proves the excellent performance of the method. This method provides a chance to precisely determine atomic interactions based on the detected atomic positions from the atomic intensity image, and hence to investigate the related physical, chemical and electrical properties. Copyright © 2014 Elsevier B.V. All rights reserved.

Instrumental requirements for the detection of electron beam-induced object excitations at the single atom level in high-resolution transmission electron microscopy.

PubMed

Kisielowski, C; Specht, P; Gygax, S M; Barton, B; Calderon, H A; Kang, J H; Cieslinski, R

2015-01-01

This contribution touches on essential requirements for instrument stability and resolution that allows operating advanced electron microscopes at the edge to technological capabilities. They enable the detection of single atoms and their dynamic behavior on a length scale of picometers in real time. It is understood that the observed atom dynamic is intimately linked to the relaxation and thermalization of electron beam-induced sample excitation. Resulting contrast fluctuations are beam current dependent and largely contribute to a contrast mismatch between experiments and theory if not considered. If explored, they open the possibility to study functional behavior of nanocrystals and single molecules at the atomic level in real time. Copyright © 2014 Elsevier Ltd. All rights reserved.

Dispersive detection of radio-frequency-dressed states

NASA Astrophysics Data System (ADS)

Jammi, Sindhu; Pyragius, Tadas; Bason, Mark G.; Florez, Hans Marin; Fernholz, Thomas

2018-04-01

We introduce a method to dispersively detect alkali-metal atoms in radio-frequency-dressed states. In particular, we use dressed detection to measure populations and population differences of atoms prepared in their clock states. Linear birefringence of the atomic medium enables atom number detection via polarization homodyning, a form of common path interferometry. In order to achieve low technical noise levels, we perform optical sideband detection after adiabatic transformation of bare states into dressed states. The balanced homodyne signal then oscillates independently of field fluctuations at twice the dressing frequency, thus allowing for robust, phase-locked detection that circumvents low-frequency noise. Using probe pulses of two optical frequencies, we can detect both clock states simultaneously and obtain population difference as well as the total atom number. The scheme also allows for difference measurements by direct subtraction of the homodyne signals at the balanced detector, which should technically enable quantum noise limited measurements with prospects for the preparation of spin squeezed states. The method extends to other Zeeman sublevels and can be employed in a range of atomic clock schemes, atom interferometers, and other experiments using dressed atoms.

Beyond mean-field effects in Bloch Oscillations of cold atoms in an optical cavity

NASA Astrophysics Data System (ADS)

Venkatesh Balasubramanian, Prasanna; O'Dell, Duncan

2012-06-01

In our earlier publication [1] we proposed using Bloch oscillations of cold atoms inside an Fabry-Perot resonator for sensitive measurements of force. The analysis in [1] was performed using a coherent mean-field description for the atoms and the light. In the current work we extend this description substantially by including the effects of fluctuations in both the atomic and light fields. This analysis is used to set realistic limits on the precision to which the force can be measured. We also make contact with the optomechanical description of the combined atom-cavity system which has proved so successful for describing recent pioneering experiments [2].[4pt] [1] B. Prasanna Venkatesh et al, Phys. Rev. A 80, 063834 (2009).[0pt] [2] S. Gupta et al, Phys. Rev. Lett. 99, 213601 (2007); F.Brennecke et al, Science 322, 235 (2008).

Quantifying polymer deformation in viscoelastic turbulence: the geometric decomposition and a Riemannian approach to scalar measures

NASA Astrophysics Data System (ADS)

Hameduddin, Ismail; Meneveau, Charles; Zaki, Tamer; Gayme, Dennice

2017-11-01

We develop a new framework to quantify the fluctuating behaviour of the conformation tensor in viscoelastic turbulent flows. This framework addresses two shortcomings of the classical approach based on Reynolds decomposition: the fluctuating part of the conformation tensor is not guaranteed to be positive definite and it does not consistently represent polymer expansions and contractions about the mean. Our approach employs a geometric decomposition that yields a positive-definite fluctuating conformation tensor with a clear physical interpretation as a deformation to the mean conformation. We propose three scalar measures of this fluctuating conformation tensor, which respect the non-Euclidean Riemannian geometry of the manifold of positive-definite tensors: fluctuating polymer volume, geodesic distance from the mean, and an anisotropy measure. We use these scalar quantities to investigate drag-reduced viscoelastic turbulent channel flow. Our approach establishes a systematic method to study viscoelastic turbulence. It also uncovers interesting phenomena that are not apparent using traditional analysis tools, including a logarithmic decrease in anisotropy of the mean conformation tensor away from the wall and polymer fluctuations peaking beyond the buffer layer. This work has been partially funded by the following NSF Grants: CBET-1652244, OCE-1633124, CBET-1511937.

Investigation of writing error in staggered heated-dot magnetic recording systems

NASA Astrophysics Data System (ADS)

Tipcharoen, W.; Warisarn, C.; Tongsomporn, D.; Karns, D.; Kovintavewat, P.

2017-05-01

To achieve an ultra-high storage capacity, heated-dot magnetic recording (HDMR) has been proposed, which heats a bit-patterned medium before recording data. Generally, an error during the HDMR writing process comes from several sources; however, we only investigate the effects of staggered island arrangement, island size fluctuation caused by imperfect fabrication, and main pole position fluctuation. Simulation results demonstrate that a writing error can be minimized by using a staggered array (hexagonal lattice) instead of a square array. Under the effect of main pole position fluctuation, the writing error is higher than the system without main pole position fluctuation. Finally, we found that the error percentage can drop below 10% when the island size is 8.5 nm and the standard deviation of the island size is 1 nm in the absence of main pole jitter.

Global and System-Specific Resting-State fMRI Fluctuations Are Uncorrelated: Principal Component Analysis Reveals Anti-Correlated Networks

PubMed Central

Carbonell, Felix; Bellec, Pierre

2011-01-01

Abstract The influence of the global average signal (GAS) on functional-magnetic resonance imaging (fMRI)–based resting-state functional connectivity is a matter of ongoing debate. The global average fluctuations increase the correlation between functional systems beyond the correlation that reflects their specific functional connectivity. Hence, removal of the GAS is a common practice for facilitating the observation of network-specific functional connectivity. This strategy relies on the implicit assumption of a linear-additive model according to which global fluctuations, irrespective of their origin, and network-specific fluctuations are super-positioned. However, removal of the GAS introduces spurious negative correlations between functional systems, bringing into question the validity of previous findings of negative correlations between fluctuations in the default-mode and the task-positive networks. Here we present an alternative method for estimating global fluctuations, immune to the complications associated with the GAS. Principal components analysis was applied to resting-state fMRI time-series. A global-signal effect estimator was defined as the principal component (PC) that correlated best with the GAS. The mean correlation coefficient between our proposed PC-based global effect estimator and the GAS was 0.97±0.05, demonstrating that our estimator successfully approximated the GAS. In 66 out of 68 runs, the PC that showed the highest correlation with the GAS was the first PC. Since PCs are orthogonal, our method provides an estimator of the global fluctuations, which is uncorrelated to the remaining, network-specific fluctuations. Moreover, unlike the regression of the GAS, the regression of the PC-based global effect estimator does not introduce spurious anti-correlations beyond the decrease in seed-based correlation values allowed by the assumed additive model. After regressing this PC-based estimator out of the original time-series, we observed robust anti-correlations between resting-state fluctuations in the default-mode and the task-positive networks. We conclude that resting-state global fluctuations and network-specific fluctuations are uncorrelated, supporting a Resting-State Linear-Additive Model. In addition, we conclude that the network-specific resting-state fluctuations of the default-mode and task-positive networks show artifact-free anti-correlations. PMID:22444074

Engineering matter interactions using squeezed vacuum

NASA Astrophysics Data System (ADS)

Zeytinoglu, Sina; Imamoglu, Atac; Huber, Sebastian

Virtually all interactions that are relevant for atomic and condensed matter physics are mediated by the quantum fluctuations of the electromagnetic field vacuum. Consequently, controlling the latter can be used to engineer the strength and the range of inter-particle interactions. Recent experiments have used this premise to demonstrate novel quantum phases or entangling gates by embedding electric dipoles in photonic cavities or waveguides which modify the electromagnetic fluctuations. In this submission, we demonstrate theoretically that the enhanced fluctuations in the anti-squeezed quadrature of a squeezed vacuum state allows for engineering interactions between electric dipoles without the need for a photonic cavity or waveguide. Thus, the strength and range of the resulting dipole-dipole coupling can be engineered by dynamically changing the spatial profile of the squeezed vacuum in a travelling-wave geometry. ETH-Zurich.

Engineering matter interactions using squeezed vacuum

NASA Astrophysics Data System (ADS)

Zeytinoglu, Sina; Imamoglu, Atac; Huber, Sebastian

Virtually all interactions that are relevant for atomic and condensed matter physics are mediated by the quantum fluctuations of the electromagnetic field vacuum. Consequently, controlling the latter can be used to engineer the strength and the range of inter-particle interactions. Recent experiments have used this premise to demonstrate novel quantum phases or entangling gates by embedding electric dipoles in photonic cavities or waveguides which modify the electromagnetic fluctuations. In this talk, we demonstrate theoretically that the enhanced fluctuations in the anti-squeezed quadrature of a squeezed vacuum state allows for engineering interactions between electric dipoles without the need for a photonic cavity or waveguide. Thus, the strength and range of the resulting dipole-dipole coupling can be engineered by dynamically changing the spatial profile of the squeezed vacuum in a travelling-wave geometry. ETH Zurich.

Mesoscopic structure formation in condensed matter due to vacuum fluctuations

NASA Astrophysics Data System (ADS)

Sen, Siddhartha; Gupta, Kumar S.; Coey, J. M. D.

2015-10-01

An observable influence of zero-point fluctuations of the vacuum electromagnetic field on bound electrons is well known in the hydrogen atom, where it produces the Lamb shift. Here, we adapt an approach used to explain the Lamb shift in terms of a slight expansion of the orbits due to interaction with the zero-point field and apply it to assemblies of N electrons that are modeled as independent atomically bound two-level systems. The effect is to stabilize a collective ground-state energy, which leads to a prediction of novel effects at room temperature for quasi-two-dimensional systems over a range of parameters in the model, namely, N , the two-level excitation energy ℏ ω and the ionization energy ℏ ω +ɛ . Some mesoscopic systems where these effects may be observable include water sheaths on protein or DNA, surfaces of gaseous nanobubbles, and the magnetic response of inhomogeneous, electronically dilute oxides. No such effects are envisaged for uniform three-dimensional systems.

Real-time observation of fluctuations in a driven-dissipative quantum many-body system undergoing a phase transition

NASA Astrophysics Data System (ADS)

Donner, Tobias

2015-03-01

A Bose-Einstein condensate whose motional degrees of freedom are coupled to a high-finesse optical cavity via a transverse pump beam constitutes a dissipative quantum many-body system with long range interactions. These interactions can induce a structural phase transition from a flat to a density-modulated state. The transverse pump field simultaneously represents a probe of the atomic density via cavity- enhanced Bragg scattering. By spectrally analyzing the light field leaking out of the cavity, we measure non-destructively the dynamic structure factor of the fluctuating atomic density while the system undergoes the phase transition. An observed asymmetry in the dynamic structure factor is attributed to the coupling to dissipative baths. Critical exponents for both sides of the phase transition can be extracted from the data. We further discuss our progress in adding strong short-range interactions to this system, in order to explore Bose-Hubbard physics with cavity-mediated long-range interactions and self-organization in lower dimensions.

High Fidelity Preparation of a Single Atom in Its 2D Center of Mass Ground State

NASA Astrophysics Data System (ADS)

Sompet, Pimonpan; Fung, Yin Hsien; Schwartz, Eyal; Hunter, Matthew D. J.; Phrompao, Jindaratsamee; Andersen, Mikkel F.

2017-04-01

Complete control over quantum states of individual atoms is important for the study of the microscopic world. Here, we present a push button method for high fidelity preparation of a single 85Rb atom in the vibrational ground state of tightly focused optical tweezers. The method combines near-deterministic preparation of a single atom with magnetically-insensitive Raman sideband cooling. We achieve 2D cooling in the radial plane with a ground state population of 0.85, which provides a fidelity of 0.7 for the entire procedure (loading and cooling). The Raman beams couple two sublevels (| F = 3 , m = 0 〉 and | F = 2 , m = 0 〉) that are indifferent to magnetic noise to first order. This leads to long atomic coherence times, and allows us to implement the cooling in an environment where magnetic field fluctuations prohibit previously demonstrated variations. Additionally, we implement the trapping and manipulation of two atoms confined in separate dynamically reconfigurable optical tweezers, to study few-body dynamics.

Laser frequency stabilization using a commercial wavelength meter

NASA Astrophysics Data System (ADS)

Couturier, Luc; Nosske, Ingo; Hu, Fachao; Tan, Canzhu; Qiao, Chang; Jiang, Y. H.; Chen, Peng; Weidemüller, Matthias

2018-04-01

We present the characterization of a laser frequency stabilization scheme using a state-of-the-art wavelength meter based on solid Fizeau interferometers. For a frequency-doubled Ti-sapphire laser operated at 461 nm, an absolute Allan deviation below 10-9 with a standard deviation of 1 MHz over 10 h is achieved. Using this laser for cooling and trapping of strontium atoms, the wavemeter scheme provides excellent stability in single-channel operation. Multi-channel operation with a multimode fiber switch results in fluctuations of the atomic fluorescence correlated to residual frequency excursions of the laser. The wavemeter-based frequency stabilization scheme can be applied to a wide range of atoms and molecules for laser spectroscopy, cooling, and trapping.

Spatial dispersion in atom-surface quantum friction

DOE PAGES

Reiche, D.; Dalvit, D. A. R.; Busch, K.; ...

2017-04-15

We investigate the influence of spatial dispersion on atom-surface quantum friction. We show that for atom-surface separations shorter than the carrier's mean free path within the material, the frictional force can be several orders of magnitude larger than that predicted by local optics. In addition, when taking into account spatial dispersion effects, we show that the commonly used local thermal equilibrium approximation underestimates by approximately 95% the drag force, obtained by employing the recently reported nonequilibrium fluctuation-dissipation relation for quantum friction. Unlike the treatment based on local optics, spatial dispersion in conjunction with corrections to local thermal equilibrium change notmore » only the magnitude but also the distance scaling of quantum friction.« less

Band structures of TiO2 doped with N, C and B*

PubMed Central

Xu, Tian-Hua; Song, Chen-Lu; Liu, Yong; Han, Gao-Rong

2006-01-01

This study on the band structures and charge densities of nitrogen (N)-, carbon (C)- and boron (B)-doped titanium dioxide (TiO2) by first-principles simulation with the CASTEP code (Segall et al., 2002) showed that the three 2p bands of impurity atom are located above the valence-band maximum and below the Ti 3d bands, and that along with the decreasing of impurity atomic number, the fluctuations become more intensive. We cannot observe obvious band-gap narrowing in our result. Therefore, the cause of absorption in visible light might be the isolated impurity atom 2p states in band-gap rather than the band-gap narrowing. PMID:16532532

How many atoms are required to characterize accurately trajectory fluctuations of a protein?

NASA Astrophysics Data System (ADS)

Cukier, Robert I.

2010-06-01

Large molecules, whose thermal fluctuations sample a complex energy landscape, exhibit motions on an extended range of space and time scales. Principal component analysis (PCA) is often used to extract dominant motions that in proteins are typically domain motions. These motions are captured in the large eigenvalue (leading) principal components. There is also information in the small eigenvalues, arising from approximate linear dependencies among the coordinates. These linear dependencies suggest that instead of using all the atom coordinates to represent a trajectory, it should be possible to use a reduced set of coordinates with little loss in the information captured by the large eigenvalue principal components. In this work, methods that can monitor the correlation (overlap) between a reduced set of atoms and any number of retained principal components are introduced. For application to trajectory data generated by simulations, where the overall translational and rotational motion needs to be eliminated before PCA is carried out, some difficulties with the overlap measures arise and methods are developed to overcome them. The overlap measures are evaluated for a trajectory generated by molecular dynamics for the protein adenylate kinase, which consists of a stable, core domain, and two more mobile domains, referred to as the LID domain and the AMP-binding domain. The use of reduced sets corresponding, for the smallest set, to one-eighth of the alpha carbon (CA) atoms relative to using all the CA atoms is shown to predict the dominant motions of adenylate kinase. The overlap between using all the CA atoms and all the backbone atoms is essentially unity for a sum over PCA modes that effectively capture the exact trajectory. A reduction to a few atoms (three in the LID and three in the AMP-binding domain) shows that at least the first principal component, characterizing a large part of the LID-binding and AMP-binding motion, is well described. Based on these results, the overlap criterion should be applicable as a guide to postulating and validating coarse-grained descriptions of generic biomolecular assemblies.

Structure and function of photosystem I–[FeFe] hydrogenase protein fusions: An all-atom molecular dynamics study

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

Harris, Bradley J.; Cheng, Xiaolin; Frymier, Paul

2015-12-15

All-atom molecular dynamics (MD) simulation was used to study the solution dynamics and protein protein interactions of protein fusions of photosystem I (PSI) from Thermosynechococcus elongatus and an [FeFe]-hydrogenase (FeFe H 2ase) from Clostridium pasteurianum, a unique complex capable of photocatalytic hydrogen production. This study involved fusions of these two proteins via dithiol linkers of different length including decanedithiol, octanedithiol, and hexanedithiol, for which experimental data had previously been obtained. Evaluation of root-mean-squared deviations (RMSDs) relative to the respective crystal structures of PSI and the FeFe H 2ase shows that these fusion complexes approach stable equilibrium conformations during the MDmore » simulations. Investigating protein mobility via root-mean-squared fluctuations (RMSFs) reveals that tethering via the shortest hexanedithiol linker results in increased atomic fluctuations of both PSI and the hydrogenase in these fusion complexes. Furthermore, evaluation of the inter- and intraprotein electron transfer distances in these fusion complexes indicates that the structural changes in the FeFe H 2ase arising from ligation to PSI via the shortest hexanedithiol linker may hinder electron transport in the hydrogenase, thus providing a molecular level explanation for the observation that the medium-length octanedithiol linker gives the highest hydrogen production rate.« less

Dielectric properties of proteins from simulations: tools and techniques

NASA Astrophysics Data System (ADS)

Simonson, Thomas; Perahia, David

1995-09-01

Tools and techniques to analyze the dielectric properties of proteins are described. Microscopic dielectric properties are determined by a susceptibility tensor of order 3 n, where n is the number of protein atoms. For perturbing charges not too close to the protein, the dielectric relaxation free energy is directly related to the dipole-dipole correlation matrix of the unperturbed protein, or equivalently to the covariance matrix of its atomic displacements. These are straightforward to obtain from existing molecular dynamics packages such as CHARMM or X- PLOR. Macroscopic dielectric properties can be derived from the dipolar fluctuations of the protein, by idealizing the protein as one or more spherical media. The dipolar fluctuations are again directly related to the covariance matrix of the atomic displacements. An interesting consequence is that the quasiharmonic approximation, which by definition exactly reproduces this covariance matrix, gives the protein dielectric constant exactly. Finally a technique is reviewed to obtain normal or quasinormal modes of vibration of symmetric protein assemblies. Using elementary group theory, and eliminating the high-frequency modes of vibration of each monomer, the limiting step in terms of memory and computation is finding the normal modes of a single monomer, with the other monomers held fixed. This technique was used to study the dielectric properties of the Tobacco Mosaic Virus protein disk.

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

Quantum Field Energy Sensor based on the Casimir Effect

NASA Astrophysics Data System (ADS)

Ludwig, Thorsten

The Casimir effect converts vacuum fluctuations into a measurable force. Some new energy technologies aim to utilize these vacuum fluctuations in commonly used forms of energy like electricity or mechanical motion. In order to study these energy technologies it is helpful to have sensors for the energy density of vacuum fluctuations. In today's scientific instrumentation and scanning microscope technologies there are several common methods to measure sub-nano Newton forces. While the commercial atomic force microscopes (AFM) mostly work with silicon cantilevers, there are a large number of reports on the use of quartz tuning forks to get high-resolution force measurements or to create new force sensors. Both methods have certain advantages and disadvantages over the other. In this report the two methods are described and compared towards their usability for Casimir force measurements. Furthermore a design for a quantum field energy sensor based on the Casimir force measurement will be described. In addition some general considerations on extracting energy from vacuum fluctuations will be given.

Absence of Local Fluctuating Dimers in Superconducting Ir 1-x(Pt,Rh) xTe 2

DOE PAGES

Yu, Runze; Banerjee, S.; Lei, H. C.; ...

2018-06-01

The compound IrTe2 is known to exhibit a transition to a modulated state featuring Ir-Ir dimers, with large associated atomic displacements. Partial substitution of Pt or Rh for Ir destabilizes the modulated structure and induces superconductivity. It has been proposed that quantum critical dimer fluctuations might be associated with the superconductivity. Here we test for such local dimer correlations and demonstrate their absence. X-ray pair distribution function approach reveals that the local structure of Ir 0.95Pt 0.05Te 2 and Ir 0.8Rh 0.2Te 2 dichalcogenide superconductors with compositions just past the dimer/superconductor boundary is explained well by a dimer-free model downmore » to 10 K, ruling out the possibility of there being nanoscale dimer fluctuations in this regime. This is inconsistent with the proposed quantum-critical-point-like interplay of the dimer state and superconductivity, and precludes scenarios for dimer fluctuations mediated superconducting pairing.« less

Absence of Local Fluctuating Dimers in Superconducting Ir 1-x(Pt,Rh) xTe 2

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

Yu, Runze; Banerjee, S.; Lei, H. C.

The compound IrTe2 is known to exhibit a transition to a modulated state featuring Ir-Ir dimers, with large associated atomic displacements. Partial substitution of Pt or Rh for Ir destabilizes the modulated structure and induces superconductivity. It has been proposed that quantum critical dimer fluctuations might be associated with the superconductivity. Here we test for such local dimer correlations and demonstrate their absence. X-ray pair distribution function approach reveals that the local structure of Ir 0.95Pt 0.05Te 2 and Ir 0.8Rh 0.2Te 2 dichalcogenide superconductors with compositions just past the dimer/superconductor boundary is explained well by a dimer-free model downmore » to 10 K, ruling out the possibility of there being nanoscale dimer fluctuations in this regime. This is inconsistent with the proposed quantum-critical-point-like interplay of the dimer state and superconductivity, and precludes scenarios for dimer fluctuations mediated superconducting pairing.« less

Absence of local fluctuating dimers in superconducting Ir1 -x(Pt,Rh ) xTe2

NASA Astrophysics Data System (ADS)

Yu, Runze; Banerjee, S.; Lei, H. C.; Sinclair, Ryan; Abeykoon, M.; Zhou, H. D.; Petrovic, C.; Guguchia, Z.; Bozin, E. S.

2018-05-01

The compound IrTe2 is known to exhibit a transition to a modulated state featuring Ir-Ir dimers, with large associated atomic displacements. Partial substitution of Pt or Rh for Ir destabilizes the modulated structure and induces superconductivity. It has been proposed that quantum critical dimer fluctuations might be associated with the superconductivity. Here we test for such local dimer correlations and demonstrate their absence. X-ray pair distribution function approach reveals that the local structure of Ir0 :95Pt0 :05Te2 and Ir0 :8Rh0 :2Te2 dichalcogenide superconductors with compositions just past the dimer/superconductor boundary is explained well by a dimer-free model down to 10 K, ruling out the possibility of there being nanoscale dimer fluctuations in this regime. This is inconsistent with the proposed quantum-critical-point-like interplay of the dimer state and superconductivity, and precludes scenarios for dimer fluctuations mediated superconducting pairing.

Direct measurement of friction of a fluctuating contact line

NASA Astrophysics Data System (ADS)

Guo, Shuo; Gao, Min; Xiong, Xiaomin; Wang, Yong Jian; Wang, Xiaoping; Sheng, Ping; Tong, Penger

2013-03-01

What happens at a moving contact line, where one fluid displaces another (immiscible) fluid over a solid surface, is a fundamental issue in fluid dynamics. In this presentation, we report a direct measurement of the friction coefficient in the immediate vicinity of a fluctuating contact line using a micron-sized vertical glass fiber with one end glued to an atomic force microscope (AFM) cantilever beam and the other end touching a liquid-air interface. By measuring the broadening of the resonance peak of the cantilever system with varying liquid viscosity η, we obtain the friction coefficient ξc associated with the contact line fluctuations on the glass fiber of diameter d and find it has the universal form, ξc = 0 . 8 πdη , independent of the contact angle. The result is further confirmed by using a soap film system whose bulk effect is negligibly small. This is the first time that the friction coefficient of a fluctuating contact line is measured. *Work supported by the Research Grants Council of Hong Kong SAR.

Convergence of sampling in protein simulations

NASA Astrophysics Data System (ADS)

Hess, Berk

2002-03-01

With molecular dynamics protein dynamics can be simulated in atomic detail. Current computers are not fast enough to probe all available conformations, but fluctuations around one conformation can be sampled to a reasonable extent. The motions with the largest fluctuations can be filtered out of a simulation using covariance or principal component analysis. A problem with this analysis is that random diffusion can appear as correlated motion. An analysis is presented of how long a simulation should be to obtain relevant results for global motions. The analysis reveals that the cosine content of the principal components is a good indicator for bad sampling.

Electrostatic force microscopy on oriented graphite surfaces: coexistence of insulating and conducting behaviors.

PubMed

Lu, Yonghua; Muñoz, M; Steplecaru, C S; Hao, Cheng; Bai, Ming; Garcia, N; Schindler, K; Esquinazi, P

2006-08-18

We present measurements of the electric potential fluctuations on the surface of highly oriented pyrolytic graphite using electrostatic force and atomic force microscopy. Micrometric domainlike potential distributions are observed even when the sample is grounded. Such potential distributions are unexpected given the good metallic conductivity of graphite because the surface should be an equipotential. Our results indicate the coexistence of regions with "metalliclike" and "insulatinglike" behaviors showing large potential fluctuations of the order of 0.25 V. In lower quality graphite, this effect is not observed. Experiments are performed in Ar and air atmospheres.

Sunlit Io Atmospheric [O I] 6300 A and the Plasma Torus

NASA Technical Reports Server (NTRS)

Oliversen, Ronald J.; Scherb, Frank; Smyth, William H.; Freed, Melanie E.; Woodward, R. Carey, Jr.; Marcone, Maximus L.; Retherford, Kurt D.; Lupie, Olivia L.; Morgenthaler, Jeffrey P.; Fisher, Richard R. (Technical Monitor)

2001-01-01

A large database of sunlit Io [O I] 6300A emission, acquired over the period 1990-1999, with extensive coverage of Io orbital phase angle phi and System III longitude lambda(sub III), exhibits significant long-term and short-term variations in [O I] 6300A emission intensities. The long-term average intensity shows a clear dependence on lambda(sub III), which establishes conclusively that the emission is produced by the interaction between Io's atmosphere and the plasma torus. Two prominent average intensity maxima, 70 deg to 90 deg wide, are centered at lambda(sub III) about 130deg. and about 295 deg. A comparison of data from October 1998 with a three-dimensional plasma torus model, based upon electron impact excitation of atomic oxygen, suggests a basis for study of the torus interaction with Io's atmosphere. The observed short-term, erratic [O I] 6300A intensity variations fluctuate approximately 20% to 50% on time scale of tens of minutes with less frequent fluctuations of a factor of about 2. The most likely candidate to produce these fluctuations is a time-variable energy flux of field-aligned nonthermal electrons identified recently in Galileo PLS data. If true, the short-term [O I] intensity fluctuations may be related to variable field-aligned currents driven by inward and outward torus plasma transport and/or transient high-latitude, field-aligned potential drops. A correlation between the intensity and emission line width indicates molecular dissociation may contribute significantly to the [O I] 6300A emission. The nonthermal electron energy flux may produce O(1-D) by electron impact dissociation of SO2 and SO, with the excess energy going into excitation of O and its kinetic energy. The [O I] 6300A emission database establishes Io as a valuable probe of the torus, responding to local conditions at Io's position.

Influence of the platform jitter on intensity fluctuation for laser launch system

NASA Astrophysics Data System (ADS)

Zhang, Pengfei; Qiao, Chunhong; Huang, Tong; Zhang, Jinghui; Fan, Chengyu

2017-10-01

The jitter of the transmitting system can cause the light intensity fluctuation at the target position of the laser transmission, which affects the performance of the laser communication, imaging and the adaptive optical system. In this paper, the platform jitter is modeled by Gaussian random fluctuation phase and the analytic expression of the system jitter effect on the fluctuation of light intensity is obtained under the vacuum condition based on extended Huygens-Fresnel principle. The numerical simulation is compared with the theoretical expression and the consistency is obtained. At the same time, the influence of the jitter of the launch system on the intensity fluctuation of the target system under different turbulence conditions is analyzed by numerical simulation. The result show that normalized intensity fluctuation variance induced by platform jitter seems to be unrestricted. The jitter of the transmitting system has a more important influence on the fluctuation of the target position caused by the atmospheric turbulence, as the jitter increase. This result provides a reference for the application of the actual laser transmission system.

A new look at the atomic level virial stress: on continuum-molecular system equivalence

NASA Astrophysics Data System (ADS)

Zhou, Min

2003-09-01

The virial stress is the most commonly used definition of stress in discrete particle systems. This quantity includes two parts. The first part depends on the mass and velocity (or, in some versions, the fluctuation part of the velocity) of atomic particles, reflecting an assertion that mass transfer causes mechanical stress to be applied on stationary spatial surfaces external to an atomic-particle system. The second part depends on interatomic forces and atomic positions, providing a continuum measure for the internal mechanical interactions between particles. Historic derivations of the virial stress include generalization from the virial theorem of Clausius (1870) for gas pressure and solution of the spatial equation of balance of momentum. The virial stress is stress-like a measure for momentum change in space. This paper shows that, contrary to the generally accepted view, the virial stress is not a measure for mechanical force between material points and cannot be regarded as a measure for mechanical stress in any sense. The lack of physical significance is both at the individual atom level in a time-resolved sense and at the system level in a statistical sense. It is demonstrated that the interatomic force term alone is a valid stress measure and can be identified with the Cauchy stress. The proof in this paper consists of two parts. First, for the simple conditions of rigid translation, uniform tension and tension with thermal oscillations, the virial stress yields clearly erroneous interpretations of stress. Second, the conceptual flaw in the generalization from the virial theorem for gas pressure to stress and the confusion over spatial and material equations of balance of momentum in theoretical derivations of the virial stress that led to its erroneous acceptance as the Cauchy stress are pointed out. Interpretation of the virial stress as a measure for mechanical force violates balance of momentum and is inconsistent with the basic definition of stress. The versions of the virial-stress formula that involve total particle velocity and the thermal fluctuation part of the velocity are demonstrated to be measures of spatial momentum flow relative to, respectively, a fixed reference frame and a moving frame with a velocity equal to the part of particle velocity not included in the virial formula. To further illustrate the irrelevance of mass transfer to the evaluation of stress, an equivalent continuum (EC) for dynamically deforming atomistic particle systems is defined. The equivalence of the continuum to discrete atomic systems includes (i) preservation of linear and angular momenta, (ii) conservation of internal, external and inertial work rates, and (iii) conservation of mass. This equivalence allows fields of work- and momentum-preserving Cauchy stress, surface traction, body force and deformation to be determined. The resulting stress field depends only on interatomic forces, providing an independent proof that as a measure for internal material interaction stress is independent of kinetic energy or mass transfer.

Constraints on stable equilibria with fluctuation-induced (Casimir) forces.

PubMed

Rahi, Sahand Jamal; Kardar, Mehran; Emig, Thorsten

2010-08-13

We examine whether fluctuation-induced forces can lead to stable levitation. First, we analyze a collection of classical objects at finite temperature that contain fixed and mobile charges and show that any arrangement in space is unstable to small perturbations in position. This extends Earnshaw's theorem for electrostatics by including thermal fluctuations of internal charges. Quantum fluctuations of the electromagnetic field are responsible for Casimir or van der Waals interactions. Neglecting permeabilities, we find that any equilibrium position of items subject to such forces is also unstable if the permittivities of all objects are higher or lower than that of the enveloping medium, the former being the generic case for ordinary materials in vacuum.

Quantum noise of a Bose-Einstein condensate in an optical cavity, correlations, and entanglement

NASA Astrophysics Data System (ADS)

Szirmai, G.; Nagy, D.; Domokos, P.

2010-04-01

A Bose-Einstein condensate of ultracold atoms inside the field of a laser-driven optical cavity exhibits dispersive optical bistability. We describe this system by using mean-field approximation and by analyzing the correlation functions of the linearized quantum fluctuations around the mean-field solution. The entanglement and the statistics of the atom-field quadratures are given in the stationary state. It is shown that the mean-field solution, that is, the Bose-Einstein condensate, is robust against entanglement generation for most of the phase diagram.

Mapping reversible photoswitching of molecular-resistance fluctuations during the conformational transformation of azobenzene-terminated molecular switches.

PubMed

Cho, Duckhyung; Yang, Myungjae; Shin, Narae; Hong, Seunghun

2018-06-07

We report a direct mapping and analysis of electrical noise in azobenzene-terminated molecular monolayers, revealing reversible photoswitching of the molecular-resistance fluctuations in the layers. In this work, a conducting atomic force microscope combined with a homemade spectrum analyzer was used to image electrical current and noise at patterned self-assembled monolayers (SAMs) of azobenzene-terminated molecular wires on a gold substrate. We analyzed the current and noise imaging data to obtain maps of molecular resistances and amount of mean-square fluctuations in the resistances of the regions of trans-azobenzene and a cis/trans-azobenzene mixture. We revealed that the fluctuations in the molecular resistances in the SAMs were enhanced after the trans-to-cis isomerization, while the resistances were reduced. This result could be attributed to enhanced disorders in the molecular arrangements in the cis-SAMs. Furthermore, we observed that the changes in the resistance fluctuations were reversible with respect to repeated trans-to-cis and cis-to-trans isomerizations, indicating that the effects originated from reversible photoswitching of the molecular structures rather than irreversible damages of the molecules. These findings provide valuable insights into the electrical fluctuations in photoswitchable molecules, which could be utilized in further studies on molecular switches and molecular electronics in general. © 2018 IOP Publishing Ltd.

Steady and unsteady calculations on thermal striping phenomena in triple-parallel jet

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

Yu, Y. Q.; Merzari, E.; Thomas, J. W.

2017-02-01

The phenomenon of thermal striping is encountered in liquid metal cooled fast reactors (LMFR), in which temperature fluctuation due to convective mixing between hot and cold fluids can lead to a possibility of crack initiation and propagation in the structure due to high cycle thermal fatigue. Using sodium experiments of parallel triple jets configuration performed by Japan Atomic Energy Agency (JAEA) as benchmark, numerical simulations were carried out to evaluate the temperature fluctuation characteristics in fluid and the transfer characteristics of temperature fluctuation from fluid to structure, which is important to assess the potential thermal fatigue damage. In this study,more » both steady (RANS) and unsteady (URANS, LES) methods were applied to predict the temperature fluctuations of thermal striping. The parametric studies on the effects of mesh density and boundary conditions on the accuracy of the overall solutions were also conducted. The velocity, temperature and temperature fluctuation intensity distribution were compared with the experimental data. As expected, steady calculation has limited success in predicting the thermal–hydraulic characteristics of the thermal striping, highlighting the limitations of the RANS approach in unsteady heat transfer simulations. The unsteady results exhibited reasonably good agreement with experimental results for temperature fluctuation intensity, as well as the average temperature and velocity components at the measurement locations.« less

Change of Energy of the Cubic Subnanocluster of Iron Under Influence of Interstitial and Substitutional Atoms.

PubMed

Nedolya, Anatoliy V; Bondarenko, Natalya V

2016-12-01

Energy change of an iron face-centred cubic subnanocluster was evaluated using molecular mechanics method depending on the position of a carbon interstitial atom and substitutional atoms of nickel. Calculations of all possible positions of impurity atoms show that the energy change of the system are discrete and at certain positions of the atoms are close to continuous.In terms of energy, when all impurity atoms are on the same edge of an atomic cluster, their positions are more advantageous. The presence of nickel atoms on the edge of a cubic cluster resulted in decrease of potential barrier for a carbon atom and decrease in energy in the whole cluster. A similar drift of a carbon atom from central octahedral interstitial site to the surface in the direction <011> occurred under the influence of surface factors.Such configuration corresponds to decreasing symmetry and increasing the number of possible energy states of a subnanocluster, and it corresponds to the condition of spontaneous crystallization process in an isolated system.Taking into account accidental positions of the nickel atom in the iron cluster, such behaviour of the carbon atom can explain the mechanism of growth of a new phase and formation of new clusters in the presence of other kind of atoms because of surface influence.

Pressure fluctuation generated by the interaction of blade and tongue

NASA Astrophysics Data System (ADS)

Zheng, Lulu; Dou, Hua-Shu; Chen, Xiaoping; Zhu, Zuchao; Cui, Baoling

2018-02-01

Pressure fluctuation around the tongue has large effect on the stable operation of a centrifugal pump. In this paper, the Reynolds averaged Navier-Stokes equations (RANS) and the RNG k-epsilon turbulence model is employed to simulate the flow in a pump. The flow field in the centrifugal pump is computed for a range of flow rate. The simulation results have been compared with the experimental data and good agreement has been achieved. In order to study the interaction of the tongue with the impeller, fifteen monitor probes are evenly distributed circumferentially at three radii around the tongue. Pressure distribution is investigated at various blade positions while the blade approaches to and leaves the tongue region. Results show that pressure signal fluctuates largely around the tongue, and it is more intense near the tongue surface. At design condition, standard deviation of pressure fluctuation is the minimum. At large flow rate, the increased low pressure region at the blade trailing edge results in the increases of pressure fluctuation amplitude and pressure spectra at the monitor probes. Minimum pressure is obtained when the blade is facing to the tongue. It is found that the amplitude of pressure fluctuation strongly depends on the blade positions at large flow rate, and pressure fluctuation is caused by the relative movement between blades and tongue. At small flow rate, the rule of pressure fluctuation is mainly depending on the structure of vortex flow at blade passage exit besides the influence from the relative position between the blade and the tongue.

An array of correlated atom interferometers to study to study the local fluctuations of the gravitational field and its impact on low fequency gravitational waves observations

NASA Astrophysics Data System (ADS)

Bouyer, P.; Canuel, B.; Pelisson, S.; Harms, J.; Bertoldi, A.; Gaffet, S.; Landragin, A.; Lefevre, G.; Riou, I.; Geiger, R.

2016-12-01

We will present here the Matter-Wave laser Interferometer Gravitation Antenna, MIGA, a hybrid instrument composed of a network of atom interferometers horizontally aligned and interrogated by the resonant field of an optical cavity. This detector will provide measurements of sub Hertz variations of the gravitational strain tensor. MIGA will bring new methods for geophysics for the characterization of spatial and temporal variations of the local gravity field and will also be a demonstrator for future low frequency Gravitational Wave (GW) detections. The recent first direct observation of gravitational radiation opens the way towards a novel astronomy requires a new class of low frequency Gravitational Wave detectors such as MIGA. Nevertheless, the fluctuations of the Earth gravitational field over different baselines are of high relevance for the functioning of such experiments. Indeed, a fluctuating gravity gradient causes a tidal effect that cannot, in principle, be distinguished from Gravitational Waves.This so-called « Newtonian Noise » is therefore considered up to now as a fundamental limit for any ground based detector and the main reason for restricting future low frequency GW detectors to space. Nevertheless, these two contributions may become discernible by the use of a network of test masses. Indeed, both GW and NN effects will have different spatial signatures over the test mass network. While GW has extremely long characteristic length, NN has shorter characteristic lengths going from the meter to a few kilometers.The array of distant Atom Interferometers in MIGA can be used as network of test masses, which can be correlated using a common laser link. Differential measurements between the atom interferometers of the Network enables for a large reduction of the effect of NN and opens the way towards the realization of low frequency GW detectors.In this paper, we will detail the projection of background NN in the underground environment of the LSBB and present GW interferometer geometries enabling its reduction.

Probing individual tunneling fluctuators with coherently controlled tunneling systems

NASA Astrophysics Data System (ADS)

Meißner, Saskia M.; Seiler, Arnold; Lisenfeld, Jürgen; Ustinov, Alexey V.; Weiss, Georg

2018-05-01

Josephson junctions made from aluminum and its oxide are the most commonly used functional elements for superconducting circuits and qubits. It is generally known that the disordered thin film AlOx contains atomic tunneling systems. Coherent tunneling systems may couple strongly to a qubit via their electric dipole moment, giving rise to spectral level repulsion. In addition, slowly fluctuating tunneling systems are observable when they are located close to coherent ones and distort their potentials. This interaction causes telegraphic switching of the coherent tunneling systems' energy splitting. Here, we measure such switching induced by individual fluctuators on timescales from hours to minutes using a superconducting qubit as a detector. Moreover, we extend the range of measurable switching times to millisecond scales by employing a highly sensitive single-photon qubit swap spectroscopy and statistical analysis of the measured qubit states.

