Structural Properties of Human IAPP Dimer in Membrane Environment Studied by All-Atom Molecular Dynamics Simulations.

PubMed

Liu, Na; Duan, Mojie; Yang, Minghui

2017-08-11

The aggregation of human islet amyloid polypeptide (hIAPP) can damage the membrane of the β-cells in the pancreatic islets and induce type 2 diabetes (T2D). Growing evidences indicated that the major toxic species are small oligomers of IAPP. Due to the fast aggregation nature, it is hard to characterize the structures of IAPP oligomers by experiments, especially in the complex membrane environment. On the other side, molecular dynamics simulation can provide atomic details of the structure and dynamics of the aggregation of IAPP. In this study, all-atom bias-exchange metadynamics (BE-Meta) and unbiased molecular dynamics simulations were employed to study the structural properties of IAPP dimer in the membranes environments. A number of intermediates, including α-helical states, β-sheet states, and fully disordered states, are identified. The formation of N-terminal β-sheet structure is prior to the C-terminal β-sheet structure towards the final fibril-like structures. The α-helical intermediates have lower propensity in the dimeric hIAPP and are off-pathway intermediates. The simulations also demonstrate that the β-sheet intermediates induce more perturbation on the membrane than the α-helical and disordered states and thus pose higher disruption ability.

Hydrogen atom in a quantum plasma environment under the influence of Aharonov-Bohm flux and electric and magnetic fields.

PubMed

Falaye, Babatunde James; Sun, Guo-Hua; Silva-Ortigoza, Ramón; Dong, Shi-Hai

2016-05-01

This study presents the confinement influences of Aharonov-Bohm (AB) flux and electric and magnetic fields directed along the z axis and encircled by quantum plasmas on the hydrogen atom. The all-inclusive effects result in a strongly attractive system while the localizations of quantum levels change and the eigenvalues decrease. We find that the combined effect of the fields is stronger than a solitary effect and consequently there is a substantial shift in the bound state energy of the system. We also find that to perpetuate a low-energy medium for the hydrogen atom in quantum plasmas, a strong electric field and weak magnetic field are required, whereas the AB flux field can be used as a regulator. The application of the perturbation technique utilized in this paper is not restricted to plasma physics; it can also be applied in molecular physics.

Nonperturbative theory of atom-surface interaction: corrections at short separations

NASA Astrophysics Data System (ADS)

Bordag, M.; Klimchitskaya, G. L.; Mostepanenko, V. M.

2018-02-01

The nonperturbative expressions for the free energy and force of interaction between a ground-state atom and a real-material surface at any temperature are presented. The transition to the Matsubara representation is performed, whereupon the comparison is made with the commonly used perturbative results based on the standard Lifshitz theory. It is shown that the Lifshitz formulas for the free energy and force of an atom-surface interaction follow from the nonperturbative ones in the lowest order of the small parameter. Numerical computations of the free energy and force for the atoms of He{\\hspace{0pt}}\\ast and Na interacting with a surface of an Au plate have been performed using the frequency-dependent dielectric permittivity of Au and highly accurate dynamic atomic polarizabilities in the framework of both the nonperturbative and perturbative theories. According to our results, the maximum deviations between the two theories are reached at the shortest atom-surface separations of about 1 nm. Simple analytic expressions for the atom-surface free energy are derived in the classical limit and for an ideal-metal plane. In the lowest order of the small parameter, they are found in agreement with the perturbative ones following from the standard Lifshitz theory. Possible applications of the obtained results in the theory of van der Waals adsorption are discussed.

On the Treatment of l-changing Proton-hydrogen Rydberg Atom Collisions

NASA Astrophysics Data System (ADS)

Vrinceanu, Daniel; Onofrio, Roberto; Sadeghpour, Hossein

2018-01-01

Energy-conserving, angular momentum-changing collisions between protons and highly excited Rydberg hydrogen atoms are important for precise understanding of the primordial recombination cascade, and the elemental abundance.Early approaches to l-changing collisions used perturbation theory for only dipole-allowed (Δl = ±1) transitions. An exact non-perturbative quantum mechanical treatment is possible, but it comes at computational cost for highly excited Rydberg states. In this note we show how to obtain a semi-classical limit that is accurate and simple, and develop further physical insights afforded by the non-perturbative quantum mechanical treatment.

Adiabatic perturbation theory of electronic stopping in insulators

DOE PAGES

Horsfield, Andrew P.; Lim, Anthony; Foulkes, W. M. C.; ...

2016-06-02

A model able to explain the complicated structure of electronic stopping at low velocities in insulating materials is presented. It is shown to be in good agreement with results obtained from time-dependent density-functional theory for the stopping of a channeling Si atom in a Si crystal. If we define the repeat frequency f=v/λ, where λ is the periodic repeat length of the crystal along the direction the channeling atom is traveling, and v is the velocity of the channeling atom, we find that electrons experience a perturbing force that varies in time at integer multiples l of f. This enablesmore » electronic excitations at low atom velocity, but their contributions diminish rapidly with increasing values of l. The expressions for stopping power are derived using adiabatic perturbation theory for many-electron systems, and they are then specialized to the case of independent electrons. Lastly, a simple model for the nonadiabatic matrix elements is described, along with the procedure for determining its parameters.« less

Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation

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

Mao, Yuezhi; Horn, Paul R.; Mardirossian, Narbe

2016-07-28

Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set producesmore » <0.15 kcal/mol root-mean-square deviations for most of the tested TC datasets, and <0.1 kcal/mol for most of the NC datasets. The performance of density functionals near the basis set limit can be even better reproduced. With further improvement to its implementation, MAB-SCF (PC) is a promising lower-cost substitute for conventional large-basis calculations as a method to approach the basis set limit of modern density functionals.« less

Quantum phase transitions of light in a dissipative Dicke-Bose-Hubbard model

NASA Astrophysics Data System (ADS)

Wu, Ren-Cun; Tan, Lei; Zhang, Wen-Xuan; Liu, Wu-Ming

2017-09-01

The impact that the environment has on the quantum phase transition of light in the Dicke-Bose-Hubbard model is investigated. Based on the quasibosonic approach, mean-field theory, and perturbation theory, the formulation of the Hamiltonian, the eigenenergies, and the superfluid order parameter are obtained analytically. Compared with the ideal cases, the order parameter of the system evolves with time as the photons naturally decay in their environment. When the system starts with the superfluid state, the dissipation makes the photons more likely to localize, and a greater hopping energy of photons is required to restore the long-range phase coherence of the localized state of the system. Furthermore, the Mott lobes depend crucially on the numbers of atoms and photons (which disappear) of each site, and the system tends to be classical with the number of atoms increasing; however, the atomic number is far lower than that expected under ideal circumstances. As there is an inevitable interaction between the coupled-cavity array and its surrounding environment in the actual experiments, the system is intrinsically dissipative. The results obtained here provide a more realistic image for characterizing the dissipative nature of quantum phase transitions in lossy platforms, which will offer valuable insight into quantum simulation of a dissipative system and which are helpful in guiding experimentalists in open quantum systems.

Imaging the effects of individual zinc impurity atoms on superconductivity in Bi2Sr2CaCu2O8+delta

PubMed

Pan; Hudson; Lang; Eisaki; Uchida; Davis

2000-02-17

Although the crystal structures of the copper oxide high-temperature superconductors are complex and diverse, they all contain some crystal planes consisting of only copper and oxygen atoms in a square lattice: superconductivity is believed to originate from strongly interacting electrons in these CuO2 planes. Substituting a single impurity atom for a copper atom strongly perturbs the surrounding electronic environment and can therefore be used to probe high-temperature superconductivity at the atomic scale. This has provided the motivation for several experimental and theoretical studies. Scanning tunnelling microscopy (STM) is an ideal technique for the study of such effects at the atomic scale, as it has been used very successfully to probe individual impurity atoms in several other systems. Here we use STM to investigate the effects of individual zinc impurity atoms in the high-temperature superconductor Bi2Sr2CaCu2O8+delta. We find intense quasiparticle scattering resonances at the Zn sites, coincident with strong suppression of superconductivity within approximately 15 A of the scattering sites. Imaging of the spatial dependence of the quasiparticle density of states in the vicinity of the impurity atoms reveals the long-sought four-fold symmetric quasiparticle 'cloud' aligned with the nodes of the d-wave superconducting gap which is believed to characterize superconductivity in these materials.

Infrared dynamics of cold atoms on hot graphene membranes

NASA Astrophysics Data System (ADS)

Sengupta, Sanghita; Kotov, Valeri N.; Clougherty, Dennis P.

2016-06-01

We study the infrared dynamics of low-energy atoms interacting with a sample of suspended graphene at finite temperature. The dynamics exhibits severe infrared divergences order by order in perturbation theory as a result of the singular nature of low-energy flexural phonon emission. Our model can be viewed as a two-channel generalization of the independent boson model with asymmetric atom-phonon coupling. This allows us to take advantage of the exact nonperturbative solution of the independent boson model in the stronger channel while treating the weaker one perturbatively. In the low-energy limit, the exact solution can be viewed as a resummation (exponentiation) of the most divergent diagrams in the perturbative expansion. As a result of this procedure, we obtain the atom's Green function which we use to calculate the atom damping rate, a quantity equal to the quantum sticking rate. A characteristic feature of our results is that the Green's function retains a weak, infrared cutoff dependence that reflects the reduced dimensionality of the problem. As a consequence, we predict a measurable dependence of the sticking rate on graphene sample size. We provide detailed predictions for the sticking rate of atomic hydrogen as a function of temperature and sample size. The resummation yields an enhanced sticking rate relative to the conventional Fermi golden rule result (equivalent to the one-loop atom self-energy), as higher-order processes increase damping at finite temperature.

Frequency Measurements of Superradiance from the Strontium Clock Transition

NASA Astrophysics Data System (ADS)

Norcia, Matthew A.; Cline, Julia R. K.; Muniz, Juan A.; Robinson, John M.; Hutson, Ross B.; Goban, Akihisa; Marti, G. Edward; Ye, Jun; Thompson, James K.

2018-04-01

We present the first characterization of the spectral properties of superradiant light emitted from the ultranarrow, 1-mHz-linewidth optical clock transition in an ensemble of cold Sr 87 atoms. Such a light source has been proposed as a next-generation active atomic frequency reference, with the potential to enable high-precision optical frequency references to be used outside laboratory environments. By comparing the frequency of our superradiant source to that of a state-of-the-art cavity-stabilized laser and optical lattice clock, we observe a fractional Allan deviation of 6.7 (1 )×10-16 at 1 s of averaging, establish absolute accuracy at the 2-Hz (4 ×10-15 fractional frequency) level, and demonstrate insensitivity to key environmental perturbations.

Estimating Atomic Contributions to Hydration and Binding Using Free Energy Perturbation.

PubMed

Irwin, Benedict W J; Huggins, David J

2018-06-12

We present a general method called atom-wise free energy perturbation (AFEP), which extends a conventional molecular dynamics free energy perturbation (FEP) simulation to give the contribution to a free energy change from each atom. AFEP is derived from an expansion of the Zwanzig equation used in the exponential averaging method by defining that the system total energy can be partitioned into contributions from each atom. A partitioning method is assumed and used to group terms in the expansion to correspond to individual atoms. AFEP is applied to six example free energy changes to demonstrate the method. Firstly, the hydration free energies of methane, methanol, methylamine, methanethiol, and caffeine in water. AFEP highlights the atoms in the molecules that interact favorably or unfavorably with water. Finally AFEP is applied to the binding free energy of human immunodeficiency virus type 1 protease to lopinavir, and AFEP reveals the contribution of each atom to the binding free energy, indicating candidate areas of the molecule to improve to produce a more strongly binding inhibitor. FEP gives a single value for the free energy change and is already a very useful method. AFEP gives a free energy change for each "part" of the system being simulated, where part can mean individual atoms, chemical groups, amino acids, or larger partitions depending on what the user is trying to measure. This method should have various applications in molecular dynamics studies of physical, chemical, or biochemical phenomena, specifically in the field of computational drug discovery.

Using the theory of small perturbations in performance calculations of the RBMK

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

Isaev, N.V.; Druzhinin, V.E.; Pogosbekyan, L.R.

The theory of small perturbations in reactor physics is discussed and applied to two-dimensional calculations of the RBMK. The classical theory of small perturbations implies considerable errors in calculations because the perturbations cannot be considered small. The modified theory of small perturbations presented here can be used in atomic power stations for determining reactivity effects and reloading rates of channels in reactors and also for assessing the reactivity storage in control rods.

Casimir forces between defects in one-dimensional quantum liquids

NASA Astrophysics Data System (ADS)

Recati, A.; Fuchs, J. N.; Peça, C. S.; Zwerger, W.

2005-08-01

We discuss the effective interactions between two localized perturbations in one-dimensional quantum liquids. For noninteracting fermions, the interactions exhibit Friedel oscillations, giving rise to a Ruderman-Kittel-Kasuya-Yosida-type interaction familiar from impurity spins in metals. In the interacting case, at low energies, a Luttinger-liquid description applies. In the case of repulsive fermions, the Friedel oscillations of the interacting system are replaced, at long distances, by a universal Casimir-type interaction which depends only on the sound velocity and decays inversely with the separation. The Casimir-type interaction between localized perturbations embedded in a fermionic environment gives rise to a long-range coupling between quantum dots in ultracold Fermi gases, opening an alternative to couple qubits with neutral atoms. We also briefly discuss the case of bosonic quantum liquids in which the interaction between weak impurities turns out to be short ranged, decaying exponentially on the scale of the healing length.

Signatures of the atomic nucleus in laser-assisted single ionization of one-electron atoms

NASA Astrophysics Data System (ADS)

Ajana, Imane; Khalil, Driss; Makhoute, Abdelkader

2018-03-01

The dynamics of the electron-impact single ionization of hydrogenic targets in the presence of a laser field (e, 2e) has been studied for different residual ion charges Z = 1, 2, 3 and 4. The state of fast electron in the laser field is described by the Volkov state, while the dressed state of the ejected slow electron and atomic target is treated perturbatively to the first-order perturbation theory. We calculate the triple differential cross section in the Ehrhardt asymmetric coplanar geometry. We have compared and analyzed the triple differential cross sections from one-electron atoms by varying the charge state of the residual ion, and evaluating the interplay between the laser influence and the role of scattering from the residual ion.

Accurate calculation of dynamic Stark shifts and depopulation rates of Rydberg energy levels induced by blackbody radiation. Hydrogen, helium, and alkali-metal atoms

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

Farley, J.W.; Wing, W.H.

1981-05-01

A highly excited (Rydberg) atom bathed in blackbody radiation is perturbed in two ways. A dynamic Stark shift is induced by the off-resonant components of the blackbody radiation. Additionally, electric-dipole transitions to other atomic energy levels are induced by the resonant components of the blackbody radiation. This depopulation effect shortens the Rydberg-state lifetime, thereby broadening the energy level. Calculations of these two effects in many states of hydrogen, helium, and the alkali-metal atoms Li, Na, K, Rb, and Cs are presented for T = 300 K. Contributions from the entire blackbody spectrum and from both discrete and continuous perturbing statesmore » are included. The accuracy is considerably greater than that of previous estimates.« less

Implementation of the NMR CHEmical Shift Covariance Analysis (CHESCA): A Chemical Biologist's Approach to Allostery.

PubMed

Boulton, Stephen; Selvaratnam, Rajeevan; Ahmed, Rashik; Melacini, Giuseppe

2018-01-01

Mapping allosteric sites is emerging as one of the central challenges in physiology, pathology, and pharmacology. Nuclear Magnetic Resonance (NMR) spectroscopy is ideally suited to map allosteric sites, given its ability to sense at atomic resolution the dynamics underlying allostery. Here, we focus specifically on the NMR CHEmical Shift Covariance Analysis (CHESCA), in which allosteric systems are interrogated through a targeted library of perturbations (e.g., mutations and/or analogs of the allosteric effector ligand). The atomic resolution readout for the response to such perturbation library is provided by NMR chemical shifts. These are then subject to statistical correlation and covariance analyses resulting in clusters of allosterically coupled residues that exhibit concerted responses to the common set of perturbations. This chapter provides a description of how each step in the CHESCA is implemented, starting from the selection of the perturbation library and ending with an overview of different clustering options.

Effects of cavity-cavity interaction on the entanglement dynamics of a generalized double Jaynes-Cummings model

NASA Astrophysics Data System (ADS)

Pandit, Mahasweta; Das, Sreetama; Singha Roy, Sudipto; Shekhar Dhar, Himadri; Sen, Ujjwal

2018-02-01

We consider a generalized double Jaynes-Cummings model consisting of two isolated two-level atoms, each contained in a lossless cavity that interact with each other through a controlled photon-hopping mechanism. We analytically show that at low values of such a mediated cavity-cavity interaction, the temporal evolution of entanglement between the atoms, under the effects of cavity perturbation, exhibits the well-known phenomenon of entanglement sudden death (ESD). Interestingly, for moderately large interaction values, a complete preclusion of ESD is achieved, irrespective of its value in the initial atomic state. Our results provide a model to sustain entanglement between two atomic qubits, under the adverse effect of cavity induced perturbation, by introducing a non-intrusive inter-cavity photon exchange that can be physically realized through cavity-QED setups in contemporary experiments.

Faraday spectroscopy of ultracold atoms guided in hollow core optical fibers

NASA Astrophysics Data System (ADS)

Fatemi, Fredrik; Pechkis, Joseph

2013-05-01

We have performed spatially and temporally resolved magnetometry using Faraday spectroscopy of ultracold rubidium atoms confined in hollow core optical fibers. We first guide 105 Rb atoms into a 3-cm-long, 100-micron-core hollow fiber using blue-detuned hollow waveguide modes. Inside the fiber, the atoms are exposed to an optical pumping pulse, and the Larmor precession is monitored by the polarization rotation of a probe laser beam detuned by 50 GHz. The intense guide beams can perturb the detected Larmor precession frequencies, but we show that by confining the atoms to the intensity null of higher order blue-detuned hollow modes, these perturbations are reduced by over 95% compared to red-detuned guides. By adjusting the guide beam detuning and polarization, the deleterious effects of both photon scattering and frequency shifts can be suppressed such that multiple magnetic field measurements with sensitivity of 30 nT per sampling pulse can be obtained throughout the length of the fiber in a single loading cycle. Work supported by ONR and DARPA.

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

Orlenko, E. V., E-mail: eorlenko@mail.ru; Evstafev, A. V.; Orlenko, F. E.

A formalism of exchange perturbation theory (EPT) is developed for the case of interactions that explicitly depend on time. Corrections to the wave function obtained in any order of perturbation theory and represented in an invariant form include exchange contributions due to intercenter electron permutations in complex multicenter systems. For collisions of atomic systems with an arbitrary type of interaction, general expressions are obtained for the transfer (T) and scattering (S) matrices in which intercenter electron permutations between overlapping nonorthogonal states belonging to different centers (atoms) are consistently taken into account. The problem of collision of alpha particles with lithiummore » atoms accompanied by the redistribution of electrons between centers is considered. The differential and total charge-exchange cross sections of lithium are calculated.« less

Dynamical screening of the van der Waals interaction between graphene layers.

PubMed

Dappe, Y J; Bolcatto, P G; Ortega, J; Flores, F

2012-10-24

The interaction between graphene layers is analyzed combining local orbital DFT and second order perturbation theory. For this purpose we use the linear combination of atomic orbitals-orbital occupancy (LCAO-OO) formalism, that allows us to separate the interaction energy as the sum of a weak chemical interaction between graphene layers plus the van der Waals interaction (Dappe et al 2006 Phys. Rev. B 74 205434). In this work, the weak chemical interaction is calculated by means of corrected-LDA calculations using an atomic-like sp(3)d(5) basis set. The van der Waals interaction is calculated by means of second order perturbation theory using an atom-atom interaction approximation and the atomic-like-orbital occupancies. We also analyze the effect of dynamical screening in the van der Waals interaction using a simple model. We find that this dynamical screening reduces by 40% the van der Waals interaction. Taking this effect into account, we obtain a graphene-graphene interaction energy of 70 ± 5 meV/atom in reasonable agreement with the experimental evidence.

Excitation energies from Görling-Levy perturbation theory along the range-separated adiabatic connection

NASA Astrophysics Data System (ADS)

Rebolini, Elisa; Teale, Andrew M.; Helgaker, Trygve; Savin, Andreas; Toulouse, Julien

2018-06-01

A Görling-Levy (GL)-based perturbation theory along the range-separated adiabatic connection is assessed for the calculation of electronic excitation energies. In comparison with the Rayleigh-Schrödinger (RS)-based perturbation theory this GL-based perturbation theory keeps the ground-state density constant at each order and thus gives the correct ionisation energy at each order. Excitation energies up to first order in the perturbation have been calculated numerically for the helium and beryllium atoms and the hydrogen molecule without introducing any density-functional approximations. In comparison with the RS-based perturbation theory, the present GL-based perturbation theory gives much more accurate excitation energies for Rydberg states but similar excitation energies for valence states.

Excitation of the hydrogen atom by fast-electron impact in the presence of a laser field

NASA Astrophysics Data System (ADS)

Bhattacharya, Manabesh; Sinha, C.; Sil, N. C.

1991-08-01

An approach has been developed to study the excitation of a ground-state H atom to the n=2 level under the simultaneous action of fast-electron impact and a monochromatic, linearly polarized, homogeneous laser beam. The laser frequency is assumed to be low (soft-photon limit) so that a stationary-state perturbation theory can be applied as is done in the adiabatic theory. An elegant method has been developed in the present work to construct the dressed excited-state wave functions of the H atom using first-order perturbation theory in the parabolic coordinate representation. By virtue of this method, the problem arising due to the degeneracy of the excited states of the H atom has been successfully overcome. The main advantage of the present approach is that the dressed wave function has been obtained in terms of a finite number of Laguerre polynomials instead of an infinite summation occurring in the usual perturbative treatment. The amplitude for direct excitation (without exchange) has been obtained in closed form. Numerical results for differential cross sections are presented for individual excitations to different Stark manifolds as well as for excitations to the n=2 level at high energies (100 and 200 eV) and for field directions both parallel and perpendicular to the incident electron momentum. Extension to a higher order of perturbation is also possible in the present approach for the construction of the dressed states, and the electron-exchange effect can also be taken into account without any further approximation.

Calculation of (P,T) -odd electric dipole moments for the diamagnetic atoms X129e , Y171b , H199g , R211n , and R225a

NASA Astrophysics Data System (ADS)

Dzuba, V. A.; Flambaum, V. V.; Porsev, S. G.

2009-09-01

Electric dipole moments of diamagnetic atoms of experimental interest are calculated using the relativistic Hartree-Fock and random-phase approximation methods, the many-body perturbation theory, and the configuration-interaction technique. We consider (P,T) -odd interactions, which give rise to atomic electric dipole moment in the second order of the perturbation theory. These include nuclear Schiff moment, (P,T) -odd electron-nucleon interaction, and electron electric dipole moment. Interpretation of an experimental constraint of a permanent electric dipole moment of H199g [W. C. Griffith, M. D. Swallows, T. H. Loftus, M. V. Romalis, B. R. Heckel, and E. N. Fortson, Phys. Rev. Lett. 102, 101601 (2009)] is discussed.

Resonantly enhanced spin-spin interaction of ultracold atoms in an optical lattice for quantum information and simulation

NASA Astrophysics Data System (ADS)

Inaba, Kensuke; Noda, Kazuto; Tokunaga, Yuuki; Tamaki, Kiyoshi; Igeta, Kazuhiro; Yamashita, Makoto

2014-05-01

Control of the spin-spin interactions between atoms in an optical lattice is a key ingredient for simulating quantum magnetism and also creating entanglement required for quantum computation. Here, we investigate the use of resonant enhancement of the perturbative spin interactions. First, we discuss entanglement generation with a tunable Ising interaction. Enhancing the interaction allows us to shorten operation time. However, it conflicts with the perturbative nature of the interaction and inevitably induces unwanted correlations that degrade fidelity. We propose a method for overcoming this difficulty. Next, we also discuss characteristic magnetism caused by the resonantly enhanced interaction. In the similar way to the above, the transition temperatures can be increased, which is limited by the breakdown of the perturbation. We will discuss the mechanism of the limitation. This work was partly supported by JST CREST.

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

Relativistic corrections for screening effects on the energies of hydrogen-like atoms embedded in plasmas

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

Poszwa, A., E-mail: poszwa@matman.uwm.edu.p; Bahar, M. K., E-mail: mussiv58@gmail.com

2015-01-15

The influence of relativistic and plasma screening effects on energies of hydrogen-like atoms embedded in plasmas has been studied. The Dirac equation with a more general exponential cosine screened potential has been solved numerically and perturbatively, by employing the direct perturbation theory. Properties of spectra corresponding to bound states and to different sets of the potential parameters have been studied both in nonrelativistic and relativistic approximations. Binding energies, fine-structure splittings, and relativistic energy shifts have been determined as functions of parameters of the potential. The results have been compared with the ones known from the literature.

Phosphorescence/microwave double-resonance spectra of tryptophan perturbed by methylmercury(II).

PubMed Central

Davis, J M; Maki, A H

1982-01-01

Amplitude-modulated phosphorescence/microwave double-resonance (AM-PMDR) spectra are reported for complexes of methylmercury(II) cation, designated CH3Hg(II), with tryptophan and glyceraldehyde-3-phosphate dehydrogenase (GPDHase; from rabbit muscle). Wavelength shifts are observed in the AM-PMDR spectra of CH3Hg(II)-tryptophan, which are obtained by microwave pumping in distinct zero-field D + E magnetic resonance transitions, demonstrating that AM-PMDR can be used to display selectively the phosphorescence spectra of structurally distinct complexes with different zero-field splittings. The AM-PMDR spectra accurately represent the phosphorescence of CH3Hg(II)-tryptophan. Binding of CH3Hg(II) to a cysteine site of GDPHase perturbs the luminescence of one of the two optically resolved tryptophan. The AM-PMDR spectrum of the perturbed tryptophan is obtained by microwave pumping of the D + E magnetic resonance signal, which can be observed optically only in the presence of a heavy atom perturbation. The resulting spectrum is broadened and shifted to the blue relative to the corresponding tryptophan phosphorescence spectrum of the uncomplexed enzyme. Comparison of the AM-PMDR spectra of CH3Hg(II)-tryptophan and CH3Hg(II)-GPDHase suggests that there are differences in the mechanisms of heavy atom perturbation in these complexes. PMID:6956860

Continued-fraction representation of the Kraus map for non-Markovian reservoir damping

NASA Astrophysics Data System (ADS)

van Wonderen, A. J.; Suttorp, L. G.

2018-04-01

Quantum dissipation is studied for a discrete system that linearly interacts with a reservoir of harmonic oscillators at thermal equilibrium. Initial correlations between system and reservoir are assumed to be absent. The dissipative dynamics as determined by the unitary evolution of system and reservoir is described by a Kraus map consisting of an infinite number of matrices. For all Laplace-transformed Kraus matrices exact solutions are constructed in terms of continued fractions that depend on the pair correlation functions of the reservoir. By performing factorizations in the Kraus map a perturbation theory is set up that conserves in arbitrary perturbative order both positivity and probability of the density matrix. The latter is determined by an integral equation for a bitemporal matrix and a finite hierarchy for Kraus matrices. In the lowest perturbative order this hierarchy reduces to one equation for one Kraus matrix. Its solution is given by a continued fraction of a much simpler structure as compared to the non-perturbative case. In the lowest perturbative order our non-Markovian evolution equations are applied to the damped Jaynes–Cummings model. From the solution for the atomic density matrix it is found that the atom may remain in the state of maximum entropy for a significant time span that depends on the initial energy of the radiation field.

Atom chip microscopy: A novel probe for strongly correlated materials

NASA Astrophysics Data System (ADS)

Kasch, Brian; Naides, Matthew; Turner, Richard; Ray, Ushnish; Lev, Benjamin

2010-03-01

Atom chip technology---substrates supporting micron-sized current-carrying wires that create magnetic microtraps near surfaces for thermal or degenerate gases of neutral atoms---will enable single-shot, large area detection of magnetic flux below the 10-7 flux quantum level. By harnessing the extreme sensitivity of Bose-Einstein condensates (BECs) to external perturbations, cryogenic atom chips could provide a magnetic flux detection capability that surpasses all other techniques by a factor of 10^2--10^3. We describe the merits of atom chip microscopy, our Rb BEC and atom chip apparatus, and prospects for imaging strongly correlated condensed matter materials.

Drifts and Environmental Disturbances in Atomic Clock Subsystems: Quantifying Local Oscillator, Control Loop, and Ion Resonance Interactions.

PubMed

Enzer, Daphna G; Diener, William A; Murphy, David W; Rao, Shanti R; Tjoelker, Robert L

2017-03-01

Linear ion trap frequency standards are among the most stable continuously operating frequency references and clocks. Depending on the application, they have been operated with a variety of local oscillators (LOs), including quartz ultrastable oscillators, hydrogen-masers, and cryogenic sapphire oscillators. The short-, intermediate-, and long-term stability of the frequency output is a complicated function of the fundamental performances, the time dependence of environmental disturbances, the atomic interrogation algorithm, the implemented control loop, and the environmental sensitivity of the LO and the atomic system components. For applications that require moving these references out of controlled lab spaces and into less stable environments, such as fieldwork or spaceflight, a deeper understanding is needed of how disturbances at different timescales impact the various subsystems of the clock and ultimately the output stability. In this paper, we analyze which perturbations have an impact and to what degree. We also report on a computational model of a control loop, which keeps the microwave source locked to the ion resonance. This model is shown to agree with laboratory measurements of how well the feedback removes various disturbances and also with a useful analytic approach we developed for predicting these impacts.

The Helium Atom and Isoelectronic Ions in Two Dimensions

ERIC Educational Resources Information Center

Patil, S. H.

2008-01-01

The energy levels of the helium atom and isoelectronic ions in two dimensions are considered. The difficulties encountered in the analytical evaluation of the perturbative and variational expressions for the ground state, promote an interesting factorization of the inter-electronic interaction, leading to simple expressions for the energy. This…

Influence of the ac-Stark shift on GPS atomic clock timekeeping

NASA Astrophysics Data System (ADS)

Formichella, V.; Camparo, J.; Tavella, P.

2017-01-01

The ac-Stark shift (or light shift) is a fundamental aspect of the field/atom interaction arising from virtual transitions between atomic states, and as Alfred Kastler noted, it is the real-photon counterpart of the Lamb shift. In the rubidium atomic frequency standards (RAFS) flying on Global Positioning System (GPS) satellites, it plays an important role as one of the major perturbations defining the RAFS' frequency: the rf-discharge lamp in the RAFS creates an atomic signal via optical pumping and simultaneously perturbs the atoms' ground-state hyperfine splitting via the light shift. Though the significance of the light shift has been known for decades, to date there has been no concrete evidence that it limits the performance of the high-quality RAFS flying on GPS satellites. Here, we show that the long-term frequency stability of GPS RAFS is primarily determined by the light shift as a consequence of stochastic jumps in lamplight intensity. Our results suggest three paths forward for improved GPS system timekeeping: (1) reduce the light-shift coefficient of the RAFS by careful control of the lamp's spectrum; (2) operate the lamp under conditions where lamplight jumps are not so pronounced; and (3) employ a light source for optical pumping that does not suffer pronounced light jumps (e.g., a diode laser).

An energy-based perturbation and a taboo strategy for improving the searching ability of stochastic structural optimization methods

NASA Astrophysics Data System (ADS)

Cheng, Longjiu; Cai, Wensheng; Shao, Xueguang

2005-03-01

An energy-based perturbation and a new idea of taboo strategy are proposed for structural optimization and applied in a benchmark problem, i.e., the optimization of Lennard-Jones (LJ) clusters. It is proved that the energy-based perturbation is much better than the traditional random perturbation both in convergence speed and searching ability when it is combined with a simple greedy method. By tabooing the most wide-spread funnel instead of the visited solutions, the hit rate of other funnels can be significantly improved. Global minima of (LJ) clusters up to 200 atoms are found with high efficiency.

Dispersion interactions between neighboring Bi atoms in (BiH3 )2 and Te(BiR2 )2.

PubMed

Haack, Rebekka; Schulz, Stephan; Jansen, Georg

2018-03-13

Triggered by the observation of a short Bi⋯Bi distance and a BiTeBi bond angle of only 86.6° in the crystal structure of bis(diethylbismuthanyl)tellurane quantum chemical computations on interactions between neighboring Bi atoms in Te(BiR 2 ) 2 molecules (R = H, Me, Et) and in (BiH 3 ) 2 were undertaken. Bi⋯Bi distances atoms were found to significantly shorten upon inclusion of the d shells of the heavy metal atoms into the electron correlation treatment, and it was confirmed that interaction energies from spin component-scaled second-order Møller-Plesset theory (SCS-MP2) agree well with coupled-cluster singles and doubles theory including perturbative triples (CCSD(T)). Density functional theory-based symmetry-adapted perturbation theory (DFT-SAPT) was used to study the anisotropy of the interplay of dispersion attraction and steric repulsion between the Bi atoms. Finally, geometries and relative stabilities of syn-syn and syn-anti conformers of Te(BiR 2 ) 2 (R = H, Me, Et) and interconversion barriers between them were computed. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Laser-enhanced dynamics in molecular rate processes

NASA Technical Reports Server (NTRS)

George, T. F.; Zimmerman, I. H.; Devries, P. L.; Yuan, J.-M.; Lam, K.-S.; Bellum, J. C.; Lee, H.-W.; Slutsky, M. S.

1978-01-01

The present discussion deals with some theoretical aspects associated with the description of molecular rate processes in the presence of intense laser radiation, where the radiation actually interacts with the molecular dynamics. Whereas for weak and even moderately intense radiation, the absorption and stimulated emission of photons by a molecular system can be described by perturbative methods, for intense radiation, perturbation theory is usually not adequate. Limiting the analysis to the gas phase, an attempt is made to describe nonperturbative approaches applicable to the description of such processes (in the presence of intense laser radiation) as electronic energy transfer in molecular (in particular atom-atom) collisions; collision-induced ionization and emission; and unimolecular dissociation.

Projector Augmented-Wave formulation of response to strain and electric field perturbation within the density-functional perturbation theory

NASA Astrophysics Data System (ADS)

Martin, Alexandre; Torrent, Marc; Caracas, Razvan

2015-03-01

A formulation of the response of a system to strain and electric field perturbations in the pseudopotential-based density functional perturbation theory (DFPT) has been proposed by D.R Hamman and co-workers. It uses an elegant formalism based on the expression of DFT total energy in reduced coordinates, the key quantity being the metric tensor and its first and second derivatives. We propose to extend this formulation to the Projector Augmented-Wave approach (PAW). In this context, we express the full elastic tensor including the clamped-atom tensor, the atomic-relaxation contributions (internal stresses) and the response to electric field change (piezoelectric tensor and effective charges). With this we are able to compute the elastic tensor for all materials (metals and insulators) within a fully analytical formulation. The comparison with finite differences calculations on simple systems shows an excellent agreement. This formalism has been implemented in the plane-wave based DFT ABINIT code. We apply it to the computation of elastic properties and seismic-wave velocities of iron with impurity elements. By analogy with the materials contained in meteorites, tested impurities are light elements (H, O, C, S, Si).

Free Energy Perturbation Calculations of the Thermodynamics of Protein Side-Chain Mutations.

PubMed

Steinbrecher, Thomas; Abel, Robert; Clark, Anthony; Friesner, Richard

2017-04-07

Protein side-chain mutation is fundamental both to natural evolutionary processes and to the engineering of protein therapeutics, which constitute an increasing fraction of important medications. Molecular simulation enables the prediction of the effects of mutation on properties such as binding affinity, secondary and tertiary structure, conformational dynamics, and thermal stability. A number of widely differing approaches have been applied to these predictions, including sequence-based algorithms, knowledge-based potential functions, and all-atom molecular mechanics calculations. Free energy perturbation theory, employing all-atom and explicit-solvent molecular dynamics simulations, is a rigorous physics-based approach for calculating thermodynamic effects of, for example, protein side-chain mutations. Over the past several years, we have initiated an investigation of the ability of our most recent free energy perturbation methodology to model the thermodynamics of protein mutation for two specific problems: protein-protein binding affinities and protein thermal stability. We highlight recent advances in the field and outline current and future challenges. Copyright © 2017 Elsevier Ltd. All rights reserved.

Modulation of individual steps in group I intron catalysis by a peripheral metal ion.

PubMed

Forconi, Marcello; Piccirilli, Joseph A; Herschlag, Daniel

2007-10-01

Enzymes are complex macromolecules that catalyze chemical reactions at their active sites. Important information about catalytic interactions is commonly gathered by perturbation or mutation of active site residues that directly contact substrates. However, active sites are engaged in intricate networks of interactions within the overall structure of the macromolecule, and there is a growing body of evidence about the importance of peripheral interactions in the precise structural organization of the active site. Here, we use functional studies, in conjunction with published structural information, to determine the effect of perturbation of a peripheral metal ion binding site on catalysis in a well-characterized catalytic RNA, the Tetrahymena thermophila group I ribozyme. We perturbed the metal ion binding site by site-specifically introducing a phosphorothioate substitution in the ribozyme's backbone, replacing the native ligands (the pro-R (P) oxygen atoms at positions 307 and 308) with sulfur atoms. Our data reveal that these perturbations affect several reaction steps, including the chemical step, despite the absence of direct contacts of this metal ion with the atoms involved in the chemical transformation. As structural probing with hydroxyl radicals did not reveal significant change in the three-dimensional structure upon phosphorothioate substitution, the effects are likely transmitted through local, rather subtle conformational rearrangements. Addition of Cd(2+), a thiophilic metal ion, rescues some reaction steps but has deleterious effects on other steps. These results suggest that native interactions in the active site may have been aligned by the naturally occurring peripheral residues and interactions to optimize the overall catalytic cycle.

The Confined Hydrogen Atom with a Moving Nucleus

ERIC Educational Resources Information Center

Fernandez, Francisco M.

2010-01-01

We study the hydrogen atom confined to a spherical box with impenetrable walls but, unlike earlier pedagogical articles on the subject, we assume that the nucleus also moves. We obtain the ground-state energy approximately by means of first-order perturbation theory and show that it is greater than that for the case in which the nucleus is clamped…

Dynamics of atom-atom correlations in the Fermi problem

NASA Astrophysics Data System (ADS)

Borrelli, Massimo; Sabín, Carlos; Adesso, Gerardo; Plastina, Francesco; Maniscalco, Sabrina

2012-10-01

We present a detailed perturbative study of the dynamics of several types of atom-atom correlations in the famous Fermi problem. This is an archetypal model to study micro-causality in the quantum domain, where two atoms, one initially excited and the other prepared in its ground state, interact with the vacuum electromagnetic field. The excitation can be transferred to the second atom via a flying photon, and various kinds of quantum correlations between the two are generated during this process. Among these, prominent examples are given by entanglement, quantum discord and non-local correlations. The aim of this paper is to analyze the role of the light cone in the emergence of such correlations.

Online time-differential perturbed angular correlation study with an 19O beam - Residence sites of oxygen atoms in highly oriented pyrolytic graphite

NASA Astrophysics Data System (ADS)

Sato, W.; Ueno, H.; Watanabe, H.; Miyoshi, H.; Yoshimi, A.; Kameda, D.; Ito, T.; Shimada, K.; Kaihara, J.; Suda, S.; Kobayashi, Y.; Shinohara, A.; Ohkubo, Y.; Asahi, K.

2008-01-01

The online time-differential perturbed angular correlation (TDPAC) method was applied to a study of the physical states of a probe 19F, the β- decay product of 19O (t1/2 = 26.9 s), implanted in highly oriented pyrolytic graphite. The observed magnitude of the electric field gradient at the probe nucleus, ∣Vzz∣ = 2.91(17) × 1022 V m-2, suggests that the incident 19O atoms are stabilized at an interlayer position with point group C3v. Exhibiting observed TDPAC spectra having a clear sample-to-detector configuration dependence, we demonstrate the applicability of the present online method with a short-lived radioactive 19O beam.

Toward controlling perturbations in robotic sensor networks

NASA Astrophysics Data System (ADS)

Banerjee, Ashis G.; Majumder, Saikat R.

2014-06-01

Robotic sensor networks (RSNs), which consist of networks of sensors placed on mobile robots, are being increasingly used for environment monitoring applications. In particular, a lot of work has been done on simultaneous localization and mapping of the robots, and optimal sensor placement for environment state estimation1. The deployment of RSNs, however, remains challenging in harsh environments where the RSNs have to deal with significant perturbations in the forms of wind gusts, turbulent water flows, sand storms, or blizzards that disrupt inter-robot communication and individual robot stability. Hence, there is a need to be able to control such perturbations and bring the networks to desirable states with stable nodes (robots) and minimal operational performance (environment sensing). Recent work has demonstrated the feasibility of controlling the non-linear dynamics in other communication networks like emergency management systems and power grids by introducing compensatory perturbations to restore network stability and operation2. In this paper, we develop a computational framework to investigate the usefulness of this approach for RSNs in marine environments. Preliminary analysis shows promising performance and identifies bounds on the original perturbations within which it is possible to control the networks.

Effects of velocity-changing collisions on two-photon and stepwise-absorption spectroscopic line shapes

NASA Astrophysics Data System (ADS)

Liao, P. F.; Bjorkholm, J. E.; Berman, P. R.

1980-06-01

We report the results of an experimental study of the effects of velocity-changing collisions on two-photon and stepwise-absorption line shapes. Excitation spectra for the 3S12-->3P12-->4D12 transitions of sodium atoms undergoing collisions with foreign gas perturbers are obtained. These spectra are obtained with two cw dye lasers. One laser, the pump laser, is tuned 1.6 GHz below the 3S12-->3P12 transition frequency and excites a nonthermal longitudinal velocity distribution of excited 3P12 atoms in the vapor. Absorption of the second (probe) laser is used to monitor the steady-state excited-state distribution which is a result of collisions with rare gas atoms. The spectra are obtained for various pressures of He, Ne, and Kr gases and are fit to a theoretical model which utilizes either the phenomenological Keilson-Störer or the classical hardsphere collision kernel. The theoretical model includes the effects of collisionally aided excitation of the 3P12 state as well as effects due to fine-structure state-changing collisions. Although both kernels are found to predict line shapes which are in reasonable agreement with the experimental results, the hard-sphere kernel is found superior as it gives a better description of the effects of large-angle scattering for heavy perturbers. Neither kernel provides a fully adequate description over the entire line profile. The experimental data is used to extract effective hard-sphere collision cross sections for collisions between sodium 3P12 atoms and helium, neon, and krypton perturbers.

Configuration-interaction relativistic-many-body-perturbation-theory calculations of photoionization cross sections from quasicontinuum oscillator strengths

DOE PAGES

Savukov, I. M.; Filin, D. V.

2014-12-29

Many applications are in need of accurate photoionization cross sections, especially in the case of complex atoms. Configuration-interaction relativistic-many-body-perturbation theory (CI-RMBPT) has been successful in predicting atomic energies, matrix elements between discrete states, and other properties, which is quite promising, but it has not been applied to photoionization problems owing to extra complications arising from continuum states. In this paper a method that will allow the conversion of discrete CI-(R)MPBT oscillator strengths (OS) to photoionization cross sections with minimal modifications of the codes is introduced and CI-RMBPT cross sections of Ne, Ar, Kr, and Xe are calculated. A consistent agreementmore » with experiment is found. RMBPT corrections are particularly significant for Ar, Kr, and Xe and improve agreement with experimental results compared to the particle-hole CI method. As a result, the demonstrated conversion method can be applied to CI-RMBPT photoionization calculations for a large number of multivalence atoms and ions.« less

Eigenstates and dynamics of Hooke's atom: Exact results and path integral simulations

NASA Astrophysics Data System (ADS)

Gholizadehkalkhoran, Hossein; Ruokosenmäki, Ilkka; Rantala, Tapio T.

2018-05-01

The system of two interacting electrons in one-dimensional harmonic potential or Hooke's atom is considered, again. On one hand, it appears as a model for quantum dots in a strong confinement regime, and on the other hand, it provides us with a hard test bench for new methods with the "space splitting" arising from the one-dimensional Coulomb potential. Here, we complete the numerous previous studies of the ground state of Hooke's atom by including the excited states and dynamics, not considered earlier. With the perturbation theory, we reach essentially exact eigenstate energies and wave functions for the strong confinement regime as novel results. We also consider external perturbation induced quantum dynamics in a simple separable case. Finally, we test our novel numerical approach based on real-time path integrals (RTPIs) in reproducing the above. The RTPI turns out to be a straightforward approach with exact account of electronic correlations for solving the eigenstates and dynamics without the conventional restrictions of electronic structure methods.

Progress Toward an Neutral Yb Frequency Standard

NASA Astrophysics Data System (ADS)

Cramer, Claire; Hong, Tao; Nagourney, Warren; Fortson, Norval

2004-05-01

We report recent progress toward a direct observation of the ^1S_0^ -- ^3P0 clock transition at 578 nm in atomic Yb and review the experimental path to an optical frequency standard based on neutral Yb confined in a Stark-free optical lattice. Lamb-Dicke confinement in an optical lattice at the ``magic wavelength'' (λ _M) at which ground and excited state light shifts cancel will free the spectrum from Doppler and recoil shifts, providing an optimal environment for a clock consisting of an ensemble of cold, trapped atoms. In^171Yb the ^3P0 level has a hfs induced lifetime of 21 s. With this isotope in a Stark-free lattice at λ M ng 750 nm, perturbations to the clock energy levels can be held below the mHz level, providing an accuracy of a few parts in 10^18[1]. To observe the clock transition we use a shelving scheme that creates a leak in a MOT on the ^1S_0^ -- ^1P1 transition. A laser resonant with the clock transition drives atoms into the ^3P0 state, in which they can escape the MOT, leading to an observable decrease in MOT fluorescence. [1] S. Porsev and A. Derevianko, to be published in PRA

Optically guided atom interferometer tuned to magic wavelength

NASA Astrophysics Data System (ADS)

Akatsuka, Tomoya; Takahashi, Tadahiro; Katori, Hidetoshi

2017-11-01

We demonstrate an atom interferometer operating on the 1S0-3P0 clock transition of 87Sr atoms in a “magic” optical guide, where the light shift perturbations of the guiding potential are canceled. As a proof-of-principle demonstration, a Mach-Zehnder interferometer is set horizontally to map the acceleration introduced by the focused optical guide. This magic guide interferometer on the clock transition is applicable to atomic elements where magic wavelengths can be found. Possible applications of the magic guide interferometer, including a hollow-core fiber interferometer and gradiometer, are discussed.

Polarization effects in recoil-induced resonances

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

Lazebnyi, D. B., E-mail: becks.ddf@gmail.com; Brazhnikov, D. V.; Taichenachev, A. V.

2017-01-15

The effect of the field polarization on the amplitude of recoil-induced resonances (RIRs) is considered for laser-cooled free atoms and for atoms in a working magneto-optical trap (MOT). For all closed dipole transitions, explicit analytical expressions are obtained for the polarization dependence of the resonance amplitudes within a perturbation theory. Optimal polarization conditions are found for the observation of resonances.

Effects of repeated walking in a perturbing environment: a 4-day locomotor learning study.

PubMed

Blanchette, Andreanne; Moffet, Helene; Roy, Jean-Sébastien; Bouyer, Laurent J

2012-07-01

Previous studies have shown that when subjects repeatedly walk in a perturbing environment, initial movement error becomes smaller, suggesting that retention of the adapted locomotor program occurred (learning). It has been proposed that the newly learned locomotor program may be stored separately from the baseline program. However, how locomotor performance evolves with repeated sessions of walking with the perturbation is not yet known. To address this question, 10 healthy subjects walked on a treadmill on 4 consecutive days. Each day, locomotor performance was measured using kinematics and surface electromyography (EMGs), before, during, and after exposure to a perturbation, produced by an elastic tubing that pulled the foot forward and up during swing, inducing a foot velocity error in the first strides. Initial movement error decreased significantly between days 1 and 2 and then remained stable. Associated changes in medial hamstring EMG activity stabilized only on day 3, however. Aftereffects were present after perturbation removal, suggesting that daily adaptation involved central command recalibration of the baseline program. Aftereffects gradually decreased across days but were still visible on day 4. Separation between the newly learned and baseline programs may take longer than suggested by the daily improvement in initial performance in the perturbing environment or may never be complete. These results therefore suggest that reaching optimal performance in a perturbing environment should not be used as the main indicator of a completed learning process, as central reorganization of the motor commands continues days after initial performance has stabilized.

An Examination of Environment Perturbation Effects on Single Event Upset Rates

NASA Technical Reports Server (NTRS)

Gates, Michele M.; Leidecker, Henning W.; Lewis, Mark J.

1997-01-01

This paper presents an analysis of the sensitivity of single event upset (SEU) rate predictions to changes in the direct ionization-inducing environment. An examination based on the nature of the SEU rate equation is presented for the case in which the perturbation is constant across varying particle linear energy transfer (LET). It is shown that the relative variation in SEU rate is equal to the relative perturbation in flux. Results are also presented for the case in which the environment perturbations exist in small LET bins. Through this analysis it is shown that the relative variation in expected SEU rate is equal to that in flux only for the LET regime in which the product of the cross section and differential flux is maximum.

A gauge-independent zeroth-order regular approximation to the exact relativistic Hamiltonian—Formulation and applications

NASA Astrophysics Data System (ADS)

Filatov, Michael; Cremer, Dieter

2005-01-01

A simple modification of the zeroth-order regular approximation (ZORA) in relativistic theory is suggested to suppress its erroneous gauge dependence to a high level of approximation. The method, coined gauge-independent ZORA (ZORA-GI), can be easily installed in any existing nonrelativistic quantum chemical package by programming simple one-electron matrix elements for the quasirelativistic Hamiltonian. Results of benchmark calculations obtained with ZORA-GI at the Hartree-Fock (HF) and second-order Møller-Plesset perturbation theory (MP2) level for dihalogens X2 (X=F,Cl,Br,I,At) are in good agreement with the results of four-component relativistic calculations (HF level) and experimental data (MP2 level). ZORA-GI calculations based on MP2 or coupled-cluster theory with single and double perturbations and a perturbative inclusion of triple excitations [CCSD(T)] lead to accurate atomization energies and molecular geometries for the tetroxides of group VIII elements. With ZORA-GI/CCSD(T), an improved estimate for the atomization energy of hassium (Z=108) tetroxide is obtained.

High-order nonlinear susceptibilities of He

NASA Astrophysics Data System (ADS)

Liu, W.-C.; Clark, Charles W.

1996-05-01

High-order nonlinear optical response of noble gases to intense laser radiation is of considerable experimental interest, but is difficult to measure or calculate accurately. We have begun a set of calculations of frequency-dependent nonlinear susceptibilities of He 1s^2, within the framework of Rayleigh-Schrödinger perturbation theory at lowest applicable order, with the goal of providing critically evaluated atomic data for modelling high harmonic generation processes. The atomic Hamiltonian is decomposed in term of Hylleraas coordinates and spherical harmonics using the formalism of Pont and Shakeshaft (M. Pont and R. Shakeshaft, Phy. Rev. A 51), 257 (1995), and the hierarchy of inhomogeneous equations of perturbation theory is solved iteratively. A combination of Hylleraas and Frankowski basis functions is used(J. D. Baker, Master thesis, U. Delaware (1988); J. D. Baker, R. N. Hill, and J. D. Morgan, AIP Conference Proceedings 189) 123(1989); the compact Hylleraas basis provides a highly accurate representation of the ground state wavefunction, whereas the diffuse Frankowski basis functions efficiently reproduce the correct asymptotic structure of the perturbed orbitals.

Manganese-Oxygen Intermediates in O-O Bond Activation and Hydrogen-Atom Transfer Reactions.

PubMed

Rice, Derek B; Massie, Allyssa A; Jackson, Timothy A

2017-11-21

Biological systems capitalize on the redox versatility of manganese to perform reactions involving dioxygen and its derivatives superoxide, hydrogen peroxide, and water. The reactions of manganese enzymes influence both human health and the global energy cycle. Important examples include the detoxification of reactive oxygen species by manganese superoxide dismutase, biosynthesis by manganese ribonucleotide reductase and manganese lipoxygenase, and water splitting by the oxygen-evolving complex of photosystem II. Although these enzymes perform very different reactions and employ structurally distinct active sites, manganese intermediates with peroxo, hydroxo, and oxo ligation are commonly proposed in catalytic mechanisms. These intermediates are also postulated in mechanisms of synthetic manganese oxidation catalysts, which are of interest due to the earth abundance of manganese. In this Account, we describe our recent efforts toward understanding O-O bond activation pathways of Mn III -peroxo adducts and hydrogen-atom transfer reactivity of Mn IV -oxo and Mn III -hydroxo complexes. In biological and synthetic catalysts, peroxomanganese intermediates are commonly proposed to decay by either Mn-O or O-O cleavage pathways, although it is often unclear how the local coordination environment influences the decay mechanism. To address this matter, we generated a variety of Mn III -peroxo adducts with varied ligand environments. Using parallel-mode EPR and Mn K-edge X-ray absorption techniques, the decay pathway of one Mn III -peroxo complex bearing a bulky macrocylic ligand was investigated. Unlike many Mn III -peroxo model complexes that decay to oxo-bridged-Mn III Mn IV dimers, decay of this Mn III -peroxo adduct yielded mononuclear Mn III -hydroxo and Mn IV -oxo products, potentially resulting from O-O bond activation of the Mn III -peroxo unit. These results highlight the role of ligand sterics in promoting the formation of mononuclear products and mark an important step in designing Mn III -peroxo complexes that convert cleanly to high-valent Mn-oxo species. Although some synthetic Mn IV -oxo complexes show great potential for oxidizing substrates with strong C-H bonds, most Mn IV -oxo species are sluggish oxidants. Both two-state reactivity and thermodynamic arguments have been put forth to explain these observations. To address these issues, we generated a series of Mn IV -oxo complexes supported by neutral, pentadentate ligands with systematically perturbed equatorial donation. Kinetic investigations of these complexes revealed a correlation between equatorial ligand-field strength and hydrogen-atom and oxygen-atom transfer reactivity. While this trend can be understood on the basis of the two-state reactivity model, the reactivity trend also correlates with variations in Mn III/IV reduction potential caused by changes in the ligand field. This work demonstrates the dramatic influence simple ligand perturbations can have on reactivity but also illustrates the difficulties in understanding the precise basis for a change in reactivity. In the enzyme manganese lipoxygenase, an active-site Mn III -hydroxo adduct initiates substrate oxidation by abstracting a hydrogen atom from a C-H bond. Precedent for this chemistry from synthetic Mn III -hydroxo centers is rare. To better understand hydrogen-atom transfer by Mn III centers, we developed a pair of Mn III -hydroxo complexes, formed in high yield from dioxygen oxidation of Mn II precursors, capable of attacking weak O-H and C-H bonds. Kinetic and computational studies show a delicate interplay between thermodynamic and steric influences in hydrogen-atom transfer reactivity, underscoring the potential of Mn III -hydroxo units as mild oxidants.

Status of the planar electrostatic gradiometer GREMLIT for airborne geodesy

NASA Astrophysics Data System (ADS)

Boulanger, D.; Foulon, B.; Lebat, V.; Bresson, A.; Christophe, B.

2016-12-01

Taking advantage of technologies, developed by ONERA for the GRACE and GOCE space missions, the GREMLIT airborne gravity gradiometer is based of a planar electrostatic gradiometer configuration. The feasibility of the instrument and of its performance was proved by realistic simulations, based on actual data and recorded environmental aircraft perturbations, with performance of about one Eötvös along the two horizontal components of the gravity gradient. In order to assess the operation of the electrostatic gradiometer on its associated stabilized platform, a one axis prototype has also been built. The next step is the realization of the stabilization platform, controlled by the common mode outputs of the instrument itself, in order to reject the perturbations induced by the airborne environment in the horizontal directions. One of the interests of the GREMLIT instrument is the possibility of an easy hybrid configuration with a vertical one axis Cold Atoms Interferometer gravity gradiometer called GIBON and also under development at ONERA. In such hybrid instrument, The CAI instrument takes also advantage of the platform stabilized by the electrostatic one. The poster will emphasize the status of realization of the instrument and of its stabilized platform.

Investigation of the collision line broadening problem as applicable to the NASA Optical Plume Anomaly Detection (OPAD) system, phase 1

NASA Astrophysics Data System (ADS)

Dean, Timothy C.; Ventrice, Carl A.

1995-05-01

As a final report for phase 1 of the project, the researchers are submitting to the Tennessee Tech Office of Research the following two papers (reprinted in this report): 'Collision Line Broadening Effects on Spectrometric Data from the Optical Plume Anomaly System (OPAD),' presented at the 30th AIAA/ASME/SAE/ASEE Joint Propulsion Conference, 27-29 June 1994, and 'Calculation of Collision Cross Sections for Atomic Line Broadening in the Plume of the Space Shuttle Main Engine (SSME),' presented at the IEEE Southeastcon '95, 26-29 March 1995. These papers fully state the problem and the progress made up to the end of NASA Fiscal Year 1994. The NASA OPAD system was devised to predict concentrations of anomalous species in the plume of the Space Shuttle Main Engine (SSME) through analysis of spectrometric data. The self absorption of the radiation of these plume anomalies is highly dependent on the line shape of the atomic transition of interest. The Collision Line Broadening paper discusses the methods used to predict line shapes of atomic transitions in the environment of a rocket plume. The Voigt profile is used as the line shape factor since both Doppler and collisional line broadening are significant. Methods used to determine the collisional cross sections are discussed and the results are given and compared with experimental data. These collisional cross sections are then incorporated into the current self absorbing radiative model and the predicted spectrum is compared to actual spectral data collected from the Stennis Space Center Diagnostic Test Facility rocket engine. The second paper included in this report investigates an analytical method for determining the cross sections for collision line broadening by molecular perturbers, using effective central force interaction potentials. These cross sections are determined for several atomic species with H2, one of the principal constituents of the SSME plume environment, and compared with experimental data.

Use of Perturbation-Based Gait Training in a Virtual Environment to Address Mediolateral Instability in an Individual With Unilateral Transfemoral Amputation

PubMed Central

Rábago, Christopher A.; Rylander, Jonathan H.; Dingwell, Jonathan B.; Wilken, Jason M.