Resolution Quality and Atom Positions in Sub-Angstrom Electron Microscopy

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

O'Keefe, Michael A.; Allard, Lawrence F.; Blom, Douglas A.

2005-02-15

Ability to determine whether an image peak represents one single atom or several depends on resolution of the HR-(S)TEM. Rayleigh's resolution criterion, an accepted standard in optics, was derived as a means for judging when two image intensity peaks from two sources of light (stars) are distinguishable from a single source. Atom spacings closer than the Rayleigh limit have been resolved in HR-TEM, suggesting that it may be useful to consider other limits, such as the Sparrow resolution criterion. From the viewpoint of the materials scientist, it is important to be able to use the image to determine whether anmore » image feature represents one or more atoms (resolution), and where the atoms (or atom columns) are positioned relative to one another (resolution quality). When atoms and the corresponding image peaks are separated by more than the Rayleigh limit of the HR-(S)TEM, it is possible to adjust imaging parameters so that relative peak positions in the image correspond to relative atom positions in the specimen. When atoms are closer than the Rayleigh limit, we must find the relationship of the peak position to the atom position by peak fitting or, if we have a suitable model, by image simulation. Our Rayleigh-Sparrow parameter QRS reveals the ''resolution quality'' of a microscope image. QRS values greater than 1 indicate a clearly resolved twin peak, while values between 1 and 0 mean a lower-quality resolution and an image with peaks displaced from the relative atom positions. The depth of the twin-peak minimum can be used to determine the value of QRS and the true separation of the atom peaks that sum to produce the twin peak in the image. The Rayleigh-Sparrow parameter can be used to refine relative atom positions in defect images where atoms are closer than the Rayleigh limit of the HR-(S)TEM, reducing the necessity for full image simulations from large defect models.« less

Resonance interatomic energy in a Schwarzschild spacetime

NASA Astrophysics Data System (ADS)

Zhou, Wenting; Yu, Hongwei

2017-08-01

We study, in the Schwarzschild spacetime, the resonance interatomic energy (RIE) of two static identical atoms with an interatomic separation L along the radial direction and correlated by a symmetric/antisymmetric entangled state. The atoms are assumed to be coupled to massless scalar fields in the Boulware, Unruh, and Hartle-Hawking vacua, and approximate analytical results are obtained both at infinity and near the horizon. Our results show that at infinity, the RIE approaches that in a flat spacetime, while, near the horizon, they can deviate dramatically from each other. Besides, different from other atomic radiative properties such as the Lamb shift of a single atom or the interatomic energy between two uncorrelated atoms, which can be obviously affected by the thermal character of quantum fields, the RIE of two atoms in a symmetric/antisymmetric entangled state in the Boulware, Unruh, and Hartle-Hawking vacua are exactly the same as a result of the fact that the RIE of two such atoms depends only on the atomic self-reaction, i.e., it does not feel the vacuum fluctuations. This suggests that the RIE of two static atoms in a symmetric/antisymmetric entangled state outside a black hole is oblivious to the Hawking radiation, in contrast to those uncorrelated atoms.

Tailoring optical metamaterials to tune the atom-surface Casimir-Polder interaction.

PubMed

Chan, Eng Aik; Aljunid, Syed Abdullah; Adamo, Giorgio; Laliotis, Athanasios; Ducloy, Martial; Wilkowski, David

2018-02-01

Metamaterials are fascinating tools that can structure not only surface plasmons and electromagnetic waves but also electromagnetic vacuum fluctuations. The possibility of shaping the quantum vacuum is a powerful concept that ultimately allows engineering the interaction between macroscopic surfaces and quantum emitters such as atoms, molecules, or quantum dots. The long-range atom-surface interaction, known as Casimir-Polder interaction, is of fundamental importance in quantum electrodynamics but also attracts a significant interest for platforms that interface atoms with nanophotonic devices. We perform a spectroscopic selective reflection measurement of the Casimir-Polder interaction between a Cs(6P 3/2 ) atom and a nanostructured metallic planar metamaterial. We show that by engineering the near-field plasmonic resonances of the metamaterial, we can successfully tune the Casimir-Polder interaction, demonstrating both a strong enhancement and reduction with respect to its nonresonant value. We also show an enhancement of the atomic spontaneous emission rate due to its coupling with the evanescent modes of the nanostructure. Probing excited-state atoms next to nontrivial tailored surfaces is a rigorous test of quantum electrodynamics. Engineering Casimir-Polder interactions represents a significant step toward atom trapping in the extreme near field, possibly without the use of external fields.

Resolution Quality and Atom Positions in Sub-?ngstr?m Electron Microscopy

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

O'Keefe, Michael A.; Allard Jr, Lawrence Frederick; Blom, Douglas Allen

2005-01-01

John Cowley pioneered use of transmission electron microscopy (TEM) for high-resolution imaging and helped spur improvements in resolution that enabled researchers to pinpoint the positions of all but the lightest atoms within a crystal structure. Sub-{angstrom} capabilities allow imaging of even the lightest atoms. Initially achieved with software aberration correction (focal-series reconstruction of the specimen exit-surface wave), sub-{angstrom} imaging will become commonplace for next-generation electron microscopes with hardware-corrected lenses and monochromated electron beams. Currently, advanced HR-TEMs can image columns of light atoms (carbon, oxygen, nitrogen) in complex structures, including the lithium atoms present in battery materials. The ability to determinemore » whether an image peak represents one single atom (or atom column) instead of several depends on the resolution of the HR-(S)TEM. Rayleigh's resolution criterion, an accepted standard in optics, was derived as a means for judging when two image intensity peaks from two sources of light (stars) are distinguishable from a single source. Atom spacings closer than the Rayleigh limit have been resolved in HR-TEM, suggesting that it may be useful to consider other limits, such as the Sparrow resolution criterion. From the viewpoint of the materials scientist, it is important to be able to use the image to determine whether an image feature represents one or more atoms (resolution), and where the atoms (or atom columns) are positioned relative to one another (resolution quality). When atoms and the corresponding image peaks are separated by more than the Rayleigh limit of the HR-(S)TEM, it is possible to adjust imaging parameters so that relative peak positions in the image correspond to relative atom positions in the specimen. When atoms are closer than the Rayleigh limit, we must find the relationship of the peak position to the atom position by peak fitting or, if we have a suitable model, by image simulation.« less

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.

The electronegativity equalization method fused with molecular mechanics: a fluctuating charge and flexible body potential function for [Emim][Gly] ionic liquids.

PubMed

Wu, Yang; Li, Yao; Hu, Na; Hong, Mei

2014-02-14

Recently, experimental and theoretical studies on amino acid ionic liquid (AAIL) systems have attracted much attention. A transferable intermolecular potential approach that includes fluctuating charges and a flexible body based on a combination of the electronegativity equalization method and molecular mechanics (EEM/MM), and its application to an AAIL system containing 1-ethyl-3-methylimidazolium ([Emim](+)) and glycine ([Gly](-)) are explored and tested in this study. A consistent integration of EEM with MM requires the input of the EEM charges of all atoms into the MM intermolecular electrostatic interaction term. Compared with ionic liquid (IL) force fields, the EEM/MM model has an outstanding feature: the EEM/MM model not only presents the electrostatic interaction of atoms and their changes in response to different ambient environments but also introduces "the H-bond interaction region" in which a new parameter kHB(RHB) is used to describe the electrostatic interaction of hydrogen atoms in [Emim](+) and oxygen atoms in [Gly](-), which can form hydrogen bonds. The EEM/MM model gives quite accurate predictions for gas-phase state properties of [Emim](+), [Gly](-), and ion pairs, such as optimized geometries, dipole moments, vibrational frequencies, and cluster interaction energies. Due to its explicit description of charges and hydrogen bonds, the EEM/MM model also performs well for the liquid-phase properties of [Emim][Gly] under ambient conditions. The calculated properties, such as density, heat of vaporization, the self-diffusion coefficient, and ionic conductivity, are fairly consistent with available experimental results.

Atom-bond electronegativity equalization method fused into molecular mechanics. I. A seven-site fluctuating charge and flexible body water potential function for water clusters.

PubMed

Yang, Zhong-Zhi; Wu, Yang; Zhao, Dong-Xia

2004-02-08

Recently, experimental and theoretical studies on the water system are very active and noticeable. A transferable intermolecular potential seven points approach including fluctuation charges and flexible body (ABEEM-7P) based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM), and its application to small water clusters are explored and tested in this paper. The consistent combination of ABEEM and molecular mechanics (MM) is to take the ABEEM charges of atoms, bonds, and lone-pair electrons into the intermolecular electrostatic interaction term in molecular mechanics. To examine the charge transfer we have used two models coming from the charge constraint types: one is a charge neutrality constraint on whole water system and the other is on each water molecule. Compared with previous water force fields, the ABEEM-7P model has two characters: (1) the ABEEM-7P model not only presents the electrostatic interaction of atoms, bonds and lone-pair electrons and their changing in respond to different ambient environment but also introduces "the hydrogen bond interaction region" in which a new parameter k(lp,H)(R(lp,H)) is used to describe the electrostatic interaction of the lone-pair electron and the hydrogen atom which can form the hydrogen bond; (2) nonrigid but flexible water body permitting the vibration of the bond length and angle is allowed due to the combination of ABEEM and molecular mechanics, and for van der Waals interaction the ABEEM-7P model takes an all atom-atom interaction, i.e., oxygen-oxygen, hydrogen-hydrogen, oxygen-hydrogen interaction into account. The ABEEM-7P model based on ABEEM/MM gives quite accurate predictions for gas-phase state properties of the small water clusters (H(2)O)(n) (n=2-6), such as optimized geometries, monomer dipole moments, vibrational frequencies, and cluster interaction energies. Due to its explicit description of charges and the hydrogen bond, the ABEEM-7P model will be applied to discuss properties of liquid water, ice, aqueous solutions, and biological systems.

Direct demodulation method for heavy atom position determination in protein crystallography

NASA Astrophysics Data System (ADS)

Zhou, Liang; Liu, Zhong-Chuan; Liu, Peng; Dong, Yu-Hui

2013-01-01

The first step of phasing in any de novo protein structure determination using isomorphous replacement (IR) or anomalous scattering (AD) experiments is to find heavy atom positions. Traditionally, heavy atom positions can be solved by inspecting the difference Patterson maps. Due to the weak signals in isomorphous or anomalous differences and the noisy background in the Patterson map, the search for heavy atoms may become difficult. Here, the direct demodulation (DD) method is applied to the difference Patterson maps to reduce the noisy backgrounds and sharpen the signal peaks. The real space Patterson search by using these optimized maps can locate the heavy atom positions more accurately. It is anticipated that the direct demodulation method can assist in heavy atom position determination and facilitate the de novo structure determination of proteins.

Optimal control of complex atomic quantum systems

PubMed Central

van Frank, S.; Bonneau, M.; Schmiedmayer, J.; Hild, S.; Gross, C.; Cheneau, M.; Bloch, I.; Pichler, T.; Negretti, A.; Calarco, T.; Montangero, S.

2016-01-01

Quantum technologies will ultimately require manipulating many-body quantum systems with high precision. Cold atom experiments represent a stepping stone in that direction: a high degree of control has been achieved on systems of increasing complexity. However, this control is still sub-optimal. In many scenarios, achieving a fast transformation is crucial to fight against decoherence and imperfection effects. Optimal control theory is believed to be the ideal candidate to bridge the gap between early stage proof-of-principle demonstrations and experimental protocols suitable for practical applications. Indeed, it can engineer protocols at the quantum speed limit – the fastest achievable timescale of the transformation. Here, we demonstrate such potential by computing theoretically and verifying experimentally the optimal transformations in two very different interacting systems: the coherent manipulation of motional states of an atomic Bose-Einstein condensate and the crossing of a quantum phase transition in small systems of cold atoms in optical lattices. We also show that such processes are robust with respect to perturbations, including temperature and atom number fluctuations. PMID:27725688

Optimal control of complex atomic quantum systems.

PubMed

van Frank, S; Bonneau, M; Schmiedmayer, J; Hild, S; Gross, C; Cheneau, M; Bloch, I; Pichler, T; Negretti, A; Calarco, T; Montangero, S

2016-10-11

Quantum technologies will ultimately require manipulating many-body quantum systems with high precision. Cold atom experiments represent a stepping stone in that direction: a high degree of control has been achieved on systems of increasing complexity. However, this control is still sub-optimal. In many scenarios, achieving a fast transformation is crucial to fight against decoherence and imperfection effects. Optimal control theory is believed to be the ideal candidate to bridge the gap between early stage proof-of-principle demonstrations and experimental protocols suitable for practical applications. Indeed, it can engineer protocols at the quantum speed limit - the fastest achievable timescale of the transformation. Here, we demonstrate such potential by computing theoretically and verifying experimentally the optimal transformations in two very different interacting systems: the coherent manipulation of motional states of an atomic Bose-Einstein condensate and the crossing of a quantum phase transition in small systems of cold atoms in optical lattices. We also show that such processes are robust with respect to perturbations, including temperature and atom number fluctuations.

Estimation of chirp rates of music-adapted prolate spheroidal atoms using reassignment

NASA Astrophysics Data System (ADS)

Mesz, Bruno; Serrano, Eduardo

2007-09-01

We introduce a modified Matching Pursuit algorithm for estimating frequency and frequency slope of FM-modulated music signals. The use of Matching Pursuit with constant frequency atoms provides coarse estimates which could be improved with chirped atoms, more suited in principle to this kind of signals. Application of the reassignment method is suggested by its good localization properties for chirps. We start considering a family of atoms generated by modulation and scaling of a prolate spheroidal wave function. These functions are concentrated in frequency on intervals of a semitone centered at the frequencies of the well-tempered scale. At each stage of the pursuit, we search the atom most correlated with the signal. We then consider the spectral peaks at each frame of the spectrogram and calculate a modified frequency and frequency slope using the derivatives of the reassignment operators; this is then used to estimate the parameters of a cubic interpolation polynomial that models local pitch fluctuations. We apply the method both to synthetic and music signals.

The influence of cavitation in the breakup of liquid free jets

NASA Astrophysics Data System (ADS)

Bode, Juergen

1991-03-01

The interaction between a diesel injection nozzle flow and the atomizing jet was investigated over a wide range of Reynolds numbers. If the pressure gradient towards the centerline of the injection nozzle, generated by the curved streamlines, becomes too large, cavitation occurs at the inlet corner. The cavitation region grows in length and boundary surface with increasing Reynolds number. The instability of the reentry flow causes unsteady fluctuations of the cavitation which influences the breakup of the liquid jet, whereby liquid films are generated which take off from the jet. Cavitation amplifies the mechanism of the atomization, based on the interaction between the jet and surrounding gas. The influence of the cavitation on the atomization is restricted to the region directly behind the nozzle exit. The injection pressure and the temperature of the gas hardly affect the atomization. The jet angle depends mainly on the density of the surrounding gas.

The role of Gouy phase on the mechanical effects of Laguerre-Gaussian light interacting with atoms

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

Lembessis, V. E., E-mail: vlempesis@ksu.edu.sa; Babiker, M.; Ellinas, D.

2016-06-10

We consider the case of Laguerre-Gaussian (LG) light with high values of radial index, p, and/or winding number l, focussing on the effects of the Gouy phase together with other phase contributions due to the curvature in a Laguerre Gaussian beam when it interacts with atoms at near resonance. We show here that these phase anomalies amount to a significant reduction of the axial wavevector and thus lead to additional contributions to the phase gradient in the vicinity of the focus plane. In consequence, the axial recoil effects due to the stimulated emission and absorption of light by the atommore » become smaller. This has important effects on the dissipative axial forces acting on the atom, on the momentum fluctuations associated with the photon absorption and stimulated emission and on diffraction of atoms through light masks created by LG beams.« less

Detecting the Curvature of de Sitter Universe with Two Entangled Atoms

NASA Astrophysics Data System (ADS)

Tian, Zehua; Wang, Jieci; Jing, Jiliang; Dragan, Andrzej

2016-10-01

Casimir-Polder interaction arises from the vacuum fluctuations of quantum field that depend on spacetime curvature and thus is spacetime-dependent. Here we show how to use the resonance Casimir-Polder interaction (RCPI) between two entangled atoms to detect spacetime curvature. We find that the RCPI of two static entangled atoms in the de Sitter-invariant vacuum depends on the de Sitter spacetime curvature relevant to the temperature felt by the static observer. It is characterized by a 1/L2 power law decay when beyond a characteristic length scale associated to the breakdown of a local inertial description of the two-atom system. However, the RCPI of the same setup embedded in a thermal bath in the Minkowski universe is temperature-independent and is always characterized by a 1/L power law decay. Therefore, although a single static atom in the de Sitter-invariant vacuum responds as if it were bathed in thermal radiation in a Minkowski universe, using the distinct difference between RCPI of two entangled atoms one can in principle distinguish these two universes.

Detecting the Curvature of de Sitter Universe with Two Entangled Atoms.

PubMed

Tian, Zehua; Wang, Jieci; Jing, Jiliang; Dragan, Andrzej

2016-10-12

Casimir-Polder interaction arises from the vacuum fluctuations of quantum field that depend on spacetime curvature and thus is spacetime-dependent. Here we show how to use the resonance Casimir-Polder interaction (RCPI) between two entangled atoms to detect spacetime curvature. We find that the RCPI of two static entangled atoms in the de Sitter-invariant vacuum depends on the de Sitter spacetime curvature relevant to the temperature felt by the static observer. It is characterized by a 1/L 2 power law decay when beyond a characteristic length scale associated to the breakdown of a local inertial description of the two-atom system. However, the RCPI of the same setup embedded in a thermal bath in the Minkowski universe is temperature-independent and is always characterized by a 1/L power law decay. Therefore, although a single static atom in the de Sitter-invariant vacuum responds as if it were bathed in thermal radiation in a Minkowski universe, using the distinct difference between RCPI of two entangled atoms one can in principle distinguish these two universes.

Detecting the Curvature of de Sitter Universe with Two Entangled Atoms

PubMed Central

Tian, Zehua; Wang, Jieci; Jing, Jiliang; Dragan, Andrzej

2016-01-01

Casimir-Polder interaction arises from the vacuum fluctuations of quantum field that depend on spacetime curvature and thus is spacetime-dependent. Here we show how to use the resonance Casimir-Polder interaction (RCPI) between two entangled atoms to detect spacetime curvature. We find that the RCPI of two static entangled atoms in the de Sitter-invariant vacuum depends on the de Sitter spacetime curvature relevant to the temperature felt by the static observer. It is characterized by a 1/L2 power law decay when beyond a characteristic length scale associated to the breakdown of a local inertial description of the two-atom system. However, the RCPI of the same setup embedded in a thermal bath in the Minkowski universe is temperature-independent and is always characterized by a 1/L power law decay. Therefore, although a single static atom in the de Sitter-invariant vacuum responds as if it were bathed in thermal radiation in a Minkowski universe, using the distinct difference between RCPI of two entangled atoms one can in principle distinguish these two universes. PMID:27731419

Matter-wave dark solitons: stochastic versus analytical results.

PubMed

Cockburn, S P; Nistazakis, H E; Horikis, T P; Kevrekidis, P G; Proukakis, N P; Frantzeskakis, D J

2010-04-30

The dynamics of dark matter-wave solitons in elongated atomic condensates are discussed at finite temperatures. Simulations with the stochastic Gross-Pitaevskii equation reveal a noticeable, experimentally observable spread in individual soliton trajectories, attributed to inherent fluctuations in both phase and density of the underlying medium. Averaging over a number of such trajectories (as done in experiments) washes out such background fluctuations, revealing a well-defined temperature-dependent temporal growth in the oscillation amplitude. The average soliton dynamics is well captured by the simpler dissipative Gross-Pitaevskii equation, both numerically and via an analytically derived equation for the soliton center based on perturbation theory for dark solitons.

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.

Nature of the transition between a ferromagnetic metal and a spin-glass insulator in pyrochlore molybdates.

PubMed

Hanasaki, N; Watanabe, K; Ohtsuka, T; Kézsmárki, I; Iguchi, S; Miyasaka, S; Tokura, Y

2007-08-24

The metal-insulator transition has been investigated for pyrochlore molybdates R(2)Mo(2)O(7) with nonmagnetic rare-earth ions R. The dynamical scaling analysis of ac susceptibility reveals that the geometrical frustration causes the atomic spin-glass state. The reentrant spin-glass phase exists below the ferromagnetic transition. The electronic specific heat is enhanced as compared to the band calculation result, perhaps due to the orbital fluctuation in the half-metallic ferromagnetic state. The large specific heat is rather reduced upon the transition, likely because the short-range antiferromagnetic fluctuation shrinks the Fermi surface.

Effect of gold nanoparticle on stability of the DNA molecule: A study of molecular dynamics simulation.

PubMed

Izanloo, Cobra

2017-09-02

An understanding of the mechanism of DNA interactions with gold nanoparticles is useful in today medicine applications. We have performed a molecular dynamics simulation on a B-DNA duplex (CCTCAGGCCTCC) in the vicinity of a gold nanoparticle with a truncated octahedron structure composed of 201 gold atoms (diameter ∼1.8 nm) to investigate gold nanoparticle (GNP) effects on the stability of DNA. During simulation, the nanoparticle is closed to DNA and phosphate groups direct the particles into the major grooves of the DNA molecule. Because of peeling and untwisting states that are occur at end of DNA, the nucleotide base lies flat on the surface of GNP. The configuration entropy is estimated using the covariance matrix of atom-positional fluctuations for different bases. The results show that when a gold nanoparticle has interaction with DNA, entropy increases. The results of conformational energy and the hydrogen bond numbers for DNA indicated that DNA becomes unstable in the vicinity of a gold nanoparticle. The radial distribution function was calculated for water hydrogen-phosphate oxygen pairs. Almost for all nucleotide, the presence of a nanoparticle around DNA caused water molecules to be released from the DNA duplex and cations were close to the DNA.

Adequacy of Si:P chains as Fermi-Hubbard simulators

NASA Astrophysics Data System (ADS)

Dusko, Amintor; Delgado, Alain; Saraiva, André; Koiller, Belita

2018-01-01

The challenge of simulating many-body models with analogue physical systems requires both experimental precision and very low operational temperatures. Atomically precise placement of dopants in Si permits the construction of nanowires by design. We investigate the suitability of these interacting electron systems as simulators of a fermionic extended Hubbard model on demand. We describe the single-particle wavefunctions as a linear combination of dopant orbitals (LCDO). The electronic states are calculated within configuration interaction (CI). Due to the peculiar oscillatory behavior of each basis orbital, properties of these chains are strongly affected by the interdonor distance R0, in a non-monotonic way. Ground state (T = 0 K) properties such as charge and spin correlations are shown to remain robust under temperatures up to 4 K for specific values of R0. The robustness of the model against disorder is also tested, allowing some fluctuation of the placement site around the target position. We suggest that finite donor chains in Si may serve as an analog simulator for strongly correlated model Hamiltonians. This simulator is, in many ways, complementary to those based on cold atoms in optical lattices—the trade-off between the tunability achievable in the latter and the survival of correlation at higher operation temperatures for the former suggests that both technologies are applicable for different regimes.

Kohn's theorem in a superfluid Fermi gas with a Feshbach resonance

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

Ohashi, Y.

2004-12-01

We investigate the dipole mode in a superfluid gas of Fermi atoms trapped in a harmonic potential. According to Kohn's theorem, the frequency of this collective mode is not affected by an interaction between the atoms and is always equal to the trap frequency. This remarkable property, however, does not necessarily hold in an approximate theory. We explicitly prove that the Hartree-Fock-Bogoliubov generalized random phase approximation (HFB-GRPA), including a coupling between fluctuations in the density and Cooper channels, is consistent with both Kohn's theorem as well as Goldstone's theorem. This proof can be immediately extended to the strong-coupling superfluid theorymore » developed by Nozieres and Schmitt-Rink (NSR), where the effect of superfluid fluctuations is included within the Gaussian level. As a result, the NSR-GRPA formalism can be used to study collective modes in the BCS-BEC crossover region in a manner which is consistent with Kohn's theorem. We also include the effect of a Feshbach resonance and a condensate of the associated molecular bound states. A detailed discussion is given of the unusual nature of the Kohn mode eigenfunctions in a Fermi superfluid, in the presence and absence of a Feshbach resonance. When the molecular bosons feel a different trap frequency from the Fermi atoms, the dipole frequency is shown to depend on the strength of effective interaction associated with the Feshbach resonance.« less

Angular-split/temporal-delay approach to ultrafast protein dynamics at XFELs.

PubMed

Ren, Zhong; Yang, Xiaojing

2016-07-01

X-ray crystallography promises direct insights into electron-density changes that lead to and arise from structural changes such as electron and proton transfer and the formation, rupture and isomerization of chemical bonds. The ultrashort pulses of hard X-rays produced by free-electron lasers present an exciting opportunity for capturing ultrafast structural events in biological macromolecules within femtoseconds after photoexcitation. However, shot-to-shot fluctuations, which are inherent to the very process of self-amplified spontaneous emission (SASE) that generates the ultrashort X-ray pulses, are a major source of noise that may conceal signals from structural changes. Here, a new approach is proposed to angularly split a single SASE pulse and to produce a temporal delay of picoseconds between the split pulses. These split pulses will allow the probing of two distinct states before and after photoexcitation triggered by a laser pulse between the split X-ray pulses. The split pulses originate from a single SASE pulse and share many common properties; thus, noise arising from shot-to-shot fluctuations is self-canceling. The unambiguous interpretation of ultrafast structural changes would require diffraction data at atomic resolution, as these changes may or may not involve any atomic displacement. This approach, in combination with the strategy of serial crystallography, offers a solution to study ultrafast dynamics of light-initiated biochemical reactions or biological processes at atomic resolution.

Shock wave oscillation driven by turbulent boundary layer fluctuations

NASA Technical Reports Server (NTRS)

Plotkin, K. J.

1972-01-01

Pressure fluctuations due to the interaction of a shock wave with a turbulent boundary layer were investigated. A simple model is proposed in which the shock wave is convected from its mean position by velocity fluctuations in the turbulent boundary layer. Displacement of the shock is assumed limited by a linear restoring mechanism. Predictions of peak root mean square pressure fluctuation and spectral density are in excellent agreement with available experimental data.

Resonant paramagnetic enhancement of the thermal and zero-point Nyquist noise

NASA Astrophysics Data System (ADS)

França, H. M.; Santos, R. B. B.

1999-01-01

The interaction between a very thin macroscopic solenoid, and a single magnetic particle precessing in a external magnetic field B0, is described by taking into account the thermal and the zero-point fluctuations of stochastic electrodynamics. The inductor belongs to a RLC circuit without batteries and the random motion of the magnetic dipole generates in the solenoid a fluctuating current Idip( t), and a fluctuating voltage εdip( t), with spectral distribution quite different from the Nyquist noise. We show that the mean square value < Idip2> presents an enormous variation when the frequency of precession approaches the frequency of the circuit, but it is still much smaller than the Nyquist current in the circuit. However, we also show that < Idip2> can reach measurable values if the inductor is interacting with a macroscopic sample of magnetic particles (atoms or nuclei) which are close enough to its coils.

Temporal fluctuation of the lead level in the cord blood of neonates in Taipei.

PubMed

Hwang, Y H; Wang, J D

1990-01-01

From August 1985 to September 1987, 9,502 cord blood samples were obtained from the Taipei Municipal Maternal and Child Hospital. A total of 205 cord blood samples chosen randomly from newborns without parental exposure to lead were analyzed by flameless atomic absorption spectrophotometry. The average blood lead level was .36 +/- .11 mumol/l (7.48 +/- 2.25 micrograms/dl). A similar analysis was performed on samples obtained from 160 newborns whose fathers had occupational lead exposure. In both groups, the average concentration of lead in cord blood in the summer was statistically greater than that in the winter. Air lead and total amount of lead in gasoline consumed in Taipei appeared to be associated with this seasonal fluctuation in the average lead level of cord blood. After considering alternative sources, we conclude that the seasonal fluctuation of cord blood lead is probably influenced by air lead produced from the combustion of gasoline.

Temperature measurement of a dust particle in a RF plasma GEC reference cell

NASA Astrophysics Data System (ADS)

Kong, Jie; Qiao, Ke; Matthews, Lorin S.; Hyde, Truell W.

2016-10-01

The thermal motion of a dust particle levitated in a plasma chamber is similar to that described by Brownian motion in many ways. The primary difference between a dust particle in a plasma system and a free Brownian particle is that in addition to the random collisions between the dust particle and the neutral gas atoms, there are electric field fluctuations, dust charge fluctuations, and correlated motions from the unwanted continuous signals originating within the plasma system itself. This last contribution does not include random motion and is therefore separable from the random motion in a `normal' temperature measurement. In this paper, we discuss how to separate random and coherent motions of a dust particle confined in a glass box in a Gaseous Electronic Conference (GEC) radio-frequency (RF) reference cell employing experimentally determined dust particle fluctuation data analysed using the mean square displacement technique.

Specific heat and effects of strong pairing fluctuations in a superfluid Fermi atom gas in the BCS-BEC crossover region

NASA Astrophysics Data System (ADS)

van Wyk, Pieter; Inotani, Daisuke; Ohashi, Yoji

2018-03-01

We theoretically investigate the specific heat at constant volume C V in the BCS(Bardeen-Cooper-Schrieffer)-BEC(Bose-Einstein-condensation)-crossover regime of an ultracold Fermi gas, below the superfluid phase transition temperature T c. Within the strong-coupling framework developed by Nozières and Schmitt-Rink, we show that the temperature dependence of C V drastically changes as one passes through the crossover region, and is sensitive to strong fluctuations in the Cooper channel near the unitarity limit. We also compare our results to a recent experiment on a 6Li unitary Fermi gas. Since fluctuation effects are a crucial key in the BCS-BEC-crossover phenomenon, our results would be helpful in considering how the fermionic BCS superfluid changes into BEC with increasing the interaction strength, from the viewpoint of specific heat.

Entropy in bimolecular simulations: A comprehensive review of atomic fluctuations-based methods.

PubMed

Kassem, Summer; Ahmed, Marawan; El-Sheikh, Salah; Barakat, Khaled H

2015-11-01

Entropy of binding constitutes a major, and in many cases a detrimental, component of the binding affinity in biomolecular interactions. While the enthalpic part of the binding free energy is easier to calculate, estimating the entropy of binding is further more complicated. A precise evaluation of entropy requires a comprehensive exploration of the complete phase space of the interacting entities. As this task is extremely hard to accomplish in the context of conventional molecular simulations, calculating entropy has involved many approximations. Most of these golden standard methods focused on developing a reliable estimation of the conformational part of the entropy. Here, we review these methods with a particular emphasis on the different techniques that extract entropy from atomic fluctuations. The theoretical formalisms behind each method is explained highlighting its strengths as well as its limitations, followed by a description of a number of case studies for each method. We hope that this brief, yet comprehensive, review provides a useful tool to understand these methods and realize the practical issues that may arise in such calculations. Copyright © 2015 Elsevier Inc. All rights reserved.

Non-Markovianity in atom-surface dispersion forces

DOE PAGES

Intravaia, F.; Behunin, R. O.; Henkel, C.; ...

2016-10-18

Here, we discuss the failure of the Markov approximation in the description of atom-surface fluctuation-induced interactions, both in equilibrium (Casimir-Polder forces) and out of equilibrium (quantum friction). Using general theoretical arguments, we show that the Markov approximation can lead to erroneous predictions of such phenomena with regard to both strength and functional dependencies on system parameters. Particularly, we show that the long-time power-law tails of two-time dipole correlations and their corresponding low-frequency behavior, neglected in the Markovian limit, affect the prediction of the force. These findings highlight the importance of non-Markovian effects in dispersion interactions.

Quantum effect on the nucleation of plastic deformation carriers and destruction in crystals

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

Khon, Yury A., E-mail: khon@ispms.tsc.ru; Kaminskii, Petr P., E-mail: ppk@ispms.tsc.ru

2015-10-27

New concepts on the irreversible crystal deformation as a structure transformation caused by a change in interatomic interactions at fluctuations of the electron density under loading are described. The change in interatomic interactions lead to the excitation of dynamical displacements of atoms. A model and a theory of a deformable pristine crystal taking into account the excitation of thermally activated and dynamical displacements of atoms are suggested. New mechanisms of the nucleation of plastic deformation carriers and destruction in pristine crystals at the real value of the deforming stress are studied.

Non-Markovianity in atom-surface dispersion forces

NASA Astrophysics Data System (ADS)

Intravaia, F.; Behunin, R. O.; Henkel, C.; Busch, K.; Dalvit, D. A. R.

2016-10-01

We discuss the failure of the Markov approximation in the description of atom-surface fluctuation-induced interactions, both in equilibrium (Casimir-Polder forces) and out of equilibrium (quantum friction). Using general theoretical arguments, we show that the Markov approximation can lead to erroneous predictions of such phenomena with regard to both strength and functional dependencies on system parameters. In particular, we show that the long-time power-law tails of two-time dipole correlations and their corresponding low-frequency behavior, neglected in the Markovian limit, affect the prediction of the force. Our findings highlight the importance of non-Markovian effects in dispersion interactions.

Steady state quantum discord for circularly accelerated atoms

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

Hu, Jiawei, E-mail: hujiawei@nbu.edu.cn; Yu, Hongwei, E-mail: hwyu@hunnu.edu.cn; Synergetic Innovation Center for Quantum Effects and Applications, Hunan Normal University, Changsha, Hunan 410081

2015-12-15

We study, in the framework of open quantum systems, the dynamics of quantum entanglement and quantum discord of two mutually independent circularly accelerated two-level atoms in interaction with a bath of fluctuating massless scalar fields in the Minkowski vacuum. We assume that the two atoms rotate synchronically with their separation perpendicular to the rotating plane. The time evolution of the quantum entanglement and quantum discord of the two-atom system is investigated. For a maximally entangled initial state, the entanglement measured by concurrence diminishes to zero within a finite time, while the quantum discord can either decrease monotonically to an asymptoticmore » value or diminish to zero at first and then followed by a revival depending on whether the initial state is antisymmetric or symmetric. When both of the two atoms are initially excited, the generation of quantum entanglement shows a delayed feature, while quantum discord is created immediately. Remarkably, the quantum discord for such a circularly accelerated two-atom system takes a nonvanishing value in the steady state, and this is distinct from what happens in both the linear acceleration case and the case of static atoms immersed in a thermal bath.« less

Ionization equilibrium at the transition from valence-band to acceptor-band migration of holes in boron-doped diamond

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

Poklonski, N. A., E-mail: poklonski@bsu.by; Vyrko, S. A.; Poklonskaya, O. N.

A quasi-classical model of ionization equilibrium in the p-type diamond between hydrogen-like acceptors (boron atoms which substitute carbon atoms in the crystal lattice) and holes in the valence band (v-band) is proposed. The model is applicable on the insulator side of the insulator–metal concentration phase transition (Mott transition) in p-Dia:B crystals. The densities of the spatial distributions of impurity atoms (acceptors and donors) and of holes in the crystal are considered to be Poissonian, and the fluctuations of their electrostatic potential energy are considered to be Gaussian. The model accounts for the decrease in thermal ionization energy of boron atomsmore » with increasing concentration, as well as for electrostatic fluctuations due to the Coulomb interaction limited to two nearest point charges (impurity ions and holes). The mobility edge of holes in the v-band is assumed to be equal to the sum of the threshold energy for diffusion percolation and the exchange energy of the holes. On the basis of the virial theorem, the temperature T{sub j} is determined, in the vicinity of which the dc band-like conductivity of holes in the v-band is approximately equal to the hopping conductivity of holes via the boron atoms. For compensation ratio (hydrogen-like donor to acceptor concentration ratio) K ≈ 0.15 and temperature T{sub j}, the concentration of “free” holes in the v-band and their jumping (turbulent) drift mobility are calculated. Dependence of the differential energy of thermal ionization of boron atoms (at the temperature 3T{sub j}/2) as a function of their concentration N is calculated. The estimates of the extrapolated into the temperature region close to T{sub j} hopping drift mobility of holes hopping from the boron atoms in the charge states (0) to the boron atoms in the charge states (−1) are given. Calculations based on the model show good agreement with electrical conductivity and Hall effect measurements for p-type diamond with boron atom concentrations in the range from 3 × 10{sup 17} to 3 × 10{sup 20 }cm{sup −3}, i.e., up to the Mott transition. The model uses no fitting parameters.« less

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

Stochastic characteristics and Second Law violations of atomic fluids in Couette flow

NASA Astrophysics Data System (ADS)

Raghavan, Bharath V.; Karimi, Pouyan; Ostoja-Starzewski, Martin

2018-04-01

Using Non-equilibrium Molecular Dynamics (NEMD) simulations, we study the statistical properties of an atomic fluid undergoing planar Couette flow, in which particles interact via a Lennard-Jones potential. We draw a connection between local density contrast and temporal fluctuations in the shear stress, which arise naturally through the equivalence between the dissipation function and entropy production according to the fluctuation theorem. We focus on the shear stress and the spatio-temporal density fluctuations and study the autocorrelations and spectral densities of the shear stress. The bispectral density of the shear stress is used to measure the degree of departure from a Gaussian model and the degree of nonlinearity induced in the system owing to the applied strain rate. More evidence is provided by the probability density function of the shear stress. We use the Information Theory to account for the departure from Gaussian statistics and to develop a more general probability distribution function that captures this broad range of effects. By accounting for negative shear stress increments, we show how this distribution preserves the violations of the Second Law of Thermodynamics observed in planar Couette flow of atomic fluids, and also how it captures the non-Gaussian nature of the system by allowing for non-zero higher moments. We also demonstrate how the temperature affects the band-width of the shear-stress and how the density affects its Power Spectral Density, thus determining the conditions under which the shear-stress acts is a narrow-band or wide-band random process. We show that changes in the statistical characteristics of the parameters of interest occur at a critical strain rate at which an ordering transition occurs in the fluid causing shear thinning and affecting its stability. A critical strain rate of this kind is also predicted by the Loose-Hess stability criterion.

Directed Atom-by-Atom Assembly of Dopants in Silicon.

PubMed

Hudak, Bethany M; Song, Jiaming; Sims, Hunter; Troparevsky, M Claudia; Humble, Travis S; Pantelides, Sokrates T; Snijders, Paul C; Lupini, Andrew R

2018-05-17

The ability to controllably position single atoms inside materials is key for the ultimate fabrication of devices with functionalities governed by atomic-scale properties. Single bismuth dopant atoms in silicon provide an ideal case study in view of proposals for single-dopant quantum bits. However, bismuth is the least soluble pnictogen in silicon, meaning that the dopant atoms tend to migrate out of position during sample growth. Here, we demonstrate epitaxial growth of thin silicon films doped with bismuth. We use atomic-resolution aberration-corrected imaging to view the as-grown dopant distribution and then to controllably position single dopants inside the film. Atomic-scale quantum-mechanical calculations corroborate the experimental findings. These results indicate that the scanning transmission electron microscope is of particular interest for assembling functional materials atom-by-atom because it offers both real-time monitoring and atom manipulation. We envision electron-beam manipulation of atoms inside materials as an achievable route to controllable assembly of structures of individual dopants.

Site-selective substitutional doping with atomic precision on stepped Al (111) surface by single-atom manipulation

PubMed Central

2014-01-01

In fabrication of nano- and quantum devices, it is sometimes critical to position individual dopants at certain sites precisely to obtain the specific or enhanced functionalities. With first-principles simulations, we propose a method for substitutional doping of individual atom at a certain position on a stepped metal surface by single-atom manipulation. A selected atom at the step of Al (111) surface could be extracted vertically with an Al trimer-apex tip, and then the dopant atom will be positioned to this site. The details of the entire process including potential energy curves are given, which suggests the reliability of the proposed single-atom doping method. PMID:24899871

Site-selective substitutional doping with atomic precision on stepped Al (111) surface by single-atom manipulation.

PubMed

Chen, Chang; Zhang, Jinhu; Dong, Guofeng; Shao, Hezhu; Ning, Bo-Yuan; Zhao, Li; Ning, Xi-Jing; Zhuang, Jun

2014-01-01

In fabrication of nano- and quantum devices, it is sometimes critical to position individual dopants at certain sites precisely to obtain the specific or enhanced functionalities. With first-principles simulations, we propose a method for substitutional doping of individual atom at a certain position on a stepped metal surface by single-atom manipulation. A selected atom at the step of Al (111) surface could be extracted vertically with an Al trimer-apex tip, and then the dopant atom will be positioned to this site. The details of the entire process including potential energy curves are given, which suggests the reliability of the proposed single-atom doping method.

Improving the phase response of an atom interferometer by means of temporal pulse shaping

NASA Astrophysics Data System (ADS)

Fang, Bess; Mielec, Nicolas; Savoie, Denis; Altorio, Matteo; Landragin, Arnaud; Geiger, Remi

2018-02-01

We study theoretically and experimentally the influence of temporally shaping the light pulses in an atom interferometer, with a focus on the phase response of the interferometer. We show that smooth light pulse shapes allow rejecting high frequency phase fluctuations (above the Rabi frequency) and thus relax the requirements on the phase noise or frequency noise of the interrogation lasers driving the interferometer. The light pulse shape is also shown to modify the scale factor of the interferometer, which has to be taken into account in the evaluation of its accuracy budget. We discuss the trade-offs to operate when choosing a particular pulse shape, by taking into account phase noise rejection, velocity selectivity, and applicability to large momentum transfer atom interferometry.

Note: Directly measuring the direct digital synthesizer frequency chirp-rate for an atom interferometer

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

Tao, Juan-Juan; Zhou, Min-Kang, E-mail: zkhu@hust.edu.cn, E-mail: zmk@hust.edu.cn; Zhang, Qiao-Zhen

2015-09-15

During gravity measurements with Raman type atom interferometry, the frequency of the laser used to drive Raman transition is scanned by chirping the frequency of a direct digital synthesizer (DDS), and the local gravity is determined by precisely measuring the chip rate α of DDS. We present an effective method that can directly evaluate the frequency chirp rate stability of our DDS. By mixing a pair of synchronous linear sweeping signals, the chirp rate fluctuation is precisely measured with a frequency counter. The measurement result shows that the relative α instability can reach 5.7 × 10{sup −11} in 1 s,more » which is neglectable in a 10{sup −9} g level atom interferometry gravimeter.« less

Quantum friction in arbitrarily directed motion

DOE PAGES

Klatt, J.; Farías, M. Belen; Dalvit, D. A. R.; ...

2017-05-30

In quantum friction, the electromagnetic fluctuation-induced frictional force decelerating an atom which moves past a macroscopic dielectric body, has so far eluded experimental evidence despite more than three decades of theoretical studies. Inspired by the recent finding that dynamical corrections to such an atom's internal dynamics are enhanced by one order of magnitude for vertical motion—compared with the paradigmatic setup of parallel motion—here we generalize quantum friction calculations to arbitrary angles between the atom's direction of motion and the surface in front of which it moves. Motivated by the disagreement between quantum friction calculations based on Markovian quantum master equationsmore » and time-dependent perturbation theory, we carry out our derivations of the quantum frictional force for arbitrary angles by employing both methods and compare them.« less

Atomic structures of Ruddlesden-Popper faults in LaCoO3/SrRuO3 multilayer thin films induced by epitaxial strain

NASA Astrophysics Data System (ADS)

Wang, Wei; Zhang, Hui; Shen, Xi; Guan, Xiangxiang; Yao, Yuan; Wang, Yanguo; Sun, Jirong; Yu, Richeng

2018-05-01

In this paper, scanning transmission electron microscopy is used to study the microstructures of the defects in LaCoO3/SrRuO3 multilayer films grown on the SrTiO3 substrates, and these films have different thickness of SrRuO3 (SRO) layers. Several types of Ruddlesden-Popper (R.P.) faults at an atomic level are found, and these chemical composition fluctuations in the growth process are induced by strain fields originating from the film-film and film-substrate lattice mismatches. Furthermore, we propose four types of structural models based on the atomic arrangements of the R.P. planar faults, which severely affect the functional properties of the films.

Structural Studies of Amorphous Materials by Fluctuation Electron Microscopy

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

Treacy, Michael M. J.

Fluctuation Electron Microscopy (FEM) is a technique that examines the fluctuations in electron scattering across a uniformly thin amorphous sample. The statistics of the intensity fluctuations, mean and variance, reveal any underlying medium-range order present in the structure. The goals of this project were: (1) To determine the fundamentals of the scattering physics that gives rise to the variance signal in fluctuation electron microscopy (FEM); (2) To use these discoveries to find ways to quantify FEM; (3) To apply the FEM method to interesting and technologically important families of amorphous materials, particularly those with important applications in energy-related processes. Excellent progress was made in items (1) and (2). In stage (3) we did not examine the metamict zircons, as proposed. Instead, we examined films of polycrystalline and amorphous semi-conducting diamond. Significant accomplishments are: (1) A Reverse Monte Carlo procedure was successfully implemented to invert FEM data into a structural model. This is computer-intensive, but it demonstrated that diffraction and FEM data from amorphous silicon are most consistent with a paracrystallite model. This means that there is more diamond-like topology present in amorphous silicon than is predicted by the continuous random network model. (2) There is significant displacement decoherence arising in diffraction from amorphous silicon and carbon. The samples are being bombarded by the electron beam and atoms do not stay still while being irradiated – much more than was formerly understood. The atom motions cause the destructive and constructive interferences in the diffraction pattern to fluctuate with time, and it is the time-averaged speckle that is being measured. The variance is reduced by a factor m, 4 ≤ m ≤ 1000, relative to that predicted by kinematical scattering theory. (3) Speckle intensity obeys a gamma distribution, where the mean intensitymore » $$ \\overline{I}\\ $$ and m are the two parameters governing the shape of the gamma distribution profile. m is determined by the illumination spatial coherence, which is normally very high, and mostly by the displacement decoherence within the sample. (4) Amorphous materials are more affected by the electron beam than are crystalline materials. Different samples exhibit different disruptibility, as measured by the effective values of m that fit the data. (5) Understanding the origin of the displacement decoherence better should lead to efficient methods for computing the observed variance from amorphous materials.« less

Plasma Turbulence Imaging via Beam Emission Spectroscopy in the Core of the DIII-D Tokamak

NASA Astrophysics Data System (ADS)

McKee, George R.; Fonck, Raymond J.; Gupta, Deepak K.; Schlossberg, David J.; Shafer, Morgan W.; Boivin, Réjean L.; Solomon, Wayne

Beam Emission Spectroscopy (BES), a high-sensitivity, good spatial resolution imaging diagnostic system, has been deployed and recently upgraded and expanded at the DIII-D tokamak to better understand density fluctuations arising from plasma turbulence. The currently deployed system images density fluctuations over an approximately 5 × 7 cm region at the plasma mid-plane (radially scannable over 0.2 < r/a ≤ 1) with a 5 × 6 (radial × poloidal) grid of rectangular detection channels, with one microsecond time resolution. BES observes collisionally-induced, Doppler-shifted Dα fluorescence (λ = 652-655 nm) of injected deuterium neutral beam atoms. The diagnostic wavenumber sensitivity is approximately k⊥ < 2.5 cm-1, allowing measurement of longwavelength (k⊥ρI < 1) density fluctuations. The recent upgrade includes expanded fiber optics bundles, customdesigned high-transmission, sharp-edge interference filters, ultra fast collection optics, and enlarged photodiode detectors that together provide nearly an order of magnitude increase in sensitivity relative to an earlier generation BES system. The high sensitivity allows visualization of turbulence at normalized density fluctuation amplitudes of ‾n/n < 1%, typical of fluctuation levels in the core region. The imaging array allows for sampling over 2-3 turbulent eddy scale lengths, which captures the essential dynamics of eddy evolution, interaction and shearing.

Optimized atom position and coefficient coding for matching pursuit-based image compression.

PubMed

Shoa, Alireza; Shirani, Shahram

2009-12-01

In this paper, we propose a new encoding algorithm for matching pursuit image coding. We show that coding performance is improved when correlations between atom positions and atom coefficients are both used in encoding. We find the optimum tradeoff between efficient atom position coding and efficient atom coefficient coding and optimize the encoder parameters. Our proposed algorithm outperforms the existing coding algorithms designed for matching pursuit image coding. Additionally, we show that our algorithm results in better rate distortion performance than JPEG 2000 at low bit rates.

Modeling DNA bubble formation at the atomic scale

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

Beleva, V; Rasmussen, K. O.; Garcia, A. E.

We describe the fluctuations of double stranded DNA molecules using a minimalist Go model over a wide range of temperatures. Minimalist models allow us to describe, at the atomic level, the opening and formation of bubbles in DNA double helices. This model includes all the geometrical constraints in helix melting imposed by the 3D structure of the molecule. The DNA forms melted bubbles within double helices. These bubbles form and break as a function of time. The equilibrium average number of broken base pairs shows a sharp change as a function of T. We observe a temperature profile of sequencemore » dependent bubble formation similar to those measured by Zeng et al. Long nuclei acid molecules melt partially through the formations of bubbles. It is known that CG rich sequences melt at higher temperatures than AT rich sequences. The melting temperature, however, is not solely determined by the CG content, but by the sequence through base stacking and solvent interactions. Recently, models that incorporate the sequence and nonlinear dynamics of DNA double strands have shown that DNA exhibits a very rich dynamics. Recent extensions of the Bishop-Peyrard model show that fluctuations in the DNA structure lead to opening in localized regions, and that these regions in the DNA are associated with transcription initiation sites. 1D and 2D models of DNA may contain enough information about stacking and base pairing interactions, but lack the coupling between twisting, bending and base pair opening imposed by the double helical structure of DNA that all atom models easily describe. However, the complexity of the energy function used in all atom simulations (including solvent, ions, etc) does not allow for the description of DNA folding/unfolding events that occur in the microsecond time scale.« less

Homogenization of Doppler broadening in spin-noise spectroscopy

NASA Astrophysics Data System (ADS)

Petrov, M. Yu.; Ryzhov, I. I.; Smirnov, D. S.; Belyaev, L. Yu.; Potekhin, R. A.; Glazov, M. M.; Kulyasov, V. N.; Kozlov, G. G.; Aleksandrov, E. B.; Zapasskii, V. S.

2018-03-01

The spin-noise spectroscopy, being a nonperturbative linear optics tool, is still reputed to reveal a number of capabilities specific to nonlinear optics techniques. The effect of the Doppler broadening homogenization discovered in this work essentially widens these unique properties of spin-noise spectroscopy. We investigate spin noise of a classical system—cesium atoms vapor with admixture of buffer gas—by measuring the spin-induced Faraday rotation fluctuations in the region of D 2 line. The line, under our experimental conditions, is strongly inhomogeneously broadened due to the Doppler effect. Despite that, optical spectrum of the spin-noise power has the shape typical for the homogeneously broadened line with a dip at the line center. This fact is in stark contrast with the results of previous studies of inhomogeneous quantum dot ensembles and Doppler broadened atomic systems. In addition, the two-color spin-noise measurements have shown, in a highly spectacular way, that fluctuations of the Faraday rotation within the line are either correlated or anticorrelated depending on whether the two wavelengths lie on the same side or on different sides of the resonance. The experimental data are interpreted in the frame of the developed theoretical model which takes into account both kinetics and spin dynamics of Cs atoms. It is shown that the unexpected behavior of the Faraday rotation noise spectra and effective homogenization of the optical transition in the spin-noise measurements are related to smallness of the momentum relaxation time of the atoms as compared with their spin-relaxation time. Our findings demonstrate abilities of spin-noise spectroscopy for studying dynamic properties of inhomogeneously broadened ensembles of randomly moving spins.

Probability distribution functions for intermittent scrape-off layer plasma fluctuations

NASA Astrophysics Data System (ADS)

Theodorsen, A.; Garcia, O. E.

2018-03-01

A stochastic model for intermittent fluctuations in the scrape-off layer of magnetically confined plasmas has been constructed based on a super-position of uncorrelated pulses arriving according to a Poisson process. In the most common applications of the model, the pulse amplitudes are assumed exponentially distributed, supported by conditional averaging of large-amplitude fluctuations in experimental measurement data. This basic assumption has two potential limitations. First, statistical analysis of measurement data using conditional averaging only reveals the tail of the amplitude distribution to be exponentially distributed. Second, exponentially distributed amplitudes leads to a positive definite signal which cannot capture fluctuations in for example electric potential and radial velocity. Assuming pulse amplitudes which are not positive definite often make finding a closed form for the probability density function (PDF) difficult, even if the characteristic function remains relatively simple. Thus estimating model parameters requires an approach based on the characteristic function, not the PDF. In this contribution, the effect of changing the amplitude distribution on the moments, PDF and characteristic function of the process is investigated and a parameter estimation method using the empirical characteristic function is presented and tested on synthetically generated data. This proves valuable for describing intermittent fluctuations of all plasma parameters in the boundary region of magnetized plasmas.

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.

Kinetic-freezing and unfreezing of local-region fluctuations in a glass structure observed by heat capacity hysteresis

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

Aji, D. P. B.; Johari, G. P., E-mail: joharig@mcmaster.ca

Fluctuations confined to local regions in the structure of a glass are observed as the Johari-Goldstein (JG) relaxation. Properties of these regions and their atomic configuration are currently studied by relaxation techniques, by electron microscopy, and by high-energy X-ray scattering and extended x-ray absorption fine structure methods. One expects that these fluctuations (i) would kinetically freeze on cooling a glass, and the temperature coefficient of its enthalpy, dH/dT, would consequently show a gradual decrease with decrease in T, (ii) would kinetically unfreeze on heating the glass toward the glass-liquid transition temperature, T{sub g}, and dH/dT would gradually increase, and (iii)more » there would be a thermal hysteresis indicating the time and temperature dependence of the enthalpy. Since no such features have been found, thermodynamic consequences of these fluctuations are debated. After searching for these features in glasses of different types, we found it in one of the most stable metal alloy glasses of composition Pd{sub 40}Ni{sub 10}Cu{sub 30}P{sub 20}. On cooling from its T{sub g}, dH/dT decreased along a broad sigmoid-shape path as local-region fluctuations kinetically froze. On heating thereafter, dH/dT increased along a similar path as these fluctuations unfroze, and there is hysteresis in the cooling and heating paths, similar to that observed in the T{sub g}-endotherm range. After eliminating other interpretations, we conclude that local-region fluctuations seen as the JG relaxation in the non-equilibrium state of a glass contribute to its entropy, and we suggest conditions under which such fluctuations may be observed.« less

Kinetic-freezing and unfreezing of local-region fluctuations in a glass structure observed by heat capacity hysteresis.

PubMed

Aji, D P B; Johari, G P

2015-06-07

Fluctuations confined to local regions in the structure of a glass are observed as the Johari-Goldstein (JG) relaxation. Properties of these regions and their atomic configuration are currently studied by relaxation techniques, by electron microscopy, and by high-energy X-ray scattering and extended x-ray absorption fine structure methods. One expects that these fluctuations (i) would kinetically freeze on cooling a glass, and the temperature coefficient of its enthalpy, dH/dT, would consequently show a gradual decrease with decrease in T, (ii) would kinetically unfreeze on heating the glass toward the glass-liquid transition temperature, Tg, and dH/dT would gradually increase, and (iii) there would be a thermal hysteresis indicating the time and temperature dependence of the enthalpy. Since no such features have been found, thermodynamic consequences of these fluctuations are debated. After searching for these features in glasses of different types, we found it in one of the most stable metal alloy glasses of composition Pd40Ni10Cu30P20. On cooling from its Tg, dH/dT decreased along a broad sigmoid-shape path as local-region fluctuations kinetically froze. On heating thereafter, dH/dT increased along a similar path as these fluctuations unfroze, and there is hysteresis in the cooling and heating paths, similar to that observed in the Tg-endotherm range. After eliminating other interpretations, we conclude that local-region fluctuations seen as the JG relaxation in the non-equilibrium state of a glass contribute to its entropy, and we suggest conditions under which such fluctuations may be observed.

Phenomenological picture of fluctuations in branching random walks

NASA Astrophysics Data System (ADS)

Mueller, A. H.; Munier, S.

2014-10-01

We propose a picture of the fluctuations in branching random walks, which leads to predictions for the distribution of a random variable that characterizes the position of the bulk of the particles. We also interpret the 1 /√{t } correction to the average position of the rightmost particle of a branching random walk for large times t ≫1 , computed by Ebert and Van Saarloos, as fluctuations on top of the mean-field approximation of this process with a Brunet-Derrida cutoff at the tip that simulates discreteness. Our analytical formulas successfully compare to numerical simulations of a particular model of a branching random walk.

Study of Magnetic Reconnection

DTIC Science & Technology

1988-11-01

and disruptions in the Tosca tokamak, Nuclear Fusion 19, 115-119, 1979. 9. Stenzel, R. L., W. Gekelman and N. Wild, Magnetic field line reconnection...Acknowledgments. The authors gratefully acknowledge the techni- plasma diffusion due to polycliromatic fluctuations, Nucl. Fussion , cal support and...sans collisions, in: Proceedings of the Conference on Plasma Physics and Controlled Nuclear Fusion, International Atomic Energy Agency, Vienna

Structural, electronic and vibrational properties of small GaxNy (x+y = 2 5) nanoclusters: a B3LYP-DFT study

NASA Astrophysics Data System (ADS)

Yadav, P. S.; Yadav, R. K.; Agrawal, B. K.

2007-02-01

An ab initio study of the stability, structural and electronic properties has been made for 49 gallium nitride nanoclusters, GaxNy (x+y = 2-5). Among the various configurations corresponding to a fixed x+y = n value, the configuration possessing the maximum value of binding energy (BE) is named as the most stable structure. The vibrational and optical properties have been investigated only for the most stable structures. A B3LYP-DFT/6-311G(3df) method has been employed to optimize the geometries of the nanoclusters fully. The binding energies (BEs), highest-occupied and lowest-unoccupied molecular orbital (HOMO-LUMO) gaps and the bond lengths have been obtained for all the clusters. We have considered the zero-point energy (ZPE) corrections ignored by the earlier workers. The adiabatic and vertical ionization potentials (IPs) and electron affinities (EAs), charge on atoms, dipole moments, vibrational frequencies, infrared intensities (IR Int.), relative infrared intensities (Rel. IR Int.) and Raman scattering activities have been investigated for the most stable structures. The configurations containing the N atoms in majority are seen to be the most stable structures. The strong N-N bond has an important role in stabilizing the clusters. For clusters containing one Ga atom and all the others as N atoms, the BE increases monotonically with the number of the N atoms. The HOMO-LUMO gap and IP fluctuate with the cluster size n, having larger values for the clusters containing odd number of N atoms. On the other hand, the EA decreases with the cluster size up to n = 3, and shows slow fluctuations thereafter for the larger clusters. In general, the adiabatic IP (EA) is smaller (greater) than the vertical IP (EA) because of the lower energies of the most stable ground state of the cationic (anionic) clusters. The optical absorption spectrum or electron energy loss spectrum (EELS) is unique for every cluster, and may be used to characterize a specific cluster. All the predicted physical quantities are in good agreement with the experimental data wherever available. The growth of these most stable structures should be possible in experiments.

Determining probability distribution of coherent integration time near 133 Hz and 1346 km in the Pacific Ocean.

PubMed

Spiesberger, John L

2013-02-01

The hypothesis tested is that internal gravity waves limit the coherent integration time of sound at 1346 km in the Pacific ocean at 133 Hz and a pulse resolution of 0.06 s. Six months of continuous transmissions at about 18 min intervals are examined. The source and receiver are mounted on the bottom of the ocean with timing governed by atomic clocks. Measured variability is only due to fluctuations in the ocean. A model for the propagation of sound through fluctuating internal waves is run without any tuning with data. Excellent resemblance is found between the model and data's probability distributions of integration time up to five hours.

Colonial, more widely distributed and less abundant bird species undergo wider population fluctuations independent of their population trend

PubMed Central

Møller, Anders P.

2017-01-01

Understanding temporal variability in population size is important for conservation biology because wide population fluctuations increase the risk of extinction. Previous studies suggested that certain ecological, demographic, life-history and genetic characteristics of species might be related to the degree of their population fluctuations. We checked whether that was the case in a large sample of 231 European breeding bird species while taking a number of potentially confounding factors such as population trends or similarities among species due to common descent into account. When species-specific characteristics were analysed one by one, the magnitude of population fluctuations was positively related to coloniality, habitat, total breeding range, heterogeneity of breeding distribution and natal dispersal, and negatively related to urbanisation, abundance, relative number of subspecies, parasitism and proportion of polymorphic loci. However, when abundance (population size) was included in the analyses of the other parameters, only coloniality, habitat, total breeding range and abundance remained significantly related to population fluctuations. The analysis including all these predictors simultaneously showed that population size fluctuated more in colonial, less abundant species with larger breeding ranges. Other parameters seemed to be related to population fluctuations only because of their association with abundance or coloniality. The unexpected positive relationship between population fluctuations and total breeding range did not seem to be mediated by abundance. The link between population fluctuations and coloniality suggests a previously unrecognized cost of coloniality. The negative relationship between population size and population fluctuations might be explained by at least three types of non-mutually exclusive stochastic processes: demographic, environmental and genetic stochasticity. Measurement error in population indices, which was unknown, may have contributed to the negative relationship between population size and fluctuations, but apparently only to a minor extent. The association between population size and fluctuations suggests that populations might be stabilized by increasing population size. PMID:28253345

Multiscale molecular dynamics simulations of rotary motor proteins.

PubMed

Ekimoto, Toru; Ikeguchi, Mitsunori

2018-04-01

Protein functions require specific structures frequently coupled with conformational changes. The scale of the structural dynamics of proteins spans from the atomic to the molecular level. Theoretically, all-atom molecular dynamics (MD) simulation is a powerful tool to investigate protein dynamics because the MD simulation is capable of capturing conformational changes obeying the intrinsically structural features. However, to study long-timescale dynamics, efficient sampling techniques and coarse-grained (CG) approaches coupled with all-atom MD simulations, termed multiscale MD simulations, are required to overcome the timescale limitation in all-atom MD simulations. Here, we review two examples of rotary motor proteins examined using free energy landscape (FEL) analysis and CG-MD simulations. In the FEL analysis, FEL is calculated as a function of reaction coordinates, and the long-timescale dynamics corresponding to conformational changes is described as transitions on the FEL surface. Another approach is the utilization of the CG model, in which the CG parameters are tuned using the fluctuation matching methodology with all-atom MD simulations. The long-timespan dynamics is then elucidated straightforwardly by using CG-MD simulations.

Spray formation processes of impinging jet injectors

NASA Technical Reports Server (NTRS)

Anderson, W. E.; Ryan, H. M.; Pal, S.; Santoro, R. J.

1993-01-01

A study examining impinging liquid jets has been underway to determine physical mechanisms responsible for combustion instabilities in liquid bi-propellant rocket engines. Primary atomization has been identified as an important process. Measurements of atomization length, wave structure, and drop size and velocity distribution were made under various ambient conditions. Test parameters included geometric effects and flow effects. It was observed that pre-impingement jet conditions, specifically whether they were laminar or turbulent, had the major effect on primary atomization. Comparison of the measurements with results from a two dimensional linear aerodynamic stability model of a thinning, viscous sheet were made. Measured turbulent impinging jet characteristics were contrary to model predictions; the structure of waves generated near the point of jet impingement were dependent primarily on jet diameter and independent of jet velocity. It has been postulated that these impact waves are related to pressure and momentum fluctuations near the impingement region and control the eventual disintegration of the liquid sheet into ligaments. Examination of the temporal characteristics of primary atomization (ligament shedding frequency) strongly suggests that the periodic nature of primary atomization is a key process in combustion instability.

Density functional theory studies of methyl dissociation on a Ni(111) surface in the presence of an external electric field.

PubMed

Che, Fanglin; Zhang, Renqin; Hensley, Alyssa J; Ha, Su; McEwen, Jean-Sabin

2014-02-14

To provide a basis for understanding the reactive processes on nickel surfaces at fuel cell anodes, we investigate the influence of an external electric field on the dehydrogenation of methyl species on a Ni(111) surface using density functional theory calculations. The structures, adsorption energies and reaction barriers for all methyl species dissociation on the Ni(111) surface are identified. Our results show that the presence of an external electric field does not affect the structures and favorable adsorption sites of the adsorbed species, but causes the adsorption energies of the CHx species at the stable site to fluctuate around 0.2 eV. Calculations give an energy barrier of 0.692 eV for CH3* → CH2* + H*, 0.323 eV for CH2* → CH* + H* and 1.373 eV for CH* → C* + H*. Finally, we conclude that the presence of a large positive electric field significantly increases the energy barrier of the CH* → C* + H* reaction more than the other two reactions, suggesting that the presence of pure C atoms on Ni(111) are impeded in the presence of an external positive electric field.

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

Reiche, D.; Dalvit, D. A. R.; Busch, K.

We investigate the influence of spatial dispersion on atom-surface quantum friction. We show that for atom-surface separations shorter than the carrier's mean free path within the material, the frictional force can be several orders of magnitude larger than that predicted by local optics. In addition, when taking into account spatial dispersion effects, we show that the commonly used local thermal equilibrium approximation underestimates by approximately 95% the drag force, obtained by employing the recently reported nonequilibrium fluctuation-dissipation relation for quantum friction. Unlike the treatment based on local optics, spatial dispersion in conjunction with corrections to local thermal equilibrium change notmore » only the magnitude but also the distance scaling of quantum friction.« less

Spin noise spectroscopy of rubidium atomic gas under resonant and non-resonant conditions

NASA Astrophysics Data System (ADS)

Ma, Jian; Shi, Ping; Qian, Xuan; Li, Wei; Ji, Yang

2016-11-01

The spin fluctuation in rubidium atom gas is studied via all-optical spin noise spectroscopy (SNS). Experimental results show that the integrated SNS signal and its full width at half maximum (FWHM) strongly depend on the frequency detuning of the probe light under resonant and non-resonant conditions. The total integrated SNS signal can be well fitted with a single squared Faraday rotation spectrum and the FWHM dependence may be related to the absorption profile of the sample. Project supported by the National Natural Science Foundation of China (Grant Nos. 91321310 and 11404325) and the National Basic Research Program of China (Grant No. 2013CB922304).

Diffusion coefficients of Fokker-Planck equation for rotating dust grains in a fusion plasma

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

Bakhtiyari-Ramezani, M., E-mail: mahdiyeh.bakhtiyari@gmail.com; Alinejad, N., E-mail: nalinezhad@aeoi.org.ir; Mahmoodi, J., E-mail: mahmoodi@qom.ac.ir

2015-11-15

In the fusion devices, ions, H atoms, and H{sub 2} molecules collide with dust grains and exert stochastic torques which lead to small variations in angular momentum of the grain. By considering adsorption of the colliding particles, thermal desorption of H atoms and normal H{sub 2} molecules, and desorption of the recombined H{sub 2} molecules from the surface of an oblate spheroidal grain, we obtain diffusion coefficients of the Fokker-Planck equation for the distribution function of fluctuating angular momentum. Torque coefficients corresponding to the recombination mechanism show that the nonspherical dust grains may rotate with a suprathermal angular velocity.

Remnants of semiclassical bistability in the few-photon regime of cavity QED.

PubMed

Kerckhoff, Joseph; Armen, Michael A; Mabuchi, Hideo

2011-11-21

Broadband homodyne detection of the light transmitted by a Fabry-Perot cavity containing a strongly-coupled (133)Cs atom is used to probe the dynamic optical response in a regime where semiclassical theory predicts bistability but strong quantum corrections should apply. While quantum fluctuations destabilize true equilibrium bistability, our observations confirm the existence of metastable states with finite lifetimes and a hysteretic response is apparent when the optical drive is modulated on comparable timescales. Our experiment elucidates remnant semiclassical behavior in the attojoule (~10 photon) regime of single-atom cavity QED, of potential significance for ultra-low power photonic signal processing. © 2011 Optical Society of America

Diffusion coefficients of Fokker-Planck equation for rotating dust grains in a fusion plasma

NASA Astrophysics Data System (ADS)

Bakhtiyari-Ramezani, M.; Mahmoodi, J.; Alinejad, N.

2015-11-01

In the fusion devices, ions, H atoms, and H2 molecules collide with dust grains and exert stochastic torques which lead to small variations in angular momentum of the grain. By considering adsorption of the colliding particles, thermal desorption of H atoms and normal H2 molecules, and desorption of the recombined H2 molecules from the surface of an oblate spheroidal grain, we obtain diffusion coefficients of the Fokker-Planck equation for the distribution function of fluctuating angular momentum. Torque coefficients corresponding to the recombination mechanism show that the nonspherical dust grains may rotate with a suprathermal angular velocity.

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.

Understanding volatility correlation behavior with a magnitude cross-correlation function

NASA Astrophysics Data System (ADS)

Jun, Woo Cheol; Oh, Gabjin; Kim, Seunghwan

2006-06-01

We propose an approach for analyzing the basic relation between correlation properties of the original signal and its magnitude fluctuations by decomposing the original signal into its positive and negative fluctuation components. We use this relation to understand the following phenomenon found in many naturally occurring time series: the magnitude of the signal exhibits long-range correlation, whereas the original signal is short-range correlated. The applications of our approach to heart rate variability signals and high-frequency foreign exchange rates reveal that the difference between the correlation properties of the original signal and its magnitude fluctuations is induced by the time organization structure of the correlation function between the magnitude fluctuations of positive and negative components. We show that this correlation function can be described well by a stretched-exponential function and is related to the nonlinearity and the multifractal structure of the signals.

Understanding volatility correlation behavior with a magnitude cross-correlation function.

PubMed

Jun, Woo Cheol; Oh, Gabjin; Kim, Seunghwan

2006-06-01

We propose an approach for analyzing the basic relation between correlation properties of the original signal and its magnitude fluctuations by decomposing the original signal into its positive and negative fluctuation components. We use this relation to understand the following phenomenon found in many naturally occurring time series: the magnitude of the signal exhibits long-range correlation, whereas the original signal is short-range correlated. The applications of our approach to heart rate variability signals and high-frequency foreign exchange rates reveal that the difference between the correlation properties of the original signal and its magnitude fluctuations is induced by the time organization structure of the correlation function between the magnitude fluctuations of positive and negative components. We show that this correlation function can be described well by a stretched-exponential function and is related to the nonlinearity and the multifractal structure of the signals.

State-dependent fluorescence of neutral atoms in optical potentials

NASA Astrophysics Data System (ADS)

Martinez-Dorantes, M.; Alt, W.; Gallego, J.; Ghosh, S.; Ratschbacher, L.; Meschede, D.

2018-02-01

Recently we have demonstrated scalable, nondestructive, and high-fidelity detection of the internal state of 87Rb neutral atoms in optical dipole traps using state-dependent fluorescence imaging [M. Martinez-Dorantes, W. Alt, J. Gallego, S. Ghosh, L. Ratschbacher, Y. Völzke, and D. Meschede, Phys. Rev. Lett. 119, 180503 (2017), 10.1103/PhysRevLett.119.180503]. In this paper we provide experimental procedures and interpretations to overcome the detrimental effects of heating-induced trap losses and state leakage. We present models for the dynamics of optically trapped atoms during state-dependent fluorescence imaging and verify our results by comparing Monte Carlo simulations with experimental data. Our systematic study of dipole force fluctuations heating in optical traps during near-resonant illumination shows that off-resonant light is preferable for state detection in tightly confining optical potentials.

Efficient frequency doubler of 1560 nm laser based on a semi-monolithic resonant cavity with a PPKTP crystal

NASA Astrophysics Data System (ADS)

Wang, Junmin; Zhang, Kong; Ge, Yulong; Guo, Shanlong

2016-06-01

We have demonstrated 1.61 W of 780 nm single-frequency continuous-wave laser output with a semi-monolithic periodically poled potassium titanyl phosphate (PPKTP) crystal doubler pumped by a 2-W erbium-doped fiber amplifier boosted 1560 nm diode laser. The measured maximum doubling efficiency is 77%, and the practical value should be 80% when taking into account the fundamental-wave mode matching efficiency. The measured beam quality factor of 780 nm output, M2, is better than 1.04. Typical root-mean-square fluctuation of 780 nm output is less than 0.5% in 30 minutes. This compact frequency doubler has good mechanical stability, and can be employed for many applications, such as laser cooling and trapping, atomic coherent control, atomic interferometer, and quantum frequency standard with rubidium atoms.

Ultracold atoms in an optical lattice one millimeter from air

NASA Astrophysics Data System (ADS)

Jervis, Dylan; Edge, Graham; Trotzky, Stefan; McKay, David; Thywissen, Joseph

2013-05-01

Over the past decade, ultracold atoms in optical lattices have shown to be versatile systems able to realize canonical Hamiltonians of condensed matter. High-resolution in-situ imaging of ultracold clouds has furthermore enabled thermometry, equation of state measurements, direct measurement of fluctuations, and unprecedented control. We report on microscopy of ultracold bosons and fermions in a novel configuration where the atoms are harmonically trapped 800 microns away from a 200 micron-thick vacuum window. This window also serves as a retro-reflecting mirror for an optical lattice, into which the atoms can be loaded. Two additional transverse standing waves complete the three-dimensional lattice setup. In free space, we have shown that laser cooling with 405 nm light, on the open 4S1/2-5P3/2 transition, allows for temperatures below the Doppler temperature of the 4S1/2-4P3/2 cycling transition at 767 nm. Microscopy with 405 nm light furthermore reduces the diffraction limit of in-situ imaging.

Intrinsic retrieval efficiency for quantum memories: A three-dimensional theory of light interaction with an atomic ensemble

NASA Astrophysics Data System (ADS)

Gujarati, Tanvi P.; Wu, Yukai; Duan, Luming

2018-03-01

Duan-Lukin-Cirac-Zoller quantum repeater protocol, which was proposed to realize long distance quantum communication, requires usage of quantum memories. Atomic ensembles interacting with optical beams based on off-resonant Raman scattering serve as convenient on-demand quantum memories. Here, a complete free space, three-dimensional theory of the associated read and write process for this quantum memory is worked out with the aim of understanding intrinsic retrieval efficiency. We develop a formalism to calculate the transverse mode structure for the signal and the idler photons and use the formalism to study the intrinsic retrieval efficiency under various configurations. The effects of atomic density fluctuations and atomic motion are incorporated by numerically simulating this system for a range of realistic experimental parameters. We obtain results that describe the variation in the intrinsic retrieval efficiency as a function of the memory storage time for skewed beam configuration at a finite temperature, which provides valuable information for optimization of the retrieval efficiency in experiments.

Understanding the mechanisms of amorphous creep through molecular simulation

NASA Astrophysics Data System (ADS)

Cao, Penghui; Short, Michael P.; Yip, Sidney

2017-12-01

Molecular processes of creep in metallic glass thin films are simulated at experimental timescales using a metadynamics-based atomistic method. Space-time evolutions of the atomic strains and nonaffine atom displacements are analyzed to reveal details of the atomic-level deformation and flow processes of amorphous creep in response to stress and thermal activations. From the simulation results, resolved spatially on the nanoscale and temporally over time increments of fractions of a second, we derive a mechanistic explanation of the well-known variation of creep rate with stress. We also construct a deformation map delineating the predominant regimes of diffusional creep at low stress and high temperature and deformational creep at high stress. Our findings validate the relevance of two original models of the mechanisms of amorphous plasticity: one focusing on atomic diffusion via free volume and the other focusing on stress-induced shear deformation. These processes are found to be nonlinearly coupled through dynamically heterogeneous fluctuations that characterize the slow dynamics of systems out of equilibrium.

Ultralow-Noise Atomic-Scale Structures for Quantum Circuitry in Silicon.

PubMed

Shamim, Saquib; Weber, Bent; Thompson, Daniel W; Simmons, Michelle Y; Ghosh, Arindam

2016-09-14

The atomically precise doping of silicon with phosphorus (Si:P) using scanning tunneling microscopy (STM) promises ultimate miniaturization of field effect transistors. The one-dimensional (1D) Si:P nanowires are of particular interest, retaining exceptional conductivity down to the atomic scale, and are predicted as interconnects for a scalable silicon-based quantum computer. Here, we show that ultrathin Si:P nanowires form one of the most-stable electrical conductors, with the phenomenological Hooge parameter of low-frequency noise being as low as ≈10(-8) at 4.2 K, nearly 3 orders of magnitude lower than even carbon-nanotube-based 1D conductors. A in-built isolation from the surface charge fluctuations due to encapsulation of the wires within the epitaxial Si matrix is the dominant cause for the observed suppression of noise. Apart from quantum information technology, our results confirm the promising prospects for precision-doped Si:P structures in atomic-scale circuitry for the 11 nm technology node and beyond.

Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer

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

Schulz, Roland; Lindner, Benjamin; Petridis, Loukas

2009-01-01

A strategy is described for a fast all-atom molecular dynamics simulation of multimillion-atom biological systems on massively parallel supercomputers. The strategy is developed using benchmark systems of particular interest to bioenergy research, comprising models of cellulose and lignocellulosic biomass in an aqueous solution. The approach involves using the reaction field (RF) method for the computation of long-range electrostatic interactions, which permits efficient scaling on many thousands of cores. Although the range of applicability of the RF method for biomolecular systems remains to be demonstrated, for the benchmark systems the use of the RF produces molecular dipole moments, Kirkwood G factors,more » other structural properties, and mean-square fluctuations in excellent agreement with those obtained with the commonly used Particle Mesh Ewald method. With RF, three million- and five million atom biological systems scale well up to 30k cores, producing 30 ns/day. Atomistic simulations of very large systems for time scales approaching the microsecond would, therefore, appear now to be within reach.« less

Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer.

PubMed

Schulz, Roland; Lindner, Benjamin; Petridis, Loukas; Smith, Jeremy C

2009-10-13

A strategy is described for a fast all-atom molecular dynamics simulation of multimillion-atom biological systems on massively parallel supercomputers. The strategy is developed using benchmark systems of particular interest to bioenergy research, comprising models of cellulose and lignocellulosic biomass in an aqueous solution. The approach involves using the reaction field (RF) method for the computation of long-range electrostatic interactions, which permits efficient scaling on many thousands of cores. Although the range of applicability of the RF method for biomolecular systems remains to be demonstrated, for the benchmark systems the use of the RF produces molecular dipole moments, Kirkwood G factors, other structural properties, and mean-square fluctuations in excellent agreement with those obtained with the commonly used Particle Mesh Ewald method. With RF, three million- and five million-atom biological systems scale well up to ∼30k cores, producing ∼30 ns/day. Atomistic simulations of very large systems for time scales approaching the microsecond would, therefore, appear now to be within reach.

Fundamental relations between short-term RR interval and arterial pressure oscillations in humans

NASA Technical Reports Server (NTRS)

Taylor, J. A.; Eckberg, D. L.

1996-01-01

BACKGROUND: One of the principal explanations for respiratory sinus arrhythmia is that it reflects arterial baroreflex buffering of respiration-induced arterial pressure fluctuations. If this explanation is correct, then elimination of RR interval fluctuations should increase respiratory arterial pressure fluctuations. METHODS AND RESULTS: We measured RR interval and arterial pressure fluctuations during normal sinus rhythm and fixed-rate atrial pacing at 17.2+/-1.8 (SEM) beats per minute greater than the sinus rate in 16 healthy men and 4 healthy women, 20 to 34 years of age. Measurements were made during controlled-frequency breathing (15 breaths per minute or 0.25 Hz) with subjects in the supine and 40 degree head-up tilt positions. We characterized RR interval and arterial pressure variabilities in low-frequency (0.05 to 0.15 Hz) and respiratory-frequency (0.20 to 0.30 Hz) ranges with fast Fourier transform power spectra and used cross-spectral analysis to determine the phase relation between the two signals. As expected, cardiac pacing eliminated beat-to-beat RR interval variability. Against expectations, however, cardiac pacing in the supine position significantly reduced arterial pressure oscillations in the respiratory frequency (systolic, 6.8+/-1.8 to 2.9 +/-0.6 mm Hg2/Hz, P=.017). In contrast, cardiac pacing in the 40 degree tilt position increased arterial pressure variability (systolic, 8.0+/-1.8 to 10.8 +/-2.6, P=.027). Cross-spectral analysis showed that 40 degree tilt shifted the phase relation between systolic pressure and RR interval at the respiratory frequency from positive to negative (9 +/-7 degrees versus -17+/-11 degrees, P=.04); that is, in the supine position, RR interval changes appeared to lead arterial pressure changes, and in the upright position, RR interval changes appeared to follow arterial pressure changes. CONCLUSIONS: These results demonstrate that respiratory sinus arrhythmia can actually contribute to respiratory arterial pressure fluctuations. Therefore, respiratory sinus arrhythmia does not represent simple baroreflex buffering of arterial pressure.