2016-01-01

Background and Purpose Roughly 50% of individuals with lower limb amputation report a fear of falling and fall at least once a year. Perturbation-based gait training and the use of virtual environments have been shown independently to be effective at improving walking stability in patient populations. An intervention was developed combining the strengths of the 2 paradigms utilizing continuous, walking surface angle oscillations within a virtual environment. This case report describes walking function and mediolateral stability outcomes of an individual with a unilateral transfemoral amputation following a novel perturbation-based gait training intervention in a virtual environment. Case Description The patient was a 43-year-old male veteran who underwent a right transfemoral amputation 7+ years previously as a result of a traumatic blast injury. He used a microprocessor-controlled knee and an energy storage and return foot. Outcomes Following the intervention, multiple measures indicated improved function and stability, including faster self-selected walking speed and reduced functional stepping time, mean step width, and step width variability. These changes were seen during normal level walking and mediolateral visual field or platform perturbations. In addition, benefits were retained at least 5 weeks after the final training session. Discussion The perturbation-based gait training program in the virtual environment resulted in the patient's improved walking function and mediolateral stability. Although the patient had completed intensive rehabilitation following injury and was fully independent, the intervention still induced notable improvements to mediolateral stability. Thus, perturbation-based gait training in challenging simulated environments shows promise for improving walking stability and may be beneficial when integrated into a rehabilitation program. PMID:27277497

A clock transition in a solid-state system

NASA Astrophysics Data System (ADS)

Edge, G. J. A.; Potnis, S.; Vutha, A. C.

2017-04-01

With the impending redefinition of the SI second based on optical frequency standards, new secondary frequency standards are needed in order to form clock ensembles. Ideally such secondary standards will offer enhanced robustness, portability and high signal-to-noise ratios (SNR), to enable rapid and precise comparisons to be made against primary standards. A clock based on a narrow optical transition, in atoms that are doped into a solid-state host, offers the experimental simplicity and large SNR to satisfy these requirements. The intra-configuration 7F0 ->5D0 transition, in Sm2+ ions doped into a host crystal, is an attractive candidate for such secondary standards due to its low susceptibility to perturbations from the crystal environment. We present results from the interrogation of this clock transition with a narrow linewidth laser.

Optical perturbation of atoms in weak localization

NASA Astrophysics Data System (ADS)

Yedjour, A.

2018-01-01

We determine the microscopic transport parameters that are necessary to describe the diffusion process of the atomic gas in optical speckle. We use the self-consistent theory to calculate the self-energy of the atomic gas. We compute the spectral function numerically by an average over disorder realizations in terms of the Greens function. We focus mainly on the behaviour of the energy distribution of the atoms to estimate a correction to the mobility edge. Our results show that the energy distribution of the atoms locates the mobility edge position under the disorder amplitude. This behaviour changes for each disorder parameter. We conclude that the disorder amplitude potential induced modification of the energy distribution of the atoms that plays a major role for the prediction of the mobility edge.

Investigation of the 6 p 2(3 P 0) n p Rydberg series of bismuth by multiphoton excitation

NASA Astrophysics Data System (ADS)

Bühler, B.; Cremer, C.; Gerber, G.

1985-03-01

Rydberg states of the odd-parity series 6 p 2(3 p 0) n p of BiI are excited by a three-photon process. A two-photon dissociation of Bi2 into excited atomic states followed by a one-photon absorption leads to highly excited atomic Rydberg states up to n = 32. States of the even-parity Rydberg series 6 p 2(3 p 0) nsJ=1/2, ndJ=3/2 and ndJ=5/2 are also observed. In order to avoid the background caused by ionization of the bismuth molecules we performed a two-color excitation with pulsed dye lasers. With this experiment the 6 p 2(3 p 0) npJ=3/2 Rydberg series could be resolved up to n=75. The increasing quantum defect of this series is due to a perturbing state close to the first ionization limit. By a MQDT analysis we obtain the energy of the perturbing state and a value of 58,761.68±0.1 cm-1 for the first ionization limit of atomic bismuth.

Analytic model of a multi-electron atom

NASA Astrophysics Data System (ADS)

Skoromnik, O. D.; Feranchuk, I. D.; Leonau, A. U.; Keitel, C. H.

2017-12-01

A fully analytical approximation for the observable characteristics of many-electron atoms is developed via a complete and orthonormal hydrogen-like basis with a single-effective charge parameter for all electrons of a given atom. The basis completeness allows us to employ the secondary-quantized representation for the construction of regular perturbation theory, which includes in a natural way correlation effects, converges fast and enables an effective calculation of the subsequent corrections. The hydrogen-like basis set provides a possibility to perform all summations over intermediate states in closed form, including both the discrete and continuous spectra. This is achieved with the help of the decomposition of the multi-particle Green function in a convolution of single-electronic Coulomb Green functions. We demonstrate that our fully analytical zeroth-order approximation describes the whole spectrum of the system, provides accuracy, which is independent of the number of electrons and is important for applications where the Thomas-Fermi model is still utilized. In addition already in second-order perturbation theory our results become comparable with those via a multi-configuration Hartree-Fock approach.

Laplace-transformed atomic orbital-based Møller–Plesset perturbation theory for relativistic two-component Hamiltonians

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

Helmich-Paris, Benjamin, E-mail: b.helmichparis@vu.nl; Visscher, Lucas, E-mail: l.visscher@vu.nl; Repisky, Michal, E-mail: michal.repisky@uit.no

2016-07-07

We present a formulation of Laplace-transformed atomic orbital-based second-order Møller–Plesset perturbation theory (MP2) energies for two-component Hamiltonians in the Kramers-restricted formalism. This low-order scaling technique can be used to enable correlated relativistic calculations for large molecular systems. We show that the working equations to compute the relativistic MP2 energy differ by merely a change of algebra (quaternion instead of real) from their non-relativistic counterparts. With a proof-of-principle implementation we study the effect of the nuclear charge on the magnitude of half-transformed integrals and show that for light elements spin-free and spin-orbit MP2 energies are almost identical. Furthermore, we investigate themore » effect of separation of charge distributions on the Coulomb and exchange energy contributions, which show the same long-range decay with the inter-electronic/atomic distance as for non-relativistic MP2. A linearly scaling implementation is possible if the proper distance behavior is introduced to the quaternion Schwarz-type estimates as for non-relativistic MP2.« less

Intermolecular symmetry-adapted perturbation theory study of large organic complexes.

PubMed

Heßelmann, Andreas; Korona, Tatiana

2014-09-07

Binding energies for the complexes of the S12L database by Grimme [Chem. Eur. J. 18, 9955 (2012)] were calculated using intermolecular symmetry-adapted perturbation theory combined with a density-functional theory description of the interacting molecules. The individual interaction energy decompositions revealed no particular change in the stabilisation pattern as compared to smaller dimer systems at equilibrium structures. This demonstrates that, to some extent, the qualitative description of the interaction of small dimer systems may be extrapolated to larger systems, a method that is widely used in force-fields in which the total interaction energy is decomposed into atom-atom contributions. A comparison of the binding energies with accurate experimental reference values from Grimme, the latter including thermodynamic corrections from semiempirical calculations, has shown a fairly good agreement to within the error range of the reference binding energies.

Estimation of 557.7 nm Emission Altitude using Co-located Lidars and Photometers over Arecibo

NASA Astrophysics Data System (ADS)

Franco, E.; Raizada, S.; Lautenbach, J.; Brum, C. G. M.

2017-12-01

Airglow at 557.7 nm (green line emission) is generated through the Barth mechanism in the E-region altitude and is sometimes associated with red line (630.0 nm) originating at F-region altitudes. Photons at 557.7 nm are produced through the quenching of excited atomic oxygen atoms, O(1S), while 630.0 nm results through the de-excitation of O(1D) atoms. Even though, the contribution of the green line from F-region is negligible and the significant component comes from the mesosphere, this uncertainty gives rise to a question related to its precise altitude. Previous studies have shown that perturbations generated by atmospheric gravity Waves (GWs) alter the airglow intensity and can be used for studying dynamics of the region where it originates. The uncertainty in the emission altitude of green line can be resolved by using co-located lidars, which provide altitude resolved metal densities. At Arecibo, the resonance lidars tuned to Na and K resonance wavelengths at 589 nm and 770 nm can be used in conjunction with simultaneous measurements from green line photometer to resolve this issue. Both photometer and lidars have narrow field of view as compared to airglow imagers, and hence provide an added advantage that these instruments sample same GW spectrum. Hence, correlation between density perturbations inferred from lidars and airglow intensity perturbations can shed light on the exact altitude of green line emission.

Regularities And Irregularities Of The Stark Parameters For Single Ionized Noble Gases

NASA Astrophysics Data System (ADS)

Peláez, R. J.; Djurovic, S.; Cirišan, M.; Aparicio, J. A.; Mar S.

2010-07-01

Spectroscopy of ionized noble gases has a great importance for the laboratory and astrophysical plasmas. Generally, spectra of inert gases are important for many physics areas, for example laser physics, fusion diagnostics, photoelectron spectroscopy, collision physics, astrophysics etc. Stark halfwidths as well as shifts of spectral lines are usually employed for plasma diagnostic purposes. For example atomic data of argon krypton and xenon will be useful for the spectral diagnostic of ITER. In addition, the software used for stellar atmosphere simulation like TMAP, and SMART require a large amount of atomic and spectroscopic data. Availability of these parameters will be useful for a further development of stellar atmosphere and evolution models. Stark parameters data of spectral lines can also be useful for verification of theoretical calculations and investigation of regularities and systematic trends of these parameters within a multiplet, supermultiplet or transition array. In the last years, different trends and regularities of Stark parameters (halwidths and shifts of spectral lines) have been analyzed. The conditions related with atomic structure of the element as well as plasma conditions are responsible for regular or irregular behaviors of the Stark parameters. The absence of very close perturbing levels makes Ne II as a good candidate for analysis of the regularities. Other two considered elements Kr II and Xe II with complex spectra present strong perturbations and in some cases an irregularities in Stark parameters appear. In this work we analyze the influence of the perturbations to Stark parameters within the multiplets.

Spectra for the reemission of attosecond and shorter electromagnetic pulses by multielectron atoms

NASA Astrophysics Data System (ADS)

Makarov, D. N.; Matveev, V. I.

2017-08-01

Based on the analytical solution of the Schrödinger equation, we have considered the reemission of attosecond and shorter electromagnetic pulses by multielectron atoms in the sudden perturbation approximation. We have developed a technique of calculating the spectra for the reemission of attosecond and shorter electromagnetic pulses by neutral multielectron atoms with nuclear charges from 1 to 92. The results are presented in the form of analytical formulas dependent on several coefficients and screening parameters tabulated for all of the atoms whose electron densities are described by the well-known Dirac-Hartree-Fock-Slater model. As examples we have calculated the spectra for the reemission by lithium, carbon, calcium, and iron atoms for two types of incident pulse: Gaussian and "sombrero."

One-dimensional "atom" with zero-range potential perturbed by finite sequence of zero-duration laser pulses

NASA Astrophysics Data System (ADS)

Gusev, A. A.; Chuluunbaatar, O.; Popov, Yu. V.; Vinitsky, S. I.; Derbov, V. L.; Lovetskiy, K. P.

2018-04-01

The exactly soluble model of a train of zero-duration electromagnetic pulses interacting with a 1D atom with short-range interaction potential modelled by a δ-function is considered. The model is related to the up-to-date laser techniques providing the duration of pulses as short as a few attoseconds and the intensities higher than 1014 W/cm2.

Extending DFT-based genetic algorithms by atom-to-place re-assignment via perturbation theory: A systematic and unbiased approach to structures of mixed-metallic clusters

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

Weigend, Florian, E-mail: florian.weigend@kit.edu

2014-10-07

Energy surfaces of metal clusters usually show a large variety of local minima. For homo-metallic species the energetically lowest can be found reliably with genetic algorithms, in combination with density functional theory without system-specific parameters. For mixed-metallic clusters this is much more difficult, as for a given arrangement of nuclei one has to find additionally the best of many possibilities of assigning different metal types to the individual positions. In the framework of electronic structure methods this second issue is treatable at comparably low cost at least for elements with similar atomic number by means of first-order perturbation theory, asmore » shown previously [F. Weigend, C. Schrodt, and R. Ahlrichs, J. Chem. Phys. 121, 10380 (2004)]. In the present contribution the extension of a genetic algorithm with the re-assignment of atom types to atom sites is proposed and tested for the search of the global minima of PtHf{sub 12} and [LaPb{sub 7}Bi{sub 7}]{sup 4−}. For both cases the (putative) global minimum is reliably found with the extended technique, which is not the case for the “pure” genetic algorithm.« less

Collisional redistribution of radiation. II - The effects of degeneracy on the equations of motion for the density matrix. III - The equation of motion for the correlation function and the scattered spectrum

NASA Technical Reports Server (NTRS)

Burnett, K.; Cooper, J.

1980-01-01

The effect of correlations between an absorber atom and perturbers in the binary-collision approximation are applied to degenerate atomic systems. A generalized absorption profile which specifies the final state of the atom after an absorption event is related to the total intensities of Rayleigh scattering and fluorescence from the atom. It is suggested that additional dynamical information to that obtainable from ordinary absorption experiments is required in order to describe redistributed atomic radiation. The scattering of monochromatic radiation by a degenerate atom is computed in a binary-collision approximation; an equation of motion is derived for the correlation function which is valid outside the quantum-regression regime. Solutions are given for the weak-field conditions in terms of generalized absorption and emission profiles that depend on the indices of the atomic multipoles.

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.

Spin properties of charged Mn-doped quantum dota)

NASA Astrophysics Data System (ADS)

Besombes, L.; Léger, Y.; Maingault, L.; Mariette, H.

2007-04-01

The optical properties of individual quantum dots doped with a single Mn atom and charged with a single carrier are analyzed. The emission of the neutral, negatively and positively charged excitons coupled with a single magnetic atom (Mn) are observed in the same individual quantum dot. The spectrum of the charged excitons in interaction with the Mn atom shows a rich pattern attributed to a strong anisotropy of the hole-Mn exchange interaction slightly perturbed by a small valence-band mixing. The anisotropy in the exchange interaction between a single magnetic atom and a single hole is revealed by comparing the emission of a charged Mn-doped quantum dot in longitudinal and transverse magnetic field.

Line shape parameters for the H2O-H2 collision system for application to exoplanet and planetary atmospheres

NASA Astrophysics Data System (ADS)

Renaud, Candice L.; Cleghorn, Kara; Hartmann, Léna; Vispoel, Bastien; Gamache, Robert R.

2018-05-01

Water can be detected throughout the universe: in comets, asteroids, dwarf planets, the inner and outer planets in our solar system, cool stars, brown dwarfs, and on many exoplanets. Here the focus is on locations rich in hydrogen gas. To properly study these environments, there is a need for the line shape parameters for H2O transitions in collision with hydrogen. This work presents calculations of the half-width and line shift, made using the Modified Complex Robert-Bonamy (MCRB) formalism, at a number of temperatures. It is shown that this collision system is strongly off-resonance. For such conditions, the atom-atom part of the intermolecular potential dominates the interaction of the radiating and perturbing molecules. The atom-atom parameters were adjusted by fitting the H2O-H2 measurements of Brown and Plymate (1996). Several techniques were used to extract lines for which there is more confidence in the quality of the data. The final potential yields results that agree with the measurements with ∼0.3% difference and a 5.9% standard deviation. Using this potential, MCRB calculations were made for all transitions in the pure rotation, ν2, ν1, and ν3 bands. The structure of the line shape parameters and the temperature dependence of the half-width, as a function of the rotational and vibrational quantum numbers, are discussed. It is shown that the power law model of the T-dependence of the half-width is inadequate over large temperature ranges.

Materials selection for long life in low earth orbit - A critical evaluation of atomic oxygen testing with thermal atom systems

NASA Technical Reports Server (NTRS)

Koontz, S. L.; Albyn, K.; Leger, L.

1990-01-01

The use of thermal atom test methods as a materials selection and screening technique for low-earth orbit (LEO) spacecraft is critically evaluated. The chemistry and physics of thermal atom environments are compared with the LEO environment. The relative reactivities of a number of materials determined in thermal atom environments are compared with those observed in LEO and in high-quality LEO simulations. Reaction efficiencies (cu cm/atom) measured in a new type of thermal atom apparatus are one-thousandth to one ten-thousandth those observed in LEO, and many materials showing nearly identical reactivities in LEO show relative reactivities differing by as much as a factor of eight in thermal atom systems. A simple phenomenological kinetic model for the reaction of oxygen atoms with organic materials can be used to explain the differences in reactivity in different environments. Certain speciic thermal atom test environments can be used as reliable materials screening tools.

Two photon excitation of atomic oxygen

NASA Technical Reports Server (NTRS)

Pindzola, M. S.

1977-01-01

A standard perturbation expansion in the atom-radiation field interaction is used to calculate the two photon excitation cross section for 1s(2) 2s(2) 2p(4) p3 to 1s(2) 2s(2) 2p(3) (s4) 3p p3 transition in atomic oxygen. The summation over bound and continuum intermediate states is handled by solving the equivalent inhomogeneous differential equation. Exact summation results differ by a factor of 2 from a rough estimate obtained by limiting the intermediate state summation to one bound state. Higher order electron correlation effects are also examined.

Reemission spectra and inelastic processes at interaction of attosecond and shorter duration electromagnetic pulses with atoms

NASA Astrophysics Data System (ADS)

Makarov, D. N.; Matveev, V. I.

2017-01-01

Inelastic processes and the reemission of attosecond and shorter electromagnetic pulses by atoms have been considered within the analytical solution of the Schrödinger equation in the sudden perturbation approximation. A method of calculations with the exact inclusion of spatial inhomogeneity of the field of an ultrashort pulse and the momenta of photons in the reemission processes has been developed. The probabilities of inelastic processes and spectra of reemission of ultrashort electromagnetic pulses by one- and many-electron atoms have been calculated. The results have been presented in the form of analytical formulas.

Laser Cooled Atomic Clocks in Space

NASA Technical Reports Server (NTRS)

Thompson, R. J.; Kohel, J.; Klipstein, W. M.; Seidel, D. J.; Maleki, L.

2000-01-01

The goals of the Glovebox Laser-cooled Atomic Clock Experiment (GLACE) are: (1) first utilization of tunable, frequency-stabilized lasers in space, (2) demonstrate laser cooling and trapping in microgravity, (3) demonstrate longest 'perturbation-free' interaction time for a precision measurement on neutral atoms, (4) Resolve Ramsey fringes 2-10 times narrower than achievable on Earth. The approach taken is: the use of COTS components, and the utilization of prototype hardware from LCAP flight definition experiments. The launch date is scheduled for Oct. 2002. The Microgravity Science Glovebox (MSG) specifications are reviewed, and a picture of the MSG is shown.

On the role of atomic metastability in the production of Balmer line radiation from ‘cold’ atomic hydrogen, deuterium and hydrogenic ion impurities in fusion edge plasmas

NASA Astrophysics Data System (ADS)

Hey, J. D.

2012-03-01

Published arguments, which assign an important role to atomic metastability in the production of ‘narrow’ Zeeman component radiation from the boundary region of fusion plasmas, are examined critically in relation to l-redistribution by proton and electron collisions, and mixing of unperturbed atomic states by the ion microfield and microfield gradient. It is concluded that these important processes indeed severely constrain the contribution from ‘metastable’ states to the generation of the hydrogen Balmer spectra, for electron concentrations above 1012 cm-3, as pointed out before by the present author (Hey et al 1999 J. Phys. B: At. Mol. Opt. Phys. 32 3555). The analysis of collision-induced l-redistribution represents an extension of that used previously (Hey et al 1996 Contrib. Plasma Phys. 36 583), applicable up to higher electron densities. For comparison purposes, we also consider the question of metastability of ionized helium in a low-temperature plasma, and that of some common hydrogenic impurities (C5+ and Ne9+) in a hydrogen (deuterium) fusion plasma. While for low nuclear charge Z the metastability of 2s1/2 levels is quenched by the plasma environment, it is much reduced in high-Z ions owing to the rapid increase with Z of the two-photon electric dipole (2E1) and magnetic dipole (M1) spontaneous transition rates to the ground state, whereas the role of the plasma in these cases is less important. The main new principle elaborated in this work is the sensitivity of atomic line strengths, and hence collision strengths, to perturbation by the plasma environment for transitions between fine-structure sublevels of the same principal quantum number. As the plasma microfield strength grows, ‘allowed’ transitions diminish in strength, while ‘forbidden’ transitions grow. However, owing to violation of the parity selection rule, there is an overall loss of collision strength available to transitions, resulting from the appearance of significant ‘self-strength’ contributions, in accord with the sum rules for the line strengths, which remain valid over the range of fields considered. Thus, the relative effectiveness per perturber of both electron and ion collisions, for inducing population transfer between fine-structure sublevels, diminishes as the sublevels evolve from a fine-structure dominated to a Stark-effect-dominated regime. In the concluding discussion, we mention that this finding may have a bearing on discrepancies claimed between Stark broadening theory developed by Griem (1967 Astrophys. J. 148 547) and by Watson (2006 J. Phys.B: At. Mol. Opt. Phys. 39 1889), and the measurements of Bell and co-workers (2000 Publ. Astron. Soc. Pac. 112 1236; 2011 Astrophys. Space Sci. 335 451) for high-n radio recombination lines from galactic H II regions. In the absence of detailed modelling to test this suggestion, however, it would be premature to attempt to draw any firm conclusions along these lines. This manuscript is dedicated to the memory of my esteemed colleague Dr. rer. nat. Manfred Korten (1940-2010).

Representation of the exact relativistic electronic Hamiltonian within the regular approximation

NASA Astrophysics Data System (ADS)

Filatov, Michael; Cremer, Dieter

2003-12-01

The exact relativistic Hamiltonian for electronic states is expanded in terms of energy-independent linear operators within the regular approximation. An effective relativistic Hamiltonian has been obtained, which yields in lowest order directly the infinite-order regular approximation (IORA) rather than the zeroth-order regular approximation method. Further perturbational expansion of the exact relativistic electronic energy utilizing the effective Hamiltonian leads to new methods based on ordinary (IORAn) or double [IORAn(2)] perturbation theory (n: order of expansion), which provide improved energies in atomic calculations. Energies calculated with IORA4 and IORA3(2) are accurate up to c-20. Furthermore, IORA is improved by using the IORA wave function to calculate the Rayleigh quotient, which, if minimized, leads to the exact relativistic energy. The outstanding performance of this new IORA method coined scaled IORA is documented in atomic and molecular calculations.

Hg-201 (+) CO-Magnetometer for HG-199(+) Trapped Ion Space Atomic Clocks

NASA Technical Reports Server (NTRS)

Burt, Eric A. (Inventor); Taghavi, Shervin (Inventor); Tjoelker, Robert L. (Inventor)

2011-01-01

Local magnetic field strength in a trapped ion atomic clock is measured in real time, with high accuracy and without degrading clock performance, and the measurement is used to compensate for ambient magnetic field perturbations. First and second isotopes of an element are co-located within the linear ion trap. The first isotope has a resonant microwave transition between two hyperfine energy states, and the second isotope has a resonant Zeeman transition. Optical sources emit ultraviolet light that optically pump both isotopes. A microwave radiation source simultaneously emits microwave fields resonant with the first isotope's clock transition and the second isotope's Zeeman transition, and an optical detector measures the fluorescence from optically pumping both isotopes. The second isotope's Zeeman transition provides the measure of magnetic field strength, and the measurement is used to compensate the first isotope's clock transition or to adjust the applied C-field to reduce the effects of ambient magnetic field perturbations.

Exospheric perturbations by radiation pressure. II - Solution for orbits in the ecliptic plane

NASA Technical Reports Server (NTRS)

Chamberlain, J. W.

1980-01-01

A previous study (Chamberlain, 1979) gave solutions for the mean time rates of change of orbital elements of satellite atoms in an exosphere influenced by solar radiation pressure; each element was assumed to behave independently. In the present paper, the instantaneous rates of changes for three elements (e, Omega, and phi = omega + Omega) are integrated simultaneously for the case of the inclination i = 0. The results confirm the validity of using mean rates when the orbits are tighly bound to the planet, and serve as examples to be reproduced by the complicated numerical solutions required for arbitrary inclination. Strongly bound hydrogen atoms perturbed in earth orbit by radiation pressure do not seem a likely cause of the geotail extending in the anti-sun direction. Instead, radiation pressure will cause those particles' orbits to form a broad fan-shaped tail and to deteriorate into the earth's atmosphere.

Quantum-optical nonlinearities induced by Rydberg-Rydberg interactions: A perturbative approach

NASA Astrophysics Data System (ADS)

Grankin, A.; Brion, E.; Bimbard, E.; Boddeda, R.; Usmani, I.; Ourjoumtsev, A.; Grangier, P.

2015-10-01

In this article, we theoretically study the quantum statistical properties of the light transmitted through or reflected from an optical cavity, filled by an atomic medium with strong optical nonlinearity induced by Rydberg-Rydberg van der Waals interactions. Atoms are driven on a two-photon transition from their ground state to a Rydberg level via an intermediate state by the combination of a weak signal field and a strong control beam. By using a perturbative approach, we get analytic results which remain valid in the regime of weak feeding fields, even when the intermediate state becomes resonant thus generalizing our previous results. We can thus investigate quantitatively new features associated with the resonant behavior of the system. We also propose an effective nonlinear three-boson model of the system which, in addition to leading to the same analytic results as the original problem, sheds light on the physical processes at work in the system.

Enhanced sensitivity at higher-order exceptional points

NASA Astrophysics Data System (ADS)

Hodaei, Hossein; Hassan, Absar U.; Wittek, Steffen; Garcia-Gracia, Hipolito; El-Ganainy, Ramy; Christodoulides, Demetrios N.; Khajavikhan, Mercedeh

2017-08-01

Non-Hermitian degeneracies, also known as exceptional points, have recently emerged as a new way to engineer the response of open physical systems, that is, those that interact with the environment. They correspond to points in parameter space at which the eigenvalues of the underlying system and the corresponding eigenvectors simultaneously coalesce. In optics, the abrupt nature of the phase transitions that are encountered around exceptional points has been shown to lead to many intriguing phenomena, such as loss-induced transparency, unidirectional invisibility, band merging, topological chirality and laser mode selectivity. Recently, it has been shown that the bifurcation properties of second-order non-Hermitian degeneracies can provide a means of enhancing the sensitivity (frequency shifts) of resonant optical structures to external perturbations. Of particular interest is the use of even higher-order exceptional points (greater than second order), which in principle could further amplify the effect of perturbations, leading to even greater sensitivity. Although a growing number of theoretical studies have been devoted to such higher-order degeneracies, their experimental demonstration in the optical domain has so far remained elusive. Here we report the observation of higher-order exceptional points in a coupled cavity arrangement—specifically, a ternary, parity-time-symmetric photonic laser molecule—with a carefully tailored gain-loss distribution. We study the system in the spectral domain and find that the frequency response associated with this system follows a cube-root dependence on induced perturbations in the refractive index. Our work paves the way for utilizing non-Hermitian degeneracies in fields including photonics, optomechanics, microwaves and atomic physics.

Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition

NASA Astrophysics Data System (ADS)

Parrish, Robert M.; Sherrill, C. David

2014-07-01

We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work through the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-π interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in systems with up to 220 atoms and 2845 basis functions.

Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition

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

Parrish, Robert M.; Sherrill, C. David, E-mail: sherrill@gatech.edu

2014-07-28

We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work throughmore » the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-π interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in systems with up to 220 atoms and 2845 basis functions.« less

Vibrational dephasing in matter-wave interferometers

NASA Astrophysics Data System (ADS)

Rembold, A.; Schütz, G.; Röpke, R.; Chang, W. T.; Hwang, I. S.; Günther, A.; Stibor, A.

2017-03-01

Matter-wave interferometry is a highly sensitive tool to measure small perturbations in a quantum system. This property allows the creation of precision sensors for dephasing mechanisms such as mechanical vibrations. They are a challenge for phase measurements under perturbing conditions that cannot be perfectly decoupled from the interferometer, e.g. for mobile interferometric devices or vibrations with a broad frequency range. Here, we demonstrate a method based on second-order correlation theory in combination with Fourier analysis, to use an electron interferometer as a sensor that precisely characterizes the mechanical vibration spectrum of the interferometer. Using the high spatial and temporal single-particle resolution of a delay line detector, the data allows to reveal the original contrast and spatial periodicity of the interference pattern from ‘washed-out’ matter-wave interferograms that have been vibrationally disturbed in the frequency region between 100 and 1000 Hz. Other than with electromagnetic dephasing, due to excitations of higher harmonics and additional frequencies induced from the environment, the parts in the setup oscillate with frequencies that can be different to the applied ones. The developed numerical search algorithm is capable to determine those unknown oscillations and corresponding amplitudes. The technique can identify vibrational dephasing and decrease damping and shielding requirements in electron, ion, neutron, atom and molecule interferometers that generate a spatial fringe pattern on the detector plane.

Unexpected Huge Dimerization Ratio in One-Dimensional Carbon Atomic Chains.

PubMed

Lin, Yung-Chang; Morishita, Shigeyuki; Koshino, Masanori; Yeh, Chao-Hui; Teng, Po-Yuan; Chiu, Po-Wen; Sawada, Hidetaka; Suenaga, Kazutomo

2017-01-11

Peierls theory predicted atomic distortion in one-dimensional (1D) crystal due to its intrinsic instability in 1930. Free-standing carbon atomic chains created in situ in transmission electron microscope (TEM)1-3 are an ideal example to experimentally observe the dimerization behavior of carbon atomic chain within a finite length. We report here a surprisingly huge distortion found in the free-standing carbon atomic chains at 773 K, which is 10 times larger than the value expected in the system. Such an abnormally distorted phase only dominates at the elevated temperatures, while two distinct phases, distorted and undistorted, coexist at lower or ambient temperatures. Atom-by-atom spectroscopy indeed shows considerable variations in the carbon 1s spectra at each atomic site but commonly observes a slightly downshifted π* peak, which proves its sp 1 bonding feature. These results suggest that the simple model, relaxed and straight, is not fully adequate to describe the realistic 1D structure, which is extremely sensitive to perturbations such as external force or boundary conditions.