Physiological Mechanisms Mediating the Coupling between Heart Period and Arterial Pressure in Response to Postural Changes in Humans

PubMed Central

Silvani, Alessandro; Calandra-Buonaura, Giovanna; Johnson, Blair D.; van Helmond, Noud; Barletta, Giorgio; Cecere, Anna G.; Joyner, Michael J.; Cortelli, Pietro

2017-01-01

The upright posture strengthens the coupling between heart period (HP) and systolic arterial pressure (SAP) consistently with a greater contribution of the arterial baroreflex to cardiac control, while paradoxically decreasing cardiac baroreflex sensitivity (cBRS). To investigate the physiological mechanisms that mediate the coupling between HP and SAP in response to different postures, we analyzed the cross-correlation functions between low-frequency HP and SAP fluctuations and estimated cBRS with the sequence technique in healthy male subjects during passive head-up tilt test (HUTT, n = 58), during supine wakefulness, supine slow-wave sleep (SWS), and in the seated and active standing positions (n = 8), and during progressive loss of 1 L blood (n = 8) to decrease central venous pressure in the supine position. HUTT, SWS, the seated, and the standing positions, but not blood loss, entailed significant increases in the positive correlation between HP and the previous SAP values, which is the expected result of arterial baroreflex control, compared with baseline recordings in the supine position during wakefulness. These increases were mirrored by increases in the low-frequency variability of SAP in each condition but SWS. cBRS decreased significantly during HUTT, in the seated and standing positions, and after blood loss compared with baseline during wakefulness. These decreases were mirrored by decreases in the RMSSD index, which reflects cardiac vagal modulation. These results support the view that the cBRS decrease associated with the upright posture is a byproduct of decreased cardiac vagal modulation, triggered by the arterial baroreflex in response to central hypovolemia. Conversely, the greater baroreflex contribution to cardiac control associated with upright posture may be explained, at least in part, by enhanced fluctuations of SAP, which elicit a more effective entrainment of HP fluctuations by the arterial baroreflex. These SAP fluctuations may result from enhanced fluctuations of vascular resistance specific to the upright posture, and not be driven by the accompanying central hypovolemia. PMID:28396638

Physiological Mechanisms Mediating the Coupling between Heart Period and Arterial Pressure in Response to Postural Changes in Humans.

PubMed

Silvani, Alessandro; Calandra-Buonaura, Giovanna; Johnson, Blair D; van Helmond, Noud; Barletta, Giorgio; Cecere, Anna G; Joyner, Michael J; Cortelli, Pietro

2017-01-01

The upright posture strengthens the coupling between heart period (HP) and systolic arterial pressure (SAP) consistently with a greater contribution of the arterial baroreflex to cardiac control, while paradoxically decreasing cardiac baroreflex sensitivity (cBRS). To investigate the physiological mechanisms that mediate the coupling between HP and SAP in response to different postures, we analyzed the cross-correlation functions between low-frequency HP and SAP fluctuations and estimated cBRS with the sequence technique in healthy male subjects during passive head-up tilt test (HUTT, n = 58), during supine wakefulness, supine slow-wave sleep (SWS), and in the seated and active standing positions ( n = 8), and during progressive loss of 1 L blood ( n = 8) to decrease central venous pressure in the supine position. HUTT, SWS, the seated, and the standing positions, but not blood loss, entailed significant increases in the positive correlation between HP and the previous SAP values, which is the expected result of arterial baroreflex control, compared with baseline recordings in the supine position during wakefulness. These increases were mirrored by increases in the low-frequency variability of SAP in each condition but SWS. cBRS decreased significantly during HUTT, in the seated and standing positions, and after blood loss compared with baseline during wakefulness. These decreases were mirrored by decreases in the RMSSD index, which reflects cardiac vagal modulation. These results support the view that the cBRS decrease associated with the upright posture is a byproduct of decreased cardiac vagal modulation, triggered by the arterial baroreflex in response to central hypovolemia. Conversely, the greater baroreflex contribution to cardiac control associated with upright posture may be explained, at least in part, by enhanced fluctuations of SAP, which elicit a more effective entrainment of HP fluctuations by the arterial baroreflex. These SAP fluctuations may result from enhanced fluctuations of vascular resistance specific to the upright posture, and not be driven by the accompanying central hypovolemia.

Ocean acidification reverses the positive effects of seawater pH fluctuations on growth and photosynthesis of the habitat-forming kelp, Ecklonia radiata.

PubMed

Britton, Damon; Cornwall, Christopher E; Revill, Andrew T; Hurd, Catriona L; Johnson, Craig R

2016-05-27

Ocean acidification (OA) is the reduction in seawater pH due to the absorption of human-released CO2 by the world's oceans. The average surface oceanic pH is predicted to decline by 0.4 units by 2100. However, kelp metabolically modifies seawater pH via photosynthesis and respiration in some temperate coastal systems, resulting in daily pH fluctuations of up to ±0.45 units. It is unknown how these fluctuations in pH influence the growth and physiology of the kelp, or how this might change with OA. In laboratory experiments that mimicked the most extreme pH fluctuations measured within beds of the canopy-forming kelp Ecklonia radiata in Tasmania, the growth and photosynthetic rates of juvenile E. radiata were greater under fluctuating pH (8.4 in the day, 7.8 at night) than in static pH treatments (8.4, 8.1, 7.8). However, pH fluctuations had no effect on growth rates and a negative effect on photosynthesis when the mean pH of each treatment was reduced by 0.3 units. Currently, pH fluctuations have a positive effect on E. radiata but this effect could be reversed in the future under OA, which is likely to impact the future ecological dynamics and productivity of habitats dominated by E. radiata.

Generalized noise terms for the quantized fluctuational electrodynamics

NASA Astrophysics Data System (ADS)

Partanen, Mikko; Häyrynen, Teppo; Tulkki, Jukka; Oksanen, Jani

2017-03-01

The quantization of optical fields in vacuum has been known for decades, but extending the field quantization to lossy and dispersive media in nonequilibrium conditions has proven to be complicated due to the position-dependent electric and magnetic responses of the media. In fact, consistent position-dependent quantum models for the photon number in resonant structures have only been formulated very recently and only for dielectric media. Here we present a general position-dependent quantized fluctuational electrodynamics (QFED) formalism that extends the consistent field quantization to describe the photon number also in the presence of magnetic field-matter interactions. It is shown that the magnetic fluctuations provide an additional degree of freedom in media where the magnetic coupling to the field is prominent. Therefore, the field quantization requires an additional independent noise operator that is commuting with the conventional bosonic noise operator describing the polarization current fluctuations in dielectric media. In addition to allowing the detailed description of field fluctuations, our methods provide practical tools for modeling optical energy transfer and the formation of thermal balance in general dielectric and magnetic nanodevices. We use QFED to investigate the magnetic properties of microcavity systems to demonstrate an example geometry in which it is possible to probe fields arising from the electric and magnetic source terms. We show that, as a consequence of the magnetic Purcell effect, the tuning of the position of an emitter layer placed inside a vacuum cavity can make the emissivity of a magnetic emitter to exceed the emissivity of a corresponding electric emitter.

Acute Positive Effects of Exercise on Center-of-Pressure Fluctuations During Quiet Standing in Middle-Aged and Elderly Women.

PubMed

Fukusaki, Chiho; Masani, Kei; Miyasaka, Maya; Nakazawa, Kimitaka

2016-01-01

Acute effects of exercise on postural stability have been studied with a focus on fatigue. This study investigated the acute effects of moderate-intensity exercise on center-of-pressure (COP) fluctuation measures in middle-aged and elderly women. Thirty-five healthy women volunteered: 18 women performed a moderate aquatic exercise session for 80 minutes and 17 remained calm in a sitting position for the same duration. Center-of-pressure fluctuations during quiet standing were recorded for 60 seconds with eyes open and closed before and after the exercise and sitting tasks. The time- and frequency-domain measures of the COP time series were calculated. The frequency-domain measures were also calculated for the COP velocity time series. According to 2-way analysis of variance and paired t-tests with a Bonferroni's correction, mean velocity of COP fluctuations, mean velocity of COP fluctuations in the medial-lateral (ML) direction, and total power of the COP velocity time series in the ML direction exhibited significant reductions after 1 session of exercise. These results indicated that a moderate-intensity aquatic exercise decreased COP velocity, counteracting age-related and fatigue-inducing postural deterioration. Therefore, we concluded that a single session of moderate-intensity aquatic exercise has acute positive effects on postural stability in middle-aged and elderly women.

Investigation of MHD flow structure and fluctuations by potassium lineshape fitting

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

Bauman, L.E.

1993-12-31

Multiple Potassium D-line emission absorption spectra from a high temperature, coal-fired flow have been fit to a radiative transfer, boundary layer flow model. The results of fitting spectra from the aerodynamic duct of the Department of Energy Coal-Fired Flow Facility provide information about the thickness and shape of the thermal boundary layer and the bulk potassium seed atom density in a simulated magnetohydrodynamic channel flow. Probability distribution functions for the entire set of more than six thousand spectra clearly indicate the typical values and magnitude of fluctuations for the flow: core temperature of 2538 {plus_minus} 20 K, near wall temperaturemore » of 1945 {plus_minus} 135 K, boundary layer width of about 1 cm, and potassium seed atom density of (5.1 {plus_minus} 0.8)x 10{sup 22}/m{sup 3}. Probability distribution functions for selected times during the eight hours of measurements indicate occasional periods of unstable combustion. In addition, broadband particle parameters during the unstable start of the test may be related to differing particle and gas temperatures. The results clearly demonstrate the ability of lineshape fitting to provide valuable data for diagnosing the high speed turbulent flow.« less

Passive microrheology of normal and cancer cells after ML7 treatment by atomic force microscopy

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

Lyapunova, Elena, E-mail: lyapunova@icmm.ru; Ural Federal University, Kuibyishev Str. 48, Ekaterinburg, 620000; Nikituk, Alexander, E-mail: nas@icmm.ru

Mechanical properties of living cancer and normal thyroidal cells were investigated by atomic force microscopy (AFM). Cell mechanics was compared before and after treatment with ML7, which is known to reduce myosin activity and induce softening of cell structures. We recorded force curves with extended dwell time of 6 seconds in contact at maximum forces from 500 pN to 1 nN. Data were analyzed within different frameworks: Hertz fit was applied in order to evaluate differences in Young’s moduli among cell types and conditions, while the fluctuations of the cantilever in contact with cells were analyzed with both conventional algorithmsmore » (probability density function and power spectral density) and multifractal detrended fluctuation analysis (MF-DFA). We found that cancer cells were softer than normal cells and ML7 had a substantial softening effect on normal cells, but only a marginal one on cancer cells. Moreover, we observed that all recorded signals for normal and cancer cells were monofractal with small differences between their scaling parameters. Finally, the applicability of wavelet-based methods of data analysis for the discrimination of different cell types is discussed.« less

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.

The performance of fine-grained and coarse-grained elastic network models and its dependence on various factors.

PubMed

Na, Hyuntae; Song, Guang

2015-07-01

In a recent work we developed a method for deriving accurate simplified models that capture the essentials of conventional all-atom NMA and identified two best simplified models: ssNMA and eANM, both of which have a significantly higher correlation with NMA in mean square fluctuation calculations than existing elastic network models such as ANM and ANMr2, a variant of ANM that uses the inverse of the squared separation distances as spring constants. Here, we examine closely how the performance of these elastic network models depends on various factors, namely, the presence of hydrogen atoms in the model, the quality of input structures, and the effect of crystal packing. The study reveals the strengths and limitations of these models. Our results indicate that ssNMA and eANM are the best fine-grained elastic network models but their performance is sensitive to the quality of input structures. When the quality of input structures is poor, ANMr2 is a good alternative for computing mean-square fluctuations while ANM model is a good alternative for obtaining normal modes. © 2015 Wiley Periodicals, Inc.

Accurate X-ray diffraction studies of KTiOPO{sub 4} single crystals doped with niobium

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

Novikova, N. E., E-mail: natnov@ns.crys.ras.ru; Sorokina, N. I.; Alekseeva, O. A.

2017-01-15

Single crystals of potassium titanyl phosphate doped with 4% of niobium (КТР:4%Nb) and 6% of niobium (KTP:6%Nb) are studied by accurate X-ray diffraction at room temperature. The niobium atoms are localized near the Ti1 and Ti2 atomic positions, and their positions are for the first time refined independent of the titanium atomic positions. Maps of difference electron density in the vicinity of K1 and K2 atomic positions are analyzed. It is found that in the structure of crystal КТР:4%Nb, additional positions of K atoms are located farther from the main positions and from each other than in КТР and KTP:6%Nbmore » crystals. The nonuniform distribution of electron density found in the channels of the КТР:4%Nb structure is responsible for ~20% increase in the signal of second harmonic generation.« less

Spatial Organization In Europe of Decadal and Interdecadal Fluctuations In Annual Rainfall

NASA Astrophysics Data System (ADS)

Lucero, O. A.; Rodriguez, N. C.

In this research the spatial patterns of decadal and bidecadal fluctuations in annual rainfall in Europe are identified. Filtering of time series of anomaly of annual rainfall is carried out using the Morlet wavelet technique. Reconstruction is achieved by sum- ming the contributions from bands of wavelet timescales; the decadal band and the bidecadal band are composed of contributions from the band of (10- to 17-year] and (17- to 27- year] timescales respectively. Results indicate that 1) the spatial organi- zation of decadal and bidecadal components of annual rainfall are standing wave-like organized patterns. Three standing decadal fluctuations zonally aligned formed the spatial pattern from 1900 until 1931; thereafter the pattern changed into a NW-SE orientation. The decadal band shows an average 12-year period. 2) The spatial orga- nization of bidecadal component was composed of three standing fluctuations since 1903 to 1986. After 1987 two standing bidecadal fluctuations were located on Europe. The orientation of bidecadal fluctuations changed during the period under study. Until 1913 the spatial pattern of the bidecadal component was zonally aligned. Since 1913 until 1986 the three bidecadal fluctuations composing the spatial pattern were aligned SW U NE; starting 1987 the spatial pattern is composed of two standing fluctuations zonally aligned. The bidecadal spatial pattern shows an average period of 20- to 22- year length. 3) At decadal and bidecadal timescales, the first principal component of the spatial field of anomaly of annual rainfall and the NAO index are connected. The upper positive third (lower negative third) of values of first principal component are indicative of extensive area with positive (negative) anomaly of annual rainfall. 4) At decadal timescale the relative phase between the first PC and the NAO index changes through the period under study; these changes define three regimes: 1) Dur- ing the regime covering the period 1900 (start of period under study) to about 1945, at the time of peak values of decadal NAO-index it takes place a transition between extremes (a neutral state) of the decadal rainfall spatial pattern (first PC takes small absolute values). Besides, for positive (negative) peak value of NAO index the spatial pattern of annual rainfall is evolving toward an area of predominantly positive (nega- tive) anomaly. 2) The second regime starts about 1946 and reaches up to early 1980s. At the time of negative (positive) peak of decadal NAO there is a prevailing spatial pattern of positive (negative) anomaly of decadal rainfall. 3) The third regime starts 1 about late 1970s and reaches to the end of the period under study (in 1996). There is a change of relative phase within this period in late 1980s. In this regime a spatial pattern of prevailing positive or negative anomaly of decadal rainfall takes place dur- ing values of decadal NAO close to zero. 5) At bidecadal timescale the relative phase between the first PC and the NAO index remains almost constant through the period under study. The first PC of the transformed bidecadal component of annual rainfall anomaly attains its positive (negative) peak about three years before the bidecadal component of NAO reaches its negative (positive) peak. 2

Molecular Dynamics Study on Nucleation Behavior and Lamellar Mergence of Polyethylene Globule Crystallization

NASA Astrophysics Data System (ADS)

Yang, Xiaozhen; Wang, Simiao

2012-02-01

The site order parameter (SOP) has been adopted to analyze various order structure formation and distribution during the crystallization of a multi-chain polyethylene globule simulated by molecular dynamics. We found that the nucleation relies on crystallinity fluctuation with increase of amplitude, and the baby nucleus in the fluctuation suddenly appears with different shape and increasing size. In the growth stage, a number of lamellar mergence was observed and their selective behaviors were suggested to be related to the orientation difference between the merging lamellae. We obtained that SOP distribution of all atoms in the system during crystallization appears with two peaks: one for the amorphous phase and the other for the crystalline phase. Mesomorphic structures with medium orders locate between the two peaks as an order promotion pathway. Obtained data show that the medium order structure fluctuates at the growth front and does not always be available; the medium order structure existing at the front is not always good for developing. It is possibly caused by chain entanglement.

Fluctuations Magnetiques des Gaz D'electrons Bidimensionnels: Application AU Compose Supraconducteur LANTHANE(2-X) Strontium(x) Cuivre OXYGENE(4)

NASA Astrophysics Data System (ADS)

Benard, Pierre

Nous presentons une etude des fluctuations magnetiques de la phase normale de l'oxyde de cuivre supraconducteur La_{2-x}Sr _{x}CuO_4 . Le compose est modelise par le Hamiltonien de Hubbard bidimensionnel avec un terme de saut vers les deuxiemes voisins (modele tt'U). Le modele est etudie en utilisant l'approximation de la GRPA (Generalized Random Phase Approximation) et en incluant les effets de la renormalisation de l'interaction de Hubbard par les diagrammes de Brueckner-Kanamori. Dans l'approche presentee dans ce travail, les maximums du facteur de structure magnetique observes par les experiences de diffusion de neutrons sont associes aux anomalies 2k _{F} de reseau du facteur de structure des gaz d'electrons bidimensionnels sans interaction. Ces anomalies proviennent de la diffusion entre particules situees a des points de la surface de Fermi ou les vitesses de Fermi sont tangentes, et conduisent a des divergences dont la nature depend de la geometrie de la surface de Fermi au voisinage de ces points. Ces resultats sont ensuite appliques au modele tt'U, dont le modele de Hubbard usuel tU est un cas particulier. Dans la majorite des cas, les interactions ne determinent pas la position des maximums du facteur de structure. Le role de l'interaction est d'augmenter l'intensite des structures du facteur de structure magnetique associees a l'instabilite magnetique du systeme. Ces structures sont souvent deja presentes dans la partie imaginaire de la susceptibilite sans interaction. Le rapport d'intensite entre les maximums absolus et les autres structures du facteur de structure magnetique permet de determiner le rapport U_ {rn}/U_{c} qui mesure la proximite d'une instabilite magnetique. Le diagramme de phase est ensuite etudie afin de delimiter la plage de validite de l'approximation. Apres avoir discute des modes collectifs et de l'effet d'une partie imaginaire non-nulle de la self-energie, l'origine de l'echelle d'energie des fluctuations magnetiques est examinee. Il est ensuite demontre que le modele a trois bandes predit les memes resultats pour la position des structures du facteur de structure magnetique que le modele a une bande, dans la limite ou l'hybridation des orbitales des atomes d'oxygene des plans Cu-O_2 et l'amplitude de sauts vers les seconds voisins sont nulles. Il est de plus constate que l'effet de l'hybridation des orbitales des atomes d'oxygene est bien modelise par le terme de saut vers les seconds voisins. Meme si ils decrivent correctement le comportement qualitatif des maximums du facteur de structure magnetique, les modeles a trois bandes et a une bande ne permettent pas d'obtenir une position de ces structures conforme avec les mesures experimentales, si on suppose que la bande est rigide, c'est-a-dire que les parametres du Hamiltonien sont independants de la concentration de strontium. Ceci peut etre cause par la dependance des parametres du Hamiltonien sur la concentration de strontium. Finalement, les resultats sont compares avec les experiences de diffusion de neutrons et les autres theories, en particulier celles de Littlewood et al. (1993) et de Q. Si et al. (1993). La comparaison avec les resultats experimentaux pour le compose de lanthane suggere que le liquide de Fermi possede une surface de Fermi disjointe, et qu'il est situe pres d'une instabilite magnetique incommensurable.

A (201)Hg+ Comagnetometer for (199)Hg+ Trapped Ion Space Atomic Clocks

NASA Technical Reports Server (NTRS)

Burt, Eric A.; Taghavi, Shervin; Tjoelker, Robert L.

2011-01-01

A method has been developed for unambiguously measuring the exact magnetic field experienced by trapped mercury ions contained within an atomic clock intended for space applications. In general, atomic clocks are insensitive to external perturbations that would change the frequency at which the clocks operate. On a space platform, these perturbative effects can be much larger than they would be on the ground, especially in dealing with the magnetic field environment. The solution is to use a different isotope of mercury held within the same trap as the clock isotope. The magnetic field can be very accurately measured with a magnetic-field-sensitive atomic transition in the added isotope. Further, this measurement can be made simultaneously with normal clock operation, thereby not degrading clock performance. Instead of using a conventional magnetometer to measure ambient fields, which would necessarily be placed some distance away from the clock atoms, first order field-sensitive atomic transition frequency changes in the atoms themselves determine the variations in the magnetic field. As a result, all ambiguity over the exact field value experienced by the atoms is removed. Atoms used in atomic clocks always have an atomic transition (often referred to as the clock transition) that is sensitive to magnetic fields only in second order, and usually have one or more transitions that are first-order field sensitive. For operating parameters used in the (199)Hg(+) clock, the latter can be five orders of magnitude or more sensitive to field fluctuations than the clock transition, thereby providing an unambiguous probe of the magnetic field strength.

Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography.

PubMed

Gardberg, Anna S; Del Castillo, Alexis Rae; Weiss, Kevin L; Meilleur, Flora; Blakeley, Matthew P; Myles, Dean A A

2010-05-01

The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 A resolution neutron diffraction studies of fully perdeuterated and selectively CH(3)-protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 A resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the sigma level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 A resolution RT neutron data for perdeuterated rubredoxin are approximately 8 times more likely overall to provide high-confidence positions for D atoms than 1.1 A resolution X-ray data at 100 K or RT. At or above the 1.0sigma level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 A resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0sigma level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.

Odd-even parity splittings and octupole correlations in neutron-rich Ba isotopes

NASA Astrophysics Data System (ADS)

Fu, Y.; Wang, H.; Wang, L.-J.; Yao, J. M.

2018-02-01

The odd-even parity splittings in low-lying parity-doublet states of atomic nuclei with octupole correlations have usually been interpreted as rotational excitations on top of octupole vibration in the language of collective models. In this paper, we report a deep analysis of the odd-even parity splittings in the parity-doublet states of neutron-rich Ba isotopes around neutron number N =88 within a full microscopic framework of beyond-mean-field multireference covariant energy density functional theory. The dynamical correlations related to symmetry restoration and quadrupole-octupole shape fluctuation are taken into account with a generator coordinate method combined with parity, particle-number, and angular-momentum projections. We show that the behavior of odd-even parity splittings is governed by the interplay of rotation, quantum tunneling, and shape evolution. Similar to 224Ra, a picture of rotation-induced octupole shape stabilization in the positive-parity states is exhibited in the neutron-rich Ba isotopes.

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

Videla, Pablo E.; Rossky, Peter J.; Laria, D., E-mail: dhlaria@cnea.gov.ar

We present results of ring polymer molecular dynamics simulations that shed light on the effects of nuclear quantum fluctuations on tunneling motions in cyclic [H{sub 2}O]{sub 3} and [D{sub 2}O]{sub 3}, at the representative temperature of T = 75 K. In particular, we focus attention on free energies associated with two key isomerization processes: The first one corresponds to flipping transitions of dangling OH bonds, between up and down positions with respect to the O–O–O plane of the cluster; the second involves the interchange between connecting and dangling hydrogen bond character of the H-atoms in a tagged water molecule. Zeromore » point energy and tunneling effects lead to sensible reductions of the free energy barriers. Due to the lighter nature of the H nuclei, these modifications are more marked in [H{sub 2}O]{sub 3} than in [D{sub 2}O]{sub 3}. Estimates of the characteristic time scales describing the flipping transitions are consistent with those predicted based on standard transition-state-approximation arguments.« less

Communication: Isotopic effects on tunneling motions in the water trimer.

PubMed

Videla, Pablo E; Rossky, Peter J; Laria, D

2016-02-14

We present results of ring polymer molecular dynamics simulations that shed light on the effects of nuclear quantum fluctuations on tunneling motions in cyclic [H2O]3 and [D2O]3, at the representative temperature of T = 75 K. In particular, we focus attention on free energies associated with two key isomerization processes: The first one corresponds to flipping transitions of dangling OH bonds, between up and down positions with respect to the O-O-O plane of the cluster; the second involves the interchange between connecting and dangling hydrogen bond character of the H-atoms in a tagged water molecule. Zero point energy and tunneling effects lead to sensible reductions of the free energy barriers. Due to the lighter nature of the H nuclei, these modifications are more marked in [H2O]3 than in [D2O]3. Estimates of the characteristic time scales describing the flipping transitions are consistent with those predicted based on standard transition-state-approximation arguments.

Fluctuations in Mass-Action Equilibrium of Protein Binding Networks

NASA Astrophysics Data System (ADS)

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

2008-12-01

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

Restoring the lattice of Si-based atom probe reconstructions for enhanced information on dopant positioning.

PubMed

Breen, Andrew J; Moody, Michael P; Ceguerra, Anna V; Gault, Baptiste; Araullo-Peters, Vicente J; Ringer, Simon P

2015-12-01

The following manuscript presents a novel approach for creating lattice based models of Sb-doped Si directly from atom probe reconstructions for the purposes of improving information on dopant positioning and directly informing quantum mechanics based materials modeling approaches. Sophisticated crystallographic analysis techniques are used to detect latent crystal structure within the atom probe reconstructions with unprecedented accuracy. A distortion correction algorithm is then developed to precisely calibrate the detected crystal structure to the theoretically known diamond cubic lattice. The reconstructed atoms are then positioned on their most likely lattice positions. Simulations are then used to determine the accuracy of such an approach and show that improvements to short-range order measurements are possible for noise levels and detector efficiencies comparable with experimentally collected atom probe data. Copyright © 2015 Elsevier B.V. All rights reserved.

Control of transcriptional pausing by biased thermal fluctuations on repetitive genomic sequences

PubMed Central

Imashimizu, Masahiko; Afek, Ariel; Takahashi, Hiroki; Lubkowska, Lucyna; Lukatsky, David B.

2016-01-01

In the process of transcription elongation, RNA polymerase (RNAP) pauses at highly nonrandom positions across genomic DNA, broadly regulating transcription; however, molecular mechanisms responsible for the recognition of such pausing positions remain poorly understood. Here, using a combination of statistical mechanical modeling and high-throughput sequencing and biochemical data, we evaluate the effect of thermal fluctuations on the regulation of RNAP pausing. We demonstrate that diffusive backtracking of RNAP, which is biased by repetitive DNA sequence elements, causes transcriptional pausing. This effect stems from the increased microscopic heterogeneity of an elongation complex, and thus is entropy-dominated. This report shows a linkage between repetitive sequence elements encoded in the genome and regulation of RNAP pausing driven by thermal fluctuations. PMID:27830653

Compact Optical Atomic Clock Based on a Two-Photon Transition in Rubidium

NASA Astrophysics Data System (ADS)

Martin, Kyle W.; Phelps, Gretchen; Lemke, Nathan D.; Bigelow, Matthew S.; Stuhl, Benjamin; Wojcik, Michael; Holt, Michael; Coddington, Ian; Bishop, Michael W.; Burke, John H.

2018-01-01

Extralaboratory atomic clocks are necessary for a wide array of applications (e.g., satellite-based navigation and communication). Building upon existing vapor-cell and laser technologies, we describe an optical atomic clock, designed around a simple and manufacturable architecture, that utilizes the 778-nm two-photon transition in rubidium and yields fractional-frequency instabilities of 4 ×10-13/√{τ (s ) } for τ from 1 to 10 000 s. We present a complete stability budget for this system and explore the required conditions under which a fractional-frequency instability of 1 ×10-15 can be maintained on long time scales. We provide a precise characterization of the leading sensitivities to external processes, including magnetic fields and fluctuations of the vapor-cell temperature and 778-nm laser power. The system is constructed primarily from commercially available components, an attractive feature from the standpoint of the commercialization and deployment of optical frequency standards.

[Application of atomic absorption spectrometry in the engine knock detection].

PubMed

Chen, Li-Dan

2013-02-01

Because existing human experience diagnosis method and apparatus for auxiliary diagnosis method are difficult to diagnose quickly engine knock. Atomic absorption spectrometry was used to detect the automobile engine knock in in innovative way. After having determined Fe, Al, Cu, Cr and Pb content in the 35 groups of Audi A6 engine oil whose travel course is 2 000 -70 000 kilometers and whose sampling interval is 2 000 kilometers by atomic absorption spectrometry, the database of primary metal content in the same automobile engine at different mileage was established. The research shows that the main metal content fluctuates within a certain range. In practical engineering applications, after the determination of engine oil main metal content and comparison with its database value, it can not only help to diagnose the type and location of engine knock without the disintegration and reduce vehicle maintenance costs and improve the accuracy of engine knock fault diagnosis.

Thermal effects in light scattering from ultracold bosons in an optical lattice

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

Lakomy, Kazimierz; Idziaszek, Zbigniew; Trippenbach, Marek

2009-10-15

We study the scattering of a weak and far-detuned light from a system of ultracold bosons in one-dimensional and three-dimensional optical lattices. We show the connection between angular distributions of the scattered light and statistical properties of a Bose gas in a periodic potential. The angular patterns are determined by the Fourier transform of the second-order correlation function, and thus they can be used to retrieve information on particle number fluctuations and correlations. We consider superfluid and Mott-insulator phases of the Bose gas in a lattice and we analyze in detail how the scattering depends on the system dimensionality, temperature,more » and atom-atom interactions.« less

Aberration corrected 1.2-MV cold field-emission transmission electron microscope with a sub-50-pm resolution

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

Akashi, Tetsuya; Takahashi, Yoshio; Tanigaki, Toshiaki, E-mail: toshiaki.tanigaki.mv@hitachi.com

2015-02-16

Atomic-resolution electromagnetic field observation is critical to the development of advanced materials and to the unveiling of their fundamental physics. For this purpose, a spherical-aberration corrected 1.2-MV cold field-emission transmission electron microscope has been developed. The microscope has the following superior properties: stabilized accelerating voltage, minimized electrical and mechanical fluctuation, and coherent electron emission. These properties have enabled to obtain 43-pm information transfer. On the bases of these performances, a 43-pm resolution has been obtained by correcting lens aberrations up to the third order. Observations of GaN [411] thin crystal showed a projected atomic locations with a separation of 44 pm.

Additional motional-magnetic-field considerations for electric-dipole-moment experiments

NASA Astrophysics Data System (ADS)

Lamoreaux, S. K.

1996-06-01

Electric-dipole-moment experiments based on spin-precession measurements of stored atoms or neutrons are generally considered to be immune from the effects of v×E or motional magnetic fields. This is because the average velocity for such systems is zero. We show here that the fluctuating field associated with the random velocity, heretofore not considered, can in fact lead to sizable systematic effects.

The theory of spin noise spectroscopy: a review

DOE PAGES

Sinitsyn, Nikolai A.; Pershin, Yuriy V.

2016-09-12

Direct measurements of spin fluctuations are becoming the mainstream approach for studies of complex condensed matter, molecular, nuclear, and atomic systems. Our review covers recent progress in the field of optical spin noise spectroscopy (SNS) with an additional goal to establish an introduction into its theoretical foundations. Finally we used various theoretical techniques recently to interpret results of SNS measurements are explained alongside examples of their applications.

Sub-poissonian photon statistics in the coherent state Jaynes-Cummings model in non-resonance

NASA Astrophysics Data System (ADS)

Zhang, Jia-tai; Fan, An-fu

1992-03-01

We study a model with a two-level atom (TLA) non-resonance interacting with a single-mode quantized cavity field (QCF). The photon number probability function, the mean photon number and Mandel's fluctuation parameter are calculated. The sub-Poissonian distributions of the photon statistics are obtained in non-resonance interaction. This statistical properties are strongly dependent on the detuning parameters.

Spontaneous time reversal symmetry breaking in atomically confined two-dimensional impurity bands in silicon and germanium

NASA Astrophysics Data System (ADS)

Ghosh, Arindam

Three-dimensional bulk-doped semiconductors, in particular phosphorus (P)-doped silicon (Si) and germanium (Ge), are among the best studied systems for many fundamental concepts in solid state physics, ranging from the Anderson metal-insulator transition to the many-body Coulomb interaction effects on quantum transport. Recent advances in material engineering have led to vertically confined doping of phosphorus (P) atoms inside bulk crystalline silicon and germanium, where the electron transport occurs through one or very few atomic layers, constituting a new and unique platform to investigate many of these phenomena at reduced dimensions. In this talk I shall present results of extensive quantum transport experiments in delta-doped silicon and germanium epilayers, over a wide range of doping density that allow independent tuning of the on-site Coulomb interaction and hopping energy scales. We find that low-frequency flicker noise, or the 1 / f noise, in the electrical conductance of these systems is exceptionally low, and in fact among the lowest when compared with other low-dimensional materials. This is attributed to the physical separation of the conduction electrons, embedded inside the crystalline semiconductor matrix, from the charged fluctuators at the surface. Most importantly, we find a remarkable suppression of weak localization effects, including the quantum correction to conductivity and universal conductance fluctuations, with decreasing doping density or, equivalently, increasing effective on-site Coulomb interaction. In-plane magneto-transport measurements indicate the presence of intrinsic local spin fluctuations at low doping although no signatures of long range magnetic order could be identified. We argue that these results indicate a spontaneous breakdown of time reversal symmetry, which is one of the most fundamental and robust symmetries of nonmagnetic quantum systems. While the microscopic origin of this spontaneous time reversal symmetry breaking remains unknown, we believe this indicates a new many-body electronic phase in two-dimensionally doped silicon and germanium with a half-filled impurity band. We acknowledge financial support from Department of Science and Technology, Government of India, and Australia-India Strategic Research Fund (AISRF).

LETTER: Biased limiter experiments on the Advanced Toroidal Facility (ATF) torsatron

NASA Astrophysics Data System (ADS)

Uckan, T.; Isler, R. C.; Jernigan, T. C.; Lyon, J. F.; Mioduszewski, P. K.; Murakami, M.; Rasmussen, D. A.; Wilgen, J. B.; Aceto, S. C.; Zielinski, J. J.

1994-02-01

The Advanced Toroidal Facility (ATF) torsatron incorporates two rail limiters that can be positioned by external controls. The influence on the plasma parameters of biasing these limiters both positively and negatively with respect to the walls has been investigated. Experiments have been carried out in the electron cyclotron heated plasmas at 200 kW with a typical density of 5 × 1012 cm-3 and a central electron temperature of ~900 eV. Negative biasing produces only small changes in the plasma parameters, but positive biasing increases the particle confinement by about a factor of 5, although the plasma stored energy does fall at the higher voltages. In addition, positive biasing produces the following effects compared with floating limiter discharges: the core density profiles become peaked rather than hollow, the electric field at the edge becomes more negative (pointing radially inward), the magnitudes of the edge fluctuations and the fluctuation induced transport are reduced, the fluctuation wavelengths become longer and their propagation direction reverses from the electron to the ion diamagnetic direction. Neither polarity of biasing appears to affect the impurity content or transport

High-precision two-dimensional atom localization from four-wave mixing in a double-Λ four-level atomic system

NASA Astrophysics Data System (ADS)

Shui, Tao; Yang, Wen-Xing; Chen, Ai-Xi; Liu, Shaopeng; Li, Ling; Zhu, Zhonghu

2018-03-01

We propose a scheme for high-precision two-dimensional (2D) atom localization via the four-wave mixing (FWM) in a four-level double-Λ atomic system. Due to the position-dependent atom-field interaction, the 2D position information of the atoms can be directly determined by the measurement of the normalized light intensity of output FWM-generated field. We further show that, when the position-dependent generated FWM field has become sufficiently intense, efficient back-coupling to the FWM generating state becomes important. This back-coupling pathway leads to competitive multiphoton destructive interference of the FWM generating state by three supplied and one internally generated fields. We find that the precision of 2D atom localization can be improved significantly by the multiphoton destructive interference and depends sensitively on the frequency detunings and the pump field intensity. Interestingly enough, we show that adjusting the frequency detunings and the pump field intensity can modify significantly the FWM efficiency, and consequently lead to a redistribution of the atoms. As a result, the atom can be localized in one of four quadrants with holding the precision of atom localization.

Solvation and Spectral Line Shifts of Chromium Atoms in Helium Droplets Based on a Density Functional Theory Approach

PubMed Central

2014-01-01

The interaction of an electronically excited, single chromium (Cr) atom with superfluid helium nanodroplets of various size (10 to 2000 helium (He) atoms) is studied with helium density functional theory. Solvation energies and pseudo-diatomic potential energy surfaces are determined for Cr in its ground state as well as in the y7P, a5S, and y5P excited states. The necessary Cr–He pair potentials are calculated by standard methods of molecular orbital-based electronic structure theory. In its electronic ground state the Cr atom is found to be fully submerged in the droplet. A solvation shell structure is derived from fluctuations in the radial helium density. Electronic excitations of an embedded Cr atom are simulated by confronting the relaxed helium density (ρHe), obtained for Cr in the ground state, with interaction pair potentials of excited states. The resulting energy shifts for the transitions z7P ← a7S, y7P ← a7S, z5P ← a5S, and y5P ← a5S are compared to recent fluorescence and photoionization experiments. PMID:24906160

Solvation and spectral line shifts of chromium atoms in helium droplets based on a density functional theory approach.

PubMed

Ratschek, Martin; Pototschnig, Johann V; Hauser, Andreas W; Ernst, Wolfgang E

2014-08-21

The interaction of an electronically excited, single chromium (Cr) atom with superfluid helium nanodroplets of various size (10 to 2000 helium (He) atoms) is studied with helium density functional theory. Solvation energies and pseudo-diatomic potential energy surfaces are determined for Cr in its ground state as well as in the y(7)P, a(5)S, and y(5)P excited states. The necessary Cr-He pair potentials are calculated by standard methods of molecular orbital-based electronic structure theory. In its electronic ground state the Cr atom is found to be fully submerged in the droplet. A solvation shell structure is derived from fluctuations in the radial helium density. Electronic excitations of an embedded Cr atom are simulated by confronting the relaxed helium density (ρHe), obtained for Cr in the ground state, with interaction pair potentials of excited states. The resulting energy shifts for the transitions z(7)P ← a(7)S, y(7)P ← a(7)S, z(5)P ← a(5)S, and y(5)P ← a(5)S are compared to recent fluorescence and photoionization experiments.

Growth and characterization of epitaxial silver indium diselenide

NASA Astrophysics Data System (ADS)

Pena Martin, Pamela

Photovoltaics (solar cells) are a key player in the renewable energy frontier, and will become increasingly important as their cost per watt continues to drop, especially if fossil fuel costs increase. One particularly promising photovoltaic technology is based on chalcopyrite-structure semiconductors. Within the chalcopyrite compounds the highest efficiency thin film solar cell absorber material to date is Cu(In,Ga)Se2 (CIGS). While current efficiency records are over 21% for single-junction cells, there is still room for improvement. Replacing some of the Cu with Ag has been shown to be beneficial in CIGS devices. However, the Ag- containing chalcopyrites are still relatively unknown in terms of their growth mechanism, energetics, and surface atomic and electronic properties. These are best inferred through study of epitaxial films, yet they have little mention in literature and have not been the subject of a detailed study. This work describes the growth of epitaxial AgInSe2 (AIS) on GaAs substrates, studying the morphology, structure, and surface properties to understand how growth takes place. It also seeks to experimentally determine the surface electronic and atomic structure at the atomic scale to gain insight into the part of the material that forms the heterojunction that collects photon energy in the device. Finally, this work seeks to compare and contrast these findings with what is known about CIGS to determine where similarities and, more importantly, the differences may lie. This study has found that single phase tetragonal AIS can be epitaxially grown on GaAs, as illustrated by x-ray diffraction (XRD), transmission electron microscope (TEM), and surface morphology data. Like CIGS, the close packed polar (112) planes have the lowest energy. The morphology points to a difference in step dynamics, leading to less faceted, straight edged island shapes compared to CIGS. Epitaxial temperature as a function of growth direction shows a different trend in AIS than in CIGS. Interdiffusion of the group III elements across the substrate interface was found to result in an epitaxial intermixed layer between the film and substrate in some cases, which may help mediate the lattice mismatch. At the atomic scale, scanning tunneling microscopy (STM) was used to observe details of the surface morphology, which indicated growth of the (112)A orientation of AIS by a screw dislocation mechanism (other surfaces were not examined by STM but are expected to show similar results). The surface atomic structure was directly imaged for the first time, revealing an arrangement similar to that expected from a bulk terminated surface. The electronic structure shows a gap in surface electronic states with a width comparable to bulk AIS, n-type conduction, and a tail of states near the valence band edge that decay well into the gap. The conduction and valence bands show fluctuations as a function of position on the surface, with greater magnitude in the valence band. The fluctuations in both bands are less than those observed on the surface of CIS by STM. It seems to indicate a reduction in band tails, both in magnitude and spacial extent, in AIS compared to CIS, likely tied to a reduction in point defect concentration at the surface.

Porphyrins and their synthesis from dipyrromethanes and aldehydes

DOEpatents

Wijesekera, Tilak; Lyons, James E.; Ellis, Jr., Paul E.

1998-01-01

The invention comprises new compositions of matter, which are iron, manganese, cobalt or ruthenium complexes of porphyrins having hydrogen, haloalkyl or haloaryl groups in meso positions, two of the opposed meso atoms or groups being hydrogen or haloaryl, and two of the opposed meso atoms or groups being hydrogen or haloalkyl, but not all four of the meso atoms or groups being hydrogen. The invention also comprises new compositions of matter in which all four of the meso positions are substituted with haloalkyl groups and the beta positions are substituted with halogen atoms. A new method of synthesizing porphyrinogens is also provided.

Porphyrins and their synthesis from dipyrromethanes and aldehydes

DOEpatents

Wijesekera, T.; Lyons, J.E.; Ellis, P.E. Jr.

1998-06-02

The invention comprises new compositions of matter, which are iron, manganese, cobalt or ruthenium complexes of porphyrins having hydrogen, haloalkyl or haloaryl groups in meso positions, two of the opposed meso atoms or groups being hydrogen or haloaryl, and two of the opposed meso atoms or groups being hydrogen or haloalkyl, but not all four of the meso atoms or groups being hydrogen. The invention also comprises new compositions of matter in which all four of the meso positions are substituted with haloalkyl groups and the beta positions are substituted with halogen atoms. A new method of synthesizing porphyrinogens is also provided.

Canceling the Gravity Gradient Phase Shift in Atom Interferometry.

PubMed

D'Amico, G; Rosi, G; Zhan, S; Cacciapuoti, L; Fattori, M; Tino, G M

2017-12-22

Gravity gradients represent a major obstacle in high-precision measurements by atom interferometry. Controlling their effects to the required stability and accuracy imposes very stringent requirements on the relative positioning of freely falling atomic clouds, as in the case of precise tests of Einstein's equivalence principle. We demonstrate a new method to exactly compensate the effects introduced by gravity gradients in a Raman-pulse atom interferometer. By shifting the frequency of the Raman lasers during the central π pulse, it is possible to cancel the initial position- and velocity-dependent phase shift produced by gravity gradients. We apply this technique to simultaneous interferometers positioned along the vertical direction and demonstrate a new method for measuring local gravity gradients that does not require precise knowledge of the relative position between the atomic clouds. Based on this method, we also propose an improved scheme to determine the Newtonian gravitational constant G towards the 10 ppm relative uncertainty.

Canceling the Gravity Gradient Phase Shift in Atom Interferometry

NASA Astrophysics Data System (ADS)

D'Amico, G.; Rosi, G.; Zhan, S.; Cacciapuoti, L.; Fattori, M.; Tino, G. M.

2017-12-01

Gravity gradients represent a major obstacle in high-precision measurements by atom interferometry. Controlling their effects to the required stability and accuracy imposes very stringent requirements on the relative positioning of freely falling atomic clouds, as in the case of precise tests of Einstein's equivalence principle. We demonstrate a new method to exactly compensate the effects introduced by gravity gradients in a Raman-pulse atom interferometer. By shifting the frequency of the Raman lasers during the central π pulse, it is possible to cancel the initial position- and velocity-dependent phase shift produced by gravity gradients. We apply this technique to simultaneous interferometers positioned along the vertical direction and demonstrate a new method for measuring local gravity gradients that does not require precise knowledge of the relative position between the atomic clouds. Based on this method, we also propose an improved scheme to determine the Newtonian gravitational constant G towards the 10 ppm relative uncertainty.

Range-dependence of acoustic channel with traveling sinusoidal surface wave.

PubMed

Choo, Youngmin; Seong, Woojae; Lee, Keunhwa

2014-04-01

Range-dependence of time-varying acoustic channels caused by a traveling surface wave is investigated through water tank experiments and acoustic propagation analysis schemes. As the surface wave travels, surface reflected signals fluctuate and the fluctuation varies with source-receiver horizontal range. Amplitude fluctuations of surface reflected signals increase with increasing horizontal range whereas the opposite occurs in delay fluctuations. The scattered pressure field at a fixed time shows strong dependence on the receiver position because of caustics and shadow zones formed by the surface. The Doppler shifts of surface reflected signals also depend on the horizontal range. Comparison between measurement data and model results indicates the Doppler shift relies on the delay fluctuation under current experimental conditions.

Simultaneous Global Positioning System observations of equatorial scintillations and total electron content fluctuations

NASA Astrophysics Data System (ADS)

Beach, Theodore L.; Kintner, Paul M.

1999-10-01

One aspect of the Global Positioning System (GPS) is the potential to conduct geophysical research, and worldwide networks of GPS receivers have been established to exploit this potential. Several research groups have begun using this global GPS data to study ionospheric total electron content (TEC) variations, also referred to as GPS phase fluctuations, as surrogates for ionospheric scintillations. This paper investigates the relationship between GPS amplitude scintillations and TEC variations for the same line of sight using observations from Ancón, Peru. These observations were taken under equatorial spread F conditions for three nights in April 1997. As expected, only when the spectrum of TEC fluctuations includes significant power at the Fresnel scale do scintillations appear. We also find that when the TEC fluctuation spectrum includes the Fresnel scale, the S4 scintillation index is roughly proportional to measures of TEC fluctuation for the weak scintillations observed. The proportionality constant varies from night to night, however, casting doubt on the ability to predict GPS S4 successfully from TEC fluctuation data alone. We also present a simple theoretical phase screen model and show that if a relationship between TEC fluctuation measures and S4 exists, that relationship depends on the power spectrum of phase variations at the screen. Unfortunately, the available TEC data, at 30 s per sample (with some aliasing apparently permitted), offer limited spectral information. A preliminary comparison of 1 s/sample data with the same data decimated to a 30 s/sample interval suggests, however, that the level of successful S4 prediction, based on TEC fluctuation measures alone, is comparable at either sample rate.

Cerebellar Purkinje Cells Generate Highly Correlated Spontaneous Slow-Rate Fluctuations.

PubMed

Cao, Ying; Liu, Yu; Jaeger, Dieter; Heck, Detlef H

2017-01-01

Cerebellar Purkinje cells (PC) fire action potentials at high, sustained rates. Changes in spike rate that last a few tens of milliseconds encode sensory and behavioral events. Here we investigated spontaneous fluctuations of PC simple spike rate at a slow time scale of the order of 1 s. Simultaneous recordings from pairs of PCs that were aligned either along the sagittal or transversal axis of the cerebellar cortex revealed that simple spike rate fluctuations at the 1 s time scale were highly correlated. Each pair of PCs had either a predominantly positive or negative slow-rate correlation, with negative correlations observed only in PC pairs aligned along the transversal axis. Slow-rate correlations were independent of faster rate changes that were correlated with fluid licking behavior. Simultaneous recordings from PCs and cerebellar nuclear (CN) neurons showed that slow-rate fluctuations in PC and CN activity were also highly correlated, but their correlations continually alternated between periods of positive and negative correlation. The functional significance of this new aspect of cerebellar spike activity remains to be determined. Correlated slow-rate fluctuations seem too slow to be involved in the real-time control of ongoing behavior. However, slow-rate fluctuations of PCs converging on the same CN neuron are likely to modulate the excitability of the CN neuron, thus introduce a possible slow modulation of cerebellar output activity.

The stochastic resonance for the incidence function model of metapopulation

NASA Astrophysics Data System (ADS)

Li, Jiang-Cheng; Dong, Zhi-Wei; Zhou, Ruo-Wei; Li, Yun-Xian; Qian, Zhen-Wei

2017-06-01

A stochastic model with endogenous and exogenous periodicities is proposed in this paper on the basis of metapopulation dynamics to model the crop yield losses due to pests and diseases. The rationale is that crop yield losses occur because the physiology of the growing crop is negatively affected by pests and diseases in a dynamic way over time as crop both grows and develops. Metapopulation dynamics can thus be used to model the resultant crop yield losses. The stochastic metapopulation process is described by using the Simplified Incidence Function model (IFM). Compared to the original IFMs, endogenous and exogenous periodicities are considered in the proposed model to handle the cyclical patterns observed in pest infestations, diseases epidemics, and exogenous affecting factors such as temperature and rainfalls. Agricultural loss data in China are used to fit the proposed model. Experimental results demonstrate that: (1) Model with endogenous and exogenous periodicities is a better fit; (2) When the internal system fluctuations and external environmental fluctuations are negatively correlated, EIL or the cost of loss is monotonically increasing; when the internal system fluctuations and external environmental fluctuations are positively correlated, an outbreak of pests and diseases might occur; (3) If the internal system fluctuations and external environmental fluctuations are positively correlated, an optimal patch size can be identified which will greatly weaken the effects of external environmental influence and hence inhibit pest infestations and disease epidemics.

Vibrational spectra from atomic fluctuations in dynamics simulations. II. Solvent-induced frequency fluctuations at femtosecond time resolution

NASA Astrophysics Data System (ADS)

Schmitz, Matthias; Tavan, Paul

2004-12-01

The midinfrared (MIR) spectra of molecules in polar solvents exhibit inhomogeneously broadened bands whose spectral positions are shifted as compared to the gas phase. The shifts are caused by interactions with structured solvation shells and the broadenings by fluctuations of these interactions. The MIR spectra can be calculated from hybrid molecular dynamics (MD) simulations, which treat the solute molecule by density functional theory and the solvent by molecular mechanics by the so-called instantaneous normal mode analysis (INMA) or by Fourier transforming the time correlation function (FTTCF) of the molecular dipole moment. In Paper I of this work [M. Schmitz and P. Tavan, J. Chem. Phys. 121, 12233 (2004)] we explored an alternative method based on generalized virial (GV) frequencies noting, however, that GV systematically underestimates frequencies. As shown by us these artifacts are caused by solvent-induced fluctuations of the (i) equilibrium geometry, (ii) force constants, and (iii) normal mode directions as well as by (iv) diagonal and (v) off-diagonal anharmonicities. Here we now show, by analyzing the time scales of fluctuations and sample MD trajectories of formaldehyde in the gas phase and in water, that all these sources of computational artifacts can be made visible by a Fourier analysis of the normal coordinates. Correspondingly, the error sources (i) and (iii)-(v) can be removed by bandpass filtering, as long as the spectral signatures of the respective effects are well separated from the fundamental band. Furthermore, the artifacts arising from effect (ii) can be strongly diminished by a time-resolved version of the GV approach (TF-GV). The TF-GV method then yields for each mode j a trajectory of the vibrational frequency ωj(t|τ) at a time resolution τ>τj, which is only limited by the corresponding oscillation time τj=2π/ωj and, thus, is in the femtosecond range. A correlation analysis of these trajectories clearly separates the librational motions from the conformational dynamics of the solvation shells and yields the inhomogeneously broadened MIR spectra, if the theory of motional narrowing is properly included. The MIR spectrum of formaldehyde in solution obtained by TF-GV agrees very well with the FTTCF result, if one applies the so-called "harmonic approximation" quantum correction factor and a temperature scaling to the FTTCF intensities. Also for INMA an excellent agreement is achieved if one disregards a slight INMA overestimate of linewidths.

Hydration of Li+ -ion in atom-bond electronegativity equalization method-7P water: a molecular dynamics simulation study.

PubMed

Li, Xin; Yang, Zhong-Zhi

2005-02-22

We have carried out molecular dynamics simulations of a Li(+) ion in water over a wide range of temperature (from 248 to 368 K). The simulations make use of the atom-bond electronegativity equalization method-7P water model, a seven-site flexible model with fluctuating charges, which has accurately reproduced many bulk water properties. The recently constructed Li(+)-water interaction potential through fitting to the experimental and ab initio gas-phase binding energies and to the measured structures for Li(+)-water clusters is adopted in the simulations. ABEEM was proposed and developed in terms of partitioning the electron density into atom and bond regions and using the electronegativity equalization method (EEM) and the density functional theory (DFT). Based on a combination of the atom-bond electronegativity equalization method and molecular mechanics (ABEEM/MM), a new set of water-water and Li(+)-water potentials, successfully applied to ionic clusters Li(+)(H(2)O)(n)(n=1-6,8), are further investigated in an aqueous solution of Li(+) in the present paper. Two points must be emphasized in the simulations: first, the model allows for the charges on the interacting sites fluctuating as a function of time; second, the ABEEM-7P model has applied the parameter k(lp,H)(R(lp,H)) to explicitly describe the short-range interaction of hydrogen bond in the hydrogen bond interaction region, and has a new description for the hydrogen bond. The static, dynamic, and thermodynamic properties have been studied in detail. In addition, at different temperatures, the structural properties such as radial distribution functions, and the dynamical properties such as diffusion coefficients and residence times of the water molecules in the first hydration shell of Li(+), are also simulated well. These simulation results show that the ABEEM/MM-based water-water and Li(+)-water potentials appear to be robust giving the overall characteristic hydration properties in excellent agreement with experiments and other molecular dynamics simulations on similar system.

Precursory signatures of protein folding/unfolding: From time series correlation analysis to atomistic mechanisms

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

Hsu, P. J.; Lai, S. K., E-mail: sklai@coll.phy.ncu.edu.tw; Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan

Folded conformations of proteins in thermodynamically stable states have long lifetimes. Before it folds into a stable conformation, or after unfolding from a stable conformation, the protein will generally stray from one random conformation to another leading thus to rapid fluctuations. Brief structural changes therefore occur before folding and unfolding events. These short-lived movements are easily overlooked in studies of folding/unfolding for they represent momentary excursions of the protein to explore conformations in the neighborhood of the stable conformation. The present study looks for precursory signatures of protein folding/unfolding within these rapid fluctuations through a combination of three techniques: (1)more » ultrafast shape recognition, (2) time series segmentation, and (3) time series correlation analysis. The first procedure measures the differences between statistical distance distributions of atoms in different conformations by calculating shape similarity indices from molecular dynamics simulation trajectories. The second procedure is used to discover the times at which the protein makes transitions from one conformation to another. Finally, we employ the third technique to exploit spatial fingerprints of the stable conformations; this procedure is to map out the sequences of changes preceding the actual folding and unfolding events, since strongly correlated atoms in different conformations are different due to bond and steric constraints. The aforementioned high-frequency fluctuations are therefore characterized by distinct correlational and structural changes that are associated with rate-limiting precursors that translate into brief segments. Guided by these technical procedures, we choose a model system, a fragment of the protein transthyretin, for identifying in this system not only the precursory signatures of transitions associated with α helix and β hairpin, but also the important role played by weaker correlations in such protein folding dynamics.« less

Precursory signatures of protein folding/unfolding: From time series correlation analysis to atomistic mechanisms

NASA Astrophysics Data System (ADS)

Hsu, P. J.; Cheong, S. A.; Lai, S. K.

2014-05-01

Folded conformations of proteins in thermodynamically stable states have long lifetimes. Before it folds into a stable conformation, or after unfolding from a stable conformation, the protein will generally stray from one random conformation to another leading thus to rapid fluctuations. Brief structural changes therefore occur before folding and unfolding events. These short-lived movements are easily overlooked in studies of folding/unfolding for they represent momentary excursions of the protein to explore conformations in the neighborhood of the stable conformation. The present study looks for precursory signatures of protein folding/unfolding within these rapid fluctuations through a combination of three techniques: (1) ultrafast shape recognition, (2) time series segmentation, and (3) time series correlation analysis. The first procedure measures the differences between statistical distance distributions of atoms in different conformations by calculating shape similarity indices from molecular dynamics simulation trajectories. The second procedure is used to discover the times at which the protein makes transitions from one conformation to another. Finally, we employ the third technique to exploit spatial fingerprints of the stable conformations; this procedure is to map out the sequences of changes preceding the actual folding and unfolding events, since strongly correlated atoms in different conformations are different due to bond and steric constraints. The aforementioned high-frequency fluctuations are therefore characterized by distinct correlational and structural changes that are associated with rate-limiting precursors that translate into brief segments. Guided by these technical procedures, we choose a model system, a fragment of the protein transthyretin, for identifying in this system not only the precursory signatures of transitions associated with α helix and β hairpin, but also the important role played by weaker correlations in such protein folding dynamics.

Zn-metalloprotease sequences in extremophiles

NASA Astrophysics Data System (ADS)

Holden, T.; Dehipawala, S.; Golebiewska, U.; Cheung, E.; Tremberger, G., Jr.; Williams, E.; Schneider, P.; Gadura, N.; Lieberman, D.; Cheung, T.

2010-09-01

The Zn-metalloprotease family contains conserved amino acid structures such that the nucleotide fluctuation at the DNA level would exhibit correlated randomness as described by fractal dimension. A nucleotide sequence fractal dimension can be calculated from a numerical series consisting of the atomic numbers of each nucleotide. The structure's vibration modes can also be studied using a Gaussian Network Model. The vibration measure and fractal dimension values form a two-dimensional plot with a standard vector metric that can be used for comparison of structures. The preference for amino acid usage in extremophiles may suppress nucleotide fluctuations that could be analyzed in terms of fractal dimension and Shannon entropy. A protein level cold adaptation study of the thermolysin Zn-metalloprotease family using molecular dynamics simulation was reported recently and our results show that the associated nucleotide fluctuation suppression is consistent with a regression pattern generated from the sequences's fractal dimension and entropy values (R-square { 0.98, N =5). It was observed that cold adaptation selected for high entropy and low fractal dimension values. Extension to the Archaemetzincin M54 family in extremophiles reveals a similar regression pattern (R-square = 0.98, N = 6). It was observed that the metalloprotease sequences of extremely halophilic organisms possess high fractal dimension and low entropy values as compared with non-halophiles. The zinc atom is usually bonded to the histidine residue, which shows limited levels of vibration in the Gaussian Network Model. The variability of the fractal dimension and entropy for a given protein structure suggests that extremophiles would have evolved after mesophiles, consistent with the bias usage of non-prebiotic amino acids by extremophiles. It may be argued that extremophiles have the capacity to offer extinction protection during drastic changes in astrobiological environments.

A New Look at Rainfall Fluctuations and Scaling Properties of Spatial Rainfall Using Orthogonal Wavelets.

NASA Astrophysics Data System (ADS)

Kumar, Praveen; Foufoula-Georgiou, Efi

1993-02-01

It has been observed that the finite-dimensional distribution functions of rainfall cannot obey simple scaling laws due to rainfall intermittency (mixed distribution with an atom at zero) and the probability of rainfall being an increasing function of area. Although rainfall fluctuations do not suffer these limitations, it is interesting to note that very few attempts have been made to study them in terms of their self-similarity characteristics. This is due to the lack of unambiguous definition of fluctuations in multidimensions. This paper shows that wavelet transforms offer a convenient and consistent method for the decomposition of inhomogeneous and anisotropic rainfall fields in two dimensions and that the components of this decomposition can be looked at as fluctuations of the rainfall field. It is also shown that under some mild assumptions, the component fields can be treated as homogeneous and thus are amenable to second-order analysis, which can provide useful insight into the nature of the process. The fact that wavelet transforms are a space-scale method also provides a convenient tool to study scaling characteristics of the process. Orthogonal wavelets are used, and these properties are investigated for a squall-line storm to study the presence of self-similarity.

Locked modes in two reversed-field pinch devices of different size and shell system

NASA Astrophysics Data System (ADS)

Malmberg, J.-A.; Brunsell, P. R.; Yagi, Y.; Koguchi, H.

2000-10-01

The behavior of locked modes in two reversed-field pinch devices, the Toroidal Pinch Experiment (TPE-RX) [Y. Yagi et al., Plasma Phys. Control. Fusion 41, 2552 (1999)] and Extrap T2 [J. R. Drake et al., in Plasma Physics and Controlled Nuclear Fusion Research 1996, Montreal (International Atomic Energy Agency, Vienna, 1996), Vol. 2, p. 193] is analyzed and compared. The main characteristics of the locked mode are qualitatively similar. The toroidal distribution of the mode locking shows that field errors play a role in both devices. The probability of phase locking is found to increase with increasing magnetic fluctuation levels in both machines. Furthermore, the probability of phase locking increases with plasma current in TPE-RX despite the fact that the magnetic fluctuation levels decrease. A comparison with computations using a theoretical model estimating the critical mode amplitude for locking [R. Fitzpatrick et al., Phys. Plasmas 6, 3878 (1999)] shows a good correlation with experimental results in TPE-RX. In Extrap T2, the magnetic fluctuations scale weakly with both plasma current and electron densities. This is also reflected in the weak scaling of the magnetic fluctuation levels with the Lundquist number (˜S-0.06). In TPE-RX, the corresponding scaling is ˜S-0.18.

A new look at rainfall fluctuations and scaling properties of spatial rainfall using orthogonal wavelets

NASA Technical Reports Server (NTRS)

Kumar, Praveen; Foufoula-Georgiou, Efi

1993-01-01

It has been observed that the finite-dimensional distribution functions of rainfall cannot obey simple scaling laws due to rainfall intermittency (mixed distribution with an atom at zero) and the probability of rainfall being an increasing function of area. Although rainfall fluctuations do not suffer these limitations, it is interesting to note that very few attempts have been made to study them in terms of their self-similarity characteristics. This is due to the lack of unambiguous definition of fluctuations in multidimensions. This paper shows that wavelet transforms offer a convenient and consistent method for the decomposition of inhomogeneous and anisotropic rainfall fields in two dimensions and that the components of this decomposition can be looked at as fluctuations of the rainfall field. It is also shown that under some mild assumptions, the component fields can be treated as homogeneous and thus are amenable to second-order analysis, which can provide useful insight into the nature of the process. The fact that wavelet transforms are a space-scale method also provides a convenient tool to study scaling characteristics of the process. Orthogonal wavelets are used, and these properties are investigated for a squall-line storm to study the presence of self-similarity.

Development of a Strontium Magneto-Optical Trap for Probing Casimir-Polder Potentials

NASA Astrophysics Data System (ADS)

Martin, Paul J.

In recent years, cold atoms have been the centerpiece of many remarkably sensitive measurements, and much effort has been made to devise miniaturized quantum sensors and quantum information processing devices. At small distances, however, mechanical effects of the quantum vacuum begin to significantly impact the behavior of the cold-atom systems. A better understanding of how surface composition and geometry affect Casimir and Casimir-Polder potentials would benefit future engineering of small-scale devices. Unfortunately, theoretical solutions are limited and the number of experimental techniques that can accurately detect such short-range forces is relatively small. We believe the exemplary properties of atomic strontium--which have enabled unprecedented frequency metrology in optical lattice clocks--make it an ideal candidate for probing slight spectroscopic perturbations caused by vacuum fluctuations. To that end, we have constructed a magneto-optical trap for strontium to enable future study of atom-surface potentials, and the apparatus and proposed detection scheme are discussed herein. Of special note is a passively stable external-cavity diode laser we developed that is both affordable and competitive with high-end commercial options.

Fast, High-Precision Optical Polarization Synthesizer for Ultracold-Atom Experiments

NASA Astrophysics Data System (ADS)

Robens, Carsten; Brakhane, Stefan; Alt, Wolfgang; Meschede, Dieter; Zopes, Jonathan; Alberti, Andrea

2018-03-01

We present a technique for the precision synthesis of arbitrary polarization states of light with a high modulation bandwidth. Our approach consists of superimposing two laser light fields with the same wavelength, but with opposite circular polarizations, where the phase and the amplitude of each light field are individually controlled. We find that the polarization-synthesized beam reaches a degree of polarization of 99.99%, which is mainly limited by static spatial variations of the polarization state over the beam profile. We also find that the depolarization caused by temporal fluctuations of the polarization state is about 2 orders of magnitude smaller. In a recent work, Robens et al. [Low-Entropy States of Neutral Atoms in Polarization-Synthesized Optical Lattices, Phys. Rev. Lett. 118, 065302 (2017), 10.1103/PhysRevLett.118.065302] demonstrated an application of the polarization synthesizer to create two independently controllable optical lattices which trap atoms depending on their internal spin state. We use ultracold atoms in polarization-synthesized optical lattices to give an independent, in situ demonstration of the performance of the polarization synthesizer.

Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins.

PubMed

Nguyen, Bao Linh; Pettitt, B Montgomery

2015-04-14

The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations.

A high-pressure atomic force microscope for imaging in supercritical carbon dioxide

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

Lea, Alan S.; Higgins, Steven R.; Knauss, Kevin G.

2011-04-26

A high-pressure atomic force microscope (AFM) that enables in-situ, atomic scale measurements of topography of solid surfaces in contact with supercritical CO2 (scCO2) fluids has been developed. This apparatus overcomes the pressure limitations of the hydrothermal AFM and is designed to handle pressures up to 100 atm at temperatures up to ~ 350 K. A standard optically-based cantilever deflection detection system was chosen. When imaging in compressible supercritical fluids such as scCO2, precise control of pressure and temperature in the fluid cell is the primary technical challenge. Noise levels and imaging resolution depend on minimization of fluid density fluctuations thatmore » change the fluid refractive index and hence the laser path. We demonstrate with our apparatus in-situ atomic scale imaging of a calcite (CaCO3) mineral surface in scCO2; both single, monatomic steps and dynamic processes occurring on the (10¯14) surface are presented. This new AFM provides unprecedented in-situ access to interfacial phenomena at solid-fluid interfaces under pressure.« less

Collective emission of matter-wave jets from driven Bose-Einstein condensates.

PubMed

Clark, Logan W; Gaj, Anita; Feng, Lei; Chin, Cheng

2017-11-16

Scattering is used to probe matter and its interactions in all areas of physics. In ultracold atomic gases, control over pairwise interactions enables us to investigate scattering in quantum many-body systems. Previous experiments on colliding Bose-Einstein condensates have revealed matter-wave interference, haloes of scattered atoms, four-wave mixing and correlations between counter-propagating pairs. However, a regime with strong stimulation of spontaneous collisions analogous to superradiance has proved elusive. In this regime, the collisions rapidly produce highly correlated states with macroscopic population. Here we find that runaway stimulated collisions in Bose-Einstein condensates with periodically modulated interaction strength cause the collective emission of matter-wave jets that resemble fireworks. Jets appear only above a threshold modulation amplitude and their correlations are invariant even when the number of ejected atoms grows exponentially. Hence, we show that the structures and atom occupancies of the jets stem from the quantum fluctuations of the condensate. Our findings demonstrate the conditions required for runaway stimulated collisions and reveal the quantum nature of matter-wave emission.

3D atom microscopy in the presence of Doppler shift

NASA Astrophysics Data System (ADS)

Rahmatullah; Chuang, You-Lin; Lee, Ray-Kuang; Qamar, Sajid

2018-03-01

The interaction of hot atoms with laser fields produces a Doppler shift, which can severely affect the precise spatial measurement of an atom. We suggest an experimentally realizable scheme to address this issue in the three-dimensional position measurement of a single atom in vapors of rubidium atoms. A three-level Λ-type atom-field configuration is considered where a moving atom interacts with three orthogonal standing-wave laser fields and spatial information of the atom in 3D space is obtained via an upper-level population using a weak probe laser field. The atom moves with velocity v along the probe laser field, and due to the Doppler broadening the precision of the spatial information deteriorates significantly. It is found that via a microwave field, precision in the position measurement of a single hot rubidium atom can be attained, overcoming the limitation posed by the Doppler shift.

Scattering length of composite bosons in the three-dimensional BCS-BEC crossover

NASA Astrophysics Data System (ADS)

Salasnich, L.; Bighin, G.

2015-03-01

We study the zero-temperature grand potential of a three-dimensional superfluid made of ultracold fermionic alkali-metal atoms in the BCS-BEC crossover. In particular, we analyze the zero-point energy of both fermionic single-particle excitations and bosonic collective excitations. The bosonic elementary excitations, which are crucial to obtain a reliable equation of state in the Bose-Einstein condensate regime, are obtained with a low-momentum expansion up to the forth order of the quadratic (Gaussian) action of the fluctuating pairing field. By performing a cutoff regularization and renormalization of Gaussian fluctuations, we find that the scattering length aB of composite bosons, bound states of fermionic pairs, is given by aB=(2 /3 ) aF , where aF is the scattering length of fermions.

Efficient atom localization via probe absorption in an inverted-Y atomic system

NASA Astrophysics Data System (ADS)

Wu, Jianchun; Wu, Bo; Mao, Jiejian

2018-06-01

The behaviour of atom localization in an inverted-Y atomic system is theoretically investigated. For the atoms interacting with a weak probe field and several orthogonal standing-wave fields, their position information can be obtained by measuring the probe absorption. Compared with the traditional scheme, we couple the probe field to the transition between the middle and top levels. It is found that the probe absorption sensitively depends on the detuning and strength of the relevant light fields. Remarkably, the atom can be localized at a particular position in the standing-wave fields by coupling a microwave field to the transition between the two ground levels.

Density Fluctuation in Asymmetric Nozzle Plumes and Correlation with Far Field Noise

NASA Technical Reports Server (NTRS)

Panda, J.; Zaman, K. B. M. Q.

2001-01-01

A comparative experimental study of air density fluctuations in the unheated plumes of a circular, 4-tabbed-circular, chevron-circular and 10-lobed rectangular nozzles was performed at a fixed Mach number of 0.95 using a recently developed Rayleigh scattering based technique. Subsequently, the flow density fluctuations are cross-correlated with the far field sound pressure fluctuations to determine sources for acoustics emission. The nearly identical noise spectra from the baseline circular and the chevron nozzles are found to be in agreement with the similarity in spreading, turbulence fluctuations, and flow-sound correlations measured in the plumes. The lobed nozzle produced the least low frequency noise, in agreement with the weakest overall density fluctuations and flow-sound correlation. The tabbed nozzle took an intermediate position in the hierarchy of noise generation, intensity of turbulent fluctuation and flow-sound correlation. Some of the features in the 4-tabbed nozzle are found to be explainable in terms of splitting of the jet in a central large core and 4 side jetlets.

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.

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

Luis, Alfredo

The use of Renyi entropy as an uncertainty measure alternative to variance leads to the study of states with quantum fluctuations below the levels established by Gaussian states, which are the position-momentum minimum uncertainty states according to variance. We examine the quantum properties of states with exponential wave functions, which combine reduced fluctuations with practical feasibility.

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.

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

Li, Chunhua; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 45108; Lv, Dashuai

Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regionsmore » between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.« less

INJECTION TO RAPID DIFFUSIVE SHOCK ACCELERATION AT PERPENDICULAR SHOCKS IN PARTIALLY IONIZED PLASMAS

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

Ohira, Yutaka, E-mail: ohira@phys.aoyama.ac.jp

2016-08-10

We present a three-dimensional hybrid simulation of a collisionless perpendicular shock in a partially ionized plasma for the first time. In this simulation, the shock velocity and upstream ionization fraction are v {sub sh} ≈ 1333 km s{sup −1} and f {sub i} ∼ 0.5, which are typical values for isolated young supernova remnants (SNRs) in the interstellar medium. We confirm previous two-dimensional simulation results showing that downstream hydrogen atoms leak into the upstream region and are accelerated by the pickup process in the upstream region, and large magnetic field fluctuations are generated both in the upstream and downstream regions.more » In addition, we find that the magnetic field fluctuations have three-dimensional structures and the leaking hydrogen atoms are injected into the diffusive shock acceleration (DSA) at the perpendicular shock after the pickup process. The observed DSA can be interpreted as shock drift acceleration with scattering. In this simulation, particles are accelerated to v ∼ 100 v {sub sh} ∼ 0.3 c within ∼100 gyroperiods. The acceleration timescale is faster than that of DSA in parallel shocks. Our simulation results suggest that SNRs can accelerate cosmic rays to 10{sup 15.5} eV (the knee) during the Sedov phase.« less

The signature of the first stars in atomic hydrogen at redshift 20.

PubMed

Visbal, Eli; Barkana, Rennan; Fialkov, Anastasia; Tseliakhovich, Dmitriy; Hirata, Christopher M

2012-07-05

Dark and baryonic matter moved at different velocities in the early Universe, which strongly suppressed star formation in some regions. This was estimated to imprint a large-scale fluctuation signal of about two millikelvin in the 21-centimetre spectral line of atomic hydrogen associated with stars at a redshift of 20, although this estimate ignored the critical contribution of gas heating due to X-rays and major enhancements of the suppression. A large velocity difference reduces the abundance of haloes and requires the first stars to form in haloes of about a million solar masses, substantially greater than previously expected. Here we report a simulation of the distribution of the first stars at redshift 20 (cosmic age of around 180 million years), incorporating all these ingredients within a 400-megaparsec box. We find that the 21-centimetre hydrogen signature of these stars is an enhanced (ten millikelvin) fluctuation signal on the hundred-megaparsec scale, characterized by a flat power spectrum with prominent baryon acoustic oscillations. The required sensitivity to see this signal is achievable with an integration time of a thousand hours with an instrument like the Murchison Wide-field Array or the Low Frequency Array but designed to operate in the range of 50-100 megahertz.

Multiscale weighted colored graphs for protein flexibility and rigidity analysis

NASA Astrophysics Data System (ADS)

Bramer, David; Wei, Guo-Wei

2018-02-01

Protein structural fluctuation, measured by Debye-Waller factors or B-factors, is known to correlate to protein flexibility and function. A variety of methods has been developed for protein Debye-Waller factor prediction and related applications to domain separation, docking pose ranking, entropy calculation, hinge detection, stability analysis, etc. Nevertheless, none of the current methodologies are able to deliver an accuracy of 0.7 in terms of the Pearson correlation coefficients averaged over a large set of proteins. In this work, we introduce a paradigm-shifting geometric graph model, multiscale weighted colored graph (MWCG), to provide a new generation of computational algorithms to significantly change the current status of protein structural fluctuation analysis. Our MWCG model divides a protein graph into multiple subgraphs based on interaction types between graph nodes and represents the protein rigidity by generalized centralities of subgraphs. MWCGs not only predict the B-factors of protein residues but also accurately analyze the flexibility of all atoms in a protein. The MWCG model is validated over a number of protein test sets and compared with many standard methods. An extensive numerical study indicates that the proposed MWCG offers an accuracy of over 0.8 and thus provides perhaps the first reliable method for estimating protein flexibility and B-factors. It also simultaneously predicts all-atom flexibility in a molecule.

Study of thermal and acoustic noise interferences in low stiffness atomic force microscope cantilevers and characterization of their dynamic properties.

PubMed

Boudaoud, Mokrane; Haddab, Yassine; Le Gorrec, Yann; Lutz, Philippe

2012-01-01

The atomic force microscope (AFM) is a powerful tool for the measurement of forces at the micro/nano scale when calibrated cantilevers are used. Besides many existing calibration techniques, the thermal calibration is one of the simplest and fastest methods for the dynamic characterization of an AFM cantilever. This method is efficient provided that the Brownian motion (thermal noise) is the most important source of excitation during the calibration process. Otherwise, the value of spring constant is underestimated. This paper investigates noise interference ranges in low stiffness AFM cantilevers taking into account thermal fluctuations and acoustic pressures as two main sources of noise. As a result, a preliminary knowledge about the conditions in which thermal fluctuations and acoustic pressures have closely the same effect on the AFM cantilever (noise interference) is provided with both theoretical and experimental arguments. Consequently, beyond the noise interference range, commercial low stiffness AFM cantilevers are calibrated in two ways: using the thermal noise (in a wide temperature range) and acoustic pressures generated by a loudspeaker. We then demonstrate that acoustic noises can also be used for an efficient characterization and calibration of low stiffness AFM cantilevers. The accuracy of the acoustic characterization is evaluated by comparison with results from the thermal calibration.

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field.

PubMed

Jamroz, Michal; Orozco, Modesto; Kolinski, Andrzej; Kmiecik, Sebastian

2013-01-08

It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801]. However, atomistic MD cannot be applied to most biologically relevant processes due to its limitation to relatively short time scales. Much longer time scales can be accessed by properly designed coarse-grained models. We demonstrate that the aforementioned consensus view of protein dynamics from short (nanosecond) time scale MD simulations is fairly consistent with the dynamics of the coarse-grained protein model - the CABS model. The CABS model employs stochastic dynamics (a Monte Carlo method) and a knowledge-based force-field, which is not biased toward the native structure of a simulated protein. Since CABS-based dynamics allows for the simulation of entire folding (or multiple folding events) in a single run, integration of the CABS approach with all-atom MD promises a convenient (and computationally feasible) means for the long-time multiscale molecular modeling of protein systems with atomistic resolution.

Interactive Web-based Visualization of Atomic Position-time Series Data

NASA Astrophysics Data System (ADS)

Thapa, S.; Karki, B. B.

2017-12-01

Extracting and interpreting the information contained in large sets of time-varying three dimensional positional data for the constituent atoms of simulated material is a challenging task. We have recently implemented a web-based visualization system to analyze the position-time series data extracted from the local or remote hosts. It involves a pre-processing step for data reduction, which involves skipping uninteresting parts of the data uniformly (at full atomic configuration level) or non-uniformly (at atomic species level or individual atom level). Atomic configuration snapshot is rendered using the ball-stick representation and can be animated by rendering successive configurations. The entire atomic dynamics can be captured as the trajectories by rendering the atomic positions at all time steps together as points. The trajectories can be manipulated at both species and atomic levels so that we can focus on one or more trajectories of interest, and can be also superimposed with the instantaneous atomic structure. The implementation was done using WebGL and Three.js for graphical rendering, HTML5 and Javascript for GUI, and Elasticsearch and JSON for data storage and retrieval within the Grails Framework. We have applied our visualization system to the simulation datatsets for proton-bearing forsterite (Mg2SiO4) - an abundant mineral of Earths upper mantle. Visualization reveals that protons (hydrogen ions) incorporated as interstitials are much more mobile than protons substituting the host Mg and Si cation sites. The proton diffusion appears to be anisotropic with high mobility along the x-direction, showing limited discrete jumps in other two directions.

Coated armor system and process for making the same

DOEpatents

Chu, Henry S.; Lillo, Thomas M.; McHugh, Kevin M.

2010-11-23

An armor system and method involves providing a core material and a stream of atomized coating material that comprises a liquid fraction and a solid fraction. An initial layer is deposited on the core material by positioning the core material in the stream of atomized coating material wherein the solid fraction of the stream of atomized coating material is less than the liquid fraction of the stream of atomized coating material on a weight basis. An outer layer is then deposited on the initial layer by positioning the core material in the stream of atomized coating material wherein the solid fraction of the stream of atomized coating material is greater than the liquid fraction of the stream of atomized coating material on a weight basis.

Armor systems including coated core materials

DOEpatents

Chu, Henry S [Idaho Falls, ID; Lillo, Thomas M [Idaho Falls, ID; McHugh, Kevin M [Idaho Falls, ID

2012-07-31

An armor system and method involves providing a core material and a stream of atomized coating material that comprises a liquid fraction and a solid fraction. An initial layer is deposited on the core material by positioning the core material in the stream of atomized coating material wherein the solid fraction of the stream of atomized coating material is less than the liquid fraction of the stream of atomized coating material on a weight basis. An outer layer is then deposited on the initial layer by positioning the core material in the stream of atomized coating material wherein the solid fraction of the stream of atomized coating material is greater than the liquid fraction of the stream of atomized coating material on a weight basis.

Armor systems including coated core materials

DOEpatents

Chu, Henry S; Lillo, Thomas M; McHugh, Kevin M

2013-10-08

An armor system and method involves providing a core material and a stream of atomized coating material that comprises a liquid fraction and a solid fraction. An initial layer is deposited on the core material by positioning the core material in the stream of atomized coating material wherein the solid fraction of the stream of atomized coating material is less than the liquid fraction of the stream of atomized coating material on a weight basis. An outer layer is then deposited on the initial layer by positioning the core material in the stream of atomized coating material wherein the solid fraction of the stream of atomized coating material is greater than the liquid fraction of the stream of atomized coating material on a weight basis.

Temperature dependent structural properties and bending rigidity of pristine and defective hexagonal boron nitride

NASA Astrophysics Data System (ADS)

Thomas, Siby; Ajith, K. M.; Chandra, Sharat; Valsakumar, M. C.

2015-08-01

Structural and thermodynamical properties of monolayer pristine and defective boron nitride sheets (h-BN) have been investigated in a wide temperature range by carrying out atomistic simulations using a tuned Tersoff-type inter-atomic empirical potential. The temperature dependence of lattice parameter, radial distribution function, specific heat at constant volume, linear thermal expansion coefficient and the height correlation function of the thermally excited ripples on pristine as well as defective h-BN sheet have been investigated. Specific heat shows considerable increase beyond the Dulong-Petit limit at high temperatures, which is interpreted as a signature of strong anharmonicity present in h-BN. Analysis of the height fluctuations, < {{h}2}> , shows that the bending rigidity and variance of height fluctuations are strongly temperature dependent and this is explained using the continuum theory of membranes. A detailed study of the height-height correlation function shows deviation from the prediction of harmonic theory of membranes as a consequence of the strong anharmonicity in h-BN. It is also seen that the variance of the height fluctuations increases with defect concentration.

Inflationary preheating dynamics with two-species condensates

NASA Astrophysics Data System (ADS)

Zache, T. V.; Kasper, V.; Berges, J.