Some properties of Stark states of hydrogenic atoms and ions

NASA Astrophysics Data System (ADS)

Hey, J. D.

2007-10-01

The motivation for this work is the problem of providing accurate values of the atomic transition matrix elements for the Stark components of Rydberg Rydberg transitions in atomic hydrogen and hydrogenic ions, for use in spectral line broadening calculations applicable to cool, low-density plasmas, such as those found in H II regions. Since conventional methods of calculating these transition matrix elements cannot be used for the high principal quantum numbers now easily attained in radio astronomical spectra, we attempt to show that the recurrence relation (ladder operator) method recently employed by Watson (2006 J. Phys. B: At. Mol. Opt. Phys. 39 1889 97) and Hey (2006 J. Phys. B: At. Mol. Opt. Phys. 39 2641 64) can be taken over into the parabolic coordinate system used to describe the Stark states of the atomic (ionic) radiators. The present method is therefore suggested as potentially useful for extending the work of Griem (1967 Astrophys. J. 148 547 58, 2005 Astrophys. J. 620 L133 4), Watson (2006), Stambulchik et al (2007 Phys. Rev. E 75 016401(9 pp) on Stark broadening in transitions between states of high principal quantum number, to physical conditions where the binary, impact approximation is no longer strictly applicable to both electron and ion perturbers. Another possible field of application is the study of Stark mixing transitions in 'ultracold' Rydberg atoms perturbed by long-range interactions with slow atoms and ions. Preparatory to the derivation of recurrence relations for states of different principal quantum number, a number of properties and recurrence relations are also found for states of identical principal quantum number, including the analogue in parabolic coordinates to the relations of Pasternack (1937 Proc. Natl Acad. Sci. USA 23 91 4, 250) in spherical polar coordinates.

Advancing Efficient All-Electron Electronic Structure Methods Based on Numeric Atom-Centered Orbitals for Energy Related Materials

NASA Astrophysics Data System (ADS)

Blum, Volker

This talk describes recent advances of a general, efficient, accurate all-electron electronic theory approach based on numeric atom-centered orbitals; emphasis is placed on developments related to materials for energy conversion and their discovery. For total energies and electron band structures, we show that the overall accuracy is on par with the best benchmark quality codes for materials, but scalable to large system sizes (1,000s of atoms) and amenable to both periodic and non-periodic simulations. A recent localized resolution-of-identity approach for the Coulomb operator enables O (N) hybrid functional based descriptions of the electronic structure of non-periodic and periodic systems, shown for supercell sizes up to 1,000 atoms; the same approach yields accurate results for many-body perturbation theory as well. For molecular systems, we also show how many-body perturbation theory for charged and neutral quasiparticle excitation energies can be efficiently yet accurately applied using basis sets of computationally manageable size. Finally, the talk highlights applications to the electronic structure of hybrid organic-inorganic perovskite materials, as well as to graphene-based substrates for possible future transition metal compound based electrocatalyst materials. All methods described here are part of the FHI-aims code. VB gratefully acknowledges contributions by numerous collaborators at Duke University, Fritz Haber Institute Berlin, TU Munich, USTC Hefei, Aalto University, and many others around the globe.

Using Density Functional Theory (DFT) for the Calculation of Atomization Energies

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The calculation of atomization energies using density functional theory (DFT), using the B3LYP hybrid functional, is reported. The sensitivity of the atomization energy to basis set is studied and compared with the coupled cluster singles and doubles approach with a perturbational estimate of the triples (CCSD(T)). Merging the B3LYP results with the G2(MP2) approach is also considered. It is found that replacing the geometry optimization and calculation of the zero-point energy by the analogous quantities computed using the B3LYP approach reduces the maximum error in the G2(MP2) approach. In addition to the 55 G2 atomization energies, some results for transition metal containing systems will also be presented.

The multi-reference retaining the excitation degree perturbation theory: A size-consistent, unitary invariant, and rapidly convergent wavefunction based ab initio approach

NASA Astrophysics Data System (ADS)

Fink, Reinhold F.

2009-02-01

The retaining the excitation degree (RE) partitioning [R.F. Fink, Chem. Phys. Lett. 428 (2006) 461(20 September)] is reformulated and applied to multi-reference cases with complete active space (CAS) reference wave functions. The generalised van Vleck perturbation theory is employed to set up the perturbation equations. It is demonstrated that this leads to a consistent and well defined theory which fulfils all important criteria of a generally applicable ab initio method: The theory is proven numerically and analytically to be size-consistent and invariant with respect to unitary orbital transformations within the inactive, active and virtual orbital spaces. In contrast to most previously proposed multi-reference perturbation theories the necessary condition for a proper perturbation theory to fulfil the zeroth order perturbation equation is exactly satisfied with the RE partitioning itself without additional projectors on configurational spaces. The theory is applied to several excited states of the benchmark systems CH2 , SiH2 , and NH2 , as well as to the lowest states of the carbon, nitrogen and oxygen atoms. In all cases comparisons are made with full configuration interaction results. The multi-reference (MR)-RE method is shown to provide very rapidly converging perturbation series. Energy differences between states of similar configurations converge even faster.

Femtosecond two-photon photoassociation of hot magnesium atoms: A quantum dynamical study using thermal random phase wavefunctions

NASA Astrophysics Data System (ADS)

Amaran, Saieswari; Kosloff, Ronnie; Tomza, Michał; Skomorowski, Wojciech; Pawłowski, Filip; Moszynski, Robert; Rybak, Leonid; Levin, Liat; Amitay, Zohar; Berglund, J. Martin; Reich, Daniel M.; Koch, Christiane P.

2013-10-01

Two-photon photoassociation of hot magnesium atoms by femtosecond laser pulses, creating electronically excited magnesium dimer molecules, is studied from first principles, combining ab initio quantum chemistry and molecular quantum dynamics. This theoretical framework allows for rationalizing the generation of molecular rovibrational coherence from thermally hot atoms [L. Rybak, S. Amaran, L. Levin, M. Tomza, R. Moszynski, R. Kosloff, C. P. Koch, and Z. Amitay, Phys. Rev. Lett. 107, 273001 (2011)]. Random phase thermal wavefunctions are employed to model the thermal ensemble of hot colliding atoms. Comparing two different choices of basis functions, random phase wavefunctions built from eigenstates are found to have the fastest convergence for the photoassociation yield. The interaction of the colliding atoms with a femtosecond laser pulse is modeled non-perturbatively to account for strong-field effects.

Precise single-qubit control of the reflection phase of a photon mediated by a strongly-coupled ancilla–cavity system

NASA Astrophysics Data System (ADS)

Motzoi, F.; Mølmer, K.

2018-05-01

We propose to use the interaction between a single qubit atom and a surrounding ensemble of three level atoms to control the phase of light reflected by an optical cavity. Our scheme employs an ensemble dark resonance that is perturbed by the qubit atom to yield a single-atom single photon gate. We show here that off-resonant excitation towards Rydberg states with strong dipolar interactions offers experimentally-viable regimes of operations with low errors (in the 10‑3 range) as required for fault-tolerant optical-photon, gate-based quantum computation. We also propose and analyze an implementation within microwave circuit-QED, where a strongly-coupled ancilla superconducting qubit can be used in the place of the atomic ensemble to provide high-fidelity coupling to microwave photons.

Origins of the changing detector response in small megavoltage photon radiation fields.

PubMed

Fenwick, John D; Georgiou, Georgios; Rowbottom, Carl G; Underwood, Tracy S A; Kumar, Sudhir; Nahum, Alan E

2018-06-08

Differences in detector response between measured small fields, f clin, and wider reference fields, f msr , can be overcome by using correction factors [Formula: see text] or by designing detectors with field-size invariant responses. The changing response in small fields is caused by perturbations of the electron fluence within the detector sensitive volume. For solid-state detectors, it has recently been suggested that these perturbations might be caused by the non-water-equivalent effective atomic numbers Z of detector materials, rather than by their non-water-like densities. Using the EGSnrc Monte Carlo code we have analyzed the response of a PTW 60017 diode detector in a 6 MV beam, calculating the [Formula: see text] correction factor from computed doses absorbed by water and by the detector sensitive volume in 0.5  ×  0.5 and 4  ×  4 cm 2 fields. In addition to the 'real' detector, fully modelled according to the manufacturer's blue-prints, we calculated doses and [Formula: see text] factors for a 'Z  →  water' detector variant in which mass stopping-powers and microscopic interaction coefficients were set to those of water while preserving real material densities, and for a 'density  →  1' variant in which densities were set to 1 g cm -3 , leaving mass stopping-powers and interaction coefficients at real levels. [Formula: see text] equalled 0.910  ±  0.005 (2 standard deviations) for the real detector, was insignificantly different at 0.912  ±  0.005 for the 'Z  →  H 2 O' variant, but equalled 1.012  ±  0.006 for the 'density  →  1' variant. For the 60017 diode in a 6 MV beam, then, [Formula: see text] was determined primarily by the detector's density rather than its atomic composition. Further calculations showed this remained the case in a 15 MV beam. Interestingly, the sensitive volume electron fluence was perturbed more by detector atomic composition than by density; however, the density-dependent perturbation varied with field-size, whereas the Z-dependent perturbation was relatively constant, little affecting [Formula: see text].

Origins of the changing detector response in small megavoltage photon radiation fields

NASA Astrophysics Data System (ADS)

Fenwick, John D.; Georgiou, Georgios; Rowbottom, Carl G.; Underwood, Tracy S. A.; Kumar, Sudhir; Nahum, Alan E.

2018-06-01

Differences in detector response between measured small fields, f clin, and wider reference fields, f msr , can be overcome by using correction factors or by designing detectors with field-size invariant responses. The changing response in small fields is caused by perturbations of the electron fluence within the detector sensitive volume. For solid-state detectors, it has recently been suggested that these perturbations might be caused by the non-water-equivalent effective atomic numbers Z of detector materials, rather than by their non-water-like densities. Using the EGSnrc Monte Carlo code we have analyzed the response of a PTW 60017 diode detector in a 6 MV beam, calculating the correction factor from computed doses absorbed by water and by the detector sensitive volume in 0.5  ×  0.5 and 4  ×  4 cm2 fields. In addition to the ‘real’ detector, fully modelled according to the manufacturer’s blue-prints, we calculated doses and factors for a ‘Z  →  water’ detector variant in which mass stopping-powers and microscopic interaction coefficients were set to those of water while preserving real material densities, and for a ‘density  →  1’ variant in which densities were set to 1 g cm‑3, leaving mass stopping-powers and interaction coefficients at real levels. equalled 0.910  ±  0.005 (2 standard deviations) for the real detector, was insignificantly different at 0.912  ±  0.005 for the ‘Z  →  H2O’ variant, but equalled 1.012  ±  0.006 for the ‘density  →  1’ variant. For the 60017 diode in a 6 MV beam, then, was determined primarily by the detector’s density rather than its atomic composition. Further calculations showed this remained the case in a 15 MV beam. Interestingly, the sensitive volume electron fluence was perturbed more by detector atomic composition than by density; however, the density-dependent perturbation varied with field-size, whereas the Z-dependent perturbation was relatively constant, little affecting .

Materials selection for long life in LEO: A critical evaluation of atomic oxygen testing with thermal atom systems

NASA Technical Reports Server (NTRS)

Koontz, S. L.; Kuminecz, J.; Leger, L.; Nordine, P.

1988-01-01

The use of thermal atom test methods as a materials selection and screening technique for low-Earth orbit (LEO) spacecraft is critically evaluated. The chemistry and physics of thermal atom environments are compared with the LEO environment. The relative reactivities of a number of materials determined to be in thermal atom environments are compared to those observed in LEO and in high quality LEO simulations. Reaction efficiencies measured in a new type of thermal atom apparatus are one-hundredth to one-thousandth those observed in LEO, and many materials showing nearly identical reactivities in LEO show relative reactivities differing by as much as a factor of 8 in thermal atom systems. A simple phenomenological kinetic model for the reaction of oxygen atoms with organic materials can be used to explain the differences in reactivity in different environments. Certain specific thermal test environments can be used as reliable materials screening tools. Using thermal atom methods to predict material lifetime in LEO requires direct calibration of the method against LEO data or high quality simulation data for each material.

The nuclear size and mass effects on muonic hydrogen-like atoms embedded in Debye plasma

NASA Astrophysics Data System (ADS)

Poszwa, A.; Bahar, M. K.; Soylu, A.

2016-10-01

Effects of finite nuclear size and finite nuclear mass are investigated for muonic atoms and muonic ions embedded in the Debye plasma. Both nuclear charge radii and nuclear masses are taken into account with experimentally determined values. In particular, isotope shifts of bound state energies, radial probability densities, transition energies, and binding energies for several atoms are studied as functions of Debye length. The theoretical model based on semianalytical calculations, the Sturmian expansion method, and the perturbative approach has been constructed, in the nonrelativistic frame. For some limiting cases, the comparison with previous most accurate literature results has been made.

Is the Lamb shift chemically significant?

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.; Bauschlicher, Charles W., Jr.; Schwenke, David W.; Pyykko, Pekka; Arnold, James (Technical Monitor)

2001-01-01

The contribution of the Lamb shift to the atomization energies of some prototype molecules, BF3, AlF3, and GaF3, is estimated by a perturbation procedure. It is found to be in the range of 3-5% of the one-electron scalar relativistic contribution to the atomization energy. The maximum absolute value is 0.2 kcal/mol for GaF3. These sample calculations indicate that the Lamb shift is probably small enough to be neglected for energetics of molecules containing light atoms if the target accuracy is 1 kcal/mol, but for higher accuracy calculations and for molecules containing heavy elements it must be considered.

Theory of long-range interactions for Rydberg states attached to hyperfine-split cores

NASA Astrophysics Data System (ADS)

Robicheaux, F.; Booth, D. W.; Saffman, M.

2018-02-01

The theory is developed for one- and two-atom interactions when the atom has a Rydberg electron attached to a hyperfine-split core state. This situation is relevant for some of the rare-earth and alkaline-earth atoms that have been proposed for experiments on Rydberg-Rydberg interactions. For the rare-earth atoms, the core electrons can have a very substantial total angular momentum J and a nonzero nuclear spin I . In the alkaline-earth atoms there is a single (s ) core electron whose spin can couple to a nonzero nuclear spin for odd isotopes. The resulting hyperfine splitting of the core state can lead to substantial mixing between the Rydberg series attached to different thresholds. Compared to the unperturbed Rydberg series of the alkali-metal atoms, the series perturbations and near degeneracies from the different parity states could lead to qualitatively different behavior for single-atom Rydberg properties (polarizability, Zeeman mixing and splitting, etc.) as well as Rydberg-Rydberg interactions (C5 and C6 matrices).

Optimization of Monte Carlo dose calculations: The interface problem

NASA Astrophysics Data System (ADS)

Soudentas, Edward

1998-05-01

High energy photon beams are widely used for radiation treatment of deep-seated tumors. The human body contains many types of interfaces between dissimilar materials that affect dose distribution in radiation therapy. Experimentally, significant radiation dose perturbations has been observed at such interfaces. The EGS4 Monte Carlo code was used to calculate dose perturbations at boundaries between dissimilar materials (such as bone/water) for 60Co and 6 MeV linear accelerator beams using a UNIX workstation. A simple test of the reliability of a random number generator was also developed. A systematic study of the adjustable parameters in EGS4 was performed in order to minimize calculational artifacts at boundaries. Calculations of dose perturbations at boundaries between different materials showed that there is a 12% increase in dose at water/bone interface, and a 44% increase in dose at water/copper interface. with the increase mainly due to electrons produced in water and backscattered from the high atomic number material. The dependence of the dose increase on the atomic number was also investigated. The clinically important case of using two parallel opposed beams for radiation therapy was investigated where increased doses at boundaries has been observed. The Monte Carlo calculations can provide accurate dosimetry data under conditions of electronic non-equilibrium at tissue interfaces.

Digital Quantum Simulation of Z2 Lattice Gauge Theories with Dynamical Fermionic Matter

NASA Astrophysics Data System (ADS)

Zohar, Erez; Farace, Alessandro; Reznik, Benni; Cirac, J. Ignacio

2017-02-01

We propose a scheme for digital quantum simulation of lattice gauge theories with dynamical fermions. Using a layered optical lattice with ancilla atoms that can move and interact with the other atoms (simulating the physical degrees of freedom), we obtain a stroboscopic dynamics which yields the four-body plaquette interactions, arising in models with (2 +1 ) and higher dimensions, without the use of perturbation theory. As an example we show how to simulate a Z2 model in (2 +1 ) dimensions.

Digital Quantum Simulation of Z_{2} Lattice Gauge Theories with Dynamical Fermionic Matter.

PubMed

Zohar, Erez; Farace, Alessandro; Reznik, Benni; Cirac, J Ignacio

2017-02-17

We propose a scheme for digital quantum simulation of lattice gauge theories with dynamical fermions. Using a layered optical lattice with ancilla atoms that can move and interact with the other atoms (simulating the physical degrees of freedom), we obtain a stroboscopic dynamics which yields the four-body plaquette interactions, arising in models with (2+1) and higher dimensions, without the use of perturbation theory. As an example we show how to simulate a Z_{2} model in (2+1) dimensions.

Electron correlation in Hooke's law atom in the high-density limit.

PubMed

Gill, P M W; O'Neill, D P

2005-03-01

Closed-form expressions for the first three terms in the perturbation expansion of the exact energy and Hartree-Fock energy of the lowest singlet and triplet states of the Hooke's law atom are found. These yield elementary formulas for the exact correlation energies (-49.7028 and -5.807 65 mE(h)) of the two states in the high-density limit and lead to a pair of necessary conditions on the exact correlation kernel G(w) in Hartree-Fock-Wigner theory.

Perturbation vectors to evaluate air quality using lichens and bromeliads: a Brazilian case study.

PubMed

Monna, F; Marques, A N; Guillon, R; Losno, R; Couette, S; Navarro, N; Dongarra, G; Tamburo, E; Varrica, D; Chateau, C; Nepomuceno, F O

2017-10-17

Samples of one lichen species, Parmotrema crinitum, and one bromeliad species, Tillandsia usneoides, were collected in the state of Rio de Janeiro, Brazil, at four sites differently affected by anthropogenic pollution. The concentrations of aluminum, cadmium, copper, iron, lanthanum, lead, sulfur, titanium, zinc, and zirconium were determined by inductively coupled plasma-atomic emission spectroscopy. The environmental diagnosis was established by examining compositional changes via perturbation vectors, an underused family of methods designed to circumvent the problem of closure in any compositional dataset. The perturbation vectors between the reference site and the other three sites were similar for both species, although body concentration levels were different. At each site, perturbation vectors between lichens and bromeliads were approximately the same, whatever the local pollution level. It should thus be possible to combine these organisms, though physiologically different, for air quality surveys, after making all results comparable with appropriate correction. The use of perturbation vectors seems particularly suitable for assessing pollution level by biomonitoring, and for many frequently met situations in environmental geochemistry, where elemental ratios are more relevant than absolute concentrations.

Interplay between tetrel and triel bonds in RC6H4CN⋯MF3CN⋯BX3 complexes: A combined symmetry-adapted perturbation theory, Møller-Plesset, and quantum theory of atoms-in-molecules study.

PubMed

Yourdkhani, Sirous; Korona, Tatiana; Hadipour, Nasser L

2015-12-15

Intermolecular ternary complexes composed of: (1) the centrally placed trifluoroacetonitrile or its higher analogs with central carbon exchanged by silicon or germanium (M = C, Si, Ge), (2) the benzonitrile molecule or its para derivatives on one side, and (3) the boron trifluoride of trichloride molecule (X = F, Cl) on the opposite side as well as the corresponding intermolecular tetrel- and triel-bonded binary complexes, were investigated by symmetry-adapted perturbation theory (SAPT) and the supermolecular Møller-Plesset method (MP2) at the complete basis set limit for optimized geometries. A character of interactions was studied by quantum theory of atoms-in-molecules (QTAIM). A comparison of interaction energies and QTAIM bond descriptors for dimers and trimers reveals that tetrel and triel bonds increase in their strength if present together in the trimer. For the triel-bonded complex, this growth leads to a change of the bond character from closed-shell to partly covalent for Si or Ge tetrel atoms, so the resulting bonding scheme corresponds to a preliminary stage of the SN2 reaction. Limitations of the Lewis theory of acids and bases were shown by its failure in predicting the stability order of the triel complexes. The necessity of including interaction energy terms beyond the electrostatic component for an elucidation of the nature of σ- and π-holes was presented by a SAPT energy decomposition and by a study of differences in monomer electrostatic potentials obtained either from isolated monomer densities, or from densities resulting from a perturbation with the effective field of another monomer. © 2015 Wiley Periodicals, Inc.

Generalized Autobalanced Ramsey Spectroscopy of Clock Transitions

NASA Astrophysics Data System (ADS)

Yudin, V. I.; Taichenachev, A. V.; Basalaev, M. Yu.; Zanon-Willette, T.; Pollock, J. W.; Shuker, M.; Donley, E. A.; Kitching, J.

2018-05-01

When performing precision measurements, the quantity being measured is often perturbed by the measurement process itself. Such measurements include precision frequency measurements for atomic clock applications carried out with Ramsey spectroscopy. With the aim of eliminating probe-induced perturbations, a method of generalized autobalanced Ramsey spectroscopy (GABRS) is presented and rigorously substantiated. The usual local-oscillator frequency control loop is augmented with a second control loop derived from secondary Ramsey sequences interspersed with the primary sequences and with a different Ramsey period. This second loop feeds back to a secondary clock variable and ultimately compensates for the perturbation of the clock frequency caused by the measurements in the first loop. We show that such a two-loop scheme can lead to perfect compensation for measurement-induced light shifts and does not suffer from the effects of relaxation, time-dependent pulse fluctuations and phase-jump modulation errors that are typical of other hyper-Ramsey schemes. Several variants of GABRS are explored based on different secondary variables including added relative phase shifts between Ramsey pulses, external frequency-step compensation, and variable second-pulse duration. We demonstrate that a universal antisymmetric error signal, and hence perfect compensation at a finite modulation amplitude, is generated only if an additional frequency step applied during both Ramsey pulses is used as the concomitant variable parameter. This universal technique can be applied to the fields of atomic clocks, high-resolution molecular spectroscopy, magnetically induced and two-photon probing schemes, Ramsey-type mass spectrometry, and the field of precision measurements. Some variants of GABRS can also be applied for rf atomic clocks using coherent-population-trapping-based Ramsey spectroscopy of the two-photon dark resonance.

Molecule-specific determination of atomic polarizabilities with the polarizable atomic multipole model.

PubMed

Woo Kim, Hyun; Rhee, Young Min

2012-07-30

Recently, many polarizable force fields have been devised to describe induction effects between molecules. In popular polarizable models based on induced dipole moments, atomic polarizabilities are the essential parameters and should be derived carefully. Here, we present a parameterization scheme for atomic polarizabilities using a minimization target function containing both molecular and atomic information. The main idea is to adopt reference data only from quantum chemical calculations, to perform atomic polarizability parameterizations even when relevant experimental data are scarce as in the case of electronically excited molecules. Specifically, our scheme assigns the atomic polarizabilities of any given molecule in such a way that its molecular polarizability tensor is well reproduced. We show that our scheme successfully works for various molecules in mimicking dipole responses not only in ground states but also in valence excited states. The electrostatic potential around a molecule with an externally perturbing nearby charge also exhibits a near-quantitative agreement with the reference data from quantum chemical calculations. The limitation of the model with isotropic atoms is also discussed to examine the scope of its applicability. Copyright © 2012 Wiley Periodicals, Inc.

Determination of formal redox potentials in aqueous solution of copper(II) complexes with ligands having nitrogen and oxygen donor atoms and comparison with their EPR and UV-Vis spectral features.

PubMed

Tabbì, Giovanni; Giuffrida, Alessandro; Bonomo, Raffaele P

2013-11-01

Formal redox potentials in aqueous solution were determined for copper(II) complexes with ligands having oxygen and nitrogen as donor atoms. All the chosen copper(II) complexes have well-known stereochemistries (pseudo-octahedral, square planar, square-based pyramidal, trigonal bipyramidal or tetrahedral) as witnessed by their reported spectroscopic, EPR and UV-visible (UV-Vis) features, so that a rough correlation between the measured redox potential and the typical geometrical arrangement of the copper(II) complex could be established. Negative values have been obtained for copper(II) complexes in tetragonally elongated pseudo-octahedral geometries, when measured against Ag/AgCl reference electrode. Copper(II) complexes in tetrahedral environments (or flattened tetrahedral geometries) show positive redox potential values. There is a region, always in the field of negative redox potentials which groups the copper(II) complexes exhibiting square-based pyramidal arrangements. Therefore, it is suggested that a measurement of the formal redox potential could be of great help, when some ambiguities might appear in the interpretation of spectroscopic (EPR and UV-Vis) data. Unfortunately, when the comparison is made between copper(II) complexes in square-based pyramidal geometries and those in square planar environments (or a pseudo-octahedral) a little perturbed by an equatorial tetrahedral distortion, their redox potentials could fall in the same intermediate region. In this case spectroscopic data have to be handled with great care in order to have an answer about a copper complex geometrical characteristics. © 2013.

Theoretical investigation of HNgNH{sub 3}{sup +} ions (Ng = He, Ne, Ar, Kr, and Xe)

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

Gao, Kunqi; Sheng, Li, E-mail: shengli@hit.edu.cn

2015-04-14

The equilibrium geometries, harmonic frequencies, and dissociation energies of HNgNH{sub 3}{sup +} ions (Ng = He, Ne, Ar, Kr, and Xe) were investigated using the following method: Becke-3-parameter-Lee-Yang-Parr (B3LYP), Boese-Matrin for Kinetics (BMK), second-order Møller-Plesset perturbation theory (MP2), and coupled-cluster with single and double excitations as well as perturbative inclusion of triples (CCSD(T)). The results indicate that HHeNH{sub 3}{sup +}, HArNH{sub 3}{sup +}, HKrNH{sub 3}{sup +}, and HXeNH{sub 3}{sup +} ions are metastable species that are protected from decomposition by high energy barriers, whereas the HNeNH{sub 3}{sup +} ion is unstable because of its relatively small energy barrier for decomposition.more » The bonding nature of noble-gas atoms in HNgNH{sub 3}{sup +} was also analyzed using the atoms in molecules approach, natural energy decomposition analysis, and natural bond orbital analysis.« less

Shape resonances of Be- and Mg- investigated with the method of analytic continuation

NASA Astrophysics Data System (ADS)

Čurík, Roman; Paidarová, I.; Horáček, J.

2018-05-01

The regularized method of analytic continuation is used to study the low-energy negative-ion states of beryllium (configuration 2 s2ɛ p 2P ) and magnesium (configuration 3 s2ɛ p 2P ) atoms. The method applies an additional perturbation potential and requires only routine bound-state multi-electron quantum calculations. Such computations are accessible by most of the free or commercial quantum chemistry software available for atoms and molecules. The perturbation potential is implemented as a spherical Gaussian function with a fixed width. Stability of the analytic continuation technique with respect to the width and with respect to the input range of electron affinities is studied in detail. The computed resonance parameters Er=0.282 eV, Γ =0.316 eV for the 2 p state of Be- and Er=0.188 eV, Γ =0.167 for the 3 p state of Mg- agree well with the best results obtained by much more elaborate and computationally demanding present-day methods.

A variation-perturbation method for atomic and molecular interactions. I - Theory. II - The interaction potential and van der Waals molecule for Ne-HF

NASA Astrophysics Data System (ADS)

Gallup, G. A.; Gerratt, J.

1985-09-01

The van der Waals energy between the two parts of a system is a very small fraction of the total electronic energy. In such cases, calculations have been based on perturbation theory. However, such an approach involves certain difficulties. For this reason, van der Waals energies have also been directly calculated from total energies. But such a method has definite limitations as to the size of systems which can be treated, and recently ab initio calculations have been combined with damped semiempirical long-range dispersion potentials to treat larger systems. In this procedure, large basis set superposition errors occur, which must be removed by the counterpoise method. The present investigation is concerned with an approach which is intermediate between the previously considered procedures. The first step in the new approach involves a variational calculation based upon valence bond functions. The procedure includes also the optimization of excited orbitals, and an approximation of atomic integrals and Hamiltonian matrix elements.

Collisional perturbation of radio-frequency E1 transitions in an atomic beam of dysprosium

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

Cingoez, A.; Lapierre, Alain; Nguyen, A.-T.

2005-12-15

We have studied collisional perturbations of radio-frequency (rf) electric-dipole (E1) transitions between the nearly degenerate opposite-parity levels in atomic dysprosium (Dy) in the presence of 10 to 80 {mu}Torr of H{sub 2}, N{sub 2}, He, Ar, Ne, Kr, and Xe. Collisional broadening and shift of the resonance, as well as the attenuation of the signal amplitude are observed to be proportional to the foreign-gas density with the exception of H{sub 2} and Ne, for which no shifts were observed. Corresponding rates and cross sections are presented. In addition, rates and cross sections for O{sub 2} are extracted from measurements usingmore » air as foreign gas. The primary motivation for this study is the need for accurate determination of the shift rates, which are needed in a laboratory search for the temporal variation of the fine-structure constant [A. T. Nguyen, D. Budker, S. K. Lamoreaux, and J. R. Torgerson, Phys. Rev. A 69, 22105 (2004)].« less

First order perturbations of the Einstein-Straus and Oppenheimer-Snyder models

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

Mars, Marc; Mena, Filipe C.; Vera, Rauel

We derive the linearly perturbed matching conditions between a Schwarzschild spacetime region with stationary and axially symmetric perturbations and a Friedmann-Lemaitre-Robertson-Walker (FLRW) spacetime with arbitrary perturbations. The matching hypersurface is also perturbed arbitrarily and, in all cases, the perturbations are decomposed into scalars using the Hodge operator on the sphere. This allows us to write down the matching conditions in a compact way. In particular, we find that the existence of a perturbed (rotating, stationary, and vacuum) Schwarzschild cavity in a perturbed FLRW universe forces the cosmological perturbations to satisfy constraints that link rotational and gravitational wave perturbations. We alsomore » prove that if the perturbation on the FLRW side vanishes identically, then the vacuole must be perturbatively static and hence Schwarzschild. By the dual nature of the problem, the first result translates into links between rotational and gravitational wave perturbations on a perturbed Oppenheimer-Snyder model, where the perturbed FLRW dust collapses in a perturbed Schwarzschild environment which rotates in equilibrium. The second result implies, in particular, that no region described by FLRW can be a source of the Kerr metric.« less

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

Geltman, S.

Recent measurements on CO{sub 2}-laser-assisted electron-atom collisions have shown large inconsistencies with the Kroll-Watson formula for small-angle scattering. We have carried out a detailed study to compare the predictions of Kroll-Watson theory (for both single and multimode fields) with those of conventional perturbation theory for stimulated free-free transitions. It is found that for {ital E}{sub 0}/2{omega}{sup 2}{lt}1, where perturbation theory is valid, there are large differences with the Kroll-Watson theory. Comparisons of experimental variations with respect to scattering angle and electron energy show much better agreement with perturbation theory than with Kroll-Watson theory. A study of the angular variations inmore » perturbation theory shows that use of the {open_quote}{open_quote}outgoing{close_quote}{close_quote} wave final state gives much better agreement with experiment than does the {open_quote}{open_quote}ingoing{close_quote}{close_quote} wave final state, which is different from the choice made in early bremsstrahlung theory. {copyright} {ital 1996 The American Physical Society.}« less

Analytic energy derivatives for the calculation of the first-order molecular properties using the domain-based local pair-natural orbital coupled-cluster theory

NASA Astrophysics Data System (ADS)

Datta, Dipayan; Kossmann, Simone; Neese, Frank

2016-09-01

The domain-based local pair-natural orbital coupled-cluster (DLPNO-CC) theory has recently emerged as an efficient and powerful quantum-chemical method for the calculation of energies of molecules comprised of several hundred atoms. It has been demonstrated that the DLPNO-CC approach attains the accuracy of a standard canonical coupled-cluster calculation to about 99.9% of the basis set correlation energy while realizing linear scaling of the computational cost with respect to system size. This is achieved by combining (a) localized occupied orbitals, (b) large virtual orbital correlation domains spanned by the projected atomic orbitals (PAOs), and (c) compaction of the virtual space through a truncated pair natural orbital (PNO) basis. In this paper, we report on the implementation of an analytic scheme for the calculation of the first derivatives of the DLPNO-CC energy for basis set independent perturbations within the singles and doubles approximation (DLPNO-CCSD) for closed-shell molecules. Perturbation-independent one-particle density matrices have been implemented in order to account for the response of the CC wave function to the external perturbation. Orbital-relaxation effects due to external perturbation are not taken into account in the current implementation. We investigate in detail the dependence of the computed first-order electrical properties (e.g., dipole moment) on the three major truncation parameters used in a DLPNO-CC calculation, namely, the natural orbital occupation number cutoff used for the construction of the PNOs, the weak electron-pair cutoff, and the domain size cutoff. No additional truncation parameter has been introduced for property calculation. We present benchmark calculations on dipole moments for a set of 10 molecules consisting of 20-40 atoms. We demonstrate that 98%-99% accuracy relative to the canonical CCSD results can be consistently achieved in these calculations. However, this comes with the price of tightening the threshold for the natural orbital occupation number cutoff by an order of magnitude compared to the DLPNO-CCSD energy calculations.

How predictive could alchemical derivatives be?

PubMed

Muñoz, Macarena; Cárdenas, Carlos

2017-06-21

The chemical space contains all possible compounds that can be imagined. Its size easily equals the number of fundamental particles in the observable universe. Rational design of compounds aims to find those sectors of the chemical space where compounds optimize a set of desired properties. Then, rational design demands tools to efficiently navigate the chemical space. Ab initio alchemical derivatives offer the possibility to navigate, without empiricism, the energy landscape through alchemical transformations. An alchemical transformation is any process, physical or fictitious, that connects to points in the chemical space. In this work, those transformations are constructed as a perturbative expansion of the energy with respect to perturbations in the stoichiometry. The response functions of that expansion are what is called alchemical derivatives. In this work we assess how effective alchemical derivatives are in predicting energy changes associated to changes in the composition. We do this by including in the expansion, for the first time, electrostatic, polarization and electron-transfer effects. The system we chose is one that challenges alchemical derivatives because none of these effects dominates its behavior. The transmutations studied here correspond to substitutional doping of Al 13 with up to four atoms of Si, Al 13-n Si n . Two types of transformations are considered, those in which the number of electrons remains constant and those in which the number of electrons also changes. It is found that contrary to what has been reported before, polarization cannot be neglected. If polarization is not included, alchemical derivatives fail to predict the change of energy and the relative energy between isomers. For isoelectronic substitution of four or more atoms, the perturbative approach collapses because the strength of the perturbation becomes too strong to guarantee convergence of the series. It is shown, however, that if only one atom is mutated at a time, alchemical derivatives rank pretty well the isomers of Al 13-n Si n according to their energy. In the case of non-isoelectronic transformations, it is observed that the series rapidly diverges with increasing number of electrons. In this situation, it becomes more important to keep the degree of transmutation of the parent system small.

The Dalgarno-Lewis summation technique: Some comments and examples

NASA Astrophysics Data System (ADS)

Mavromatis, Harry A.

1991-08-01

The Dalgarno-Lewis technique [A. Dalgarno and J. T. Lewis, ``The exact calculation of long-range forces between atoms by perturbation theory,'' Proc. R. Soc. London Ser. A 233, 70-74 (1955)] provides an elegant method to obtain exact results for various orders in perturbation theory, while avoiding the infinite sums which arise in each order. In the present paper this technique, which perhaps has not been exploited as much as it could be, is first reviewed with attention to some of its not-so-straightforward details, and then six examples of the method are given using three different one-dimensional bases.

Mechanisms of dust grain charging in plasma with allowance for electron emission processes

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

Mol’kov, S. I.; Savin, V. N., E-mail: moped@onego.ru

2017-02-15

The process of dust grain charging is described with allowance for secondary, ion-induced, photoelectric, and thermal electron emission from the grain surface. The roughness of the grain surface is taken into account. An intermediate charging regime involving ion–atom collisions and electron ionization in the perturbed plasma region is analyzed using the moment equations and Poisson’s equation. A calculation method is proposed that allows one to take into account the influence of all the above effects and determine the radius of the plasma region perturbed by the dust grain.

Topological bound states of a quantum walk with cold atoms

NASA Astrophysics Data System (ADS)

Mugel, Samuel; Celi, Alessio; Massignan, Pietro; Asbóth, János K.; Lewenstein, Maciej; Lobo, Carlos

2016-08-01

We suggest a method for engineering a quantum walk, with cold atoms as walkers, which presents topologically nontrivial properties. We derive the phase diagram, and show that we are able to produce a boundary between topologically distinct phases using the finite beam width of the applied lasers. A topologically protected bound state can then be observed, which is pinned to the interface and is robust to perturbations. We show that it is possible to identify this bound state by averaging over spin sensitive measures of the atom's position, based on the spin distribution that these states display. Interestingly, there exists a parameter regime in which our system maps on to the Creutz ladder.

Oxidation kinetics and soot formation

NASA Technical Reports Server (NTRS)

Glassman, I.; Brezinsky, K.

1983-01-01

The research objective is to clarify the role of aromaticity in the soot nucleation process by determining the relative importance of phenyl radical/molecular oxygen and benzene/atomic oxygen reactions in the complex combustion of aromatic compounds. Three sets of chemical flow reactor experiments have been designed to determine the relative importance of the phenyl radical/molecular oxygen and benzene/atomic oxygen reactions. The essential elements of these experiments are 1) the use of cresols and anisole formed during the high temperature oxidation of toluene as chemical reaction indicators; 2) the in situ photolysis of molecular oxygen to provide an oxygen atom perturbation in the reacting aromatic system; and 3) the high temperature pyrolysis of phenol, the cresols and possibly anisole.

Selection rule engineering of forbidden transitions of a hydrogen atom near a nanogap

NASA Astrophysics Data System (ADS)

Kim, Hyunyoung Y.; Kim, Daisik S.

2018-01-01

We perform an analytical study on the allowance of forbidden transitions for a hydrogen atom placed near line dipole sources, mimicking light emanating from a one-dimensional metallic nanogap. It is shown that the rapid variation of the electric field vector, inevitable in the near zone, completely breaks the selection rule of Δl=±1. While the forbidden transitions between spherically symmetric S states, such as 2S to 1S or 3S to 1S (Δl=0), are rather robust against selection rule breakage, Δl=±2 transitions such as between 3D and 1S or 3D and 2S states are very vulnerable to the spatial variation of the perturbing electric field. Transitions between 2S and 3D states are enhanced by many orders of magnitude, aided by the quadratic nature of both the perturbing Hamiltonian and D wavefunctions. The forbidden dipole moment, which approaches one Bohr radius times the electric charge in the vicinity of the gap, can be written in a simple closed form owing to the one-dimensional nature of our gap. With large enough effective volume together with the symmetric nature of the excited state wavefunctions, our work paves way towards atomic physics application of infinitely long nanogaps.

Theoretical Study of Energy Levels and Transition Probabilities of Boron Atom

NASA Astrophysics Data System (ADS)

Tian Yi, Zhang; Neng Wu, Zheng

2009-08-01

Full Text PDF Though the electrons configuration for boron atom is simple and boron atom has long been of interest for many researchers, the theoretical studies for properties of BI are not systematic, there are only few results reported on energy levels of high excited states of boron, and transition measurements are generally restricted to transitions involving ground states and low excited states without considering fine structure effects, provided only multiplet results, values for transitions between high excited states are seldom performed. In this article, by using the scheme of the weakest bound electron potential model theory calculations for energy levels of five series are performed and with the same method we give the transition probabilities between excited states with considering fine structure effects. The comprehensive set of calculations attempted in this paper could be of some value to workers in the field because of the lack of published calculations for the BI systems. The perturbations coming from foreign perturbers are taken into account in studying the energy levels. Good agreement between our results and the accepted values taken from NIST has been obtained. We also reported some values of energy levels and transition probabilities not existing on the NIST data bases.

Atomic force microscopy for two-dimensional materials: A tutorial review

NASA Astrophysics Data System (ADS)

Zhang, Hang; Huang, Junxiang; Wang, Yongwei; Liu, Rui; Huai, Xiulan; Jiang, Jingjing; Anfuso, Chantelle

2018-01-01

Low dimensional materials exhibit distinct properties compared to their bulk counterparts. A plethora of examples have been demonstrated in two-dimensional (2-D) materials, including graphene and transition metal dichalcogenides (TMDCs). These novel and intriguing properties at the nano-, molecular- and even monatomic scales have triggered tremendous interest and research, from fundamental studies to practical applications and even device fabrication. The unique behaviors of 2-D materials result from the special structure-property relationships that exist between surface topographical variations and mechanical responses, electronic structures, optical characteristics, and electrochemical properties. These relationships are generally convoluted and sensitive to ambient and external perturbations. Characterizing these systems thus requires techniques capable of providing multidimensional information under controlled environments, such as atomic force microscopy (AFM). Today, AFM plays a key role in exploring the basic principles underlying the functionality of 2-D materials. In this tutorial review, we provide a brief introduction to some of the unique properties of 2-D materials, followed by a summary of the basic principles of AFM and the various AFM modes most appropriate for studying these systems. Following that, we will focus on five important properties of 2-D materials and their characterization in more detail, including recent literature examples. These properties include nanomechanics, nanoelectromechanics, nanoelectrics, nanospectroscopy, and nanoelectrochemistry.

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

Santos, O. L.; Fonseca, T. L., E-mail: tertius@ufg.br; Sabino, J. R.

We present theoretical results for the dipole moment, linear polarizability, and first hyperpolarizability of the urea and thiourea molecules in solid phase. The in-crystal electric properties were determined by applying a supermolecule approach in combination with an iterative electrostatic scheme, in which the surrounding molecules are represented by point charges. It is found for both urea and thiourea molecules that the influence of the polarization effects is mild for the linear polarizability, but it is marked for the dipole moment and first hyperpolarizability. The replacement of oxygen atoms by sulfur atoms increases, in general, the electric responses. Our second-order Møller–Plessetmore » perturbation theory based iterative scheme predicts for the in-crystal dipole moment of urea and thiourea the values of 7.54 and 9.19 D which are, respectively, increased by 61% and 58%, in comparison with the corresponding isolated values. The result for urea is in agreement with the available experimental result of 6.56 D. In addition, we present an estimate of macroscopic quantities considering explicit unit cells of urea and thiourea crystals including environment polarization effects. These supermolecule calculations take into account partially the exchange and dispersion effects. The results illustrate the role played by the electrostatic interactions on the static second-order nonlinear susceptibility of the urea crystal.« less

Flexibility of the Cu,Zn superoxide dismutase structure investigated at 0.57 GPa.

PubMed

Ascone, Isabella; Savino, Carmelinda; Kahn, Richard; Fourme, Roger

2010-06-01

The 2 A resolution crystal structure of bovine erythrocyte Cu,Zn superoxide dismutase (CuZnSOD) has been determined by X-ray diffraction at high pressure (0.57 GPa) and room temperature. At 0.57 GPa the secondary, tertiary and quaternary structures are similar to other previously determined bovine erythrocyte CuZnSOD structures. Nevertheless, pressure has a localized impact on the atomic coordinates of C(alpha) atoms and on side chains. The compression of the crystal and of the protein backbone is anisotropic. This anisotropy is discussed, taking into account intermolecular contacts and protein conformation. Pressure perturbation highlights the more flexible zones in the protein such as the electrostatic loop. At 0.57 GPa, a global shift of the dimetallic sites in both subunits and changes in the oxidation state of Cu were observed. The flexibility of the electrostatic loop may be useful for the interaction of different metal carriers in the copper-uptake process, whereas the flexibility of the metal sites involved in the activity of the protein could contribute to explaining the ubiquitous character of CuZnSODs, which are found in organisms living in very different conditions, including the deep-sea environment. This work illustrates the potential of combining X-ray crystallography with high pressure to promote and stabilize higher energy conformational substates.

The importance of the intensity and frequency of perturbations on the germination delay.

PubMed

Garmendia, Alfonso; Garmendia, Luis; Salvador, Adela

2008-01-01

An iterative model is developed to evaluate the reproductive strategies of plants in environments with different frequencies and intensities of disturbance. Two extreme reproductive strategies are compared: the "homocarpic" strategy, in which all the seeds germinate the following spring, without dormancy, and the "heterocarpic" strategy, whereby, each year, half of the existing seeds germinate. It is observed that this sort of heterocarpy is beneficial in environments with strong perturbations, in which a high percentage of the population dies. However, the frequency of such perturbations does not cause changes in the advantage of one strategy over the other. The results suggest that the intensity of the disturbance is much more important than the frequency.

Inhomogeneous atomic Bose-Fermi mixtures in cubic lattices.

PubMed

Cramer, M; Eisert, J; Illuminati, F

2004-11-05

We determine the ground state properties of inhomogeneous mixtures of bosons and fermions in cubic lattices and parabolic confining potentials. For finite hopping we determine the domain boundaries between Mott-insulator plateaux and hopping-dominated regions for lattices of arbitrary dimension within mean-field and perturbation theory. The results are compared with a new numerical method that is based on a Gutzwiller variational approach for the bosons and an exact treatment for the fermions. The findings can be applied as a guideline for future experiments with trapped atomic Bose-Fermi mixtures in optical lattices.

Traces of Lorentz symmetry breaking in a hydrogen atom at ground state

NASA Astrophysics Data System (ADS)

Borges, L. H. C.; Barone, F. A.

2016-02-01

Some traces of a specific Lorentz symmetry breaking scenario in the ground state of the hydrogen atom are investigated. We use standard Rayleigh-Schrödinger perturbation theory in order to obtain the corrections to the ground state energy and the wave function. It is shown that an induced four-pole moment arises, due to the Lorentz symmetry breaking. The model considered is the one studied in Borges et al. (Eur Phys J C 74:2937, 2014), where the Lorentz symmetry is broken in the electromagnetic sector.

Reconstructing the ideal results of a perturbed analog quantum simulator

NASA Astrophysics Data System (ADS)

Schwenk, Iris; Reiner, Jan-Michael; Zanker, Sebastian; Tian, Lin; Leppäkangas, Juha; Marthaler, Michael

2018-04-01

Well-controlled quantum systems can potentially be used as quantum simulators. However, a quantum simulator is inevitably perturbed by coupling to additional degrees of freedom. This constitutes a major roadblock to useful quantum simulations. So far there are only limited means to understand the effect of perturbation on the results of quantum simulation. Here we present a method which, in certain circumstances, allows for the reconstruction of the ideal result from measurements on a perturbed quantum simulator. We consider extracting the value of the correlator 〈Ôi(t ) Ôj(0 ) 〉 from the simulated system, where Ôi are the operators which couple the system to its environment. The ideal correlator can be straightforwardly reconstructed by using statistical knowledge of the environment, if any n -time correlator of operators Ôi of the ideal system can be written as products of two-time correlators. We give an approach to verify the validity of this assumption experimentally by additional measurements on the perturbed quantum simulator. The proposed method can allow for reliable quantum simulations with systems subjected to environmental noise without adding an overhead to the quantum system.

CI+MBPT calculations of Ar I energies, g factors, and transition line strengths

NASA Astrophysics Data System (ADS)

Savukov, I. M.

2018-03-01

Excited states of noble gas atoms present certain challenges to atomic theory for several reasons: first, relativistic effects are important and LS coupling is not optimal; second, energy intervals can be quite small, leading to strong mixing of states; third, many-body perturbation theory for hole states does not converge well. Previously, some attempts were made to solve this problem, using for example the all-order coupled-cluster approach and particle-hole configuration-interaction many-body perturbation theory (CI-MBPT) with modified denominators. However, while these approaches were promising, the accuracy was still limited. In this paper, we calculate Ar I energies, g factors, and transition amplitudes using ab initio CI-MBPT with eight valence electrons to avoid the problem of slow convergence of MBPT due to strong interaction between 3p and 3s states. We also included in CI many dominant states obtained by double excitations of the ground state configuration. Thus perturbation corrections were needed only for 1s, 2s, 2p core electrons non-included in valence-valence CI, which are quite small. We found that energy, g factors, and electric dipole matrix elements are in reasonable agreement with experiments. It is noteworthy that the theory agreed well with accurately measured g factors. Experimental oscillator strengths have large uncertainty, so in some cases we made a comparison with average values.

Atomic orbital-based SOS-MP2 with tensor hypercontraction. I. GPU-based tensor construction and exploiting sparsity

NASA Astrophysics Data System (ADS)

Song, Chenchen; Martínez, Todd J.

2016-05-01

We present a tensor hypercontracted (THC) scaled opposite spin second order Møller-Plesset perturbation theory (SOS-MP2) method. By using THC, we reduce the formal scaling of SOS-MP2 with respect to molecular size from quartic to cubic. We achieve further efficiency by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs) to accelerate integral construction and matrix multiplication. The practical scaling of GPU-accelerated atomic orbital-based THC-SOS-MP2 calculations is found to be N2.6 for reference data sets of water clusters and alanine polypeptides containing up to 1600 basis functions. The errors in correlation energy with respect to density-fitting-SOS-MP2 are less than 0.5 kcal/mol for all systems tested (up to 162 atoms).

Atomic orbital-based SOS-MP2 with tensor hypercontraction. I. GPU-based tensor construction and exploiting sparsity.

PubMed

Song, Chenchen; Martínez, Todd J

2016-05-07

We present a tensor hypercontracted (THC) scaled opposite spin second order Møller-Plesset perturbation theory (SOS-MP2) method. By using THC, we reduce the formal scaling of SOS-MP2 with respect to molecular size from quartic to cubic. We achieve further efficiency by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs) to accelerate integral construction and matrix multiplication. The practical scaling of GPU-accelerated atomic orbital-based THC-SOS-MP2 calculations is found to be N(2.6) for reference data sets of water clusters and alanine polypeptides containing up to 1600 basis functions. The errors in correlation energy with respect to density-fitting-SOS-MP2 are less than 0.5 kcal/mol for all systems tested (up to 162 atoms).

ProteinAC: a frequency domain technique for analyzing protein dynamics

NASA Astrophysics Data System (ADS)

Bozkurt Varolgunes, Yasemin; Demir, Alper

2018-03-01

It is widely believed that the interactions of proteins with ligands and other proteins are determined by their dynamic characteristics as opposed to only static, time-invariant processes. We propose a novel computational technique, called ProteinAC (PAC), that can be used to analyze small scale functional protein motions as well as interactions with ligands directly in the frequency domain. PAC was inspired by a frequency domain analysis technique that is widely used in electronic circuit design, and can be applied to both coarse-grained and all-atom models. It can be considered as a generalization of previously proposed static perturbation-response methods, where the frequency of the perturbation becomes the key. We discuss the precise relationship of PAC to static perturbation-response schemes. We show that the frequency of the perturbation may be an important factor in protein dynamics. Perturbations at different frequencies may result in completely different response behavior while magnitude and direction are kept constant. Furthermore, we introduce several novel frequency dependent metrics that can be computed via PAC in order to characterize response behavior. We present results for the ferric binding protein that demonstrate the potential utility of the proposed techniques.

Relativistic radiationless transitions in atoms

NASA Technical Reports Server (NTRS)

Huang, K.-N.

1978-01-01

The perturbing interaction appropriate for the Dirac-Fock formalism is used to formulate relativistic radiationless transitions. The transition rate between two jj-coupled many-electron configurations is expressed as a linear combination of radial integrals, suitable for numerical computation. The correlation and relaxation effects and the generalisation of the present work are discussed briefly.

Stability investigation of a high number density Pt1/Fe2O3 single-atom catalyst under different gas environments by HAADF-STEM

NASA Astrophysics Data System (ADS)

Duan, Sibin; Wang, Rongming; Liu, Jingyue

2018-05-01

Catalysis by supported single metal atoms has demonstrated tremendous potential for practical applications due to their unique catalytic properties. Unless they are strongly anchored to the support surfaces, supported single atoms, however, are thermodynamically unstable, which poses a major obstacle for broad applications of single-atom catalysts (SACs). In order to develop strategies to improve the stability of SACs, we need to understand the intrinsic nature of the sintering processes of supported single metal atoms, especially under various gas environments that are relevant to important catalytic reactions. We report on the synthesis of high number density Pt1/Fe2O3 SACs using a facial strong adsorption method and the study of the mobility of these supported Pt single atoms at 250 °C under various gas environments that are relevant to CO oxidation, water–gas shift, and hydrogenation reactions. Under the oxidative gas environment, Fe2O3 supported Pt single atoms are stable even at high temperatures. The presence of either CO or H2 molecules in the gas environment, however, facilitates the movement of the Pt atoms. The strong interaction between CO and Pt weakens the binding between the Pt atoms and the support, facilitating the movement of the Pt single atoms. The dissociation of H2 molecules on the Pt atoms and their subsequent interaction with the oxygen species of the support surfaces dislodge the surface oxygen anchored Pt atoms, resulting in the formation of Pt clusters. The addition of H2O molecules to the CO or H2 significantly accelerates the sintering of the Fe2O3 supported Pt single atoms. An anchoring-site determined sintering mechanism is further proposed, which is related to the metal–support interaction.

Stability investigation of a high number density Pt1/Fe2O3 single-atom catalyst under different gas environments by HAADF-STEM.

PubMed

Duan, Sibin; Wang, Rongming; Liu, Jingyue

2018-05-18

Catalysis by supported single metal atoms has demonstrated tremendous potential for practical applications due to their unique catalytic properties. Unless they are strongly anchored to the support surfaces, supported single atoms, however, are thermodynamically unstable, which poses a major obstacle for broad applications of single-atom catalysts (SACs). In order to develop strategies to improve the stability of SACs, we need to understand the intrinsic nature of the sintering processes of supported single metal atoms, especially under various gas environments that are relevant to important catalytic reactions. We report on the synthesis of high number density Pt 1 /Fe 2 O 3 SACs using a facial strong adsorption method and the study of the mobility of these supported Pt single atoms at 250 °C under various gas environments that are relevant to CO oxidation, water-gas shift, and hydrogenation reactions. Under the oxidative gas environment, Fe 2 O 3 supported Pt single atoms are stable even at high temperatures. The presence of either CO or H 2 molecules in the gas environment, however, facilitates the movement of the Pt atoms. The strong interaction between CO and Pt weakens the binding between the Pt atoms and the support, facilitating the movement of the Pt single atoms. The dissociation of H 2 molecules on the Pt atoms and their subsequent interaction with the oxygen species of the support surfaces dislodge the surface oxygen anchored Pt atoms, resulting in the formation of Pt clusters. The addition of H 2 O molecules to the CO or H 2 significantly accelerates the sintering of the Fe 2 O 3 supported Pt single atoms. An anchoring-site determined sintering mechanism is further proposed, which is related to the metal-support interaction.

An NMR Study of Microvoids in Polymers

NASA Technical Reports Server (NTRS)

Toy, James; Mattrix, Larry

1996-01-01

An understanding of polymer defect structures, like microvoids in polymeric matrices, is most crucial to their fabrication and application potential. In this project guest atoms are introduced into the microvoids in PMR-15 and NMR is used to determine microvoid sizes and locations. Xenon is a relatively inert probe that would normally not be found naturally in polymer or in NMR probe materials. There are two NMR active Xenon isotopes, Xe-129 and Xe-131. The Xe atom has a very high polarizability, which makes it sensitive to the intracrystalline environment of polymers. Interactions between the Xe atoms and the host matrix perturb and Xe electron cloud, deshielding the nuclei, and thereby expanding the range of the observed NMR chemical shifts. This chemical shift range which may be as large as 5000 ppm, permits subtle structural and chemical effects to be studied with high sensitivity. The Xe-129-NMR line shape has been found to vary in response to changes in the pore symmetry of the framework hosts in Zeolites and Clathrasil compounds. Before exposure to Xe gas, the PMR-15 samples were dried in a vacuum oven at 150 C for 48 hours. The samples were then exposed to Xe gas at 30 psi for 72 hours and sealed in glass tubes with 1 atmosphere of Xenon gas. Xenon gas at 1 atmosphere was used to tune up the spectrometer and to set up the appropriate NMR parameters. A series of spectra were obtained interspersed with applications of vacuum and heating to drive out the adsorbed Xe and determine the role of Xe-Xe interactions in the observed chemical shift.

Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program

NASA Astrophysics Data System (ADS)

Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A.

2017-12-01

In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program.

PubMed

Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A

2017-12-28

In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

Spray combustion under oscillatory pressure conditions

NASA Technical Reports Server (NTRS)

Jacobs, H. R.; Santoro, R. J.

1991-01-01

The performance and stability of liquid rocket engines is often argued to be significantly impacted by atomization and droplet vaporization processes. In particular, combustion instability phenomena may result from the interactions between the oscillating pressure field present in the rocket combustor and the fuel and oxidizer injection process. Few studies have been conducted to examine the effects of oscillating pressure fields on spray formation and its evolution under rocket engine conditions. The pressure study is intended to address the need for such studies. In particular, two potentially important phenomena are addressed in the present effort. The first involves the enhancement of the atomization process for a liquid jet subjected to an oscillating pressure field of known frequency and amplitude. The objective of this part of the study is to examine the coupling between the pressure field and or the resulting periodically perturbed velocity field on the breakup of the liquid jet. In particular, transverse mode oscillations are of interest since such modes are considered of primary importance in combustion instability phenomena. The second aspect of the project involves the effects of an oscillating pressure on droplet coagulation and secondary atomization. The objective of this study is to examine the conditions under which phenomena following the atomization process are affected by perturbations to the pressure or velocity fields. Both coagulation and represent a coupling mechanism between the pressure field and the energy release process in rocket combustors. It is precisely this coupling which drives combustion instability phenomena. Consequently, the present effort is intended to provide the fundamental insights needed to evaluate these processes as important mechanisms in liquid rocket instability phenomena.

Correlation study of sodium-atom chemisorption on the GaAs(110) surface

NASA Astrophysics Data System (ADS)

Song, K. M.; Khan, D. C.; Ray, A. K.

1994-01-01

Different possible adsorption sites of sodium atoms on a gallium arsenide surface have been investigated using ab initio self-consistent unrestricted Hartree-Fock total-energy cluster calculations with Hay-Wadt effective core potentials. The effects of electron correlation have been included by invoking the concepts of many-body perturbation theory and are found to be highly significant. We find that the Na-atom adsorption at a site modeled with an NaGa5As4H12 cluster is most favored energetically followed by Na adsorption at the site modeled with the NaGa4As5H12 cluster. The effects of charge transfer from Na to the GaAs surface as also possibilities of metallization are also analyzed and discussed.