2017-06-01

We investigate both analytically and numerically a two-component ultracold atom system in one spatial dimension. The model features a tachyonic instability, which incorporates characteristic aspects of the mechanisms for particle production in early universe inflaton models. We establish a direct correspondence between measurable macroscopic growth rates for occupation numbers of the ultracold Bose gas and the underlying microscopic processes in terms of Feynman loop diagrams. We analyze several existing ultracold atom setups featuring dynamical instabilities and propose optimized protocols for their experimental realization. We demonstrate that relevant dynamical processes can be enhanced using a seeding procedure for unstable modes and clarify the role of initial quantum fluctuations and the generation of a nonlinear secondary stage for the amplification of modes.

Car-Parrinello molecular dynamics study of the melting behaviors of n-atom (n = 6, 10) graphene quantum dots

NASA Astrophysics Data System (ADS)

Shekaari, Ashkan; Abolhassani, Mohammad Reza

2017-06-01

First-principles molecular dynamics has been applied to inquire into the melting behaviors of n-atom (n = 6, 10) graphene quantum dots (GQD6 and zigzag GQD10) within the temperature range of T = 0-500 K. The temperature dependence of the geometry of each quantum dot is thoroughly evaluated via calculating the related shape deformation parameters and the eigenvalues of the quadrupole tensors. Examining the variations of some phase-transition indicators such as root-mean-square bond length fluctuations and mean square displacements broadly proposes the value of Tm = 70 K for the melting point of GQD6 while a continuous, two-stage phase transition has been concluded for zigzag GQD10.

Deformation in Metallic Glass: Connecting Atoms to Continua

NASA Astrophysics Data System (ADS)

Hinkle, Adam R.; Falk, Michael L.; Rycroft, Chris H.; Shields, Michael D.

Metallic glasses like other amorphous solids experience strain localization as the primary mode of failure. However, the development of continuum constitutive laws which provide a quantitative description of disorder and mechanical deformation remains an open challenge. Recent progress has shown the necessity of accurately capturing fluctuations in material structure, in particular the statistical changes in potential energy of the atomic constituents during the non-equilibrium process of applied shear. Here we directly cross-compare molecular dynamics shear simulations of a ZrCu glass with continuum shear transformation zone (STZ) theory representations. We present preliminary results for a methodology to coarse-grain detailed molecular dynamics data with the goal of initializing a continuum representation in the STZ theory. NSF Grants Awards 1107838, 1408685, and 0801471.

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

Cable, J.W.

The diffuse scattering of neutrons from magnetic materials provides unique and important information regarding the spatial correlations of the atoms and the spins. Such measurements have been extensively applied to magnetically ordered systems, such as the ferromagnetic binary alloys, for which the observed correlations describe the magnetic moment fluctuations associated with local environment effects. With the advent of polarization analysis, these techniques are increasingly being applied to study disordered paramagnetic systems such as the spin-glasses and the diluted magnetic semiconductors. The spin-pair correlations obtained are essential in understanding the exchange interactions of such systems. In this paper, we describe recentmore » neutron diffuse scattering results on the atom-pair and spin-pair correlations in some of these disordered magnetic systems. 56 refs.« less

Instability of Fulde-Ferrell-Larkin-Ovchinnikov states in atomic Fermi gases in three and two dimensions

NASA Astrophysics Data System (ADS)

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

2018-04-01

The exotic Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) states have been actively searched for experimentally since the mean-field based FFLO theories were put forward half a century ago. Here, we investigate the stability of FFLO states in the presence of pairing fluctuations. We conclude that FFLO superfluids cannot exist in continuum in three and two dimensions, due to their intrinsic instability, associated with infinite quantum degeneracy of the pairs. These results address the absence of convincing experimental observations of FFLO phases in both condensed matter and in ultracold atomic Fermi gases with a population imbalance. We predict that the true ground state has a pair momentum distribution highly peaked on an entire constant energy surface.

Results of the AEROS satellite program: Summary

NASA Technical Reports Server (NTRS)

Lammerzahl, P.; Rawer, K.; Roemer, N.

1980-01-01

Published literature reporting aeronomic data collected on two AEROS missions is summarized. The extreme ultraviolet solar radiation and other significant parameters of the thermosphere/ionosphere were investigated. Kinetic pressure, the quantity of atomic nitrogen, and partial densities of helium, oxygen, nitrogen, argon, and atomic nitrogen were determined. The thermal electron population, superthermal energy distribution, plasma density, ion temperature, and composition according to ion types were measured. The chief energy supply in the thermosphere was calculated. Aeronomic calculations showing that variations in the parameters of the ionosphere cannot be correlated with fluctuations of extreme ultraviolet solar radiation were performed. The AEROS data were compared with data from S3-1, ISIS, and AE-C satellites. Models of the thermosphere and ionosphere were developed.

Quantum liquid droplets in a mixture of Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Cabrera, C. R.; Tanzi, L.; Sanz, J.; Naylor, B.; Thomas, P.; Cheiney, P.; Tarruell, L.

2018-01-01

Quantum droplets are small clusters of atoms self-bound by the balance of attractive and repulsive forces. Here, we report on the observation of droplets solely stabilized by contact interactions in a mixture of two Bose-Einstein condensates. We demonstrate that they are several orders of magnitude more dilute than liquid helium by directly measuring their size and density via in situ imaging. We show that the droplets are stablized against collapse by quantum fluctuations and that they require a minimum atom number to be stable. Below that number, quantum pressure drives a liquid-to-gas transition that we map out as a function of interaction strength. These ultradilute isotropic liquids remain weakly interacting and constitute an ideal platform to benchmark quantum many-body theories.

NOVA SCIENCE UNIT 15, FUNDAMENTAL PARTICLES 4.

ERIC Educational Resources Information Center

1964

THE PRINCIPLES OF ATOMIC STRUCTURE WHICH ARE STRESSED ARE THAT ATOMS ARE MADE UP OF A NUCLEUS WITH A POSITIVE CHARGE, SURROUNDED BY ELECTRONS WITH A NEGATIVE CHARGE, AND THAT THERE IS NO CHANGE IN THE ATOM WHEN THE POSITIVE AND NEGATIVE CHARGES ARE EQUAL. EXPERIMENTS ILLUSTRATE THAT CURRENT ELECTRICITY IS ACTUALLY ELECTRONS IN MOTION, THAT THERE…

A stochastic differential equations approach for the description of helium bubble size distributions in irradiated metals

NASA Astrophysics Data System (ADS)

Seif, Dariush; Ghoniem, Nasr M.

2014-12-01

A rate theory model based on the theory of nonlinear stochastic differential equations (SDEs) is developed to estimate the time-dependent size distribution of helium bubbles in metals under irradiation. Using approaches derived from Itô's calculus, rate equations for the first five moments of the size distribution in helium-vacancy space are derived, accounting for the stochastic nature of the atomic processes involved. In the first iteration of the model, the distribution is represented as a bivariate Gaussian distribution. The spread of the distribution about the mean is obtained by white-noise terms in the second-order moments, driven by fluctuations in the general absorption and emission of point defects by bubbles, and fluctuations stemming from collision cascades. This statistical model for the reconstruction of the distribution by its moments is coupled to a previously developed reduced-set, mean-field, rate theory model. As an illustrative case study, the model is applied to a tungsten plasma facing component under irradiation. Our findings highlight the important role of stochastic atomic fluctuations on the evolution of helium-vacancy cluster size distributions. It is found that when the average bubble size is small (at low dpa levels), the relative spread of the distribution is large and average bubble pressures may be very large. As bubbles begin to grow in size, average bubble pressures decrease, and stochastic fluctuations have a lessened effect. The distribution becomes tighter as it evolves in time, corresponding to a more uniform bubble population. The model is formulated in a general way, capable of including point defect drift due to internal temperature and/or stress gradients. These arise during pulsed irradiation, and also during steady irradiation as a result of externally applied or internally generated non-homogeneous stress fields. Discussion is given into how the model can be extended to include full spatial resolution and how the implementation of a path-integral approach may proceed if the distribution is known experimentally to significantly stray from a Gaussian description.

Irregular-regular mode oscillations inside plasma bubble and its fractal analysis in glow discharge magnetized plasma

NASA Astrophysics Data System (ADS)

Megalingam, Mariammal; Hari Prakash, N.; Solomon, Infant; Sarma, Arun; Sarma, Bornali

2017-04-01

Experimental evidence of different kinds of oscillations in floating potential fluctuations of glow discharge magnetized plasma is being reported. A spherical gridded cage is inserted into the ambient plasma volume for creating plasma bubbles. Plasma is produced between a spherical mesh grid and chamber. The spherical mesh grid of 80% optical transparency is connected to the positive terminal of power supply and considered as anode. Two Langmuir probes are kept in the ambient plasma to measure the floating potential fluctuations in different positions within the system, viz., inside and outside the spherical mesh grid. At certain conditions of discharge voltage (Vd) and magnetic field, irregular to regular mode appears, and it shows chronological changes with respect to magnetic field. Further various nonlinear analyses such as Recurrence Plot, Hurst exponent, and Lyapunov exponent have been carried out to investigate the dynamics of oscillation at a range of discharge voltages and external magnetic fields. Determinism, entropy, and Lmax are important measures of Recurrence Quantification Analysis which indicate an irregular to regular transition in the dynamics of the fluctuations. Furthermore, behavior of the plasma oscillation is characterized by the technique called multifractal detrended fluctuation analysis to explore the nature of the fluctuations. It reveals that it has a multifractal nature and behaves as a long range correlated process.

Extremely high wall-shear stress events in a turbulent boundary layer

NASA Astrophysics Data System (ADS)

Pan, Chong; Kwon, Yongseok

2018-04-01

The present work studies the fluctuating characteristics of the streamwise wall-shear stress in a DNS of a turbulent boundary layer at Re τ =1500 from a structural view. The two-dimensional field of the fluctuating friction velocity u‧ τ (x,z) is decomposed into the large- and small-scale components via a recently proposed scale separation algorithm, Quasi-bivariate Variational Mode Decomposition (QB-VMD). Both components are found to be dominated by streak-like structures, which can be regarded as the wall signature of the inner-layer streaks and the outer-layer LSMs, respectively. Extreme positive/negative wall-shear stress fluctuation events are detected in the large-scale component. The former’s occurrence frequency is nearly one order of magnitude higher than the latter; therefore, they contribute a significant portion of the long tail of the wall-shear stress distribution. Both two-point correlations and conditional averages show that these extreme positive wall-shear stress events are embedded in the large-scale positive u‧ τ streaks. They seem to be formed by near-wall ‘splatting’ process, which are related to strong finger-like sweeping (Q4) events originated from the outer-layer positive LSMs.

Impact of proton transfer phenomena on the electronic structure of model Schiff bases: an AIM/NBO/ELF study.

PubMed

Panek, Jarosław J; Filarowski, Aleksander; Jezierska-Mazzarello, Aneta

2013-10-21

Understanding of the electronic structure evolution due to a proton dynamics is a key issue in biochemistry and material science. This paper reports on density functional theory calculations of Schiff bases containing short, strong intramolecular hydrogen bonds where the bridged proton is located: (i) at the donor site, (ii) strongly delocalized, and (iii) at the acceptor site. The mobility of the bridged proton and its influence on the molecular structure and properties of the chosen Schiff base derivatives have been investigated on the basis of Atoms in Molecules, Natural Bond Orbitals, and Electron Localization Function theories. It has been observed that the extent of the bridged proton delocalization is strongly modified by the steric and inductive effects present in the studied compounds introduced by various substituents. It has been shown that: (i) potential energy profiles for the proton motion are extremely dependent on the substitution of the aromatic ring, (ii) the topology of the free electron pairs present at the donor∕acceptor site, as well as their electron populations, are affected qualitatively by the bridged proton position, (iii) the distortion of the molecular structure due to the bridged proton dynamics includes the atomic charge fluctuations, which are in some cases non-monotonic, and (iv) topology of the ELF recognizes events of proton detachment from the donor and attachment to the acceptor. The quantitative and qualitative results shed light onto molecular consequences of the proton transfer phenomena.

Perturbational formulation of principal component analysis in molecular dynamics simulation.

PubMed

Koyama, Yohei M; Kobayashi, Tetsuya J; Tomoda, Shuji; Ueda, Hiroki R

2008-10-01

Conformational fluctuations of a molecule are important to its function since such intrinsic fluctuations enable the molecule to respond to the external environmental perturbations. For extracting large conformational fluctuations, which predict the primary conformational change by the perturbation, principal component analysis (PCA) has been used in molecular dynamics simulations. However, several versions of PCA, such as Cartesian coordinate PCA and dihedral angle PCA (dPCA), are limited to use with molecules with a single dominant state or proteins where the dihedral angle represents an important internal coordinate. Other PCAs with general applicability, such as the PCA using pairwise atomic distances, do not represent the physical meaning clearly. Therefore, a formulation that provides general applicability and clearly represents the physical meaning is yet to be developed. For developing such a formulation, we consider the conformational distribution change by the perturbation with arbitrary linearly independent perturbation functions. Within the second order approximation of the Kullback-Leibler divergence by the perturbation, the PCA can be naturally interpreted as a method for (1) decomposing a given perturbation into perturbations that independently contribute to the conformational distribution change or (2) successively finding the perturbation that induces the largest conformational distribution change. In this perturbational formulation of PCA, (i) the eigenvalue measures the Kullback-Leibler divergence from the unperturbed to perturbed distributions, (ii) the eigenvector identifies the combination of the perturbation functions, and (iii) the principal component determines the probability change induced by the perturbation. Based on this formulation, we propose a PCA using potential energy terms, and we designate it as potential energy PCA (PEPCA). The PEPCA provides both general applicability and clear physical meaning. For demonstrating its power, we apply the PEPCA to an alanine dipeptide molecule in vacuum as a minimal model of a nonsingle dominant conformational biomolecule. The first and second principal components clearly characterize two stable states and the transition state between them. Positive and negative components with larger absolute values of the first and second eigenvectors identify the electrostatic interactions, which stabilize or destabilize each stable state and the transition state. Our result therefore indicates that PCA can be applied, by carefully selecting the perturbation functions, not only to identify the molecular conformational fluctuation but also to predict the conformational distribution change by the perturbation beyond the limitation of the previous methods.

Perturbational formulation of principal component analysis in molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Koyama, Yohei M.; Kobayashi, Tetsuya J.; Tomoda, Shuji; Ueda, Hiroki R.

2008-10-01

Conformational fluctuations of a molecule are important to its function since such intrinsic fluctuations enable the molecule to respond to the external environmental perturbations. For extracting large conformational fluctuations, which predict the primary conformational change by the perturbation, principal component analysis (PCA) has been used in molecular dynamics simulations. However, several versions of PCA, such as Cartesian coordinate PCA and dihedral angle PCA (dPCA), are limited to use with molecules with a single dominant state or proteins where the dihedral angle represents an important internal coordinate. Other PCAs with general applicability, such as the PCA using pairwise atomic distances, do not represent the physical meaning clearly. Therefore, a formulation that provides general applicability and clearly represents the physical meaning is yet to be developed. For developing such a formulation, we consider the conformational distribution change by the perturbation with arbitrary linearly independent perturbation functions. Within the second order approximation of the Kullback-Leibler divergence by the perturbation, the PCA can be naturally interpreted as a method for (1) decomposing a given perturbation into perturbations that independently contribute to the conformational distribution change or (2) successively finding the perturbation that induces the largest conformational distribution change. In this perturbational formulation of PCA, (i) the eigenvalue measures the Kullback-Leibler divergence from the unperturbed to perturbed distributions, (ii) the eigenvector identifies the combination of the perturbation functions, and (iii) the principal component determines the probability change induced by the perturbation. Based on this formulation, we propose a PCA using potential energy terms, and we designate it as potential energy PCA (PEPCA). The PEPCA provides both general applicability and clear physical meaning. For demonstrating its power, we apply the PEPCA to an alanine dipeptide molecule in vacuum as a minimal model of a nonsingle dominant conformational biomolecule. The first and second principal components clearly characterize two stable states and the transition state between them. Positive and negative components with larger absolute values of the first and second eigenvectors identify the electrostatic interactions, which stabilize or destabilize each stable state and the transition state. Our result therefore indicates that PCA can be applied, by carefully selecting the perturbation functions, not only to identify the molecular conformational fluctuation but also to predict the conformational distribution change by the perturbation beyond the limitation of the previous methods.

Weight Fluctuation and Postmenopausal Breast Cancer in the National Health and Nutrition Examination Survey I Epidemiologic Follow-Up Study.

PubMed

Komaroff, Marina

2016-01-01

The aim of this study is to investigate if weight fluctuation is an independent risk factor for postmenopausal breast cancer (PBC) among women who gained weight in adult years. NHANES I Epidemiologic Follow-Up Study (NHEFS) database was used in the study. Women that were cancers-free at enrollment and diagnosed for the first time with breast cancer at age 50 or greater were considered cases. Controls were chosen from the subset of cancers-free women and matched to cases by years of follow-up and status of body mass index (BMI) at 25 years of age. Weight fluctuation was measured by the root-mean-square-error (RMSE) from a simple linear regression model for each woman with their body mass index (BMI) regressed on age (started at 25 years) while women with the positive slope from this regression were defined as weight gainers. Data were analyzed using conditional logistic regression models. A total of 158 women were included into the study. The conditional logistic regression adjusted for weight gain demonstrated positive association between weight fluctuation in adult years and postmenopausal breast cancers (odds ratio/OR = 1.67; 95% confidence interval/CI: 1.06-2.66). The data suggested that long-term weight fluctuation was significant risk factor for PBC among women who gained weight in adult years. This finding underscores the importance of maintaining lost weight and avoiding weight fluctuation.

Weight Fluctuation and Postmenopausal Breast Cancer in the National Health and Nutrition Examination Survey I Epidemiologic Follow-Up Study

PubMed Central

Komaroff, Marina

2016-01-01

Objective. The aim of this study is to investigate if weight fluctuation is an independent risk factor for postmenopausal breast cancer (PBC) among women who gained weight in adult years. Methods. NHANES I Epidemiologic Follow-Up Study (NHEFS) database was used in the study. Women that were cancers-free at enrollment and diagnosed for the first time with breast cancer at age 50 or greater were considered cases. Controls were chosen from the subset of cancers-free women and matched to cases by years of follow-up and status of body mass index (BMI) at 25 years of age. Weight fluctuation was measured by the root-mean-square-error (RMSE) from a simple linear regression model for each woman with their body mass index (BMI) regressed on age (started at 25 years) while women with the positive slope from this regression were defined as weight gainers. Data were analyzed using conditional logistic regression models. Results. A total of 158 women were included into the study. The conditional logistic regression adjusted for weight gain demonstrated positive association between weight fluctuation in adult years and postmenopausal breast cancers (odds ratio/OR = 1.67; 95% confidence interval/CI: 1.06–2.66). Conclusions. The data suggested that long-term weight fluctuation was significant risk factor for PBC among women who gained weight in adult years. This finding underscores the importance of maintaining lost weight and avoiding weight fluctuation. PMID:26953120

Superimposition of protein structures with dynamically weighted RMSD.

PubMed

Wu, Di; Wu, Zhijun

2010-02-01

In protein modeling, one often needs to superimpose a group of structures for a protein. A common way to do this is to translate and rotate the structures so that the square root of the sum of squares of coordinate differences of the atoms in the structures, called the root-mean-square deviation (RMSD) of the structures, is minimized. While it has provided a general way of aligning a group of structures, this approach has not taken into account the fact that different atoms may have different properties and they should be compared differently. For this reason, when superimposed with RMSD, the coordinate differences of different atoms should be evaluated with different weights. The resulting RMSD is called the weighted RMSD (wRMSD). Here we investigate the use of a special wRMSD for superimposing a group of structures with weights assigned to the atoms according to certain thermal motions of the atoms. We call such an RMSD the dynamically weighted RMSD (dRMSD). We show that the thermal motions of the atoms can be obtained from several sources such as the mean-square fluctuations that can be estimated by Gaussian network model analysis. We show that the superimposition of structures with dRMSD can successfully identify protein domains and protein motions, and that it has important implications in practice, e.g., in aligning the ensemble of structures determined by nuclear magnetic resonance.

Laser Cooling and Trapping of Neutral Strontium for Spectroscopic Measurements of Casimir-Polder Potentials

NASA Astrophysics Data System (ADS)

Cook, Eryn C.

Casimir and Casimir-Polder effects are forces between electrically neutral bodies and particles in vacuum, arising entirely from quantum fluctuations. The modification to the vacuum electromagnetic-field modes imposed by the presence of any particle or surface can result in these mechanical forces, which are often the dominant interaction at small separations. These effects play an increasingly critical role in the operation of micro- and nano-mechanical systems as well as miniaturized atomic traps for precision sensors and quantum-information devices. Despite their fundamental importance, calculations present theoretical and numeric challenges, and precise atom-surface potential measurements are lacking in many geometric and distance regimes. The spectroscopic measurement of Casimir-Polder-induced energy level shifts in optical-lattice trapped atoms offers a new experimental method to probe atom-surface interactions. Strontium, the current front-runner among optical frequency metrology systems, has demonstrated characteristics ideal for such precision measurements. An alkaline earth atom possessing ultra-narrow intercombination transitions, strontium can be loaded into an optical lattice at the "magic" wavelength where the probe transition is unperturbed by the trap light. Translation of the lattice will permit controlled transport of tightly-confined atomic samples to well-calibrated atom-surface separations, while optical transition shifts serve as a direct probe of the Casimir-Polder potential. We have constructed a strontium magneto-optical trap (MOT) for future Casimir-Polder experiments. This thesis will describe the strontium apparatus, initial trap performance, and some details of the proposed measurement procedure.

Relationship between frequency power spectra and intermittent, large-amplitude bursts in the Alcator C-Mod scrape-off layer

NASA Astrophysics Data System (ADS)

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

2017-11-01

Fluctuations in the boundary region of the Alcator C-Mod tokamak have been analyzed using gas puff imaging data from a set of Ohmically heated plasma density scan experiments. It is found that the relative fluctuation amplitudes are modest and close to normally distributed at the separatrix but become increasingly larger and skewed towards the main chamber wall. The frequency power spectra are nevertheless similar for all radial positions and line-averaged densities. Predictions of a stochastic model, describing the plasma fluctuations as a super-position of uncorrelated pulses, are shown to be in excellent agreement with the measurements. This implies that the pulse duration is the same, while the degree of pulse overlap decreases radially outwards in the scrape-off layer. The universal frequency power spectral density is thus determined by the shape and duration of the large-amplitude bursts associated with blob-like structures. The model also describes the rate of threshold level crossings, for which the exponential tails underline the intermittency of the fluctuations in the far scarpe-off layer.

An experimental test of the fluctuation relation in an active camphor boat system

NASA Astrophysics Data System (ADS)

Paroor, H. M.; Nambiar, N.; Bandi, M. M.

The Gallavotti-Cohen fluctuation relation (FR) posits a specific symmetry between positive and negative fluctuations in entropy production, or a related quantity (e.g power) for systems in non-equilibrium stationary state. Successful tests in a variety of systems suggest the FR may be more generally applicable than the conditions under which it was originally derived. Systems where the FR fails are therefore valuable for the insight they provide into the FR's general success. It has recently been suggested that ``active matter'' should not satisfy the fluctuation-dissipation theorem or FR. We experimentally test this possibility in a system of active camphor boats, self-propelled by surface tension gradients at air-water interfaces. The boats interact via short-range capillary attraction which competes with long-range surface tension mediated repulsion. Tuning interaction strength with number density, we test the FR through the statistics of power as one goes from a free non-interacting camphor boat, through a few weakly interacting boats to several, strongly interacting boats. We present preliminary results of our experiments and data analysis.

Molecular dynamics simulation of the Escherichia coli NikR protein: equilibrium conformational fluctuations reveal interdomain allosteric communication pathways.

PubMed

Bradley, Michael J; Chivers, Peter T; Baker, Nathan A

2008-05-16

Escherichia coli NikR is a homotetrameric Ni(2+)- and DNA-binding protein that functions as a transcriptional repressor of the NikABCDE nickel permease. The protein is composed of two distinct domains. The N-terminal 50 amino acids of each chain forms part of the dimeric ribbon-helix-helix (RHH) domains, a well-studied DNA-binding fold. The 83-residue C-terminal nickel-binding domain forms an ACT (aspartokinase, chorismate mutase, and TyrA) fold and contains the tetrameric interface. In this study, we have utilized an equilibrium molecular dynamics simulation in order to explore the conformational dynamics of the NikR tetramer and determine important residue interactions within and between the RHH and ACT domains to gain insight into the effects of Ni(2+) on DNA-binding activity. The molecular simulation data were analyzed using two different correlation measures based on fluctuations in atomic position and noncovalent contacts together with a clustering algorithm to define groups of residues with similar correlation patterns for both types of correlation measure. Based on these analyses, we have defined a series of residue interrelationships that describe an allosteric communication pathway between the Ni(2+)- and DNA-binding sites, which are separated by 40 A. Several of the residues identified by our analyses have been previously shown experimentally to be important for NikR function. An additional subset of the identified residues structurally connects the experimentally implicated residues and may help coordinate the allosteric communication between the ACT and RHH domains.

Proton transfer in a short hydrogen bond caused by solvation shell fluctuations: an ab initio MD and NMR/UV study of an (OHO)(-) bonded system.

PubMed

Pylaeva, Svetlana; Allolio, Christoph; Koeppe, Benjamin; Denisov, Gleb S; Limbach, Hans-Heinrich; Sebastiani, Daniel; Tolstoy, Peter M

2015-02-14

We present a joint experimental and quantum chemical study on the influence of solvent dynamics on the protonation equilibrium in a strongly hydrogen bonded phenol-acetate complex in CD2Cl2. Particular attention is given to the correlation of the proton position distribution with the internal conformation of the complex itself and with fluctuations of the aprotic solvent. Specifically, we have focused on a complex formed by 4-nitrophenol and tetraalkylammonium-acetate in CD2Cl2. Experimentally we have used combined low-temperature (1)H and (13)C NMR and UV-vis spectroscopy and showed that a very strong OHO hydrogen bond is formed with proton tautomerism (PhOH···(-)OAc and PhO(-)···HOAc forms, both strongly hydrogen bonded). Computationally, we have employed ab initio molecular dynamics (70 and 71 solvent molecules, with and without the presence of a counter-cation, respectively). We demonstrate that the relative motion of the counter-cation and the "free" carbonyl group of the acid plays the major role in the OHO bond geometry and causes proton "jumps", i.e. interconversion of PhOH···(-)OAc and PhO(-)···HOAc tautomers. Weak H-bonds between CH(CD) groups of the solvent and the oxygen atom of carbonyl stabilize the PhOH···(-)OAc type of structures. Breaking of CH···O bonds shifts the equilibrium towards PhO(-)···HOAc form.

Molecular dynamics simulation of the Escherichia coli NikR protein: Equilibrium conformational fluctuations reveal inter-domain allosteric communication pathways

PubMed Central

Bradley, Michael J.; Chivers, Peter T.; Baker, Nathan A.

2008-01-01

Summary E. coliNikR is a homotetrameric Ni2+- and DNA-binding protein that functions as a transcriptional repressor of the NikABCDE nickel permease. The protein is composed of 2 distinct domains. The N-terminal fifty amino acids of each chain forms part of the dimeric ribbon-helix-helix (RHH) domains, a well-studied DNA-binding fold. The eighty-three residue C-terminal nickel-binding domain forms an ACT-fold and contains the tetrameric interface. In this study, we have utilized an equilibrium molecular dynamics (MD) simulation in order to explore the conformational dynamics of the NikR tetramer and determine important residue interactions within and between the RHH and ACT domains to gain insight into the effects of Ni on DNA-binding activity. The molecular simulation data was analyzed using two different correlation measures based on fluctuations in atomic position and non-covalent contacts, together with a clustering algorithm to define groups of residues with similar correlation patterns for both types of correlation measure. Based on these analyses, we have defined a series of residue interrelationships that describe an allosteric communication pathway between the Ni2+ and DNA binding sites, which are separated by 40 Å. Several of the residues identified by our analyses have been previously shown experimentally to be important for NikR function. An additional subset of the identified residues structurally connects the experimentally implicated residues and may help coordinate the allosteric communication between the ACT and RHH domains. PMID:18433769

Computational design of a thermostable mutant of cocaine esterase via molecular dynamics simulations.

PubMed

Huang, Xiaoqin; Gao, Daquan; Zhan, Chang-Guo

2011-06-07

Cocaine esterase (CocE) has been known as the most efficient native enzyme for metabolizing naturally occurring cocaine. A major obstacle to the clinical application of CocE is the thermoinstability of native CocE with a half-life of only ∼11 min at physiological temperature (37 °C). It is highly desirable to develop a thermostable mutant of CocE for therapeutic treatment of cocaine overdose and addiction. To establish a structure-thermostability relationship, we carried out molecular dynamics (MD) simulations at 400 K on wild-type CocE and previously known thermostable mutants, demonstrating that the thermostability of the active form of the enzyme correlates with the fluctuation (characterized as the root-mean square deviation and root-mean square fluctuation of atomic positions) of the catalytic residues (Y44, S117, Y118, H287, and D259) in the simulated enzyme. In light of the structure-thermostability correlation, further computational modelling including MD simulations at 400 K predicted that the active site structure of the L169K mutant should be more thermostable. The prediction has been confirmed by wet experimental tests showing that the active form of the L169K mutant had a half-life of 570 min at 37 °C, which is significantly longer than those of the wild-type and previously known thermostable mutants. The encouraging outcome suggests that the high-temperature MD simulations and the structure-thermostability relationship may be considered as a valuable tool for the computational design of thermostable mutants of an enzyme.

Method for oxidizing alkanes using novel porphyrins synthesized from dipyrromethanes and aldehydes

DOEpatents

Wijesekera, Tilak; Lyons, James E.; Ellis, Jr., Paul E.

1999-01-01

The invention comprises a method for the oxidation of alkanes to alcohols and for decomposition of hydroperoxides to alcohols utilizing new compositions of matter, which are metal complexes of porphyrins. Preferred complexes have hydrogen, haloalkyl or haloaryl groups in meso positions, two of the opposed meso atoms or groups being hydrogen or haloaryl, and two of the opposed meso atoms or groups being hydrogen or haloalkyl, but not all four of the meso atoms or groups being hydrogen. Other preferred complexes are ones in which all four of the meso positions are substituted with haloalkyl groups and the beta positions are substituted with halogen atoms. A new method of synthesizing porphyrinogens is also disclosed.

Method for hydroperoxide decomposition using novel porphyrins synthesized from dipyrromethanes and aldehydes

DOEpatents

Wijesekera, T.; Lyons, J.E.; Ellis, P.E. Jr.

1998-03-03

The invention comprises a method for the oxidation of alkanes to alcohols and for decomposition of hydroperoxides to alcohols utilizing new compositions of matter, which are metal complexes of porphyrins. Preferred complexes have hydrogen, haloalkyl or haloaryl groups in meso positions, two of the opposed meso atoms or groups being hydrogen or haloaryl, and two of the opposed meso atoms or groups being hydrogen or haloalkyl, but not all four of the meso atoms or groups being hydrogen. Other preferred complexes are ones in which all four of the meso positions are substituted with haloalkyl groups and the beta positions are substituted with halogen atoms. A new method of synthesizing porphyrinogens is also disclosed.

Method for hydroperoxide decomposition using novel porphyrins synthesized from dipyrromethanes and aldehydes

DOEpatents

Wijesekera, Tilak; Lyons, James E.; Ellis, Jr., Paul E.

1998-01-01

The invention comprises a method for the oxidation of alkanes to alcohols and for decomposition of hydroperoxides to alcohols utilizing new compositions of matter, which are metal complexes of porphyrins. Preferred complexes have hydrogen, haloalkyl or haloaryl groups in meso positions, two of the opposed meso atoms or groups being hydrogen or haloaryl, and two of the opposed meso atoms or groups being hydrogen or haloalkyl, but not all four of the meso atoms or groups being hydrogen. Other preferred complexes are ones in which all four of the meso positions are substituted with haloalkyl groups and the beta positions are substituted with halogen atoms. A new method of synthesizing porphyrinogens is also disclosed.

Single-shot imaging of trapped Fermi gas

NASA Astrophysics Data System (ADS)

Gajda, Mariusz; Mostowski, Jan; Sowiński, Tomasz; Załuska-Kotur, Magdalena

2016-07-01

Recently developed techniques allow for simultaneous measurements of the positions of all ultra-cold atoms in a trap with high resolution. Each such single-shot experiment detects one element of the quantum ensemble formed by the cloud of atoms. Repeated single-shot measurements can be used to determine all correlations between particle positions as opposed to standard measurements that determine particle density or two-particle correlations only. In this paper we discuss the possible outcomes of such single-shot measurements in the case of cloud of ultra-cold noninteracting Fermi atoms. We show that the Pauli exclusion principle alone leads to correlations between particle positions that originate from unexpected spatial structures formed by the atoms.

Methods of producing armor systems, and armor systems produced using such methods

DOEpatents

Chu, Henry S; Lillo, Thomas M; McHugh, Kevin M

2013-02-19

An armor system and method involves providing a core material and a stream of atomized coating material that comprises a liquid fraction and a solid fraction. An initial layer is deposited on the core material by positioning the core material in the stream of atomized coating material wherein the solid fraction of the stream of atomized coating material is less than the liquid fraction of the stream of atomized coating material on a weight basis. An outer layer is then deposited on the initial layer by positioning the core material in the stream of atomized coating material wherein the solid fraction of the stream of atomized coating material is greater than the liquid fraction of the stream of atomized coating material on a weight basis.

Imaging Dirac-mass disorder from magnetic dopant atoms in the ferromagnetic topological insulator Crx(Bi0.1Sb0.9)2-xTe3.

PubMed

Lee, Inhee; Kim, Chung Koo; Lee, Jinho; Billinge, Simon J L; Zhong, Ruidan; Schneeloch, John A; Liu, Tiansheng; Valla, Tonica; Tranquada, John M; Gu, Genda; Davis, J C Séamus

2015-02-03

To achieve and use the most exotic electronic phenomena predicted for the surface states of 3D topological insulators (TIs), it is necessary to open a "Dirac-mass gap" in their spectrum by breaking time-reversal symmetry. Use of magnetic dopant atoms to generate a ferromagnetic state is the most widely applied approach. However, it is unknown how the spatial arrangements of the magnetic dopant atoms influence the Dirac-mass gap at the atomic scale or, conversely, whether the ferromagnetic interactions between dopant atoms are influenced by the topological surface states. Here we image the locations of the magnetic (Cr) dopant atoms in the ferromagnetic TI Cr0.08(Bi0.1Sb0.9)1.92Te3. Simultaneous visualization of the Dirac-mass gap Δ(r) reveals its intense disorder, which we demonstrate is directly related to fluctuations in n(r), the Cr atom areal density in the termination layer. We find the relationship of surface-state Fermi wavevectors to the anisotropic structure of Δ(r) not inconsistent with predictions for surface ferromagnetism mediated by those states. Moreover, despite the intense Dirac-mass disorder, the anticipated relationship [Formula: see text] is confirmed throughout and exhibits an electron-dopant interaction energy J* = 145 meV·nm(2). These observations reveal how magnetic dopant atoms actually generate the TI mass gap locally and that, to achieve the novel physics expected of time-reversal symmetry breaking TI materials, control of the resulting Dirac-mass gap disorder will be essential.

Direct Observation of Inherent Atomic-Scale Defect Disorders responsible for High-Performance Ti1-x Hfx NiSn1-y Sby Half-Heusler Thermoelectric Alloys.

PubMed

Kim, Ki Sung; Kim, Young-Min; Mun, Hyeona; Kim, Jisoo; Park, Jucheol; Borisevich, Albina Y; Lee, Kyu Hyoung; Kim, Sung Wng

2017-09-01

Structural defects often dominate the electronic- and thermal-transport properties of thermoelectric (TE) materials and are thus a central ingredient for improving their performance. However, understanding the relationship between TE performance and the disordered atomic defects that are generally inherent in nanostructured alloys remains a challenge. Herein, the use of scanning transmission electron microscopy to visualize atomic defects directly is described and disordered atomic-scale defects are demonstrated to be responsible for the enhancement of TE performance in nanostructured Ti 1- x Hf x NiSn 1- y Sb y half-Heusler alloys. The disordered defects at all atomic sites induce a local composition fluctuation, effectively scattering phonons and improving the power factor. It is observed that the Ni interstitial and Ti,Hf/Sn antisite defects are collectively formed, leading to significant atomic disorder that causes the additional reduction of lattice thermal conductivity. The Ti 1- x Hf x NiSn 1- y Sb y alloys containing inherent atomic-scale defect disorders are produced in one hour by a newly developed process of temperature-regulated rapid solidification followed by sintering. The collective atomic-scale defect disorder improves the zT to 1.09 ± 0.12 at 800 K for the Ti 0.5 Hf 0.5 NiSn 0.98 Sb 0.02 alloy. These results provide a promising avenue for improving the TE performance of state-of-the-art materials. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Imaging Dirac-mass disorder from magnetic dopant atoms in the ferromagnetic topological insulator Crx(Bi0.1Sb0.9)2-xTe3

PubMed Central

Lee, Inhee; Kim, Chung Koo; Lee, Jinho; Billinge, Simon J. L.; Zhong, Ruidan; Schneeloch, John A.; Liu, Tiansheng; Valla, Tonica; Tranquada, John M.; Gu, Genda; Davis, J. C. Séamus

2015-01-01

To achieve and use the most exotic electronic phenomena predicted for the surface states of 3D topological insulators (TIs), it is necessary to open a “Dirac-mass gap” in their spectrum by breaking time-reversal symmetry. Use of magnetic dopant atoms to generate a ferromagnetic state is the most widely applied approach. However, it is unknown how the spatial arrangements of the magnetic dopant atoms influence the Dirac-mass gap at the atomic scale or, conversely, whether the ferromagnetic interactions between dopant atoms are influenced by the topological surface states. Here we image the locations of the magnetic (Cr) dopant atoms in the ferromagnetic TI Cr0.08(Bi0.1Sb0.9)1.92Te3. Simultaneous visualization of the Dirac-mass gap Δ(r) reveals its intense disorder, which we demonstrate is directly related to fluctuations in n(r), the Cr atom areal density in the termination layer. We find the relationship of surface-state Fermi wavevectors to the anisotropic structure of Δ(r) not inconsistent with predictions for surface ferromagnetism mediated by those states. Moreover, despite the intense Dirac-mass disorder, the anticipated relationship Δ(r)∝n(r) is confirmed throughout and exhibits an electron–dopant interaction energy J* = 145 meV·nm2. These observations reveal how magnetic dopant atoms actually generate the TI mass gap locally and that, to achieve the novel physics expected of time-reversal symmetry breaking TI materials, control of the resulting Dirac-mass gap disorder will be essential. PMID:25605947

Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme.

PubMed

Levitt, M; Sander, C; Stern, P S

1985-02-05

We have developed a new method for modelling protein dynamics using normal-mode analysis in internal co-ordinates. This method, normal-mode dynamics, is particularly well suited for modelling collective motion, makes possible direct visualization of biologically interesting modes, and is complementary to the more time-consuming simulation of molecular dynamics trajectories. The essential assumption and limitation of normal-mode analysis is that the molecular potential energy varies quadratically. Our study starts with energy minimization of the X-ray co-ordinates with respect to the single-bond torsion angles. The main technical task is the calculation of second derivative matrices of kinetic and potential energy with respect to the torsion angle co-ordinates. These enter into a generalized eigenvalue problem, and the final eigenvalues and eigenvectors provide a complete description of the motion in the basic 0.1 to 10 picosecond range. Thermodynamic averages of amplitudes, fluctuations and correlations can be calculated efficiently using analytical formulae. The general method presented here is applied to four proteins, trypsin inhibitor, crambin, ribonuclease and lysozyme. When the resulting atomic motion is visualized by computer graphics, it is clear that the motion of each protein is collective with all atoms participating in each mode. The slow modes, with frequencies of below 10 cm-1 (a period of 3 ps), are the most interesting in that the motion in these modes is segmental. The root-mean-square atomic fluctuations, which are dominated by a few slow modes, agree well with experimental temperature factors (B values). The normal-mode dynamics of these four proteins have many features in common, although in the larger molecules, lysozyme and ribonuclease, there is low frequency domain motion about the active site.