Lattice dynamics calculations based on density-functional perturbation theory in real space

NASA Astrophysics Data System (ADS)

Shang, Honghui; Carbogno, Christian; Rinke, Patrick; Scheffler, Matthias

2017-06-01

A real-space formalism for density-functional perturbation theory (DFPT) is derived and applied for the computation of harmonic vibrational properties in molecules and solids. The practical implementation using numeric atom-centered orbitals as basis functions is demonstrated exemplarily for the all-electron Fritz Haber Institute ab initio molecular simulations (FHI-aims) package. The convergence of the calculations with respect to numerical parameters is carefully investigated and a systematic comparison with finite-difference approaches is performed both for finite (molecules) and extended (periodic) systems. Finally, the scaling tests and scalability tests on massively parallel computer systems demonstrate the computational efficiency.

Chiral dynamics with (non)strange quarks

NASA Astrophysics Data System (ADS)

Kubis, Bastian; Meißner, Ulf-G.

2017-01-01

We review the results and achievements of the project B.3. Topics addressed include pion photoproduction off the proton and off deuterium, three-flavor chiral perturbation theory studies, chiral symmetry tests in Goldstone boson decays, the development of unitarized chiral perturbation theory to next-to-leading order, the two-pole structure of the Λ(1405), the dynamical generation of the lowest S11 resonances, the theory of hadronic atoms and its application to various systems, precision studies in light-meson decays based on dispersion theory, the Roy-Steiner analysis of pion-nucleon scattering, a high-precision extraction of the elusive pion-nucleon σ-term, and aspects of chiral dynamics in few-nucleon systems.

Electronic structures of rutile (011)(2 × 1) surfaces: A many-body perturbation theory study.

PubMed

Liu, Guokui; Chen, Tingwei; Liu, Xiaobiao; Jin, Fan; Yuan, Shiling; Ma, Yuchen

2017-03-28

Using the GW method within many-body perturbation theory, we investigate the electronic properties of the rutile (011) surfaces with different reconstruction patterns. We find that keeping the Ti:O ratio on the reconstructedsurface to 1:2 enlarges the bandgap of the rutile (011) surface to ca. 4.0 eV. Increasing the content of O atoms in the surface can turn rutile into a semi-metal. For some surfaces, it is important to apply self-consistent GW calculation to get the correct charge distributions for the frontier orbitals, which are relevant to the photocatalytic behavior of TiO 2 .

Collisional transfer of population and orientation in NaK

NASA Astrophysics Data System (ADS)

Wolfe, C. M.; Ashman, S.; Bai, J.; Beser, B.; Ahmed, E. H.; Lyyra, A. M.; Huennekens, J.

2011-05-01

Collisional satellite lines with |ΔJ| ≤ 58 have been identified in recent polarization spectroscopy V-type optical-optical double resonance (OODR) excitation spectra of the Rb2 molecule [H. Salami et al., Phys. Rev. A 80, 022515 (2009)]. Observation of these satellite lines clearly requires a transfer of population from the rotational level directly excited by the pump laser to a neighboring level in a collision of the molecule with an atomic perturber. However to be observed in polarization spectroscopy, the collision must also partially preserve the angular momentum orientation, which is at least somewhat surprising given the extremely large values of ΔJ that were observed. In the present work, we used the two-step OODR fluorescence and polarization spectroscopy techniques to obtain quantitative information on the transfer of population and orientation in rotationally inelastic collisions of the NaK molecules prepared in the 2(A)1Σ+(v' = 16, J' = 30) rovibrational level with argon and potassium perturbers. A rate equation model was used to study the intensities of these satellite lines as a function of argon pressure and heat pipe oven temperature, in order to separate the collisional effects of argon and potassium atoms. Using a fit of this rate equation model to the data, we found that collisions of NaK molecules with potassium atoms are more likely to transfer population and destroy orientation than collisions with argon atoms. Collisions with argon atoms show a strong propensity for population transfer with ΔJ = even. Conversely, collisions with potassium atoms do not show this ΔJ = even propensity, but do show a propensity for ΔJ = positive compared to ΔJ = negative, for this particular initial state. The density matrix equations of motion have also been solved numerically in order to test the approximations used in the rate equation model and to calculate fluorescence and polarization spectroscopy line shapes. In addition, we have measured rate coefficients for broadening of NaK 31Π ← 2(A)1Σ+spectral lines due to collisions with argon and potassium atoms. Additional broadening, due to velocity changes occurring in rotationally inelastic collisions, has also been observed.

Collisional transfer of population and orientation in NaK.

PubMed

Wolfe, C M; Ashman, S; Bai, J; Beser, B; Ahmed, E H; Lyyra, A M; Huennekens, J

2011-05-07

Collisional satellite lines with |ΔJ| ≤ 58 have been identified in recent polarization spectroscopy V-type optical-optical double resonance (OODR) excitation spectra of the Rb(2) molecule [H. Salami et al., Phys. Rev. A 80, 022515 (2009)]. Observation of these satellite lines clearly requires a transfer of population from the rotational level directly excited by the pump laser to a neighboring level in a collision of the molecule with an atomic perturber. However to be observed in polarization spectroscopy, the collision must also partially preserve the angular momentum orientation, which is at least somewhat surprising given the extremely large values of ΔJ that were observed. In the present work, we used the two-step OODR fluorescence and polarization spectroscopy techniques to obtain quantitative information on the transfer of population and orientation in rotationally inelastic collisions of the NaK molecules prepared in the 2(A)(1)Σ(+)(v' = 16, J' = 30) rovibrational level with argon and potassium perturbers. A rate equation model was used to study the intensities of these satellite lines as a function of argon pressure and heat pipe oven temperature, in order to separate the collisional effects of argon and potassium atoms. Using a fit of this rate equation model to the data, we found that collisions of NaK molecules with potassium atoms are more likely to transfer population and destroy orientation than collisions with argon atoms. Collisions with argon atoms show a strong propensity for population transfer with ΔJ = even. Conversely, collisions with potassium atoms do not show this ΔJ = even propensity, but do show a propensity for ΔJ = positive compared to ΔJ = negative, for this particular initial state. The density matrix equations of motion have also been solved numerically in order to test the approximations used in the rate equation model and to calculate fluorescence and polarization spectroscopy line shapes. In addition, we have measured rate coefficients for broadening of NaK 3(1)Π ← 2(A)(1)Σ(+)spectral lines due to collisions with argon and potassium atoms. Additional broadening, due to velocity changes occurring in rotationally inelastic collisions, has also been observed.

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.

Testing general relativity and alternative theories of gravity with space-based atomic clocks and atom interferometers

NASA Astrophysics Data System (ADS)

Bondarescu, Ruxandra; Schärer, Andreas; Jetzer, Philippe; Angélil, Raymond; Saha, Prasenjit; Lundgren, Andrew

2015-05-01

The successful miniaturisation of extremely accurate atomic clocks and atom interferometers invites prospects for satellite missions to perform precision experiments. We discuss the effects predicted by general relativity and alternative theories of gravity that can be detected by a clock, which orbits the Earth. Our experiment relies on the precise tracking of the spacecraft using its observed tick-rate. The spacecraft's reconstructed four-dimensional trajectory will reveal the nature of gravitational perturbations in Earth's gravitational field, potentially differentiating between different theories of gravity. This mission can measure multiple relativistic effects all during the course of a single experiment, and constrain the Parametrized Post-Newtonian Parameters around the Earth. A satellite carrying a clock of fractional timing inaccuracy of Δ f / f ˜ 10-16 in an elliptic orbit around the Earth would constrain the PPN parameters |β - 1|, |γ - 1| ≲ 10-6. We also briefly review potential constraints by atom interferometers on scalar tensor theories and in particular on Chameleon and dilaton models.

An ab initio cluster study of the chemisorption of atomic cesium and hydrogen on reconstructed surfaces of gallium rich gallium arsenide

NASA Astrophysics Data System (ADS)

Schailey, Ronald

1999-11-01

Chemisorption properties of cesium and hydrogen atoms on the Ga-rich GaAs (100) (2 x 1), (2 x 2), and β(4 x 2) surfaces are investigated using ab initio self-consistent restricted open shell Hartree-Fock (ROHF) total energy calculations with Hay- Wadt effective core potentials. The effects of electron correlation have been included using many-body perturbation theory through second order, with the exception of β(4 x 2) symmetry due to computational limitations. The semiconductor surface is modeled by finite sized hydrogen saturated clusters. The effects of surface relaxation and reconstruction have been investigated in detail. Results are given for the energetics of chemisorption, charge population analysis, HOMO-LUMO gaps, and consequent possibilities of metallization for atomic cesium adsorption. For the chemisorption of atomic hydrogen, the experimentally verified mechanism of surface dimer bond breaking is investigated in detail.

Approaching the theoretical limit in periodic local MP2 calculations with atomic-orbital basis sets: the case of LiH.

PubMed

Usvyat, Denis; Civalleri, Bartolomeo; Maschio, Lorenzo; Dovesi, Roberto; Pisani, Cesare; Schütz, Martin

2011-06-07

The atomic orbital basis set limit is approached in periodic correlated calculations for solid LiH. The valence correlation energy is evaluated at the level of the local periodic second order Møller-Plesset perturbation theory (MP2), using basis sets of progressively increasing size, and also employing "bond"-centered basis functions in addition to the standard atom-centered ones. Extended basis sets, which contain linear dependencies, are processed only at the MP2 stage via a dual basis set scheme. The local approximation (domain) error has been consistently eliminated by expanding the orbital excitation domains. As a final result, it is demonstrated that the complete basis set limit can be reached for both HF and local MP2 periodic calculations, and a general scheme is outlined for the definition of high-quality atomic-orbital basis sets for solids. © 2011 American Institute of Physics

Theory of the stopping power of fast multicharged ions

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

Yudin, G.L.

1991-12-01

The processes of Coulomb excitation and ionization of atoms by a fast charged particle moving along a classical trajectory are studied. The target electrons are described by the Dirac equation, while the field of the incident particle is described by the Lienard-Wiechert potential. The theory is formulated in the form most convenient for investigation of various characteristics of semiclassical atomic collisions. The theory of sudden perturbations, which is valid at high enough velocities for a high projectile charge, is employed to obtain probabilities and cross sections of the Coulomb excitation and ionization of atomic hydrogen by fast multiply charged ions.more » Based on the semiclassical sudden Born approximation, the ionization cross section and the average electronic energy loss of a fast ion in a single collision with an atom are investigated over a wide specific energy range from 500 keV/amu to 50 MeV/amu.« less

Atomic orbital-based SOS-MP2 with tensor hypercontraction. I. GPU-based tensor construction and exploiting sparsity

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

Song, Chenchen; Martínez, Todd J.; SLAC National Accelerator Laboratory, Menlo Park, California 94025

We present a tensor hypercontracted (THC) scaled opposite spin second order Møller-Plesset perturbation theory (SOS-MP2) method. By using THC, we reduce the formal scaling of SOS-MP2 with respect to molecular size from quartic to cubic. We achieve further efficiency by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs) to accelerate integral construction and matrix multiplication. The practical scaling of GPU-accelerated atomic orbital-based THC-SOS-MP2 calculations is found to be N{sup 2.6} for reference data sets of water clusters and alanine polypeptides containing up to 1600 basis functions. The errors in correlation energy with respect to density-fitting-SOS-MP2 aremore » less than 0.5 kcal/mol for all systems tested (up to 162 atoms).« less

Energy gap states and tunneling currents in semiconducting graphene

NASA Astrophysics Data System (ADS)

Szczesniak, Dominik; Hoehn, Ross; Kais, Sabre

It has been predicted that when graphene is supported on a substrate or doped with foreign atom species, the inherent linear electronic dispersion of its pristine form can be strongly altered. Worthy of special attention is the situation when the interactions between graphene and the substrate or dopants lead to an opening of the finite electronic gap in the fermionic spectrum of this nano-material, and strongly influence its transport and optical properties. Herein, the fundamental electronic transport properties of such perturbed graphene are discussed in the framework of the complex band structure analysis, which not only accounts for the propagating but also the evanescent electronic states. Various scenarios responsible for the band gap opening and manipulation of its characteristics are considered, these considerations may entirely account for the aforementioned perturbations to the pristine graphene. It is shown, that the these perturbations are responsible for inducing gap states which allow electrons to directly tunnel between the conduction and valence bands in perturbed graphene. The resulting tunneling states are analyzed in a comprehensive manner, suggesting their great importance for the transport processes across graphene-based semiconducting nanostructures.

Effect of the nonlocal exchange on the performance of the orbital-dependent correlation functionals from second-order perturbation theory.

PubMed

Schweigert, Igor V; Bartlett, Rodney J

2008-09-28

Adding a fraction of the nonlocal exchange operator to the local orbital-dependent exchange potential improves the many-body perturbation expansion based on the Kohn-Sham determinant. The effect of such a hybrid scheme on the performance of the orbital-dependent correlation functional from the second-order perturbation theory (PT2H) is investigated numerically. A small fraction of the nonlocal exchange is often sufficient to ensure the existence of the self-consistent solution for the PT2H potential. In the He and Be atoms, including 37% of the nonlocal exchange leads to the correlation energies and electronic densities that are very close to the exact ones. In molecules, varying the fraction of the nonlocal exchange may result in the PT2H energy closely reproducing the CCSD(T) value; however such a fraction depends on the system and does not always result in an accurate electronic density. We also numerically verify that the "semicanonical" perturbation series includes most of the beneficial effects of the nonlocal exchange without sacrificing the locality of the exchange potential.

Laser-assisted coplanar symmetric (e, 2e) triple differential cross sections

NASA Astrophysics Data System (ADS)

Khalil, D.; Tlidi, M.; Makhoute, A.; Ajana, I.

2017-04-01

The modification due to an external linearly polarized monochromatic laser field on the dynamics of the ionization process of an atomic hydrogen by electron-impact is studied theoretically for a coplanar symmetric geometry. The interaction of the laser field with the unbound electrons is treated in a non-perturbative way. The wave functions of the ingoing and outgoing electrons in the laser field are treated as non-relativistic Volkov waves, while the interaction of the bound electron with the laser field is treated by using first-order perturbation theory, assuming that the electric field strength associated with the external laser field is much less than the atomic unit e/{a}2=5× {10}9 {{V}} {{{cm}}}-1. The influence of the laser parameters on the angular distribution is analyzed and several illustrative examples are discussed. Significant changes are noted both in the shape and magnitude of the triple differential cross sections (TDCS) by the application of the laser field. Numerical results show that the TDCS are strongly dependent on the dressing of the projectile by the laser field at low frequency in (e, 2e) spectroscopy region.

molgw 1: Many-body perturbation theory software for atoms, molecules, and clusters

DOE PAGES

Bruneval, Fabien; Rangel, Tonatiuh; Hamed, Samia M.; ...

2016-07-12

Here, we summarize the MOLGW code that implements density-functional theory and many-body perturbation theory in a Gaussian basis set. The code is dedicated to the calculation of the many-body self-energy within the GW approximation and the solution of the Bethe–Salpeter equation. These two types of calculations allow the user to evaluate physical quantities that can be compared to spectroscopic experiments. Quasiparticle energies, obtained through the calculation of the GW self-energy, can be compared to photoemission or transport experiments, and neutral excitation energies and oscillator strengths, obtained via solution of the Bethe–Salpeter equation, are measurable by optical absorption. The implementation choicesmore » outlined here have aimed at the accuracy and robustness of calculated quantities with respect to measurements. Furthermore, the algorithms implemented in MOLGW allow users to consider molecules or clusters containing up to 100 atoms with rather accurate basis sets, and to choose whether or not to apply the resolution-of-the-identity approximation. Finally, we demonstrate the parallelization efficacy of the MOLGW code over several hundreds of processors.« less

Linear-scaling method for calculating nuclear magnetic resonance chemical shifts using gauge-including atomic orbitals within Hartree-Fock and density-functional theory.

PubMed

Kussmann, Jörg; Ochsenfeld, Christian

2007-08-07

Details of a new density matrix-based formulation for calculating nuclear magnetic resonance chemical shifts at both Hartree-Fock and density functional theory levels are presented. For systems with a nonvanishing highest occupied molecular orbital-lowest unoccupied molecular orbital gap, the method allows us to reduce the asymptotic scaling order of the computational effort from cubic to linear, so that molecular systems with 1000 and more atoms can be tackled with today's computers. The key feature is a reformulation of the coupled-perturbed self-consistent field (CPSCF) theory in terms of the one-particle density matrix (D-CPSCF), which avoids entirely the use of canonical MOs. By means of a direct solution for the required perturbed density matrices and the adaptation of linear-scaling integral contraction schemes, the overall scaling of the computational effort is reduced to linear. A particular focus of our formulation is to ensure numerical stability when sparse-algebra routines are used to obtain an overall linear-scaling behavior.

Trapping ultracold gases near cryogenic materials with rapid reconfigurability

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

Naides, Matthew A.; Turner, Richard W.; Lai, Ruby A.

We demonstrate an atom chip trapping system that allows the placement and high-resolution imaging of ultracold atoms within microns from any ≲100 μm-thin, UHV-compatible material, while also allowing sample exchange with minimal experimental downtime. The sample is not connected to the atom chip, allowing rapid exchange without perturbing the atom chip or laser cooling apparatus. Exchange of the sample and retrapping of atoms has been performed within a week turnaround, limited only by chamber baking. Moreover, the decoupling of sample and atom chip provides the ability to independently tune the sample temperature and its position with respect to the trapped ultracoldmore » gas, which itself may remain in the focus of a high-resolution imaging system. As a first demonstration of this system, we have confined a 700-nK cloud of 8 × 10{sup 4} {sup 87}Rb atoms within 100 μm of a gold-mirrored 100-μm-thick silicon substrate. The substrate was cooled to 35 K without use of a heat shield, while the atom chip, 120 μm away, remained at room temperature. Atoms may be imaged and retrapped every 16 s, allowing rapid data collection.« less

Intensities of K-X-ray satellite and hypersatellite target radiation in Bi83+-Xe @70 MeV/u collisions

NASA Astrophysics Data System (ADS)

Kozhedub, Y. S.; Bondarev, A. I.; Cai, X.; Gumberidze, A.; Hagmann, S.; Kozhuharov, C.; Maltsev, I. A.; Plunien, G.; Shabaev, V. M.; Shao, C.; Stöhlker, Th.; Tupitsyn, I. I.; Yang, B.; Yu, D.

2017-10-01

Non-perturbative calculations of the relativistic quantum dynamics of electrons in the Bi83+-Xe collisions at 70 AMeV are performed. A method of calculation employs an independent particle model with effective single-electron Dirac-Kohn-Sham operator. Solving of the single-electron equations is based on the coupled-channel approach with atomic-like Dirac-Sturm-Fock orbitals, localized at the ions (atoms). Special attention is paid to the inner-shell processes. Intensities of the K satellite and hypersatellite target radiation are evaluated. The role of the relativistic effects is studied.

Optical nonlinearities of excitonic states in atomically thin 2D transition metal dichalcogenides

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

Soh, Daniel Beom Soo

We calculated the optical nonlinearities of the atomically thin monolayer transition metal dichalcogenide material (particularly MoS 2), particularly for those linear and nonlinear transition processes that utilize the bound exciton states. We adopted the bound and the unbound exciton states as the basis for the Hilbert space, and derived all the dynamical density matrices that provides the induced current density, from which the nonlinear susceptibilities can be drawn order-by-order via perturbative calculations. We provide the nonlinear susceptibilities for the linear, the second-harmonic, the third-harmonic, and the kerr-type two-photon processes.

Incipient plasticity and indentation response of MgO surfaces using molecular dynamics

NASA Astrophysics Data System (ADS)

Tran, Anh-Son; Hong, Zheng-Han; Chen, Ming-Yuan; Fang, Te-Hua

2018-05-01

The mechanical characteristics of magnesium oxide (MgO) based on nanoindentation are studied using molecular dynamics (MD) simulation. The effects of indenting speed and temperature on the structural deformation and loading-unloading curve are investigated. Results show that the strained surface of the MgO expands to produce a greater relaxation of atoms in the surroundings of the indent. The dislocation propagation and pile-up for MgO occur more significantly with the increasing temperature from 300 K to 973 K. In addition, with increasing temperature, the high strained atoms with a great perturbation appearing at the groove location.

How to Connect Cardiac Excitation to the Atomic Interactions of Ion Channels.

PubMed

Silva, Jonathan R

2018-01-23

Many have worked to create cardiac action potential models that explicitly represent atomic-level details of ion channel structure. Such models have the potential to define new therapeutic directions and to show how nanoscale perturbations to channel function predispose patients to deadly cardiac arrhythmia. However, there have been significant experimental and theoretical barriers that have limited model usefulness. Recently, many of these barriers have come down, suggesting that considerable progress toward creating these long-sought models may be possible in the near term. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Low Earth orbit atomic oxygen simulation for durability evaluation of solar reflector surfaces

NASA Technical Reports Server (NTRS)

Degroh, Kim K.; Banks, Bruce A.

1992-01-01

To evaluate the performance and durability of solar reflector surfaces in the atomic oxygen environment typical of low Earth orbit (LEO), one must expose the reflector surface either directly to LEO or to ground-laboratory atomic oxygen environments. Although actual LEO exposures are most desired, such opportunities are typically scarce, expensive, and of limited duration. As a result, ground-laboratory exposures must be relied upon as the most practical long-term durability evaluation technique. Plasma ashers are widely used as LEO simulation facilities by producing atomic oxygen environments for durability evaluation of potential spacecraft materials. Atomic oxygen arrival differs between ground and space exposure in that plasma asher exposure produces isotropic arrival and space solar tracking produces sweeping arrival. Differences in initial impact reaction probability occur, dependent upon the energy and species existing in these environments. Due to the variations in ground-laboratory and space atomic oxygen, quantification of in-space performance based on plasma asher testing is not straightforward. The various atomic oxygen interactions that can occur with reflector surfaces, such as undercutting in organic substrates at protective coating defect sites, ground-laboratory techniques recommended for evaluating the atomic oxygen durability of reflectors based on asher exposures, and computational techniques which make use of ground-laboratory atomic oxygen exposure to predict in-space LEO durability are addressed.

High viscosity environments: an unexpected route to obtain true atomic resolution with atomic force microscopy.

PubMed

Weber, Stefan A L; Kilpatrick, Jason I; Brosnan, Timothy M; Jarvis, Suzanne P; Rodriguez, Brian J

2014-05-02

Atomic force microscopy (AFM) is widely used in liquid environments, where true atomic resolution at the solid-liquid interface can now be routinely achieved. It is generally expected that AFM operation in more viscous environments results in an increased noise contribution from the thermal motion of the cantilever, thereby reducing the signal-to-noise ratio (SNR). Thus, viscous fluids such as ionic and organic liquids have been generally avoided for high-resolution AFM studies despite their relevance to, e.g. energy applications. Here, we investigate the thermal noise limitations of dynamic AFM operation in both low and high viscosity environments theoretically, deriving expressions for the amplitude, phase and frequency noise resulting from the thermal motion of the cantilever, thereby defining the performance limits of amplitude modulation, phase modulation and frequency modulation AFM. We show that the assumption of a reduced SNR in viscous environments is not inherent to the technique and demonstrate that SNR values comparable to ultra-high vacuum systems can be obtained in high viscosity environments under certain conditions. Finally, we have obtained true atomic resolution images of highly ordered pyrolytic graphite and mica surfaces, thus revealing the potential of high-resolution imaging in high viscosity environments.

High viscosity environments: an unexpected route to obtain true atomic resolution with atomic force microscopy

NASA Astrophysics Data System (ADS)

Weber, Stefan A. L.; Kilpatrick, Jason I.; Brosnan, Timothy M.; Jarvis, Suzanne P.; Rodriguez, Brian J.

2014-05-01

Atomic force microscopy (AFM) is widely used in liquid environments, where true atomic resolution at the solid-liquid interface can now be routinely achieved. It is generally expected that AFM operation in more viscous environments results in an increased noise contribution from the thermal motion of the cantilever, thereby reducing the signal-to-noise ratio (SNR). Thus, viscous fluids such as ionic and organic liquids have been generally avoided for high-resolution AFM studies despite their relevance to, e.g. energy applications. Here, we investigate the thermal noise limitations of dynamic AFM operation in both low and high viscosity environments theoretically, deriving expressions for the amplitude, phase and frequency noise resulting from the thermal motion of the cantilever, thereby defining the performance limits of amplitude modulation, phase modulation and frequency modulation AFM. We show that the assumption of a reduced SNR in viscous environments is not inherent to the technique and demonstrate that SNR values comparable to ultra-high vacuum systems can be obtained in high viscosity environments under certain conditions. Finally, we have obtained true atomic resolution images of highly ordered pyrolytic graphite and mica surfaces, thus revealing the potential of high-resolution imaging in high viscosity environments.

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.

Structure and hydration of membranes embedded with voltage-sensing domains.

PubMed

Krepkiy, Dmitriy; Mihailescu, Mihaela; Freites, J Alfredo; Schow, Eric V; Worcester, David L; Gawrisch, Klaus; Tobias, Douglas J; White, Stephen H; Swartz, Kenton J

2009-11-26

Despite the growing number of atomic-resolution membrane protein structures, direct structural information about proteins in their native membrane environment is scarce. This problem is particularly relevant in the case of the highly charged S1-S4 voltage-sensing domains responsible for nerve impulses, where interactions with the lipid bilayer are critical for the function of voltage-activated ion channels. Here we use neutron diffraction, solid-state nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics simulations to investigate the structure and hydration of bilayer membranes containing S1-S4 voltage-sensing domains. Our results show that voltage sensors adopt transmembrane orientations and cause a modest reshaping of the surrounding lipid bilayer, and that water molecules intimately interact with the protein within the membrane. These structural findings indicate that voltage sensors have evolved to interact with the lipid membrane while keeping energetic and structural perturbations to a minimum, and that water penetrates the membrane, to hydrate charged residues and shape the transmembrane electric field.

Structure and hydration of membranes embedded with voltage-sensing domains

PubMed Central

Krepkiy, Dmitriy; Mihailescu, Mihaela; Freites, J. Alfredo; Schow, Eric V.; Worcester, David L.; Gawrisch, Klaus; Tobias, Douglas; White, Stephen H.; Swartz, Kenton J.

2009-01-01

Despite the growing number of atomic-resolution membrane protein structures, direct structural information about proteins in their native membrane environment is scarce. This problem is particularly relevant in the case of the highly-charged S1–S4 voltage-sensing domains responsible for nerve impulses, where interactions with the lipid bilayer are critical for the function of voltage-activated potassium channels. Here we use neutron diffraction, solid-state nuclear magnetic resonance spectroscopy, and molecular dynamics simulations to investigate the structure and hydration of bilayer membranes containing S1–S4 voltage-sensing domains. Our results show that voltage sensors adopt transmembrane orientations, cause a modest reshaping of the surrounding lipid bilayer, and that water molecules intimately interact with the protein within the membrane. These structural findings reveal that voltage sensors have evolved to interact with the lipid membrane while keeping the energetic and structural perturbations to a minimum, and that water penetrates into the membrane to hydrate charged residues and shape the transmembrane electric field. PMID:19940918

A Neutron View of Proteins in Lipid Bilayers

NASA Astrophysics Data System (ADS)

White, Stephen

2012-02-01

Despite the growing number of atomic-resolution membrane protein structures, direct structural information about proteins in their native membrane environment is scarce. This problem is particularly relevant in the case of the highly-charged S1-S4 voltage- sensing domains responsible for nerve impulses, where interactions with the lipid bilayer are critical for the function of voltage-activated potassium channels. We have used neutron diffraction, solid-state nuclear magnetic resonance spectroscopy, and molecular dynamics simulations to investigate the structure and hydration of bilayer membranes containing S1-S4 voltage-sensing domains. Our results show that voltage sensors adopt transmembrane orientations, cause a modest reshaping of the surrounding lipid bilayer, and that water molecules intimately interact with the protein within the membrane. These structural findings reveal that voltage sensors have evolved to interact with the lipid membrane while keeping the energetic and structural perturbations to a minimum, and that water penetrates into the membrane to hydrate charged residues and shape the transmembrane electric field.

PubChem atom environments.

PubMed

Hähnke, Volker D; Bolton, Evan E; Bryant, Stephen H

2015-01-01

Atom environments and fragments find wide-spread use in chemical information and cheminformatics. They are the basis of prediction models, an integral part in similarity searching, and employed in structure search techniques. Most of these methods were developed and evaluated on the relatively small sets of chemical structures available at the time. An analysis of fragment distributions representative of most known chemical structures was published in the 1970s using the Chemical Abstracts Service data system. More recently, advances in automated synthesis of chemicals allow millions of chemicals to be synthesized by a single organization. In addition, open chemical databases are readily available containing tens of millions of chemical structures from a multitude of data sources, including chemical vendors, patents, and the scientific literature, making it possible for scientists to readily access most known chemical structures. With this availability of information, one can now address interesting questions, such as: what chemical fragments are known today? How do these fragments compare to earlier studies? How unique are chemical fragments found in chemical structures? For our analysis, after hydrogen suppression, atoms were characterized by atomic number, formal charge, implicit hydrogen count, explicit degree (number of neighbors), valence (bond order sum), and aromaticity. Bonds were differentiated as single, double, triple or aromatic bonds. Atom environments were created in a circular manner focused on a central atom with radii from 0 (atom types) up to 3 (representative of ECFP_6 fragments). In total, combining atom types and atom environments that include up to three spheres of nearest neighbors, our investigation identified 28,462,319 unique fragments in the 46 million structures found in the PubChem Compound database as of January 2013. We could identify several factors inflating the number of environments involving transition metals, with many seemingly due to erroneous interpretation of structures from patent data. Compared to fragmentation statistics published 40 years ago, the exponential growth in chemistry is mirrored in a nearly eightfold increase in the number of unique chemical fragments; however, this result is clearly an upper bound estimate as earlier studies employed structure sampling approaches and this study shows that a relatively high rate of atom fragments are found in only a single chemical structure (singletons). In addition, the percentage of singletons grows as the size of the chemical fragment is increased. The observed growth of the numbers of unique fragments over time suggests that many chemically possible connections of atom types to larger fragments have yet to be explored by chemists. A dramatic drop in the relative rate of increase of atom environments from smaller to larger fragments shows that larger fragments mainly consist of diverse combinations of a limited subset of smaller fragments. This is further supported by the observed concomitant increase of singleton atom environments. Combined, these findings suggest that there is considerable opportunity for chemists to combine known fragments to novel chemical compounds. The comparison of PubChem to an older study of known chemical structures shows noticeable differences. The changes suggest advances in synthetic capabilities of chemists to combine atoms in new patterns. Log-log plots of fragment incidence show small numbers of fragments are found in many structures and that large numbers of fragments are found in very few structures, with nearly half being novel using the methods in this work. The relative decrease in the count of new fragments as a function of size further suggests considerable opportunity for more novel chemicals exists. Lastly, the differences in atom environment diversity between PubChem Substance and Compound showcase the effect of PubChem standardization protocols, but also indicate that a normalization procedure for atom types, functional groups, and tautomeric/resonance forms based on atom environments is possible. The complete sets of atom types and atom environments are supplied as supporting information.

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

Change in the frequency and intensity of the spectral lines of a hydrogen-like atom in the field of a point charge

NASA Astrophysics Data System (ADS)

Ovsyannikov, V. D.; Kamenskii, A. A.

2002-03-01

The changes in the wave functions and the energies of a hydrogen-like atom in the static field of a structureless charged particle are calculated in the asymptotic approximation. The corrections to the energy of states, as well as to the dipole matrix elements of radiative transitions caused by the interaction of the atom with the point charge at long range are calculated using the perturbation theory and the Sturm series for a reduced Coulomb Green’s function in parabolic coordinates. The analytical expressions are derived and tables of numerical values of the coefficients of asymptotic series that determine the corrections to the matrix elements and the intensities of transitions of the Lyman and Balmer series are presented.

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

PubMed

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

2014-04-03

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

Study of Dose Perturbation at Bone-Tissue Interfaces in Megavoltage Photon Beam Therapy.

NASA Astrophysics Data System (ADS)

Das, Indra Jeet

Dose perturbations during photon beam irradiation occur at interfaces between two dissimilar media due to the loss of electronic equilibrium. The human body contains many different types of interfaces between soft tissue and other media such as, air cavities, lungs, bones, and high atomic number (Z) materials. The dose to critical organs in the vicinity of high Z interfaces, is what leads to this project. This work describes the dose perturbation at high Z (from bone to lead) interfaces with soft tissue for clinically used megavoltage photon beams in the range of CO-60 gamma rays to 24 MV X-rays. It is divided into three main sections: (1) the dose outside the inhomogeneity in the direction of backscatter, (2) the dose inside the inhomogeneity, and (3) the dose on the photon transmission side of the inhomogeneity. Using different types of parallel plate ion chambers, TLD (powder and chip), and film as dosimeters, the dose perturbation is studied as a function of photon energy, thickness, width, and depth of inhomogeneity, distance from the interface and radiation field size. The concept of Bragg-Gray cavity theory is applied and verified for dose determination inside the inhomogeneity. A significant dose enhancement has been observed on the backscatter side for all photon energies. It is strongly dependent on the atomic number of the inhomogeneity and less dependent on the photon energy, thickness, depth, width, and field size. In the forward direction, a dose reduction occurs at the interface at beam energies lower than 10 MV, whereas a dose enhancement occurs for higher photon energies. The interface effect persists up to a few millimeters on the backscatter side but a distance equivalent to the secondary electron range for the particular photon beams in the forward direction. The dose perturbation is explained on the basis of production and transport of secondary electrons. Empirical functions are derived from the experimental data to predict the dose distribution in the vicinity of an inhomogeneity. These equations could form the basis of a treatment planning system that would accurately represent the dose both at the interface and surrounding tissue.

Studies of dispersion energy in hydrogen-bonded systems. H2O-HOH, H2O-HF, H3N-HF, HF-HF

NASA Astrophysics Data System (ADS)

Szcześniak, M. M.; Scheiner, Steve

1984-02-01

Dispersion energy is calculated in the systems H2O-HOH, H2O-HF, H3N-HF, and HF-HF as a function of the intermolecular separation using a variety of methods. M≂ller-Plesset perturbation theory to second and third orders is applied in conjunction with polarized basis sets of 6-311G** type and with an extended basis set including a second set of polarization functions (DZ+2P). These results are compared to a multipole expansion of the dispersion energy, based on the Unsöld approximation, carried out to the inverse tenth power of the intermolecular distance. Pairwise evaluation is also carried out using both atom-atom and bond-bond formulations. The MP3/6-311G** results are in generally excellent accord with the leading R-6 term of the multipole expansion. This expansion, if carried out to the R-10 term, reproduces extremely well previously reported dispersion energies calculated via variation-perturbation theory. Little damping of the expansion is required for intermolecular distances equal to or greater than the equilibrium separation. Although the asymptotic behavior of the MP2 dispersion energy is somewhat different than that of the other methods, augmentation of the basis set by a second diffuse set of d functions leads to quite good agreement in the vicinity of the minima. Both the atom-atom and bond-bond parametrization schemes are in good qualitative agreement with the other methods tested. All approaches produce similar dependence of the dispersion energy upon the angular orientation between the two molecules involved in the H bond.

The life of a meander bend: Connecting shape and dynamics via analysis of a numerical model

NASA Astrophysics Data System (ADS)

Schwenk, Jon; Lanzoni, Stefano; Foufoula-Georgiou, Efi

2015-04-01

Analysis of bend-scale meandering river dynamics is a problem of theoretical and practical interest. This work introduces a method for extracting and analyzing the history of individual meander bends from inception until cutoff (called "atoms") by tracking backward through time the set of two cutoff nodes in numerical meander migration models. Application of this method to a simplified yet physically based model provides access to previously unavailable bend-scale meander dynamics over long times and at high temporal resolutions. We find that before cutoffs, the intrinsic model dynamics invariably simulate a prototypical cutoff atom shape we dub simple. Once perturbations from cutoffs occur, two other archetypal cutoff planform shapes emerge called long and round that are distinguished by a stretching along their long and perpendicular axes, respectively. Three measures of meander migration—growth rate, average migration rate, and centroid migration rate—are introduced to capture the dynamic lives of individual bends and reveal that similar cutoff atom geometries share similar dynamic histories. Specifically, through the lens of the three shape types, simples are seen to have the highest growth and average migration rates, followed by rounds, and finally longs. Using the maximum average migration rate as a metric describing an atom's dynamic past, we show a strong connection between it and two metrics of cutoff geometry. This result suggests both that early formative dynamics may be inferred from static cutoff planforms and that there exists a critical period early in a meander bend's life when its dynamic trajectory is most sensitive to cutoff perturbations. An example of how these results could be applied to Mississippi River oxbow lakes with unknown historic dynamics is shown. The results characterize the underlying model and provide a framework for comparisons against more complex models and observed dynamics.

Coherent manipulation of a solid-state artificial atom with few photons.

PubMed

Giesz, V; Somaschi, N; Hornecker, G; Grange, T; Reznychenko, B; De Santis, L; Demory, J; Gomez, C; Sagnes, I; Lemaître, A; Krebs, O; Lanzillotti-Kimura, N D; Lanco, L; Auffeves, A; Senellart, P

2016-06-17

In a quantum network based on atoms and photons, a single atom should control the photon state and, reciprocally, a single photon should allow the coherent manipulation of the atom. Both operations require controlling the atom environment and developing efficient atom-photon interfaces, for instance by coupling the natural or artificial atom to cavities. So far, much attention has been drown on manipulating the light field with atomic transitions, recently at the few-photon limit. Here we report on the reciprocal operation and demonstrate the coherent manipulation of an artificial atom by few photons. We study a quantum dot-cavity system with a record cooperativity of 13. Incident photons interact with the atom with probability 0.95, which radiates back in the cavity mode with probability 0.96. Inversion of the atomic transition is achieved for 3.8 photons on average, showing that our artificial atom performs as if fully isolated from the solid-state environment.

Cytochrome C in a dry trehalose matrix: structural and dynamical effects probed by x-ray absorption spectroscopy.

PubMed

Giachini, Lisa; Francia, Francesco; Cordone, Lorenzo; Boscherini, Federico; Venturoli, Giovanni

2007-02-15

We report on the structure and dynamics of the Fe ligand cluster of reduced horse heart cytochrome c in solution, in a dried polyvinyl alcohol (PVA) film, and in two trehalose matrices characterized by different contents of residual water. The effect of the solvent/matrix environment was studied at room temperature using Fe K-edge x-ray absorption fine structure (XAFS) spectroscopy. XAFS data were analyzed by combining ab initio simulations and multi-parameter fitting in an attempt to disentangle structural from disorder parameters. Essentially the same structural and disorder parameters account adequately for the XAFS spectra measured in solution, both in the absence and in the presence of glycerol, and in the PVA film, showing that this polymer interacts weakly with the embedded protein. Instead, incorporation in trehalose leads to severe structural changes, more prominent in the more dried matrix, consisting of 1), an increase up to 0.2 A of the distance between Fe and the imidazole N atom of the coordinating histidine residue and 2), an elongation up to 0.16 A of the distance between Fe and the fourth-shell C atoms of the heme pyrrolic units. These structural distortions are accompanied by a substantial decrease of the relative mean-square displacements of the first ligands. In the extensively dried trehalose matrix, extremely low values of the Debye Waller factors are obtained for the pyrrolic and for the imidazole N atoms. This finding is interpreted as reflecting a drastic hindering in the relative motions of the Fe ligand cluster atoms and an impressive decrease in the static disorder of the local Fe structure. It appears, therefore, that the dried trehalose matrix dramatically perturbs the energy landscape of cytochrome c, giving rise, at the level of local structure, to well-resolved structural distortions and restricting the ensemble of accessible conformational substates.

The challenge of detecting gravitational radiation is creating a new chapter in quantum electronics: Quantum nondemolition measurements

NASA Technical Reports Server (NTRS)

Braginsky, V. B.; Vorontsov, Y. I.; Thorne, K. S.

1979-01-01

Future gravitational wave antennas will be approximately 100 kilogram cylinders, whose end-to-end vibrations must be measured so accurately (10 to the -19th power centimeters) that they behave quantum mechanically. Moreover, the vibration amplitude must be measured over and over again without perturbing it (quantum nondemolition measurement). This contrasts with quantum chemistry, quantum optics, or atomic, nuclear, and elementary particle physics where measurements are usually made on an ensemble of identical objects, and care is not given to whether any single object is perturbed or destroyed by the measurement. Electronic techniques required for quantum nondemolition measurements are described as well as the theory underlying them.

A reformulation of the coupled perturbed self-consistent field equations entirely within a local atomic orbital density matrix-based scheme

NASA Astrophysics Data System (ADS)

Ochsenfeld, Christian; Head-Gordon, Martin

1997-05-01

To exploit the exponential decay found in numerical studies for the density matrix and its derivative with respect to nuclear displacements, we reformulate the coupled perturbed self-consistent field (CPSCF) equations and a quadratically convergent SCF (QCSCF) method for Hartree-Fock and density functional theory within a local density matrix-based scheme. Our D-CPSCF (density matrix-based CPSCF) and D-QCSCF schemes open the way for exploiting sparsity and to achieve asymptotically linear scaling of computational complexity with molecular size ( M), in case of D-CPSCF for all O( M) derivative densities. Furthermore, these methods are even for small molecules strongly competitive to conventional algorithms.

Simple turbulence measurements with azopolymer thin films.

PubMed

Barillé, Regis; Pérez, Darío G; Morille, Yohann; Zielińska, Sonia; Ortyl, Ewelina

2013-04-01

A simple method to measure the influence on the laser beam propagation by a turbid medium is proposed. This measurement is based on the inscription of a surface relief grating (SRG) on an azopolymer thin film. The grating obtained with a single laser beam after propagation into a turbulent medium is perturbed and directly analyzed by a CCD camera through its diffraction pattern. Later, by scanning the surface pattern with an atomic force microscope, the inscribed SRG is analyzed with the Radon transform. This method has the advantage of using a single beam to remotely inscribe a grating detecting perturbations during the beam path. A method to evaluate the refractive index constant structure is developed.

Margins of stability in young adults with traumatic transtibial amputation walking in destabilizing environments✫

PubMed Central

Beltran, Eduardo J.; Dingwell, Jonathan B.; Wilken, Jason M.

2014-01-01

Understanding how lower-limb amputation affects walking stability, specifically in destabilizing environments, is essential for developing effective interventions to prevent falls. This study quantified mediolateral margins of stability (MOS) and MOS sub-components in young individuals with traumatic unilateral transtibial amputation (TTA) and young able-bodied individuals (AB). Thirteen AB and nine TTA completed five 3-minute walking trials in a Computer Assisted Rehabilitation ENvironment (CAREN) system under three each of three test conditions: no perturbations, pseudo-random mediolateral translations of the platform, and pseudo-random mediolateral translations of the visual field. Compared to the unperturbed trials, TTA exhibited increased mean MOS and MOS variability during platform and visual field perturbations (p < 0.010). Also, AB exhibited increased mean MOS during visual field perturbations and increased MOS variability during both platform and visual field perturbations (p < 0.050). During platform perturbations, TTA exhibited significantly greater values than AB for mean MOS (p < 0.050) and MOS variability (p < 0.050); variability of the lateral distance between the center of mass (COM) and base of support at initial contact (p < 0.005); mean and variability of the range of COM motion (p < 0.010); and variability of COM peak velocity (p < 0.050). As determined by mean MOS and MOS variability, young and otherwise healthy individuals with transtibial amputation achieved stability similar to that of their able-bodied counterparts during unperturbed and visually-perturbed walking. However, based on mean and variability of MOS, unilateral transtibial amputation was shown to have affected walking stability during platform perturbations. PMID:24444777

On the relationship between residue structural environment and sequence conservation in proteins.

PubMed

Liu, Jen-Wei; Lin, Jau-Ji; Cheng, Chih-Wen; Lin, Yu-Feng; Hwang, Jenn-Kang; Huang, Tsun-Tsao

2017-09-01

Residues that are crucial to protein function or structure are usually evolutionarily conserved. To identify the important residues in protein, sequence conservation is estimated, and current methods rely upon the unbiased collection of homologous sequences. Surprisingly, our previous studies have shown that the sequence conservation is closely correlated with the weighted contact number (WCN), a measure of packing density for residue's structural environment, calculated only based on the C α positions of a protein structure. Moreover, studies have shown that sequence conservation is correlated with environment-related structural properties calculated based on different protein substructures, such as a protein's all atoms, backbone atoms, side-chain atoms, or side-chain centroid. To know whether the C α atomic positions are adequate to show the relationship between residue environment and sequence conservation or not, here we compared C α atoms with other substructures in their contributions to the sequence conservation. Our results show that C α positions are substantially equivalent to the other substructures in calculations of various measures of residue environment. As a result, the overlapping contributions between C α atoms and the other substructures are high, yielding similar structure-conservation relationship. Take the WCN as an example, the average overlapping contribution to sequence conservation is 87% between C α and all-atom substructures. These results indicate that only C α atoms of a protein structure could reflect sequence conservation at the residue level. © 2017 Wiley Periodicals, Inc.

Low Earth Orbital Atomic Oxygen Interactions With Materials

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Miller, Sharon K.; deGroh, Kim K.

2004-01-01

Atomic oxygen is formed in the low Earth orbital environment (LEO) by photo dissociation of diatomic oxygen by short wavelength (< 243 nm) solar radiation which has sufficient energy to break the 5.12 eV O2 diatomic bond in an environment where the mean free path is sufficiently long ( 108 meters) that the probability of reassociation or the formation of ozone (O3) is small. As a consequence, between the altitudes of 180 and 650 km, atomic oxygen is the most abundant species. Spacecraft impact the atomic oxygen resident in LEO with sufficient energy to break hydrocarbon polymer bonds, causing oxidation and thinning of the polymers due to loss of volatile oxidation products. Mitigation techniques, such as the development of materials with improved durability to atomic oxygen attack, as well as atomic oxygen protective coatings, have been employed with varying degrees of success to improve durability of polymers in the LEO environment. Atomic oxygen can also oxidize silicones and silicone contamination to produce non-volatile silica deposits. Such contaminants are present on most LEO missions and can be a threat to performance of optical surfaces. The LEO atomic oxygen environment, its interactions with materials, results of space testing, computational modeling, mitigation techniques, and ground laboratory simulation procedures and issues are presented.

Simulation of charge transfer and orbital rehybridization in molecular and condensed matter systems

NASA Astrophysics Data System (ADS)

Nistor, Razvan A.

The mixing and shifting of electronic orbitals in molecules, or between atoms in bulk systems, is crucially important to the overall structure and physical properties of materials. Understanding and accurately modeling these orbital interactions is of both scientific and industrial relevance. Electronic orbitals can be perturbed in several ways. Doping, adding or removing electrons from systems, can change the bond-order and the physical properties of certain materials. Orbital rehybridization, driven by either thermal or pressure excitation, alters the short-range structure of materials and changes their long-range transport properties. Macroscopically, during bond formation, the shifting of electronic orbitals can be interpreted as a charge transfer phenomenon, as electron density may pile up around, and hence, alter the effective charge of, a given atom in the changing chemical environment. Several levels of theory exist to elucidate the mechanisms behind these orbital interactions. Electronic structure calculations solve the time-independent Schrodinger equation to high chemical accuracy, but are computationally expensive and limited to small system sizes and simulation times. Less fundamental atomistic calculations use simpler parameterized functional expressions called force-fields to model atomic interactions. Atomistic simulations can describe systems and time-scales larger and longer than electronic-structure methods, but at the cost of chemical accuracy. In this thesis, both first-principles and phenomenological methods are addressed in the study of several encompassing problems dealing with charge transfer and orbital rehybridization. Firstly, a new charge-equilibration method is developed that improves upon existing models to allow next-generation force-fields to describe the electrostatics of changing chemical environments. Secondly, electronic structure calculations are used to investigate the doping dependent energy landscapes of several high-temperature superconducting materials in order to parameterize the apparently large nonlinear electron-phonon coupling. Thirdly, ab initio simulations are used to investigate the role of pressure-driven structural re-organization in the crystalline-to-amorphous (or, metallic-to-insulating) transition of a common binary phase-change material composed of Ge and Sb. Practical applications of each topic will be discussed. Keywords. Charge-equilibration methods, molecular dynamics, electronic structure calculations, ab initio simulations, high-temperature superconductors, phase-change materials.

Environment-Assisted Speed-up of the Field Evolution in Cavity Quantum Electrodynamics

DOE PAGES

Cimmarusti, A. D.; Yan, Z.; Patterson, B. D.; ...

2015-06-11

We measure the quantum speed of the state evolution of the field in a weakly-driven optical cavity QED system. To this end, the mode of the electromagnetic field is considered as a quantum system of interest with a preferential coupling to a tunable environment: the atoms. By controlling the environment, i.e., changing the number of atoms coupled to the optical cavity mode, an environment assisted speed-up is realized: the quantum speed of the state re-population in the optical cavity increases with the coupling strength between the optical cavity mode and this non-Markovian environment (the number of atoms).

Do dihydroxymagnesium carboxylates form Grignard-type reagents? A theoretical investigation on decarboxylative fragmentation.

PubMed

Ruf, Alexander; Kanawati, Basem; Schmitt-Kopplin, Philippe

2018-03-27

Dihydroxymagnesium carboxylates [(OH) 2 MgO 2 CR] were probed for decarboxylation on a theoretical level, by utilizing both Møller-Plesset perturbation theory (MP2) and density functional theory (B3LYP-DFT) computations. This study is connected to the question of whether this recently introduced, astrobiologically relevant chemical class may form Grignard-type reagent molecules. To extract trends for a broad molecular mass range, different linear alkyl chain lengths between C 4 and C 11 were computed. The forward energy barrier for decarboxylation reactions increases linearly as a function of the ligand's chain length. Decarboxylation-type fragmentations of these organomagnesium compounds seem to be improbable in non-catalytic, low energetic environments. A high forward energy barrier (E MP2  > 55 kcal mol -1 ) towards a described transition state restricts the release of CO 2 . Nevertheless, we propose the release of CO 2 on a theoretical level, as been revealed via an intramolecular nucleophilic attack mechanism. Once the challenging transition state for decarboxylation is overcome, a stable Mg-C bond is formed. These mechanistic insights were gained by help of natural bond orbital analysis. The Cα atom (first carbon atom in the ligand chain attached to the carboxyl group) is thought to prefer binding towards the electrophilic magnesium coordination center, rather than towards the electrophilic CO 2 -carbon atom. Additionally, the putatively formed Grignard-type OH-bearing product molecules possess a more polarized Mg-C bond in comparison to RMgCl species. Therefore, carbanion formation from OH-bearing Grignard-type molecules is made feasible for triggering C-C bond formation reactions. Graphical abstract This study asks whether recently introduced, astrobiologically dihydroxymagnesium carboxylates form Grignard-type reagent molecules via decarboxylative fragmentation.

Active System for Electromagnetic Perturbation Monitoring in Vehicles

NASA Astrophysics Data System (ADS)

Matoi, Adrian Marian; Helerea, Elena

Nowadays electromagnetic environment is rapidly expanding in frequency domain and wireless services extend in terms of covered area. European electromagnetic compatibility regulations refer to limit values regarding emissions, as well as procedures for determining susceptibility of the vehicle. Approval procedure for a series of cars is based on determining emissions/immunity level for a few vehicles picked randomly from the entire series, supposing that entire vehicle series is compliant. During immunity assessment, the vehicle is not subjected to real perturbation sources, but exposed to electric/magnetic fields generated by laboratory equipment. Since current approach takes into account only partially real situation regarding perturbation sources, this paper proposes an active system for determining electromagnetic parameters of vehicle's environment, that implements a logical diagram for measurement, satisfying the imposed requirements. This new and original solution is useful for EMC assessment of hybrid and electrical vehicles.

Studies of Ionic Photoionization Using Relativistic Random Phase Approximation and Relativistic Multichannel Quantum Defect Theory

NASA Astrophysics Data System (ADS)

Haque, Ghousia Nasreen

The absorption of electromagnetic radiation by positive ions is one of the fundamental processes of nature which occurs in every intensely hot environment. Due to the difficulties in producing sufficient densities of ions in a laboratory, there are very few measurements of ionic photoabsorption parameters. On the theoretical side, some calculations have been made of a few major photoionization parameters, but generally speaking, most of the work done so far has employed rather simple single particle models and any theoretical work which has adequately taken into account intricate atomic many-body and relativistic effects is only scanty. In the present work, several complex aspects of atomic/ionic photoabsorption parameters have been studied. Non -resonant photoionization in neon and argon isonuclear as well as isoelectronic sequences has been studied using a very sophisticated technique, namely the relativistic random phase approximation (RRPA). This technique takes into account relativistic effects as well as an important class of major many-body effects on the same footing. The present calculations confirmed that gross features of photoionization parameters calculated using simpler models were not an artifact of the simple model. Also, the present RRPA calculations on K^+ ion and neutral Ar brought out the relative importance of various many-body effects such the inter-channel coupling. Inter-channel coupling between discrete bound state photoexcitation channels from an inner atomic/ionic level and photoionization continuum channels from an outer atomic/ionic level leads to the phenomena of autoionization resonances in the photoionization process. These resonances lead to very complex effects in the atomic/ionic photoabsorption spectra. These resonances have been calculated and studied in the present work in the neon and magnesium isoelectronic sequences using the relativistic multi-channel quantum defect theory (RMQDT) within the framework of the RRPA. The character of the autoionization resonances studied was determined in the present work and the effect of series perturbations in the Rydberg series due to interference between various multichannel processes was quantitatively determined. Furthermore, results of the present calculations also serve as important pointer to measure the relative strengths of radiative (fluorescence) decay modes and non -radiative (autoionization/auger) decay modes in an isoelectronic sequence.

40 CFR 23.9 - Timing of Administrator's action under the Atomic Energy Act.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 1 2014-07-01 2014-07-01 false Timing of Administrator's action under the Atomic Energy Act. 23.9 Section 23.9 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Atomic Energy Act. Unless the Administrator otherwise explicitly provides in a particular order, the time...

40 CFR 23.9 - Timing of Administrator's action under the Atomic Energy Act.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 1 2010-07-01 2010-07-01 false Timing of Administrator's action under the Atomic Energy Act. 23.9 Section 23.9 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Atomic Energy Act. Unless the Administrator otherwise explicitly provides in a particular order, the time...

40 CFR 23.9 - Timing of Administrator's action under the Atomic Energy Act.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 1 2011-07-01 2011-07-01 false Timing of Administrator's action under the Atomic Energy Act. 23.9 Section 23.9 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Atomic Energy Act. Unless the Administrator otherwise explicitly provides in a particular order, the time...

40 CFR 23.9 - Timing of Administrator's action under the Atomic Energy Act.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 1 2012-07-01 2012-07-01 false Timing of Administrator's action under the Atomic Energy Act. 23.9 Section 23.9 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Atomic Energy Act. Unless the Administrator otherwise explicitly provides in a particular order, the time...

40 CFR 23.9 - Timing of Administrator's action under the Atomic Energy Act.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 1 2013-07-01 2013-07-01 false Timing of Administrator's action under the Atomic Energy Act. 23.9 Section 23.9 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Atomic Energy Act. Unless the Administrator otherwise explicitly provides in a particular order, the time...

Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program

PubMed Central

Miller, Edward B.; Murrett, Colleen S.; Zhu, Kai; Zhao, Suwen; Goldfeld, Dahlia A.; Bylund, Joseph H.; Friesner, Richard A.

2013-01-01

Robust homology modeling to atomic-level accuracy requires in the general case successful prediction of protein loops containing small segments of secondary structure. Further, as loop prediction advances to success with larger loops, the exclusion of loops containing secondary structure becomes awkward. Here, we extend the applicability of the Protein Local Optimization Program (PLOP) to loops up to 17 residues in length that contain either helical or hairpin segments. In general, PLOP hierarchically samples conformational space and ranks candidate loops with a high-quality molecular mechanics force field. For loops identified to possess α-helical segments, we employ an alternative dihedral library composed of (ϕ,ψ) angles commonly found in helices. The alternative library is searched over a user-specified range of residues that define the helical bounds. The source of these helical bounds can be from popular secondary structure prediction software or from analysis of past loop predictions where a propensity to form a helix is observed. Due to the maturity of our energy model, the lowest energy loop across all experiments can be selected with an accuracy of sub-Ångström RMSD in 80% of cases, 1.0 to 1.5 Å RMSD in 14% of cases, and poorer than 1.5 Å RMSD in 6% of cases. The effectiveness of our current methods in predicting hairpin-containing loops is explored with hairpins up to 13 residues in length and again reaching an accuracy of sub-Ångström RMSD in 83% of cases, 1.0 to 1.5 Å RMSD in 10% of cases, and poorer than 1.5 Å RMSD in 7% of cases. Finally, we explore the effect of an imprecise surrounding environment, in which side chains, but not the backbone, are initially in perturbed geometries. In these cases, loops perturbed to 3Å RMSD from the native environment were restored to their native conformation with sub-Ångström RMSD. PMID:23814507

Systematics of Rydberg Series of Diatomic Molecules and Correlation Diagrams

NASA Astrophysics Data System (ADS)

Lee, Chun-Woo

2015-06-01

Rydberg states are studied for H2, Li2, HeH, LiH and BeH using the multi-reference configuration interaction (MRCI) method. The systematics and regularities of the physical properties such as potential energies curves (PECs), quantum defect curves, permanent dipole moment and transition dipole moment curves of the Rydberg series are studied. They are explained using united atom perturbation theory by Bingel and Byers-Brown, Fermi model, Stark theory, and Mulliken's theory. Interesting mirror relationships of the dipole moments are observed between l-mixed Rydberg series, indicating that the members of the l-mixed Rydberg series have dipole moments with opposite directions, which are related to the reversal of the polarity of a dipole moment at the avoided crossing points. The assignment of highly excited states is difficult because of the usual absence of the knowledge on the behaviors of potential energy curves at small internuclear separation whereby the correlation between the united atom limit and separated atoms limit cannot be given. All electron MRCI calculations of PECs are performed to obtain the correlation diagrams between Rydberg orbitals at the united-atom and separated atoms limits.

Quantum-mechanical elaboration for the description of low- and high-order harmonics generated by extended gas media: prospects to the efficiency enhancement in spatially modulated media

NASA Astrophysics Data System (ADS)

Stremoukhov, Sergey Yu; Andreev, Anatoly V.

2018-03-01

A simple model fully matching the description of the low- and high-order harmonic generation in extended media interacting with multicolor laser fields is proposed. The extended atomic media is modeled by a 1D chain of atoms, the number of atoms and the distance between them depend on the pressure of the gas and the length of the gas cell. The response of the individual atoms is calculated accurately in the frame of the non-perturbative theory where the driving field for each atom is calculated with account of dispersion properties of any multicolor field component. In spite of the simplicity of the proposed model it provides the detailed description of behaviour of harmonic spectra under variation of the gas pressure and medium length, it also predicts a scaling law for harmonic generation (an invariant). To demonstrate the wide range of applications of the model we have simulated the results of recent experiments dealing with spatially modulated media and obtained good coincidence between the numerical results and the experimental ones.

Communication: Finite size correction in periodic coupled cluster theory calculations of solids.