Interdependence of Inhibitor Recognition in HIV-1 Protease

PubMed Central

2017-01-01

Molecular recognition is a highly interdependent process. Subsite couplings within the active site of proteases are most often revealed through conditional amino acid preferences in substrate recognition. However, the potential effect of these couplings on inhibition and thus inhibitor design is largely unexplored. The present study examines the interdependency of subsites in HIV-1 protease using a focused library of protease inhibitors, to aid in future inhibitor design. Previously a series of darunavir (DRV) analogs was designed to systematically probe the S1′ and S2′ subsites. Co-crystal structures of these analogs with HIV-1 protease provide the ideal opportunity to probe subsite interdependency. All-atom molecular dynamics simulations starting from these structures were performed and systematically analyzed in terms of atomic fluctuations, intermolecular interactions, and water structure. These analyses reveal that the S1′ subsite highly influences other subsites: the extension of the hydrophobic P1′ moiety results in 1) reduced van der Waals contacts in the P2′ subsite, 2) more variability in the hydrogen bond frequencies with catalytic residues and the flap water, and 3) changes in the occupancy of conserved water sites both proximal and distal to the active site. In addition, one of the monomers in this homodimeric enzyme has atomic fluctuations more highly correlated with DRV than the other monomer. These relationships intricately link the HIV-1 protease subsites and are critical to understanding molecular recognition and inhibitor binding. More broadly, the interdependency of subsite recognition within an active site requires consideration in the selection of chemical moieties in drug design; this strategy is in contrast to what is traditionally done with independent optimization of chemical moieties of an inhibitor. PMID:28358514

Interdependence of Inhibitor Recognition in HIV-1 Protease.

PubMed

Paulsen, Janet L; Leidner, Florian; Ragland, Debra A; Kurt Yilmaz, Nese; Schiffer, Celia A

2017-05-09

Molecular recognition is a highly interdependent process. Subsite couplings within the active site of proteases are most often revealed through conditional amino acid preferences in substrate recognition. However, the potential effect of these couplings on inhibition and thus inhibitor design is largely unexplored. The present study examines the interdependency of subsites in HIV-1 protease using a focused library of protease inhibitors, to aid in future inhibitor design. Previously a series of darunavir (DRV) analogs was designed to systematically probe the S1' and S2' subsites. Co-crystal structures of these analogs with HIV-1 protease provide the ideal opportunity to probe subsite interdependency. All-atom molecular dynamics simulations starting from these structures were performed and systematically analyzed in terms of atomic fluctuations, intermolecular interactions, and water structure. These analyses reveal that the S1' subsite highly influences other subsites: the extension of the hydrophobic P1' moiety results in 1) reduced van der Waals contacts in the P2' subsite, 2) more variability in the hydrogen bond frequencies with catalytic residues and the flap water, and 3) changes in the occupancy of conserved water sites both proximal and distal to the active site. In addition, one of the monomers in this homodimeric enzyme has atomic fluctuations more highly correlated with DRV than the other monomer. These relationships intricately link the HIV-1 protease subsites and are critical to understanding molecular recognition and inhibitor binding. More broadly, the interdependency of subsite recognition within an active site requires consideration in the selection of chemical moieties in drug design; this strategy is in contrast to what is traditionally done with independent optimization of chemical moieties of an inhibitor.

Positive and negative contribution to birefringence in a family of carbonates: A Born effective charges analysis

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

Jing, Qun; Yang, Guang; Hou, Juan

It is an important topic to investigate the birefringence and reveal the contribution from ions to birefringence because it plays an important role in nonlinear optical materials. In this paper, the birefringence of carbonates with coplanar CO{sub 3} groups were investigated using the first-principles method. The results show that the lead carbonates exhibit relative large birefringence. After detailed investigate the electronic structures, and Born effective charges, the authors find out that anisotropic electron distribution in the CO{sub 3} groups and Pb atoms give positive contribution, while the negative contribution was found from fluorine atoms, meanwhile the Ca, Mg, and Cdmore » atoms give very small contribution to birefringence. - Graphical abstract: Using the DFT and Born effective charges, the birefringence and the contribution of ions were investigated, the positive and negative contribution was found from Pb and F ions, respectively. - Highlights: • Optical properties and Born effective charges of carbonates are investigated. • Lead carbonates exhibit relative large birefringence. • Coplanar CO{sub 3} groups and Pb atoms give positive contribution. • F atoms give negative contribution. • Ca, Mg, and Cd atoms give very small contribution.« less

Role of the water-drinking test in medically treated primary open angle glaucoma patients.

PubMed

Salcedo, H; Arciniega, D; Mayorga, M; Wu, L

2018-05-01

The water-drinking test (WDT) has recently re-emerged as a possible way to determine the competency of the trabecular meshwork. We performed a prospective interventional study to test the hypothesis that the WDT could be useful in assessing fluctuations in patients undergoing treatment for primary open angle glaucoma (POAG). We included 122 patients; 62 on medical treatment for POAG (n=123 eyes) and 60 controls (n=120 eyes). The study group had been on intraocular pressures (IOP) lowering treatment continuously for at least 3months with stable IOP. The WDT was performed during fasting and was considered positive if it fluctuated ≥6mmHg. The patients on medical treatment had a mean age of 50.56±18.45 years vs. 51.35±11.22 for the controls (P=0.34); with 71% being female in the study group and 77% in the control group. In the study group; 52% were on beta blockers (n=64), 27% combination of two or more medications (n=33), 19% prostaglandin analogues (n=24) and 2% alpha agonists (n=2). The WDT was positive in 17.07% (n=21) in the study group and 2.5% (n=3) in the control group (P=0.0001). The mean fluctuation was 7.14±2.15mmHg in the study group and 6.00±0mmHg in the controls (P=0.33). A positive WDT was found in 33.33% (n=11) of those on combination therapy; 12.5% (n=3) prostaglandin analogues and 10.94% (n=7) beta blockers (P=0.03). Combination therapy had the highest positive WDT fluctuation (7.54±2.87) followed by prostaglandin analogues (7.00±1.00) and beta blockers (6.57±0.78) with a P value of 0.44. The WDT can identify significant fluctuations in eyes with POAG that are medically treated. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Revision of the Li13Si4 structure.

PubMed

Zeilinger, Michael; Fässler, Thomas F

2013-11-06

Besides Li17Si4, Li16.42Si4, and Li15Si4, another lithium-rich representative in the Li-Si system is the phase Li13Si4 (trideca-lithium tetra-silicide), the structure of which has been determined previously [Frank et al. (1975 ▶). Z. Naturforsch. Teil B, 30, 10-13]. A careful analysis of X-ray diffraction patterns of Li13Si4 revealed discrepancies between experimentally observed and calculated Bragg positions. Therefore, we redetermined the structure of Li13Si4 on the basis of single-crystal X-ray diffraction data. Compared to the previous structure report, decisive differences are (i) the introduction of a split position for one Li site [occupancy ratio 0.838 (7):0.162 (7)], (ii) the anisotropic refinement of atomic displacement parameters for all atoms, and (iii) a high accuracy of atom positions and unit-cell parameters. The asymmetric unit of Li13Si4 contains two Si and seven Li atoms. Except for one Li atom situated on a site with symmetry 2/m, all other atoms are on mirror planes. The structure consists of isolated Si atoms as well as Si-Si dumbbells surrounded by Li atoms. Each Si atom is either 12- or 13-coordinated. The isolated Si atoms are situated in the ab plane at z = 0 and are strictly separated from the Si-Si dumbbells at z = 0.5.

Vector dark matter detection using the quantum jump of atoms

NASA Astrophysics Data System (ADS)

Yang, Qiaoli; Di, Haoran

2018-05-01

The hidden sector U(1) vector bosons created from inflationary fluctuations can be a substantial fraction of dark matter if their mass is around 10-5 eV. The creation mechanism makes the vector bosons' energy spectral density ρcdm / ΔE very high. Therefore, the dark electric dipole transition rate in atoms is boosted if the energy gap between atomic states equals the mass of the vector bosons. By using the Zeeman effect, the energy gap between the 2S state and the 2P state in hydrogen atoms or hydrogen like ions can be tuned. The 2S state can be populated with electrons due to its relatively long life, which is about 1/7 s. When the energy gap between the semi-ground 2S state and the 2P state matches the mass of the cosmic vector bosons, induced transitions occur and the 2P state subsequently decays into the 1S state. The 2 P → 1 S decay emitted Lyman-α photons can then be registered. The choices of target atoms depend on the experimental facilities and the mass ranges of the vector bosons. Because the mass of the vector boson is connected to the inflation scale, the proposed experiment may provide a probe to inflation.

Superfluid qubit systems with ring shaped optical lattices

PubMed Central

Amico, Luigi; Aghamalyan, Davit; Auksztol, Filip; Crepaz, Herbert; Dumke, Rainer; Kwek, Leong Chuan

2014-01-01

We study an experimentally feasible qubit system employing neutral atomic currents. Our system is based on bosonic cold atoms trapped in ring-shaped optical lattice potentials. The lattice makes the system strictly one dimensional and it provides the infrastructure to realize a tunable ring-ring interaction. Our implementation combines the low decoherence rates of neutral cold atoms systems, overcoming single site addressing, with the robustness of topologically protected solid state Josephson flux qubits. Characteristic fluctuations in the magnetic fields affecting Josephson junction based flux qubits are expected to be minimized employing neutral atoms as flux carriers. By breaking the Galilean invariance we demonstrate how atomic currents through the lattice provide an implementation of a qubit. This is realized either by artificially creating a phase slip in a single ring, or by tunnel coupling of two homogeneous ring lattices. The single qubit infrastructure is experimentally investigated with tailored optical potentials. Indeed, we have experimentally realized scaled ring-lattice potentials that could host, in principle, n ~ 10 of such ring-qubits, arranged in a stack configuration, along the laser beam propagation axis. An experimentally viable scheme of the two-ring-qubit is discussed, as well. Based on our analysis, we provide protocols to initialize, address, and read-out the qubit. PMID:24599096

Polarization squeezing of light by single passage through an atomic vapor

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

Barreiro, S.; Valente, P.; Failache, H.

We have studied relative-intensity fluctuations for a variable set of orthogonal elliptic polarization components of a linearly polarized laser beam traversing a resonant {sup 87}Rb vapor cell. Significant polarization squeezing at the threshold level (-3dB) required for the implementation of several continuous-variable quantum protocols was observed. The extreme simplicity of the setup, which is based on standard polarization components, makes it particularly convenient for quantum information applications.

Soviet Developments in Material Science No. 1, January - June 1975

DTIC Science & Technology

1975-11-30

Zotova, T. Makhanbetaliyev, B. Ya. Mel’tser, and D. N. Nasledov. Effect of fluctuations in local composition of solid solutions on...289-297. Gurin, N. T., D. G. Semak, and V. V. Fedak. Threshold switching and local states in chalcogenide glasses. FTP, no. 4, 1975...L. N. Seregina. Crystal-glass transition in Ge0 .-Te- p. and its effect on local environment of germanium atoms. FTT, no. 2, 1975, 633

Insects in fluctuating thermal environments.

PubMed

Colinet, Hervé; Sinclair, Brent J; Vernon, Philippe; Renault, David

2015-01-07

All climate change scenarios predict an increase in both global temperature means and the magnitude of seasonal and diel temperature variation. The nonlinear relationship between temperature and biological processes means that fluctuating temperatures lead to physiological, life history, and ecological consequences for ectothermic insects that diverge from those predicted from constant temperatures. Fluctuating temperatures that remain within permissive temperature ranges generally improve performance. By contrast, those which extend to stressful temperatures may have either positive impacts, allowing repair of damage accrued during exposure to thermal extremes, or negative impacts from cumulative damage during successive exposures. We discuss the mechanisms underlying these differing effects. Fluctuating temperatures could be used to enhance or weaken insects in applied rearing programs, and any prediction of insect performance in the field-including models of climate change or population performance-must account for the effect of fluctuating temperatures.

Heritability of Intraindividual Mean and Variability of Positive and Negative Affect.

PubMed

Zheng, Yao; Plomin, Robert; von Stumm, Sophie

2016-12-01

Positive affect (e.g., attentiveness) and negative affect (e.g., upset) fluctuate over time. We examined genetic influences on interindividual differences in the day-to-day variability of affect (i.e., ups and downs) and in average affect over the duration of a month. Once a day, 17-year-old twins in the United Kingdom ( N = 447) rated their positive and negative affect online. The mean and standard deviation of each individual's daily ratings across the month were used as the measures of that individual's average affect and variability of affect. Analyses revealed that the average of negative affect was significantly heritable (.53), but the average of positive affect was not; instead, the latter showed significant shared environmental influences (.42). Fluctuations across the month were significantly heritable for both negative affect (.54) and positive affect (.34). The findings support the two-factor theory of affect, which posits that positive affect is more situational and negative affect is more dispositional.

Heritability of Intraindividual Mean and Variability of Positive and Negative Affect

PubMed Central

Zheng, Yao; Plomin, Robert; von Stumm, Sophie

2016-01-01

Positive affect (e.g., attentiveness) and negative affect (e.g., upset) fluctuate over time. We examined genetic influences on interindividual differences in the day-to-day variability of affect (i.e., ups and downs) and in average affect over the duration of a month. Once a day, 17-year-old twins in the United Kingdom (N = 447) rated their positive and negative affect online. The mean and standard deviation of each individual’s daily ratings across the month were used as the measures of that individual’s average affect and variability of affect. Analyses revealed that the average of negative affect was significantly heritable (.53), but the average of positive affect was not; instead, the latter showed significant shared environmental influences (.42). Fluctuations across the month were significantly heritable for both negative affect (.54) and positive affect (.34). The findings support the two-factor theory of affect, which posits that positive affect is more situational and negative affect is more dispositional. PMID:27729566

REVIEWS OF TOPICAL PROBLEMS: Instabilities of a multicomponent plasma with accelerated particles and magnetic field generation in astrophysical objects

NASA Astrophysics Data System (ADS)

Bykov, Andrei M.; Toptygin, Igor'N.

2007-02-01

A system of MHD equations for the description of a magnetized nonequilibrium astrophysical plasma with neutral atoms and suprathermal (in particular, relativistic) particles is formulated. The instabilities of such a plasma, which arise from the presence of neutral and relativistic components, are considered. It is shown that the presence of nonthermal particles interacting with the thermal plasma component via regular and fluctuating electromagnetic fields is responsible for the emergence of specific mechanisms of MHD wave generation. The main generation mechanisms of static and turbulent magnetic fields near shock wave fronts in the Galaxy and interplanetary space are analyzed. We discuss the application of the generation effects of long-wave magnetic fluctuations to the problems of magnetic field origin and relativistic particle acceleration in astrophysical objects of various natures.

LETTER TO THE EDITOR: Phase transition in a random fragmentation problem with applications to computer science

NASA Astrophysics Data System (ADS)

Dean, David S.; Majumdar, Satya N.

2002-08-01

We study a fragmentation problem where an initial object of size x is broken into m random pieces provided x > x0 where x0 is an atomic cut-off. Subsequently, the fragmentation process continues for each of those daughter pieces whose sizes are bigger than x0. The process stops when all the fragments have sizes smaller than x0. We show that the fluctuation of the total number of splitting events, characterized by the variance, generically undergoes a nontrivial phase transition as one tunes the branching number m through a critical value m = mc. For m < mc, the fluctuations are Gaussian where as for m > mc they are anomalously large and non-Gaussian. We apply this general result to analyse two different search algorithms in computer science.

Directed Field Ionization

NASA Astrophysics Data System (ADS)

Gregoric, Vincent C.; Kang, Xinyue; Liu, Zhimin Cheryl; Rowley, Zoe A.; Carroll, Thomas J.; Noel, Michael W.

2017-04-01

Selective field ionization is an important experimental technique used to study the state distribution of Rydberg atoms. This is achieved by applying a steadily increasing electric field, which successively ionizes more tightly bound states. An atom prepared in an energy eigenstate encounters many avoided Stark level crossings on the way to ionization. As it traverses these avoided crossings, its amplitude is split among multiple different states, spreading out the time resolved electron ionization signal. By perturbing the electric field ramp, we can change how the atoms traverse the avoided crossings, and thus alter the shape of the ionization signal. We have used a genetic algorithm to evolve these perturbations in real time in order to arrive at a target ionization signal shape. This process is robust to large fluctuations in experimental conditions. This work was supported by the National Science Foundation under Grants No. 1607335 and No. 1607377 and used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant Number OCI-1053575.

vmdICE: a plug-in for rapid evaluation of molecular dynamics simulations using VMD.

PubMed

Knapp, Bernhard; Lederer, Nadja; Omasits, Ulrich; Schreiner, Wolfgang

2010-12-01

Molecular dynamics (MD) is a powerful in silico method to investigate the interactions between biomolecules. It solves Newton's equations of motion for atoms over a specified period of time and yields a trajectory file, containing the different spatial arrangements of atoms during the simulation. The movements and energies of each single atom are recorded. For evaluating of these simulation trajectories with regard to biomedical implications, several methods are available. Three well-known ones are the root mean square deviation (RMSD), the root mean square fluctuation (RMSF) and solvent accessible surface area (SASA). Herein, we present a novel plug-in for the software "visual molecular dynamics" (VMD) that allows an interactive 3D representation of RMSD, RMSF, and SASA, directly on the molecule. On the one hand, our plug-in is easy to handle for inexperienced users, and on the other hand, it provides a fast and flexible graphical impression of the spatial dynamics of a system for experts in the field. © 2010 Wiley Periodicals, Inc.

Point-by-point compositional analysis for atom probe tomography.

PubMed

Stephenson, Leigh T; Ceguerra, Anna V; Li, Tong; Rojhirunsakool, Tanaporn; Nag, Soumya; Banerjee, Rajarshi; Cairney, Julie M; Ringer, Simon P

2014-01-01

This new alternate approach to data processing for analyses that traditionally employed grid-based counting methods is necessary because it removes a user-imposed coordinate system that not only limits an analysis but also may introduce errors. We have modified the widely used "binomial" analysis for APT data by replacing grid-based counting with coordinate-independent nearest neighbour identification, improving the measurements and the statistics obtained, allowing quantitative analysis of smaller datasets, and datasets from non-dilute solid solutions. It also allows better visualisation of compositional fluctuations in the data. Our modifications include:.•using spherical k-atom blocks identified by each detected atom's first k nearest neighbours.•3D data visualisation of block composition and nearest neighbour anisotropy.•using z-statistics to directly compare experimental and expected composition curves. Similar modifications may be made to other grid-based counting analyses (contingency table, Langer-Bar-on-Miller, sinusoidal model) and could be instrumental in developing novel data visualisation options.

Probing density and spin correlations in two-dimensional Hubbard model with ultracold fermions

NASA Astrophysics Data System (ADS)

Chan, Chun Fai; Drewes, Jan Henning; Gall, Marcell; Wurz, Nicola; Cocchi, Eugenio; Miller, Luke; Pertot, Daniel; Brennecke, Ferdinand; Koehl, Michael

2017-04-01

Quantum gases of interacting fermionic atoms in optical lattices is a promising candidate to study strongly correlated quantum phases of the Hubbard model such as the Mott-insulator, spin-ordered phases, or in particular d-wave superconductivity. We experimentally realise the two-dimensional Hubbard model by loading a quantum degenerate Fermi gas of 40 K atoms into a three-dimensional optical lattice geometry. High-resolution absorption imaging in combination with radiofrequency spectroscopy is applied to spatially resolve the atomic distribution in a single 2D layer. We investigate in local measurements of spatial correlations in both the density and spin sector as a function of filling, temperature and interaction strength. In the density sector, we compare the local density fluctuations and the global thermodynamic quantities, and in the spin sector, we observe the onset of non-local spin correlation, signalling the emergence of the anti-ferromagnetic phase. We would report our recent experimental endeavours to investigate further down in temperature in the spin sector.

Correlation between micrometer-scale ripple alignment and atomic-scale crystallographic orientation of monolayer graphene

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

Choi, Jin Sik; Chang, Young Jun; Woo, Sungjong

Deformation normal to the surface is intrinsic in two-dimensional materials due to phononic thermal fluctuations at finite temperatures. Graphene's negative thermal expansion coefficient is generally explained by such an intrinsic property. Recently, friction measurements on graphene exfoliated on a silicon oxide surface revealed an anomalous anisotropy whose origin was believed to be the formation of ripple domains. Here, we uncover the atomistic origin of the observed friction domains using a cantilever torsion microscopy in conjunction with angle-resolved photoemission spectroscopy. We experimentally demonstrate that ripples on graphene are formed along the zigzag direction of the hexagonal lattice. The formation of zigzagmore » directional ripple is consistent with our theoretical model that takes account of the atomic-scale bending stiffness of carbon-carbon bonds and the interaction of graphene with the substrate. Lastly, the correlation between micrometer-scale ripple alignment and atomic-scale arrangement of exfoliated monolayer graphene is first discovered and suggests a practical tool for measuring lattice orientation of graphene.« less

Correlation between micrometer-scale ripple alignment and atomic-scale crystallographic orientation of monolayer graphene

DOE PAGES

Choi, Jin Sik; Chang, Young Jun; Woo, Sungjong; ...

2014-12-01

Deformation normal to the surface is intrinsic in two-dimensional materials due to phononic thermal fluctuations at finite temperatures. Graphene's negative thermal expansion coefficient is generally explained by such an intrinsic property. Recently, friction measurements on graphene exfoliated on a silicon oxide surface revealed an anomalous anisotropy whose origin was believed to be the formation of ripple domains. Here, we uncover the atomistic origin of the observed friction domains using a cantilever torsion microscopy in conjunction with angle-resolved photoemission spectroscopy. We experimentally demonstrate that ripples on graphene are formed along the zigzag direction of the hexagonal lattice. The formation of zigzagmore » directional ripple is consistent with our theoretical model that takes account of the atomic-scale bending stiffness of carbon-carbon bonds and the interaction of graphene with the substrate. Lastly, the correlation between micrometer-scale ripple alignment and atomic-scale arrangement of exfoliated monolayer graphene is first discovered and suggests a practical tool for measuring lattice orientation of graphene.« less

Correlation between micrometer-scale ripple alignment and atomic-scale crystallographic orientation of monolayer graphene.

PubMed

Choi, Jin Sik; Chang, Young Jun; Woo, Sungjong; Son, Young-Woo; Park, Yeonggu; Lee, Mi Jung; Byun, Ik-Su; Kim, Jin-Soo; Choi, Choon-Gi; Bostwick, Aaron; Rotenberg, Eli; Park, Bae Ho

2014-12-01

Deformation normal to the surface is intrinsic in two-dimensional materials due to phononic thermal fluctuations at finite temperatures. Graphene's negative thermal expansion coefficient is generally explained by such an intrinsic property. Recently, friction measurements on graphene exfoliated on a silicon oxide surface revealed an anomalous anisotropy whose origin was believed to be the formation of ripple domains. Here, we uncover the atomistic origin of the observed friction domains using a cantilever torsion microscopy in conjunction with angle-resolved photoemission spectroscopy. We experimentally demonstrate that ripples on graphene are formed along the zigzag direction of the hexagonal lattice. The formation of zigzag directional ripple is consistent with our theoretical model that takes account of the atomic-scale bending stiffness of carbon-carbon bonds and the interaction of graphene with the substrate. The correlation between micrometer-scale ripple alignment and atomic-scale arrangement of exfoliated monolayer graphene is first discovered and suggests a practical tool for measuring lattice orientation of graphene.

Analysis of Meniscus Fluctuation in a Continuous Casting Slab Mold

NASA Astrophysics Data System (ADS)

Zhang, Kaitian; Liu, Jianhua; Cui, Heng; Xiao, Chao

2018-06-01

A water model of slab mold was established to analyze the microscopic and macroscopic fluctuation of meniscus. The fast Fourier transform and wavelet entropy were adopted to analyze the wave amplitude, frequency, and components of fluctuation. The flow patterns under the meniscus were measured by using particle image velocimetry measurement and then the mechanisms of meniscus fluctuation were discussed. The results reflected that wavelet entropy had multi-scale and statistical properties, and it was suitable for the study of meniscus fluctuation details both in time and frequency domain. The basic wave, frequency of which exceeding 1 Hz in the condition of no mold oscillation, was demonstrated in this work. In fact, three basic waves were found: long-wave with low frequency, middle-wave with middle frequency, and short-wave with high frequency. In addition, the upper roll flow in mold had significant effect on meniscus fluctuation. When the position of flow impinged was far from the meniscus, long-wave dominated the fluctuation and the stability of meniscus was enhanced. However, when the velocity of flow was increased, the short-wave dominated the meniscus fluctuation and the meniscus stability was decreased.

Poynting vector, energy densities, and pressure of collective transverse electromagnetic fluctuations in unmagnetized plasmas

NASA Astrophysics Data System (ADS)

Schlickeiser, R.

2012-01-01

A systematic calculation of the electromagnetic properties (Poynting vector, electromagnetic energy, and pressure) of the collective transverse fluctuations in unmagnetized plasmas with velocity-anisotropic plasma particle distributions functions is presented. Time-averaged electromagnetic properties for monochromatic weakly damped wave-like fluctuations and space-averaged electromagnetic properties for monochromatic weakly propagating and aperiodic fluctuations are calculated. For aperiodic fluctuations, the Poynting vector as well as the sum of the space-averaged electric and magnetic field energy densities vanish. However, aperiodic fluctuations possess a positive pressure given by its magnetic energy density. This finite pressure density pa of aperiodic fluctuations has important consequences for the dynamics of cosmic unmagnetized plasmas such as the intergalactic medium after reionization. Adopting the standard cosmological evolution model, we show that this additional pressure changes the expansion law of the universe leading to further deceleration. Negative vacuum pressure counterbalances this deceleration to an accelerating universe provided that the negative vacuum pressure is greater than 1.5pa, which we estimate to be of the order 2.1 . 10-16 dyn cm-2.

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.

FLUCTUATING JAUNDICE IN THE ADENOCARCINOMA OF THE AMPULLA OF VATER: a classic sign or an exception?

PubMed

Alves, José Roberto; Amico, Enio Campos; Souza, Dyego Leandro Bezerra de; Oliveira, Patrick Vanttinny Vieira de; Maranhão, Ícaro Godeiro de Oliveira

2015-01-01

Some authors consider the fluctuating jaundice as a classic sign of the adenocarcinoma of the ampulla of Vater. Assessing the frequency of fluctuating jaundice in their forms of its depiction in the patients with adenocarcinoma of the ampulla of Vater. Observational and retrospective study, conducted through analyses of medical records from patients subjected to pancreatic cephalic resections between February 2008 and July 2013. The pathological examination of the surgical specimen was positive to adenocarcinoma of the ampulla of Vater. Concepts and differences on clinical and laboratory fluctuating jaundice were standardized. It was subdivided into type A and type B laboratory fluctuating jaundice. Twenty patients were selected. One of them always remained anicteric, 11 patients developed progressive jaundice, 2 of them developed clinical and laboratory fluctuating jaundice, 5 presented only laboratory fluctuating jaundice and one did not present significant variations on total serum bilirubin levels. Among the seven patients with fluctuating jaundice, two were classified as type A, one as type B and four were not classified due to lack information. Finally, progressive jaundice was the prevailing presentation form in these patients (11 cases). This series of cases suggested that clinical fluctuating jaundice is a uncommon signal in adenocarcinoma of the ampulla of Vater.

A study on suppressing transmittance fluctuations for air-gapped Glan-type polarizing prisms

NASA Astrophysics Data System (ADS)

Zhang, Chuanfa; Li, Dailin; Zhu, Huafeng; Li, Chuanzhi; Jiao, Zhiyong; Wang, Ning; Xu, Zhaopeng; Wang, Xiumin; Song, Lianke

2018-05-01

Light intensity transmittance is a key parameter for the design of polarizing prisms, while sometimes its experimental curves based on spatial incident angle presents periodical fluctuations. Here, we propose a novel method for completely suppressing these fluctuations via setting a glued error angle in the air gap of Glan-Taylor prisms. The proposal consists of: an accurate formula of the intensity transmittance for Glan-Taylor prisms, a numerical simulation and a contrast experiment of Glan-Taylor prisms for analyzing the causes of the fluctuations, and a simple method for accurately measuring the glued error angle. The result indicates that when the setting glued error angle is larger than the critical angle for a certain polarizing prism, the fluctuations can be completely suppressed, and a smooth intensity transmittance curve can be obtained. Besides, the critical angle in the air gap for suppressing the fluctuations is decreased with the increase of beam spot size. This method has the advantage of having less demand for the prism position in optical systems.

Short-term fluctuations in motivation to quit smoking in a sample of smokers in Hawaii.

PubMed

Herzog, Thaddeus; Pokhrel, Pallav; Kawamoto, Crissy T

2015-01-01

Despite its potential for usefulness in informing the development of smoking cessation interventions, short-term fluctuations in motivation to quit is a relatively understudied topic. To assess the prevalence of smokers' day-to-day fluctuations in motivation to quit, and to assess associations of day-to-day fluctuations in motivation to quit with several established cessation-related variables. A cross-sectional survey was administered to smokers in Hawaii (N = 1,567). To assess short-term fluctuations in motivation to quit smoking, participants were asked to respond "True" or "False" to the statement: "My motivation to quit smoking changes from one day to the next." Other items measured desire to quit smoking, intention to quit, confidence in quitting, cigarette dependence, and other cessation-related variables. "My motivation to quit smoking changes from one day to the next" was endorsed as true by 64.7% of smokers, and false by 35.3%. Analyses revealed that smokers who indicated fluctuating motivation were significantly more interested in quitting as compared to smokers without fluctuations. Fluctuations in motivation to quit also were associated with greater confidence in quitting, lesser cigarette dependence, and more recent quitting activity (all p < .01). Day-to-day fluctuations in motivation to quit are common. Day-to-day fluctuations in motivation to quit are strongly associated with higher motivation to quit, greater confidence in future quitting, and other positive cessation-relevant trends.

High-frequency fluctuations of surface temperatures in an urban environment

NASA Astrophysics Data System (ADS)

Christen, Andreas; Meier, Fred; Scherer, Dieter

2012-04-01

This study presents an attempt to resolve fluctuations in surface temperatures at scales of a few seconds to several minutes using time-sequential thermography (TST) from a ground-based platform. A scheme is presented to decompose a TST dataset into fluctuating, high-frequency, and long-term mean parts. To demonstrate the scheme's application, a set of four TST runs (day/night, leaves-on/leaves-off) recorded from a 125-m-high platform above a complex urban environment in Berlin, Germany is used. Fluctuations in surface temperatures of different urban facets are measured and related to surface properties (material and form) and possible error sources. A number of relationships were found: (1) Surfaces with surface temperatures that were significantly different from air temperature experienced the highest fluctuations. (2) With increasing surface temperature above (below) air temperature, surface temperature fluctuations experienced a stronger negative (positive) skewness. (3) Surface materials with lower thermal admittance (lawns, leaves) showed higher fluctuations than surfaces with high thermal admittance (walls, roads). (4) Surface temperatures of emerged leaves fluctuate more compared to trees in a leaves-off situation. (5) In many cases, observed fluctuations were coherent across several neighboring pixels. The evidence from (1) to (5) suggests that atmospheric turbulence is a significant contributor to fluctuations. The study underlines the potential of using high-frequency thermal remote sensing in energy balance and turbulence studies at complex land-atmosphere interfaces.

Chlorine adsorption on the InAs (001) surface

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

Bakulin, A. V.; Eremeev, S. V.; Tereshchenko, O. E.

2011-01-15

Chlorine adsorption on the In-stabilized InAs(001) surface with {zeta}-(4 Multiplication-Sign 2) and {beta}3 Prime -(4 Multiplication-Sign 2) reconstructions and on the Ga-stabilized GaAs (001)-{zeta}-(4 Multiplication-Sign 2) surface has been studied within the electron density functional theory. The equilibrium structural parameters of these reconstructions, surface atom positions, bond lengths in dimers, and their changes upon chlorine adsorption are determined. The electronic characteristics of the clean surface and the surface with adsorbed chlorine are calculated. It is shown that the most energetically favorable positions for chlorine adsorption are top positions over dimerized indium or gallium atoms. The mechanism of chlorine binding withmore » In(Ga)-stabilized surface is explained. The interaction of chlorine atoms with dimerized surface atoms weakens surface atom bonds and controls the initial stage of surface etching.« less

[Study of characteristics of excited O atom generated in multi-needle-to-plate corona discharge by emission spectroscopy].

PubMed

Ge, Hui; Yan, Ling; Mi, Dong; Zhu, Yi-min; Zhang, Lu

2012-04-01

The emission spectra of O(3p 5 P --> 3s 5 S2(0) 777.4 nm) produced by multi-needle-to-plate negative corona discharge and positive streamer discharge in air were successfully recorded at one atmosphere. The influences of discharge power, electrode gap, content of N2 and relative humidity on the excited O atom production were investigated in negative corona discharge. Meanwhile, the distribution of relative density of excited O atom in discharge space was also studied in positive streamer discharge. The results indicate that, for negative corona discharge, the amount of O active atom increases with the increase in power, decreases with increased discharge gap. And with the increase in relative humidity and N2 content, its amount firstly increases and then decreases; whereas for positive corona discharge, the relative density of O active atom from needlepoint to plate firstly increases and then decreases.

Effects of trace elements on the crystal field parameters of Nd ions at the surface of Nd{sub 2}Fe{sub 14}B grains

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

Toga, Yuta; Suzuki, Tsuneaki; Sakuma, Akimasa, E-mail: sakuma@solid.apph.tohoku.ac.jp

2015-06-14

Using first-principles calculations, we investigate the positional dependence of trace elements such as O and Cu on the crystal field parameter A{sub 2}{sup 0}, proportional to the magnetic anisotropy constant K{sub u} of Nd ions placed at the surface of Nd{sub 2}Fe{sub 14}B grains. The results suggest the possibility that the A{sub 2}{sup 0} parameter of Nd ions at the (001) surface of Nd{sub 2}Fe{sub 14}B grains exhibits a negative value when the O or Cu atom is located near the surface, closer than its equilibrium position. At the (110) surface, however, O atoms located at the equilibrium position providemore » a negative A{sub 2}{sup 0}, while for Cu additions A{sub 2}{sup 0} remains positive regardless of Cu's position. Thus, Cu atoms are expected to maintain a positive local K{sub u} of surface Nd ions more frequently than O atoms when they approach the grain surfaces in the Nd-Fe-B grains.« less

Molecular dynamics simulation of highly charged proteins: Comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions

PubMed Central

Gargallo, Raimundo; Hünenberger, Philippe H.; Avilés, Francesc X.; Oliva, Baldomero

2003-01-01

Molecular dynamics (MD) simulations of the activation domain of porcine procarboxypeptidase B (ADBp) were performed to examine the effect of using the particle-particle particle-mesh (P3M) or the reaction field (RF) method for calculating electrostatic interactions in simulations of highly charged proteins. Several structural, thermodynamic, and dynamic observables were derived from the MD trajectories, including estimated entropies and solvation free energies and essential dynamics (ED). The P3M method leads to slightly higher atomic positional fluctuations and deviations from the crystallographic structure, along with somewhat lower values of the total energy and solvation free energy. However, the ED analysis of the system leads to nearly identical results for both simulations. Because of the strong similarity between the results, both methods appear well suited for the simulation of highly charged globular proteins in explicit solvent. However, the lower computational demand of the RF method in the present implementation represents a clear advantage over the P3M method. PMID:14500874

Asymptotic densities from the modified Montroll-Weiss equation for coupled CTRWs

NASA Astrophysics Data System (ADS)

Aghion, Erez; Kessler, David A.; Barkai, Eli

2018-01-01

We examine the bi-scaling behavior of Lévy walks with nonlinear coupling, where χ, the particle displacement during each step, is coupled to the duration of the step, τ, by χ τβ. An example of such a process is regular Lévy walks, where β = 1. In recent years such processes were shown to be highly useful for analysis of a class of Langevin dynamics, in particular a system of Sisyphus laser-cooled atoms in an optical lattice, where β = 3/2. We discuss the well-known decoupling approximation used to describe the central part of the particles' position distribution, and use the recently introduced infinite-covariant density approach to study the large fluctuations. Since the density of the step displacements is fat-tailed, the last travel event must be treated with care for the latter. This effect requires a modification of the Montroll-Weiss equation, an equation which has proved important for the analysis of many microscopic models. Contribution to the Topical Issue "Continuous Time Random Walk Still Trendy: Fifty-year History, Current State and Outlook", edited by Ryszard Kutner and Jaume Masoliver.

Modeling of Disordered Binary Alloys Under Thermal Forcing: Effect of Nanocrystallite Dissociation on Thermal Expansion of AuCu3

NASA Astrophysics Data System (ADS)

Kim, Y. W.; Cress, R. P.

2016-11-01

Disordered binary alloys are modeled as a randomly close-packed assembly of nanocrystallites intermixed with randomly positioned atoms, i.e., glassy-state matter. The nanocrystallite size distribution is measured in a simulated macroscopic medium in two dimensions. We have also defined, and measured, the degree of crystallinity as the probability of a particle being a member of nanocrystallites. Both the distribution function and the degree of crystallinity are found to be determined by alloy composition. When heated, the nanocrystallites become smaller in size due to increasing thermal fluctuation. We have modeled this phenomenon as a case of thermal dissociation by means of the law of mass action. The crystallite size distribution function is computed for AuCu3 as a function of temperature by solving some 12 000 coupled algebraic equations for the alloy. The results show that linear thermal expansion of the specimen has contributions from the temperature dependence of the degree of crystallinity, in addition to respective thermal expansions of the nanocrystallites and glassy-state matter.

Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible ‘seed-less’ targets

PubMed Central

Xia, Zhen; Clark, Peter; Huynh, Tien; Loher, Phillipe; Zhao, Yue; Chen, Huang-Wen; Rigoutsos, Isidore; Zhou, Ruhong

2012-01-01

To better understand the recognition mechanism of RISC and the repertoire of guide-target interactions we introduced G:U wobbles and mismatches at various positions of the microRNA (miRNA) ‘seed’ region and performed all-atom molecular dynamics simulations of the resulting Ago-miRNA:mRNA ternary complexes. Our simulations reveal that many modifications, including combinations of multiple G:U wobbles and mismatches in the seed region, are admissible and result in only minor structural fluctuations that do not affect overall complex stability. These results are further supported by analyses of HITS-CLIP data. Lastly, introduction of disruptive mutations revealed a bending motion of the PAZ domain along the L1/L2 ‘hinge’ and a subsequent opening of the nucleic-acid-binding channel. Our findings suggest that the spectrum of a miRNA's admissible targets is different from what is currently anticipated by the canonical seed-model. Moreover, they provide a likely explanation for the previously reported sequence-dependent regulation of unintended targeting by siRNAs. PMID:22888400

Significance of structural changes in proteins: expected errors in refined protein structures.

PubMed Central

Stroud, R. M.; Fauman, E. B.

1995-01-01

A quantitative expression key to evaluating significant structural differences or induced shifts between any two protein structures is derived. Because crystallography leads to reports of a single (or sometimes dual) position for each atom, the significance of any structural change based on comparison of two structures depends critically on knowing the expected precision of each median atomic position reported, and on extracting it for each atom, from the information provided in the Protein Data Bank and in the publication. The differences between structures of protein molecules that should be identical, and that are normally distributed, indicating that they are not affected by crystal contacts, were analyzed with respect to many potential indicators of structure precision, so as to extract, essentially by "machine learning" principles, a generally applicable expression involving the highest correlates. Eighteen refined crystal structures from the Protein Data Bank, in which there are multiple molecules in the crystallographic asymmetric unit, were selected and compared. The thermal B factor, the connectivity of the atom, and the ratio of the number of reflections to the number of atoms used in refinement correlate best with the magnitude of the positional differences between regions of the structures that otherwise would be expected to be the same. These results are embodied in a six-parameter equation that can be applied to any crystallographically refined structure to estimate the expected uncertainty in position of each atom. Structure change in a macromolecule can thus be referenced to the expected uncertainty in atomic position as reflected in the variance between otherwise identical structures with the observed values of correlated parameters. PMID:8563637

On relaxation nature of glass transition in amorphous materials

NASA Astrophysics Data System (ADS)

Sanditov, Damba S.; Ojovan, Michael I.

2017-10-01

A short review on relaxation theories of glass transition is presented. The main attention is paid to modern aspects of the glass transition equation qτg = C, suggested by Bartenev in 1951 (q - cooling rate of the melt, τg - structural relaxation time at the glass transition temperature Tg). This equation represents a criterion of structural relaxation at transition from liquid to glass at T = Tg (analogous to the condition of mechanical relaxation ωτ = 1, where the maximum of mechanical loss is observed). The empirical parameter С = δTg has the meaning of temperature range δTg that characterizes the liquid-glass transition. Different approaches of δTg calculation are reviewed. In the framework of the model of delocalized atoms a modified kinetic criterion of glass transition is proposed (q/Tg)τg = Cg, where Cg ≅ 7·10-3 is a practically universal dimensionless constant. It depends on fraction of fluctuation volume fg, which is frozen at the glass transition temperature Cg = fg/ln(1/fg). The value of fg is approximately constant fg ≅ 0.025. At Tg the process of atom delocalization, i.e. its displacement from the equilibrium position, is frozen. In silicate glasses atom delocalization is reduced to critical displacement of bridge oxygen atom in Si-O-Si bridge necessary to switch a valence bond according to Muller and Nemilov. An equation is derived for the temperature dependence of viscosity of glass-forming liquids in the wide temperature range, including the liquid-glass transition and the region of higher temperatures. Notion of (bridge) atom delocalization is developed, which is related to necessity of local low activation deformation of structural network for realization of elementary act of viscous flow - activated switch of a valence (bridge) bond. Without atom delocalization (;trigger mechanism;) a switch of the valence bond is impossible and, consequently, the viscous flow. Thus the freezing of atom delocalization process at low temperatures, around Tg, leads to the cease of the viscous flow and transition of a melt to a glassy state. This occurs when the energy of disordered lattice thermal vibrations averaged to one atom becomes equal or less than the energy of atom delocalization. The Bartenev equation for cooling rate dependence of glass transition temperature Tg = Tg(q) is discussed. The value of fg calculated from the data on the Tg(q) dependence coincides with result of the fg calculation using the data on viscosity near the glass transition. Derivation of the Bartenev equation with the account of temperature dependence of activation energy of glass transition process is considered. The obtained generalized relation describes the Tg(q) dependence in a wider interval of the cooling rate compared Bartenev equation. Experimental data related to standard cooling rate q = 3 K/min were used in this work.

Porphyrins

DOEpatents

Wijesekera, T.; Lyons, J.E.; Ellis, P.E. Jr.

1996-11-05

The invention comprises new compositions of matter, which are iron, manganese, cobalt or ruthenium complexes of porphyrins having hydrogen, haloalkyl or haloaryl groups in meso positions, two of the opposed meso atoms or groups being hydrogen or haloaryl, and two of the opposed meso atoms or groups being hydrogen or haloalkyl, but not all four of the meso atoms or groups being hydrogen. The invention also comprises new compositions of matter in which all four of the meso positions are substituted with haloalkyl groups and the beta positions are substituted with halogen atoms. A new method of synthesizing porphyrinogens is also provided. The novel compositions and others made according to the process of the invention are useful as hydrocarbon conversion catalysts; for example, for the oxidation of alkanes and the decomposition of hydroperoxides.

Porphyrins

DOEpatents

Wijesekera, Tilak; Lyons, James E.; Ellis, Jr., Paul E.

1996-01-01

The invention comprises new compositions of matter, which are iron, manganese, cobalt or ruthenium complexes of porphyrins having hydrogen, haloalkyl or haloaryl groups in meso positions, two of the opposed meso atoms or groups being hydrogen or haloaryl, and two of the opposed meso atoms or groups being hydrogen or haloalkyl, but not all four of the meso atoms or groups being hydrogen. The invention also comprises new compositions of matter in which all four of the meso positions are substituted with haloalkyl groups and the beta positions are substituted with halogen atoms. A new method of synthesizing porphyrinogens is also provided. The novel compositions and others made according to the process of the invention are useful as hydrocarbon conversion catalysts; for example, for the oxidation of alkanes and the decomposition of hydroperoxides.

Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells

PubMed Central

McQuilken, Molly; La Riviere, Patrick J.; Occhipinti, Patricia; Verma, Amitabh; Oldenbourg, Rudolf; Gladfelter, Amy S.; Tani, Tomomi

2016-01-01

Regulation of order, such as orientation and conformation, drives the function of most molecular assemblies in living cells but remains difficult to measure accurately through space and time. We built an instantaneous fluorescence polarization microscope, which simultaneously images position and orientation of fluorophores in living cells with single-molecule sensitivity and a time resolution of 100 ms. We developed image acquisition and analysis methods to track single particles that interact with higher-order assemblies of molecules. We tracked the fluctuations in position and orientation of molecules from the level of an ensemble of fluorophores down to single fluorophores. We tested our system in vitro using fluorescently labeled DNA and F-actin, in which the ensemble orientation of polarized fluorescence is known. We then tracked the orientation of sparsely labeled F-actin network at the leading edge of migrating human keratinocytes, revealing the anisotropic distribution of actin filaments relative to the local retrograde flow of the F-actin network. Additionally, we analyzed the position and orientation of septin-GFP molecules incorporated in septin bundles in growing hyphae of a filamentous fungus. Our data indicate that septin-GFP molecules undergo positional fluctuations within ∼350 nm of the binding site and angular fluctuations within ∼30° of the central orientation of the bundle. By reporting position and orientation of molecules while they form dynamic higher-order structures, our approach can provide insights into how micrometer-scale ordered assemblies emerge from nanoscale molecules in living cells. PMID:27679846

Thermal nanostructure: An order parameter multiscale ensemble approach

NASA Astrophysics Data System (ADS)

Cheluvaraja, S.; Ortoleva, P.

2010-02-01

Deductive all-atom multiscale techniques imply that many nanosystems can be understood in terms of the slow dynamics of order parameters that coevolve with the quasiequilibrium probability density for rapidly fluctuating atomic configurations. The result of this multiscale analysis is a set of stochastic equations for the order parameters whose dynamics is driven by thermal-average forces. We present an efficient algorithm for sampling atomistic configurations in viruses and other supramillion atom nanosystems. This algorithm allows for sampling of a wide range of configurations without creating an excess of high-energy, improbable ones. It is implemented and used to calculate thermal-average forces. These forces are then used to search the free-energy landscape of a nanosystem for deep minima. The methodology is applied to thermal structures of Cowpea chlorotic mottle virus capsid. The method has wide applicability to other nanosystems whose properties are described by the CHARMM or other interatomic force field. Our implementation, denoted SIMNANOWORLD™, achieves calibration-free nanosystem modeling. Essential atomic-scale detail is preserved via a quasiequilibrium probability density while overall character is provided via predicted values of order parameters. Applications from virology to the computer-aided design of nanocapsules for delivery of therapeutic agents and of vaccines for nonenveloped viruses are envisioned.

Measurement Sensitivity Improvement of All-Optical Atomic Spin Magnetometer by Suppressing Noises

PubMed Central

Chen, Xiyuan; Zhang, Hong; Zou, Sheng

2016-01-01

Quantum manipulation technology and photoelectric detection technology have jointly facilitated the rapid development of ultra-sensitive atomic spin magnetometers. To improve the output signal and sensitivity of the spin-exchange-relaxation-free (SERF) atomic spin magnetometer, the noises influencing on the output signal and the sensitivity were analyzed, and the corresponding noise suppression methods were presented. The magnetic field noises, including the residual magnetic field noise and the light shift noise, were reduced to approximately zero by employing the magnetic field compensation method and by adjusting the frequency of the pump beam, respectively. With respect to the operation temperature, the simulation results showed that the temperature of the potassium atomic spin magnetometer realizing the spin-exchange relaxation-free regime was 180 °C. Moreover, the fluctuation noises of the frequency and the power were suppressed by using the frequency and the power stable systems. The experimental power stability results showed that the light intensity stability was enhanced 10%. Contrast experiments on the sensitivity were carried out to demonstrate the validity of the suppression methods. Finally, a sensitivity of 13 fT/Hz1/2 was successfully achieved by suppressing noises and optimizing parameters. PMID:27322272

The influence of voxel size on atom probe tomography data.

PubMed

Torres, K L; Daniil, M; Willard, M A; Thompson, G B

2011-05-01

A methodology for determining the optimal voxel size for phase thresholding in nanostructured materials was developed using an atom simulator and a model system of a fixed two-phase composition and volume fraction. The voxel size range was banded by the atom count within each voxel. Some voxel edge lengths were found to be too large, resulting in an averaging of compositional fluctuations; others were too small with concomitant decreases in the signal-to-noise ratio for phase identification. The simulated methodology was then applied to the more complex experimentally determined data set collected from a (Co(0.95)Fe(0.05))(88)Zr(6)Hf(1)B(4)Cu(1) two-phase nanocomposite alloy to validate the approach. In this alloy, Zr and Hf segregated to an intergranular amorphous phase while Fe preferentially segregated to a crystalline phase during the isothermal annealing step that promoted primary crystallization. The atom probe data analysis of the volume fraction was compared to transmission electron microscopy (TEM) dark-field imaging analysis and a lever rule analysis of the volume fraction within the amorphous and crystalline phases of the ribbon. Copyright © 2011 Elsevier B.V. All rights reserved.

Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel

PubMed Central

Li, Xianfeng; Murthy, N. Sanjeeva; Becker, Matthew L.; Latour, Robert A.

2016-01-01

A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications. PMID:27013229

Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins

PubMed Central

Nguyen, Bao Linh; Pettitt, B. Montgomery

2015-01-01

The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations. PMID:26388706

Unlocking higher harmonics in atomic force microscopy with gentle interactions.

PubMed

Santos, Sergio; Barcons, Victor; Font, Josep; Verdaguer, Albert

2014-01-01

In dynamic atomic force microscopy, nanoscale properties are encoded in the higher harmonics. Nevertheless, when gentle interactions and minimal invasiveness are required, these harmonics are typically undetectable. Here, we propose to externally drive an arbitrary number of exact higher harmonics above the noise level. In this way, multiple contrast channels that are sensitive to compositional variations are made accessible. Numerical integration of the equation of motion shows that the external introduction of exact harmonic frequencies does not compromise the fundamental frequency. Thermal fluctuations are also considered within the detection bandwidth of interest and discussed in terms of higher-harmonic phase contrast in the presence and absence of an external excitation of higher harmonics. Higher harmonic phase shifts further provide the means to directly decouple the true topography from that induced by compositional heterogeneity.

An extensive study of Bose-Einstein condensation in liquid helium using Tsallis statistics

NASA Astrophysics Data System (ADS)

Guha, Atanu; Das, Prasanta Kumar

2018-05-01

Realistic scenario can be represented by general canonical ensemble way better than the ideal one, with proper parameter sets involved. We study the Bose-Einstein condensation phenomena of liquid helium within the framework of Tsallis statistics. With a comparatively high value of the deformation parameter q(∼ 1 . 4) , the theoretically calculated value of the critical temperature (Tc) of the phase transition of liquid helium is found to agree with the experimentally determined value (Tc = 2 . 17 K), although they differs from each other for q = 1 (undeformed scenario). This throws a light on the understanding of the phenomenon and connects temperature fluctuation(non-equilibrium conditions) with the interactions between atoms qualitatively. More interactions between atoms give rise to more non-equilibrium conditions which is as expected.

Potentialities of a new sigma(+)-sigma(-)laser configuration for radiative cooling and trapping

NASA Astrophysics Data System (ADS)

Dalibard, J.; Reynaud, S.; Cohen-Tannoudji, C.

1984-11-01

In the process of cooling and trapping neutral atoms, a new laser configuration is investigated which consists of two counterpropagating laser beams with orthogonal sigma(+) and sigma(-)polarizations. It is shown that such a configuration looks more promising than an ordinary standing wave (where the two counterpropagating waves have the same polarization), and this result is explained as being due to angular momentum conservation which prevents any coherent redistribution of photons between the two waves. The present conclusions are based on a quantitative calculation of the various parameters (potential depth, friction coefficient, diffusion coefficient) describing the mean value and the fluctuations of the radiative forces experienced, in such a laser configuration, by an atom with a J = 0 ground state and a J = 1 excited state.

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

Lafuente-Sampietro, A.; CNRS, Institut Néel, F-38000 Grenoble; Institute of Materials Science, University of Tsukuba, 305-8573 Tsukuba

We studied the spin dynamics of a Cr atom incorporated in a II-VI semiconductor quantum dot using photon correlation techniques. We used recently developed singly Cr-doped CdTe/ZnTe quantum dots to access the spin of an individual magnetic atom. Auto-correlation of the photons emitted by the quantum dot under continuous wave optical excitation reveals fluctuations of the localized spin with a timescale in the 10 ns range. Cross-correlation gives quantitative transfer time between Cr spin states. A calculation of the time dependence of the spin levels population in Cr-doped quantum dots shows that the observed spin dynamics is dominated by the exciton-Crmore » interaction. These measurements also provide a lower bound in the 20 ns range for the intrinsic Cr spin relaxation time.« less

Extending the electron spin coherence time of atomic hydrogen by dynamical decoupling.

PubMed

Mitrikas, George; Efthimiadou, Eleni K; Kordas, George

2014-02-14

We study the electron spin decoherence of encapsulated atomic hydrogen in octasilsesquioxane cages induced by the (1)H and (29)Si nuclear spin bath. By applying the Carr-Purcell-Meiboom-Gill (CPMG) pulse sequence we significantly suppress the low-frequency noise due to nuclear spin flip-flops up to the point where a maximum T2 = 56 μs is observed. Moreover, dynamical decoupling with the CPMG sequence reveals the existence of two other sources of decoherence: first, a classical magnetic field noise imposed by the (1)H nuclear spins of the cage organic substituents, which can be described by a virtual fluctuating magnetic field with the proton Larmor frequency, and second, decoherence due to anisotropic hyperfine coupling between the electron and the inner (29)Si spins of the cage.

Assessing degrees of entanglement of phonon states in atomic Bose gases through the measurement of commuting observables

NASA Astrophysics Data System (ADS)

Robertson, Scott; Michel, Florent; Parentani, Renaud

2017-08-01

We show that measuring commuting observables can be sufficient to assess that a bipartite state is entangled according to either nonseparability or the stronger criterion of "steerability." Indeed, the measurement of a single observable might reveal the strength of the interferences between the two subsystems, as if an interferometer were used. For definiteness, we focus on the two-point correlation function of density fluctuations obtained by in situ measurements in homogeneous one-dimensional cold atomic Bose gases. We then compare this situation to that found in transonic stationary flows mimicking a black hole geometry where correlated phonon pairs are emitted on either side of the sonic horizon by the analogue Hawking effect. We briefly apply our considerations to two recent experiments.

Phase transition kinetics for a Bose Einstein condensate in a periodically driven band system

NASA Astrophysics Data System (ADS)

Michon, E.; Cabrera-Gutiérrez, C.; Fortun, A.; Berger, M.; Arnal, M.; Brunaud, V.; Billy, J.; Petitjean, C.; Schlagheck, P.; Guéry-Odelin, D.

2018-05-01

The dynamical transition of an atomic Bose–Einstein condensate from a spatially periodic state to a staggered state with alternating sign in its wavefunction is experimentally studied using a one-dimensional phase modulated optical lattice. We observe the crossover from quantum to thermal fluctuations as the triggering mechanism for the nucleation of staggered states. In good quantitative agreement with numerical simulations based on the truncated Wigner method, we experimentally investigate how the nucleation time varies with the renormalized tunneling rate, the atomic density, and the driving frequency. The effective inverted energy band in the driven lattice is identified as the key ingredient which explains the emergence of gap solitons as observed in numerics and the possibility to nucleate staggered states from interband excitations as reported experimentally.

Passive microrheology of soft materials with atomic force microscopy: A wavelet-based spectral analysis

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

Martinez-Torres, C.; Streppa, L.; Arneodo, A.

2016-01-18

Compared to active microrheology where a known force or modulation is periodically imposed to a soft material, passive microrheology relies on the spectral analysis of the spontaneous motion of tracers inherent or external to the material. Passive microrheology studies of soft or living materials with atomic force microscopy (AFM) cantilever tips are rather rare because, in the spectral densities, the rheological response of the materials is hardly distinguishable from other sources of random or periodic perturbations. To circumvent this difficulty, we propose here a wavelet-based decomposition of AFM cantilever tip fluctuations and we show that when applying this multi-scale methodmore » to soft polymer layers and to living myoblasts, the structural damping exponents of these soft materials can be retrieved.« less

Eccentricity fluctuation effects on elliptic flow in relativistic heavy ion collisions

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

Hirano, Tetsufumi; Nara, Yasushi

2009-06-15

We study effects of eccentricity fluctuations on the elliptic flow coefficient v{sub 2} at midrapidity in both Au+Au and Cu+Cu collisions at {radical}(s{sub NN})=200 GeV by using a hybrid model that combines ideal hydrodynamics for space-time evolution of the quark gluon plasma phase and a hadronic transport model for the hadronic matter. For initial conditions in hydrodynamic simulations, both the Glauber model and the color glass condensate model are employed to demonstrate the effect of initial eccentricity fluctuations originating from the nucleon position inside a colliding nucleus. The effect of eccentricity fluctuations is modest in semicentral Au+Au collisions, but significantlymore » enhances v{sub 2} in Cu+Cu collisions.« less

Chaotic dynamics of a microswimmer in Poiseuille flow.

PubMed

Chacón, Ricardo

2013-11-01

The chaotic dynamics of pointlike, spherical particles in cylindrical Poiseuille flow is theoretically characterized and numerically confirmed when their own intrinsic swimming velocity undergoes temporal fluctuations around an average value. Two dimensionless ratios associated with the three significant temporal scales of the problem are identified that fully determine the chaos scenario. In particular, small but finite periodic fluctuations of swimming speed result in chaotic or regular motion depending on the position and orientation of the microswimmer with respect to the flow center line. Remarkably, the spatial extension of chaotic microswimmers is found to depend crucially on the fluctuations' period and amplitude and to be highly sensitive to the Fourier spectrum of the fluctuations. This has implications for the design of artificial microswimmers.

Plasma Diffusion in Self-Consistent Fluctuations

NASA Technical Reports Server (NTRS)

Smets, R.; Belmont, G.; Aunai, N.

2012-01-01

The problem of particle diffusion in position space, as a consequence ofeleclromagnetic fluctuations is addressed. Numerical results obtained with a self-consistent hybrid code are presented, and a method to calculate diffusion coefficient in the direction perpendicular to the mean magnetic field is proposed. The diffusion is estimated for two different types of fluctuations. The first type (resuiting from an agyrotropic in itiai setting)is stationary, wide band white noise, and associated to Gaussian probability distribution function for the magnetic fluctuations. The second type (result ing from a Kelvin-Helmholtz instability) is non-stationary, with a power-law spectrum, and a non-Gaussian probabi lity distribution function. The results of the study allow revisiting the question of loading particles of solar wind origin in the Earth magnetosphere.

Revision of the Li13Si4 structure

PubMed Central

Zeilinger, Michael; Fässler, Thomas F.

2013-01-01

Besides Li17Si4, Li16.42Si4, and Li15Si4, another lithium-rich representative in the Li–Si system is the phase Li13Si4 (trideca­lithium tetra­silicide), the structure of which has been determined previously [Frank et al. (1975 ▶). Z. Naturforsch. Teil B, 30, 10–13]. A careful analysis of X-ray diffraction patterns of Li13Si4 revealed discrepancies between experimentally observed and calculated Bragg positions. Therefore, we redetermined the structure of Li13Si4 on the basis of single-crystal X-ray diffraction data. Compared to the previous structure report, decisive differences are (i) the introduction of a split position for one Li site [occupancy ratio 0.838 (7):0.162 (7)], (ii) the anisotropic refinement of atomic displacement parameters for all atoms, and (iii) a high accuracy of atom positions and unit-cell parameters. The asymmetric unit of Li13Si4 contains two Si and seven Li atoms. Except for one Li atom situated on a site with symmetry 2/m, all other atoms are on mirror planes. The structure consists of isolated Si atoms as well as Si–Si dumbbells surrounded by Li atoms. Each Si atom is either 12- or 13-coordinated. The isolated Si atoms are situated in the ab plane at z = 0 and are strictly separated from the Si–Si dumbbells at z = 0.5. PMID:24454148

Detection of stably bright squeezed light with the quantum noise reduction of 12.6  dB by mutually compensating the phase fluctuations.

PubMed

Yang, Wenhai; Shi, Shaoping; Wang, Yajun; Ma, Weiguang; Zheng, Yaohui; Peng, Kunchi

2017-11-01

We present a mutual compensation scheme of three phase fluctuations, originating from the residual amplitude modulation (RAM) in the phase modulation process, in the bright squeezed light generation system. The influence of the RAM on each locking loop is harmonized by using one electro-optic modulator (EOM), and the direction of the phase fluctuation is manipulated by positioning the photodetector (PD) that extracts the error signal before or after the optical parametric amplifier (OPA). Therefore a bright squeezed light with non-classical noise reduction of π is obtained. By fitting the squeezing and antisqueezing measurement results, we confirm that the total phase fluctuation of the system is around 3.1 mrad. The fluctuation of the noise suppression is 0.2 dB for 3 h.

Impact of economic fluctuations on suicide mortality in Canada (1926-2008): Testing the Durkheim, Ginsberg, and Henry and Short theories.

PubMed

Thibodeau, Lise; Lachaud, James

2016-01-01

Three theories have been proposed to explain the relationship between suicide and economic fluctuations, including the Durkheim (nonlinear), Ginsberg (procyclical), and Henry and Short (countercyclical) theories. This study tested the effect of economic fluctuations, measured by unemployment rate, on suicide rates in Canada from 1926 to 2008. Autoregressive integrated moving average time-series models were used. The results showed a significant relationship between suicide and economic fluctuation; this association was positive during the contraction period (1926-1950) and negative in the period of economic expansion (1951-1973). Males and females showed differential effects in the period of moderate unemployment (1974-2008). In addition, the suicide rate of mid-adults (45-64) was most impacted by economic fluctuations. Our study tends to support Durkheim's theory and suggests the need for public health responses in times of economic contraction and expansion.

Non-conventional Anderson localization in a matched quarter stack with metamaterials

NASA Astrophysics Data System (ADS)

Torres-Herrera, E. J.; Izrailev, F. M.; Makarov, N. M.

2013-05-01

We study the problem of non-conventional Anderson localization emerging in bilayer periodic-on-average structures with alternating layers of materials, with positive and negative refraction indices na and nb. Attention is paid to the model of the so-called quarter stack with perfectly matched layers (the same unperturbed by disorder impedances, Za = Zb, and optical path lengths, nada = |nb|db, with da and db being the thicknesses of basic layers). As was recently numerically discovered, in such structures with weak fluctuations of refractive indices (compositional disorder), the localization length Lloc is enormously large in comparison to the conventional localization occurring in the structures with positive refraction indices only. In this paper we develop a new approach, which allows us to derive the expression for Lloc for weak disorder and any wave frequency ω. In the limit ω → 0 one gets a quite specific dependence, L-1loc∝σ4ω8, which is obtained within the fourth order of perturbation theory. We also analyze the interplay between two types of disorder, when in addition to the fluctuations of na and nb, the thicknesses da and db slightly fluctuate as well (positional disorder). We show how conventional localization recovers with the addition of positional disorder.

Analysis of Delay Fluctuations on Two-Way Time Transfer Earth Stations

DTIC Science & Technology

2007-11-01

Two Way Satellite Time and Frequency Transfer ( TWSTFT ) has become one of the major techniques to compare atomic time scales and primary clocks over...the result of TWSTFT . On the TL’s earth station, the most of the equipment is located outside, including the up- and down-converters, solid-state...light/shade, wind speed, humidity, and thermal circulation, may affect the TWSTFT earth station. These conditions may cause both the change of path

Quantized vortices in the ideal bose gas: a physical realization of random polynomials.

PubMed

Castin, Yvan; Hadzibabic, Zoran; Stock, Sabine; Dalibard, Jean; Stringari, Sandro

2006-02-03

We propose a physical system allowing one to experimentally observe the distribution of the complex zeros of a random polynomial. We consider a degenerate, rotating, quasi-ideal atomic Bose gas prepared in the lowest Landau level. Thermal fluctuations provide the randomness of the bosonic field and of the locations of the vortex cores. These vortices can be mapped to zeros of random polynomials, and observed in the density profile of the gas.

Sympathetic Cooling of Lattice Atoms by a Bose-Einstein Condensate

DTIC Science & Technology

2010-08-13

average out to zero net change in momentum. This type of cooling is the basis for techniques such as Zeeman slowing and Magneto - optical traps . On a...change in momentum. This type of cooling is the basis for techniques such as Zeeman slowing and Magneto - optical traps . On a more basic level, an excited...cause stimulated emission of a second excitation. A quantitative explanation requires the use of the density fluctuation operator . This operator

Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model

NASA Astrophysics Data System (ADS)

Li, Chunhua; Lv, Dashuai; Zhang, Lei; Yang, Feng; Wang, Cunxin; Su, Jiguo; Zhang, Yang

2016-07-01

Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regions between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.

Atomically flat superconducting nanofilms: multiband properties and mean-field theory

NASA Astrophysics Data System (ADS)

Shanenko, A. A.; Aguiar, J. Albino; Vagov, A.; Croitoru, M. D.; Milošević, M. V.

2015-05-01

Recent progress in materials synthesis enabled fabrication of superconducting atomically flat single-crystalline metallic nanofilms with thicknesses down to a few monolayers. Interest in such nano-thin systems is attracted by the dimensional 3D-2D crossover in their coherent properties which occurs with decreasing the film thickness. The first fundamental aspect of this crossover is dictated by the Mermin-Wagner-Hohenberg theorem and concerns frustration of the long-range order due to superconductive fluctuations and the possibility to track its impact with an unprecedented level of control. The second important aspect is related to the Fabri-Pérot modes of the electronic motion strongly bound in the direction perpendicular to the nanofilm. The formation of such modes results in a pronounced multiband structure that changes with the nanofilm thickness and affects both the mean-field behavior and superconductive fluctuations. Though the subject is very rich in physics, it is scarcely investigated to date. The main obstacle is that there are no manageable models to study a complex magnetic response in this case. Full microscopic consideration is rather time consuming, if practicable at all, while the standard Ginzburg-Landau theory is not applicable. In the present work we review the main achievements in the subject to date, and construct and justify an efficient multiband mean-field formalism which allows for numerical and even analytical treatment of nano-thin superconductors in applied magnetic fields.

Part-crystalline part-liquid state and electrical/thermal transport in materials with chemical-bond hierarchy

NASA Astrophysics Data System (ADS)

Zhang, Wenqng

2015-03-01

A concept of part-crystalline part-liquid state (or liquid-like), and even part-crystalline part-glass state (or glass-like), was demonstrated in some materials such as Cu3SbSe3 with chemical-bond-hierarchy, in which certain constituent species weakly bond to other part of the crystal. Such a material could intrinsically manifest the coexistence of rigid crystalline sublattices and other fluctuating noncrystalline sublattices with thermally induced large amplitude vibrations and even flow of the group of species atoms. The large-amplitude vibrations and movement of atoms can generate unusual severe phonon scattering and thermal damping due to the collective low-frequency vibrations similar to the Boson peak in amorphous or liquid materials. While different phase or state may have large energetic discrepancy, whether the thermally-induced part-crystalline state is undergoing phase transition becomes an interesting issue. In addition, our earlier work reported that second-order phase transition could induce extreme electron and phonon scattering in thermoelectrics. The above work clearly demonstrated that the unusual effect from structural fluctuations on thermal and electrical transport in thermoelectrics should be paid attention to. While materials with these structural changes can retain extremely low lattice thermal conductivity and unusual electron transport and become promising candidates for high-performance thermoelectrics, underlying mechanism is yet to be explored.

An investigation of molecular dynamics simulation and molecular docking: interaction of citrus flavonoids and bovine β-lactoglobulin in focus.

PubMed

Sahihi, M; Ghayeb, Y

2014-08-01

Citrus flavonoids are natural compounds with important health benefits. The study of their interaction with a transport protein, such as bovine β-lactoglobulin (BLG), at the atomic level could be a valuable factor to control their transport to biological sites. In the present study, molecular docking and molecular dynamics simulation methods were used to investigate the interaction of hesperetin, naringenin, nobiletin and tangeretin as citrus flavonoids and BLG as transport protein. The molecular docking results revealed that these flavonoids bind in the internal cavity of BLG and the BLG affinity for binding the flavonoids follows naringenin>hesperetin>tangeretin>nobiletin. The docking results also indicated that the BLG-flavonoid complexes are stabilized through hydrophobic interactions, hydrogen bond interactions and π-π stacking interactions. The analysis of molecular dynamics (MD) simulation trajectories showed that the root mean square deviation (RMSD) of various systems reaches equilibrium and fluctuates around the mean value at various times. Time evolution of the radius of gyration, total solvent accessible surface of the protein and the second structure of protein showed as well that BLG and BLG-flavonoid complexes were stable around 2500ps, and there was not any conformational change as for BLG-flavonoid complexes. Further, the profiles of atomic fluctuations indicated the rigidity of the ligand binding site during the simulation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Quantum conductance oscillation in linear monatomic silicon chains

NASA Astrophysics Data System (ADS)

Liu, Fu-Ti; Cheng, Yan; Yang, Fu-Bin; Chen, Xiang-Rong

2014-02-01

The conductance of linear silicon atomic chains with n=1-8 atoms sandwiched between Au electrodes is investigated by using the density functional theory combined with non-equilibrium Green's function. The results show that the conductance oscillates with a period of two atoms as the number of atoms in the chain is varied. We optimize the geometric structure of nanoscale junctions in different distances, and obtain that the average bond-length of silicon atoms in each chain at equilibrium positions is 2.15±0.03 Å. The oscillation of average Si-Si bond-length can explain the conductance oscillation from the geometric structure of atomic chains. We calculate the transmission spectrum of the chains in the equilibrium positions, and explain the conductance oscillation from the electronic structure. The transport channel is mainly contributed by px and py orbital electrons of silicon atoms. The even-odd oscillation is robust under external voltage up to 1.2 V.

Zn or O? An Atomic Level Comparison on Antibacterial Activities of Zinc Oxides.

PubMed

Yu, Fen; Fang, Xuan; Jia, Huimin; Liu, Miaoxing; Shi, Xiaotong; Xue, Chaowen; Chen, Tingtao; Wei, Zhipeng; Fang, Fang; Zhu, Hui; Xin, Hongbo; Feng, Jing; Wang, Xiaolei

2016-06-06

For the first time, the influence of different types of atoms (Zn and O) on the antibacterial activities of nanosized ZnO was quantitatively evaluated with the aid of a 3D-printing-manufactured evaluation system. Two different outermost atomic layers were manufactured separately by using an ALD (atomic layer deposition) method. Interestingly, we found that each outermost atomic layer exhibited certain differences against gram-positive or gram-negative bacterial species. Zinc atoms as outermost layer (ZnO-Zn) showed a more pronounced antibacterial effect towards gram-negative E. coli (Escherichia coli), whereas oxygen atoms (ZnO-O) showed a stronger antibacterial activity against gram-positive S. aureus (Staphylococcus aureus). A possible antibacterial mechanism has been comprehensively discussed from different perspectives, including Zn(2+) concentrations, oxygen vacancies, photocatalytic activities and the DNA structural characteristics of different bacterial species. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identifying the adaptive mechanism in globular proteins: Fluctuations in densely packed regions manipulate flexible parts

NASA Astrophysics Data System (ADS)

Yilmaz, Lutfu Safak; Atilgan, Ali Rana

2000-09-01

A low-resolution structural model based on the packing geometry of α-carbons is utilized to establish a connection between the flexible and rigid parts of a folded protein. The former commonly recognizes a complementing molecule for making a complex, while the latter manipulates the necessary conformational change for binding. We attempt analytically to distinguish this control architecture that intrinsically exists in globular proteins. First with two-dimensional simple models, then for a native protein, bovine pancreatic trypsin inhibitor, we explicitly demonstrate that inserting fluctuations in tertiary contacts supported by the stable core, one can regulate the displacement of residues on loop regions. The positional fluctuations of the flexible regions are annihilated by the rest of the protein in conformity with the Le Chatelier-Braun principle. The results indicate that the distortion of the principal nonbonded contacts between highly packed residues is accompanied by that of the slavery fluctuations that are widely distributed over the native structure. These positional arrangements do not appear in a reciprocal relation between a perturbation and the associated response; the effect of a movement of residue i on residue j is not equal to that of the same movement of residue j on residue i.

On the mass function of stars growing in a flocculent medium

NASA Astrophysics Data System (ADS)

Maschberger, Th.

2013-12-01

Stars form in regions of very inhomogeneous densities and may have chaotic orbital motions. This leads to a time variation of the accretion rate, which will spread the masses over some mass range. We investigate the mass distribution functions that arise from fluctuating accretion rates in non-linear accretion, ṁ ∝ mα. The distribution functions evolve in time and develop a power-law tail attached to a lognormal body, like in numerical simulations of star formation. Small fluctuations may be modelled by a Gaussian and develop a power-law tail ∝ m-α at the high-mass side for α > 1 and at the low-mass side for α < 1. Large fluctuations require that their distribution is strictly positive, for example, lognormal. For positive fluctuations the mass distribution function develops the power-law tail always at the high-mass hand side, independent of α larger or smaller than unity. Furthermore, we discuss Bondi-Hoyle accretion in a supersonically turbulent medium, the range of parameters for which non-linear stochastic growth could shape the stellar initial mass function, as well as the effects of a distribution of initial masses and growth times.

Imaging Dirac-mass disorder from magnetic dopant atoms in the ferromagnetic topological insulator Cr x(Bi 0.1Sb 0.9) 2-xTe 3

DOE PAGES

Lee, Inhee; Kim, Chung Koo; Lee, Jinho; ...

2015-01-20

To achieve and use the most exotic electronic phenomena predicted for the surface states of 3D topological insulators (TIs), it is necessary to open a “Dirac-mass gap” in their spectrum by breaking time-reversal symmetry. Use of magnetic dopant atoms to generate a ferromagnetic state is the most widely applied approach. However, it is unknown how the spatial arrangements of the magnetic dopant atoms influence the Dirac-mass gap at the atomic scale or, conversely, whether the ferromagnetic interactions between dopant atoms are influenced by the topological surface states. Here we image the locations of the magnetic (Cr) dopant atoms in themore » ferromagnetic TI Cr₀.₀₈(Bi₀.₁Sb₀.₉)₁.₉₂Te₃. Simultaneous visualization of the Dirac-mass gap Δ(r) reveals its intense disorder, which we demonstrate is directly related to fluctuations in n(r), the Cr atom areal density in the termination layer. We find the relationship of surface-state Fermi wavevectors to the anisotropic structure of Δ(r) not inconsistent with predictions for surface ferromagnetism mediated by those states. Moreover, despite the intense Dirac-mass disorder, the anticipated relationship Δ(r)∝n(r) is confirmed throughout and exhibits an electron–dopant interaction energy J* = 145 meV·nm². In addition, these observations reveal how magnetic dopant atoms actually generate the TI mass gap locally and that, to achieve the novel physics expected of time-reversal symmetry breaking TI materials, control of the resulting Dirac-mass gap disorder will be essential.« less

Limited Quantum Helium Transportation through Nano-channels by Quantum Fluctuation

PubMed Central

Ohba, Tomonori

2016-01-01

Helium at low temperatures has unique quantum properties such as superfluidity, which causes it to behave differently from a classical fluid. Despite our deep understanding of quantum mechanics, there are many open questions concerning the properties of quantum fluids in nanoscale systems. Herein, the quantum behavior of helium transportation through one-dimensional nanopores was evaluated by measuring the adsorption of quantum helium in the nanopores of single-walled carbon nanohorns and AlPO4-5 at 2–5 K. Quantum helium was transported unimpeded through nanopores larger than 0.7 nm in diameter, whereas quantum helium transportation was significantly restricted through 0.4-nm and 0.6-nm nanopores. Conversely, nitrogen molecules diffused through the 0.4-nm nanopores at 77 K. Therefore, quantum helium behaved as a fluid comprising atoms larger than 0.4–0.6 nm. This phenomenon was remarkable, considering that helium is the smallest existing element with a (classical) size of approximately 0.27 nm. This finding revealed the presence of significant quantum fluctuations. Quantum fluctuation determined the behaviors of quantum flux and is essential to understanding unique quantum behaviors in nanoscale systems. PMID:27363671

Phonons of Fe-based superconductor Ca 10Pt 4As 8(Fe 1-xPt xAs) 10

DOE PAGES

Ikeuchi, K.; Kobayashi, Y.; Suzuki, K.; ...

2015-10-28

In this paper, we report the results of inelastic neutron scattering measurements on particular phonons of a superconducting (SC) Ca10Pt 4As 8(Fe 1-xPt xAs) 10 with the onset transition temperature T c ~ 33 K to investigate mainly what roles orbital fluctuation plays in Cooper pairing, where we observed a slight softening of the in-plane transverse acoustic mode corresponding to the elastic constant C 66. This softening starts at temperature T well above the superconducting T c, as T decreases. An anomalously strong change of the scattering intensity of in-plane optical modes was observed at the M point of themore » pseudo tetragonal reciprocal space in the range of 35 < ω < 40 meV with decreasing T from far above T c. Finally, because this ω region mainly corresponds to the motion of Fe and As atoms in the FeAs planes, the finding presents information on the coupling between the orbital fluctuation of Fe 3d electrons and the lattice system, useful for studying the possible roles of orbital fluctuation in the pairing mechanism and/or the appearance of the so-called nematic phase.« less

Random Dopant Induced Threshold Voltage Lowering and Fluctuations in Sub-0.1 (micron)meter MOSFET's: A 3-D 'Atomistic' Simulation Study

NASA Technical Reports Server (NTRS)

Asenov, Asen

1998-01-01

A three-dimensional (3-D) "atomistic" simulation study of random dopant induced threshold voltage lowering and fluctuations in sub-0.1 microns MOSFET's is presented. For the first time a systematic analysis of random dopant effects down to an individual dopant level was carried out in 3-D on a scale sufficient to provide quantitative statistical predictions. Efficient algorithms based on a single multigrid solution of the Poisson equation followed by the solution of a simplified current continuity equation are used in the simulations. The effects of various MOSFET design parameters, including the channel length and width, oxide thickness and channel doping, on the threshold voltage lowering and fluctuations are studied using typical samples of 200 atomistically different MOSFET's. The atomistic results for the threshold voltage fluctuations were compared with two analytical models based on dopant number fluctuations. Although the analytical models predict the general trends in the threshold voltage fluctuations, they fail to describe quantitatively the magnitude of the fluctuations. The distribution of the atomistically calculated threshold voltage and its correlation with the number of dopants in the channel of the MOSFET's was analyzed based on a sample of 2500 microscopically different devices. The detailed analysis shows that the threshold voltage fluctuations are determined not only by the fluctuation in the dopant number, but also in the dopant position.

Hirshfeld atom refinement for modelling strong hydrogen bonds.

PubMed

Woińska, Magdalena; Jayatilaka, Dylan; Spackman, Mark A; Edwards, Alison J; Dominiak, Paulina M; Woźniak, Krzysztof; Nishibori, Eiji; Sugimoto, Kunihisa; Grabowsky, Simon

2014-09-01

High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first examples of Z' > 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O-H...O intramolecular hydrogen bond present in the hydrogen maleate anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM; transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body (SHADE) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment, e.g. the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.

Stochastic environmental fluctuations drive epidemiology in experimental host–parasite metapopulations

PubMed Central

Duncan, Alison B.; Gonzalez, Andrew; Kaltz, Oliver

2013-01-01

Environmental fluctuations are important for parasite spread and persistence. However, the effects of the spatial and temporal structure of environmental fluctuations on host–parasite dynamics are not well understood. Temporal fluctuations can be random but positively autocorrelated, such that the environment is similar to the recent past (red noise), or random and uncorrelated with the past (white noise). We imposed red or white temporal temperature fluctuations on experimental metapopulations of Paramecium caudatum, experiencing an epidemic of the bacterial parasite Holospora undulata. Metapopulations (two subpopulations linked by migration) experienced fluctuations between stressful (5°C) and permissive (23°C) conditions following red or white temporal sequences. Spatial variation in temperature fluctuations was implemented by exposing subpopulations to the same (synchronous temperatures) or different (asynchronous temperatures) temporal sequences. Red noise, compared with white noise, enhanced parasite persistence. Despite this, red noise coupled with asynchronous temperatures allowed infected host populations to maintain sizes equivalent to uninfected populations. It is likely that this occurs because subpopulations in permissive conditions rescue declining subpopulations in stressful conditions. We show how patterns of temporal and spatial environmental fluctuations can impact parasite spread and host population abundance. We conclude that accurate prediction of parasite epidemics may require realistic models of environmental noise. PMID:23966645

Electronic structure of graphene nanoribbons doped with nitrogen atoms: a theoretical insight.

PubMed

Torres, A E; Fomine, S

2015-04-28

The electronic structure of graphene nanoribbons doped with a graphitic type of nitrogen atoms has been studied using B3LYP, B2PLYP and CAS methods. In all but one case the restricted B3LYP solutions were unstable and the CAS calculations provided evidence for the multiconfigurational nature of the ground state with contributions from two dominant configurations. The relative stability of the doped nanoribbons depends mostly on the mutual position of the dopant atoms and notably less on the position of nitrogen atoms within the nanoribbon. N-graphitic doping affects cationic states much more than anionic ones due the participation of the nitrogen atoms in the stabilization of the positive charge, resulting in a drop in ionization energies (IPs) for N-graphitic doped systems. Nitrogen atoms do not participate in the negative charge stabilization of anionic species and, therefore, the doping does not affect the electron affinities (EAs). The unrestricted B3LYP method is the method of choice for the calculation of IPs and EAs. Restricted B3LYP and B2PLYP produces unreliable results for both IPs and EAs while CAS strongly underestimates the electron affinities. This is also true for the reorganization energies where restricted B3LYP produces qualitatively incorrect results. Doping changes the reorganization energy of the nanoribbons; the hole reorganization energy is generally higher than the corresponding electron reorganization energy due to the participation of nitrogen atoms in the stabilization of the positive charge.