PubMed

Liao, Ke; Grüneis, Andreas

2016-10-14

We present a method to correct for finite size errors in coupled cluster theory calculations of solids. The outlined technique shares similarities with electronic structure factor interpolation methods used in quantum Monte Carlo calculations. However, our approach does not require the calculation of density matrices. Furthermore we show that the proposed finite size corrections achieve chemical accuracy in the convergence of second-order Møller-Plesset perturbation and coupled cluster singles and doubles correlation energies per atom for insulating solids with two atomic unit cells using 2 × 2 × 2 and 3 × 3 × 3 k-point meshes only.

Heavy atom vibrational modes and low-energy vibrational autodetachment in nitromethane anions

NASA Astrophysics Data System (ADS)

Thompson, Michael C.; Baraban, Joshua H.; Matthews, Devin A.; Stanton, John F.; Weber, J. Mathias

2015-06-01

We report infrared spectra of nitromethane anion, CH3NO2-, in the region 700-2150 cm-1, obtained by Ar predissociation spectroscopy and electron detachment spectroscopy. The data are interpreted in the framework of second-order vibrational perturbation theory based on coupled-cluster electronic structure calculations. The modes in the spectroscopic region studied here are mainly based on vibrations involving the heavier atoms; this work complements earlier studies on nitromethane anion that focused on the CH stretching region of the spectrum. Electron detachment begins at photon energies far below the adiabatic electron affinity due to thermal population of excited vibrational states.

Heavy atom vibrational modes and low-energy vibrational autodetachment in nitromethane anions.

PubMed

Thompson, Michael C; Baraban, Joshua H; Matthews, Devin A; Stanton, John F; Weber, J Mathias

2015-06-21

We report infrared spectra of nitromethane anion, CH3NO2 (-), in the region 700-2150 cm(-1), obtained by Ar predissociation spectroscopy and electron detachment spectroscopy. The data are interpreted in the framework of second-order vibrational perturbation theory based on coupled-cluster electronic structure calculations. The modes in the spectroscopic region studied here are mainly based on vibrations involving the heavier atoms; this work complements earlier studies on nitromethane anion that focused on the CH stretching region of the spectrum. Electron detachment begins at photon energies far below the adiabatic electron affinity due to thermal population of excited vibrational states.

Temporal and spatiotemporal correlation functions for trapped Bose gases

NASA Astrophysics Data System (ADS)

Kohnen, M.; Nyman, R. A.

2015-03-01

Density correlations unambiguously reveal the quantum nature of matter. Here, we study correlations between measurements of density in cold-atom clouds at different times at one position, and also at two separated positions. We take into account the effects of finite-size and -duration measurements made by light beams passing through the atom cloud. We specialize to the case of Bose gases in harmonic traps above critical temperature, for weakly perturbative measurements. For overlapping measurement regions, shot-noise correlations revive after a trap oscillation period. For nonoverlapping regions, bosonic correlations dominate at long times, and propagate at finite speeds. Finally, we give a realistic measurement protocol for performing such experiments.

Scanning tunneling microscopy current from localized basis orbital density functional theory

NASA Astrophysics Data System (ADS)

Gustafsson, Alexander; Paulsson, Magnus

2016-03-01

We present a method capable of calculating elastic scanning tunneling microscopy (STM) currents from localized atomic orbital density functional theory (DFT). To overcome the poor accuracy of the localized orbital description of the wave functions far away from the atoms, we propagate the wave functions, using the total DFT potential. From the propagated wave functions, the Bardeen's perturbative approach provides the tunneling current. To illustrate the method we investigate carbon monoxide adsorbed on a Cu(111) surface and recover the depression/protrusion observed experimentally with normal/CO-functionalized STM tips. The theory furthermore allows us to discuss the significance of s - and p -wave tips.

Optically probing the fine structure of a single Mn atom in an InAs quantum dot.

PubMed

Kudelski, A; Lemaître, A; Miard, A; Voisin, P; Graham, T C M; Warburton, R J; Krebs, O

2007-12-14

We report on the optical spectroscopy of a single InAs/GaAs quantum dot doped with a single Mn atom in a longitudinal magnetic field of a few Tesla. Our findings show that the Mn impurity is a neutral acceptor state A0 whose effective spin J=1 is significantly perturbed by the quantum dot potential and its associated strain field. The spin interaction with photocarriers injected in the quantum dot is shown to be ferromagnetic for holes, with an effective coupling constant of a few hundreds of mueV, but vanishingly small for electrons.

Application of the Finite Element Method in Atomic and Molecular Physics

NASA Technical Reports Server (NTRS)

Shertzer, Janine

2007-01-01

The finite element method (FEM) is a numerical algorithm for solving second order differential equations. It has been successfully used to solve many problems in atomic and molecular physics, including bound state and scattering calculations. To illustrate the diversity of the method, we present here details of two applications. First, we calculate the non-adiabatic dipole polarizability of Hi by directly solving the first and second order equations of perturbation theory with FEM. In the second application, we calculate the scattering amplitude for e-H scattering (without partial wave analysis) by reducing the Schrodinger equation to set of integro-differential equations, which are then solved with FEM.

Exploring warm dense matter using quantum molecular dynamics

NASA Astrophysics Data System (ADS)

Clérouin, J.; Mazevet, S.

2006-06-01

For dense plasmas produced in shock experiments, the influence of the media on the isolated atomic properties can no longer be treated as a perturbation and conventional atomic physics approaches usually fail. Recently, quantum molecular dynamics (QMD) has been used to successfully predict static, dynamical and optical properties in this regime within the framework of a first principle method. In this short report, we illustrate the usefulness of the method for dense plasmas with a few selected examples: the equation of state of liquid deuterium, the electrical properties of expanded metals, the optical properties of shocked insulators, and the interaction of femto-second lasers with gold thin films.

Cluster formation in nuclear reactions from mean-field inhomogeneities

NASA Astrophysics Data System (ADS)

Napolitani, Paolo; Colonna, Maria; Mancini-Terracciano, Carlo

2018-05-01

Perturbing fluids of neutrons and protons (nuclear matter) may lead, as the most catastrophic effect, to the rearrangement of the fluid into clusters of nucleons. A similar process may occur in a single atomic nucleus undergoing a violent perturbation, like in heavy-ion collisions tracked in particle accelerators at around 30 to 50 MeV per nucleon: in this conditions, after the initial collision shock, the nucleus expands and then clusterises into several smaller nuclear fragments. Microscopically, when violent perturbation are applied to nuclear matter, a process of clusterisation arises from the combination of several fluctuation modes of large-amplitude where neutrons and protons may oscillate in phase or out of phase. The imposed perturbation leads to conditions of instability, the wavelengths which are the most amplified have sizes comparable to small atomic nuclei. We found that these conditions, explored in heavy-ion collisions, correspond to the splitting of a nucleus into fragments ranging from Oxygen to Neon in a time interval shorter than one zeptosecond (10 ‑ 21s). From the out-of-phase oscillations of neutrons and protons another property arises, the smaller fragments belonging to a more volatile phase get more neutron enriched: in the heavy-ion collision case this process, called distillation, reflects in the isotopic distributions of the fragments. The resulting dynamical description of heavy-ion collisions is an improvement with respect to more usual statistical approaches, based on the equilibrium assumption. It allows in fact to characterise also the very fast early stages of the collision process which are out of equilibrium. Such dynamical description is the core of the Boltzmann-Langevin One Body (BLOB) model, which in its latest development unifies in a common approach the description of fluctuations in nuclear matter, and a predictive description of the disintegration of nuclei into nuclear fragments. After a theoretical introduction, a few practical examples will be illustrated. This paper resumes the extended analysis of fluctuations in nuclear matter of ref. [2] and briefly reviews applications to heavy-ion collisions.

Study on Potential Changes in Geological and Disposal Environment Caused by 'Natural Phenomena' on a HLW Disposal System

NASA Astrophysics Data System (ADS)

Kawamura, M.; Umeda, K.; Ohi, T.; Ishimaru, T.; Niizato, T.; Yasue, K.; Makino, H.

2007-12-01

We have developed a formal evaluation method to assess the potential impact of natural phenomena (earthquakes and faulting; volcanism; uplift, subsidence, denudation and sedimentation; climatic and sea-level changes) on a High Level Radioactive Waste (HLW) Disposal System. In 2000, we had developed perturbation scenarios in a generic and conservative sense and illustrated the potential impact on a HLW disposal system. As results of the development of perturbation scenarios, two points were highlighted for consideration in subsequent work: improvement of the scenarios from the viewpoints of reality, transparency, traceability and consistency and avoiding extreme conservatism. Subsequently, we have thus developed a new procedure for describing such perturbation scenarios based on further studies of the characteristics of these natural perturbation phenomena in Japan. The approach to describing the perturbation scenario is effectively developed in five steps: Step 1: Description of potential process of phenomena and their impacts on the geological environment. Step 2: Characterization of potential changes of geological environment in terms of T-H-M-C (Thermal - Hydrological - Mechanical - Chemical) processes. The focus is on specific T-H-M-C parameters that influence geological barrier performance, utilizing the input from Step 1. Step 3: Classification of potential influences, based on similarity of T-H-M-C perturbations. This leads to development of perturbation scenarios to serve as a basis for consequence analysis. Step 4: Establishing models and parameters for performance assessment. Step 5: Calculation and assessment. This study focuses on identifying key T-H-M-C process associated with perturbations at Step 2. This framework has two advantages. First one is assuring maintenance of traceability during the scenario construction processes, facilitating the production and structuring of suitable records. The second is providing effective elicitation and organization of information from a wide range of investigations of earth sciences within a performance assessment context. In this framework, scenario development work proceeds in a stepwise manner, to ensure clear identification of the impact of processes associated with these phenomena on a HLW disposal system. Output is organized to create credible scenarios with required transparency, consistency, traceability and adequate conservatism. In this presentation, the potential impact of natural phenomena in the viewpoint of performance assessment for HLW disposal will be discussed and modeled using the approach.

Visualizing deceleration-phase instabilities in inertial confinement fusion implosions using an "enhanced self-emission" technique at the National Ignition Facility

NASA Astrophysics Data System (ADS)

Pickworth, L. A.; Hammel, B. A.; Smalyuk, V. A.; Robey, H. F.; Benedetti, L. R.; Berzak Hopkins, L.; Bradley, D. K.; Field, J. E.; Haan, S. W.; Hatarik, R.; Hartouni, E.; Izumi, N.; Johnson, S.; Khan, S.; Lahmann, B.; Landen, O. L.; Le Pape, S.; MacPhee, A. G.; Meezan, N. B.; Milovich, J.; Nagel, S. R.; Nikroo, A.; Pak, A. E.; Petrasso, R.; Remington, B. A.; Rice, N. G.; Springer, P. T.; Stadermann, M.; Widmann, K.; Hsing, W.

2018-05-01

High-mode perturbations and low-mode asymmetries were measured in the deceleration phase of indirectly driven, deuterium gas filled inertial confinement fusion capsule implosions at convergence ratios of 10 to 15, using a new "enhanced emission" technique at the National Ignition Facility [E. M. Campbell et al., AIP Conf. Proc. 429, 3 (1998)]. In these experiments, a high spatial resolution Kirkpatrick-Baez microscope was used to image the x-ray emission from the inner surface of a high-density-carbon capsule's shell. The use of a high atomic number dopant in the shell enabled time-resolved observations of shell perturbations penetrating into the hot spot. This allowed the effects of the perturbations and asymmetries on degrading neutron yield to be directly measured. In particular, mix induced radiation losses of ˜400 J from the hot spot resulted in a neutron yield reduction of a factor of ˜2. In a subsequent experiment with a significantly increased level of short-mode initial perturbations, shown through the enhanced imaging technique to be highly organized radially, the neutron yield dropped an additional factor of ˜2.

Effect of heavy atoms on photochemically induced dynamic nuclear polarization in liquids

NASA Astrophysics Data System (ADS)

Okuno, Yusuke; Cavagnero, Silvia

2018-01-01

Given its short hyperpolarization time (∼10-6 s) and mostly non-perturbative nature, photo-chemically induced dynamic nuclear polarization (photo-CIDNP) is a powerful tool for sensitivity enhancement in nuclear magnetic resonance. In this study, we explore the extent of 1H-detected 13C nuclear hyperpolarization that can be gained via photo-CIDNP in the presence of small-molecule additives containing a heavy atom. The underlying rationale for this methodology is the well-known external-heavy-atom (EHA) effect, which leads to significant enhancements in the intersystem-crossing rate of selected photosensitizer dyes from photoexcited singlet to triplet. We exploited the EHA effect upon addition of moderate amounts of halogen-atom-containing cosolutes. The resulting increase in the transient triplet-state population of the photo-CIDNP sensitizer fluorescein resulted in a significant increase in the nuclear hyperpolarization achievable via photo-CIDNP in liquids. We also explored the internal-heavy-atom (IHA) effect, which is mediated by halogen atoms covalently incorporated into the photosensitizer dye. Widely different outcomes were achieved in the case of EHA and IHA, with EHA being largely preferable in terms of net hyperpolarization.

The perturbation energy: A missing key to understand the “nobleness” of bulk gold

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

Alcántara Ortigoza, Marisol, E-mail: Marisol.AlcantaraOrtigoza@ucf.edu; Stolbov, Sergey, E-mail: Sergey.Stolbov@ucf.edu

2015-05-21

The nobleness of gold surfaces has been appreciated since long before the beginning of recorded history. Yet, the origin of this phenomenon remains open because the so far existing explanations either incorrectly imply that silver should be the noblest metal or would fail to predict the dissolution of Au in aqua regia. Here, based on our analyses of oxygen adsorption, we advance that bulk gold’s unique resistance to oxidation is traced to the large energy cost associated with the perturbation its surfaces undergo upon adsorption of highly electronegative species. This fact is related to the almost totally filled d-band ofmore » Au and relativistic effects, but does not imply that the strength of the adsorbate-Au bond is weak. The magnitude of the structural and charge-density perturbation energy upon adsorption of atomic oxygen—which is largest for Au—is assessed from first-principles calculations and confirmed via a multiple regression analysis of the binding energy of oxygen on metal surfaces.« less

Ambient atomic resolution atomic force microscopy with qPlus sensors: Part 1.

PubMed

Wastl, Daniel S

2017-01-01

Atomic force microscopy (AFM) is an enormous tool to observe nature in highest resolution and understand fundamental processes like friction and tribology on the nanoscale. Atomic resolution in highest quality was possible only in well-controlled environments like ultrahigh vacuum (UHV) or controlled buffer environments (liquid conditions) and more specified for long-term high-resolution analysis at low temperatures (∼4 K) in UHV where drift is nearly completely absent. Atomic resolution in these environments is possible and is widely used. However, in uncontrolled environments like air, with all its pollutants and aerosols, unspecified thin liquid films as thin as a single molecular water-layer of 200 pm or thicker condensation films with thicknesses up to hundred nanometer, have been a problem for highest resolution since the invention of the AFM. The goal of true atomic resolution on hydrophilic as well as hydrophobic samples was reached recently. In this manuscript we want to review the concept of ambient AFM with atomic resolution. The reader will be introduced to the phenomenology in ambient conditions and the problems will be explained and analyzed while a method for scan parameter optimization will be explained. Recently developed concepts and techniques how to reach atomic resolution in air and ultra-thin liquid films will be shown and explained in detail, using several examples. Microsc. Res. Tech. 80:50-65, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Cavity-QED interactions of two correlated atoms

NASA Astrophysics Data System (ADS)

Esfandiarpour, Saeideh; Safari, Hassan; Bennett, Robert; Yoshi Buhmann, Stefan

2018-05-01

We consider the resonant van der Waals (vdW) interaction between two correlated identical two-level atoms (at least one of which being excited) within the framework of macroscopic cavity quantum electrodynamics in linear, dispersing and absorbing media. The interaction of both atoms with the body-assisted electromagnetic field of the cavity is assumed to be strong. Our time-independent evaluation is based on an extended Jaynes–Cummings model. For a system prepared in a superposition of its dressed states, we derive the general form of the vdW forces, using a Lorentzian single-mode approximation. We demonstrate the applicability of this approach by considering the case of a planar cavity and showing the position dependence of Rabi oscillations. We also show that in the limiting case of weak coupling, our results reproduce the perturbative ones for the case where the field is initially in vacuum state while the atomic state is in a superposition of two correlated states sharing one excitation.

Progress toward studies of bubble-geometry Bose-Einstein condensates in microgravity with a ground-based prototype of NASA CAL

NASA Astrophysics Data System (ADS)

Lundblad, Nathan; Jarvis, Thomas; Paseltiner, Daniel; Lannert, Courtney

2016-05-01

We have proposed using NASA's Cold Atom Laboratory (CAL, launching to the International Space Station in 2017) to generate bubble-geometry Bose-Einstein condensates through radiofrequency dressing of an atom-chip magnetic trap. This geometry has not been truly realized terrestrially due to the perturbing influence of gravity, making it an ideal candidate for microgravity investigation aboard CAL. We report progress in the construction of a functional prototype of the orbital BEC apparatus: a compact atom-chip machine loaded by a 2D+MOT source, conventional 3D MOT, quadrupole trap, and transfer coil. We also present preliminary modeling of the dressed trap uniformity, which will crucially inform the geometric closure of the BEC shell surface as atom number, bubble radius, and bubble aspect ratio are varied. Finally, we discuss plans for experimental sequences to be run aboard CAL guided by intuition from ground-based prototype operation. JPL 1502172.

Protein side chain rotational isomerization: A minimum perturbation mapping study

NASA Astrophysics Data System (ADS)

Haydock, Christopher

1993-05-01

A theory of the rotational isomerization of the indole side chain of tryptophan-47 of variant-3 scorpion neurotoxin is presented. The isomerization potential energy, entropic part of the isomerization free energy, isomer probabilities, transition state theory reaction rates, and indole order parameters are calculated from a minimum perturbation mapping over tryptophan-47 χ1×χ2 torsion space. A new method for calculating the fluorescence anisotropy from molecular dynamics simulations is proposed. The method is based on an expansion that separates transition dipole orientation from chromophore dynamics. The minimum perturbation potential energy map is inverted and applied as a bias potential for a 100 ns umbrella sampling simulation. The entropic part of the isomerization free energy as calculated by minimum perturbation mapping and umbrella sampling are in fairly close agreement. Throughout, the approximation is made that two glutamine and three tyrosine side chains neighboring tryptophan-47 are truncated at the Cβ atom. Comparison with the previous combination thermodynamic perturbation and umbrella sampling study suggests that this truncated neighbor side chain approximation leads to at least a qualitatively correct theory of tryptophan-47 rotational isomerization in the wild type variant-3 scorpion neurotoxin. Analysis of van der Waals interactions in a transition state region indicates that for the simulation of barrier crossing trajectories a linear combination of three specially defined dihedral angles will be superior to a simple side chain dihedral reaction coordinate.

VizieR Online Data Catalog: Energy levels & transition rates for F-like ions (Si+, 2016)

NASA Astrophysics Data System (ADS)

Si, R.; Li, S.; Guo, X. L.; Chen, Z. B.; Brage, T.; Jonsson, P.; Wang, K.; Yan, J.; Chen, C. Y.; Zou, Y. M.

2017-01-01

For the multiconfiguration Dirac-Hartree-Fock (MCDHF) calculation we use the latest version of the GRASP2K code (Jonsson+ 2013CoPhC.184.2197J), while the many-body perturbation theory (MBPT) calculation is performed using the Flexible Atomic Code (FAC; Gu 2008CaJPh..86..675G). (2 data files).

Transition energy and potential energy curves for ionized inner-shell states of CO, O2 and N 2 calculated by several inner-shell multiconfigurational approaches.

PubMed

Moura, Carlos E V de; Oliveira, Ricardo R; Rocha, Alexandre B

2013-05-01

Potential energy curves and inner-shell ionization energies of carbon monoxide, oxygen and nitrogen molecules were calculated using several forms of the inner-shell multiconfigurational self-consistent field (IS-MCSCF) method-a recently proposed protocol to obtain specifically converged inner-shell states at this level. The particular forms of the IS-MCSCF method designated IS-GVB-PP, IS-FVBL and IS-CASSCF stand for perfect pairing generalized valence bond, full valence bond-like MCSCF and complete active space self consistent field, respectively. A comparison of these different versions of the IS-MCSCF method was carried out for the first time. The results indicate that inner-shell states are described accurately even for the simplest version of the method (IS-GVB-PP). Dynamic correlation was recovered by multireference configuration interaction or multireference perturbation theory. For molecules not having equivalent atoms, all methods led to comparable and accurate transition energies. For molecules with equivalent atoms, the most accurate results were obtained by multireference perturbation theory. Scalar relativistic effects were accounted for using the Douglas-Kroll-Hess Hamiltonian.

Photon and vector meson exchanges in the production of light meson pairs and elementary atoms

NASA Astrophysics Data System (ADS)

Gevorkyan, S. R.; Kuraev, E. A.; Volkov, M. K.

2013-01-01

The production of pseudoscalar and scalar meson pairs ππ, ηη, η‧η‧, σσ as well as bound states in high energy γγ collisions are considered. The exchange by a vector particle in the binary process γ + γ → ha + hb with hadronic states ha, hb in fragmentation regions of the initial particle leads to nondecreasing cross sections with increasing energy, that is a priority of peripheral kinematics. Unlike the photon exchange the vector meson exchange needs a reggeization leading to fall with energy growth. Nevertheless, due to the peripheral kinematics beyond very forward production angles the vector meson exchanges dominate over all possible exchanges. The proposed approach allows one to express the matrix elements of the considered processes through impacting factors, which can be calculated in perturbation models like chiral perturbation theory (ChPT) or the Nambu-Jona-Lasinio (NJL) model. In particular cases the impact factors can be determined from relevant γγ sub-processes or the vector meson radiative decay width. The pionium atom production in the collisions of high energy electrons and pions with protons is considered and the relevant cross sections have been estimated.

Study on using I - as heavy atom perturber in cyclodextrin-induced room temperature phosphorimetry

NASA Astrophysics Data System (ADS)

Li, Longdi; Hai, Xuan; Tong, Aijun

2000-07-01

A cyclodextrin induced room temperature phosphorimetry (CD-RTP) for determine β-NOA, which using I- as a heavy atom perturber (HAP) and sodium sulfite as a deoxygenator, was developed. The phosphorescence peak wavelength maxima λex/λem=287/496 521 nm. The analytical curve of β-NOA gives a linear dynamic range of 2.0×10-7-6.0×10-6 mol/l and a detection limit of 4×10-8 mol/l. The relative standard deviation (RSD; n=7) was 3.2% for the 4.0×10-6 mol/l β-NOA in spiked apple samples. The influence of I- concentration on RTP lifetime of β-NOA was studied in detail, the static Stern-Volmer equation for phosphorescence was derived and the luminescence kinetic parameters were calculated. It is found that the relation between I- concentration (x) and RTP lifetime (τ) can be expressed as τ=1.047 e-0.354x and the rate constants of phosphorescence emission kp and non-radiation process ki from T1→S0 were 0.9551s-1 and 0.4276 s-1l-1mol, respectively.

The molecular gradient using the divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation theory: The DEC-RI-MP2 gradient

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

Bykov, Dmytro; Kristensen, Kasper; Kjærgaard, Thomas

We report an implementation of the molecular gradient using the divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation theory (DEC-RI-MP2). The new DEC-RI-MP2 gradient method combines the precision control as well as the linear-scaling and massively parallel features of the DEC scheme with efficient evaluations of the gradient contributions using the RI approximation. We further demonstrate that the DEC-RI-MP2 gradient method is capable of calculating molecular gradients for very large molecular systems. A test set of supramolecular complexes containing up to 158 atoms and 1960 contracted basis functions has been employed to demonstrate the general applicability of the DEC-RI-MP2 methodmore » and to analyze the errors of the DEC approximation. Moreover, the test set contains molecules of complicated electronic structures and is thus deliberately chosen to stress test the DEC-RI-MP2 gradient implementation. Additionally, as a showcase example the full molecular gradient for insulin (787 atoms and 7604 contracted basis functions) has been evaluated.« less

Self-organized perturbations enhance class IV behavior and 1/f power spectrum in elementary cellular automata.

PubMed

Nakajima, Kohei; Haruna, Taichi

2011-09-01

In this paper, we propose a new class of cellular automata based on the modification of its state space. It is introduced to model a computation which is exposed to an environment. We formalized the computation as extension and projection processes of its state space and resulting misidentifications of the state. This is motivated to embed the role of an environment into the system itself, which naturally induces self-organized internal perturbations rather than the usual external perturbations. Implementing this structure into the elementary cellular automata, we characterized its effect by means of input entropy and power spectral analysis. As a result, the cellular automata with this structure showed robust class IV behavior and a 1/f power spectrum in a wide range of rule space comparative to the notion of the edge of chaos. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

The cognitive domain of a glider in the game of life.

PubMed

Beer, Randall D

2014-01-01

This article examines in some technical detail the application of Maturana and Varela's biology of cognition to a simple concrete model: a glider in the game of Life cellular automaton. By adopting an autopoietic perspective on a glider, the set of possible perturbations to it can be divided into destructive and nondestructive subsets. From a glider's reaction to each nondestructive perturbation, its cognitive domain is then mapped. In addition, the structure of a glider's possible knowledge of its immediate environment, and the way in which that knowledge is grounded in its constitution, are fully described. The notion of structural coupling is then explored by characterizing the paths of mutual perturbation that a glider and its environment can undergo. Finally, a simple example of a communicative interaction between two gliders is given. The article concludes with a discussion of the potential implications of this analysis for the enactive approach to cognition.

Effect of second-order exchange in electron-hydrogen scattering

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

Madison, D.H.; Bray, I.; McCarthy, I.

1990-05-07

The electron-hydrogen scattering problem has been a nemesis to theoretical atomic physicists due to the fact that even the most sophisticated of theoretical calculations, both perturbative and nonperturbative, do not agree with experiment. The current opinion is that the perturbative approach cannot be used for this problem since recent second-order calculations are not in agreement with the experimental data and higher-order calculations are deemed impractical. However, these second-order calculations neglected second-order exchange. We have now added exchange to the second-order calculation and have found that the primary source of disagreement between experiment and theory for intermediate energies is attributable notmore » to higher-order terms but to second-order exchange.« less

Generic equilibration dynamics of planar defects in trapped atomic superfluids

DOE PAGES

Scherpelz, Peter; Padavić, Karmela; Murray, Andy; ...

2015-03-18

Here, we investigate equilibration processes shortly after sudden perturbations are applied to ultracold trapped superfluids. We show the similarity of phase imprinting and localized density depletion perturbations, both of which initially are found to produce “phase walls”. These planar defects are associated with a sharp gradient in the phase. Importantly they relax following a quite general sequence. Our studies, based on simulations of the complex time-dependent Ginzburg-Landau equation, address the challenge posed by these experiments: how a superfluid eventually eliminatesa spatially extended planar defect. The processes involved are necessarily more complex than equilibration involving simpler line vortices. An essential mechanismmore » form relaxation involves repeated formation and loss of vortex rings near the trap edge.« less

Prediction of the electron redundant SinNn fullerenes

NASA Astrophysics Data System (ADS)

Yang, Huihui; Song, Yan; Zhang, Yan; Chen, Hongshan

2018-05-01

The stabilities and electronic structures of SimAln-mNn and SinNn (n = 16, 20, m = 12 and n = 24, m = 16) fullerene-like cages have been investigated using density functional method B3LYP and the second-order perturbation theory MP2. The results show that the SimAln-mNn and SinNn fullerenes are more stable than the AlN counterparts. Comparing with the corresponding AlnNn cages, one silicon atom in each Si2N2 square protrudes and the excess electrons reside as lone pair electrons at the outside of the protrudent Si atoms. Analyses on the electronic structures suggest that the Sisbnd N bonds are covalent bonding with strong polarity. The ELF (electron localization function) shows large electron pair probability between Si and N atoms. The orbital interactions between Si and N are stronger than that between Al and N atoms; the overlap integral is 0.40 per Sisbnd N bond in SinNn and 0.34 per Alsbnd N bond in AlnNn. The AIM (atoms in molecule) charges on the Al atoms in AlnNn and SimAln-mNn are 2.37 and 2.40. The charges on the in-plane and protrudent Si atoms are about 2.88 and 1.50 respectively. Considering the large local dipole moments around the protrudent Si atoms, the electrostatic interactions are also favorable to the SiN cages.

Enhanced one-photon double ionization of atoms and molecules in an environment of different species.

PubMed

Stumpf, V; Kryzhevoi, N V; Gokhberg, K; Cederbaum, L S

2014-05-16

The correlated nature of electronic states in atoms and molecules is manifested in the simultaneous emission of two electrons after absorption of a single photon close to the respective threshold. Numerous observations in atoms and small molecules demonstrate that the double ionization efficiency close to threshold is rather small. In this Letter we show that this efficiency can be dramatically enhanced in the environment. To be specific, we concentrate on the case where the species in question has one or several He atoms as neighbors. The enhancement is achieved by an indirect process, where a He atom of the environment absorbs a photon and the resulting He(+) cation is neutralized fast by a process known as electron transfer mediated decay, producing thereby doubly ionized species. The enhancement of the double ionization is demonstrated in detail for the example of the Mg · He cluster. We show that the double ionization cross section of Mg becomes 3 orders of magnitude larger than the respective cross section of the isolated Mg atom. The impact of more neighbors is discussed and the extension to other species and environments is addressed.

Simulation of the low earth orbital atomic oxygen interaction with materials by means of an oxygen ion beam

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Rutledge, Sharon K.; Paulsen, Phillip E.; Steuber, Thomas J.

1989-01-01

Atomic oxygen is the predominant species in low-Earth orbit between the altitudes of 180 and 650 km. These highly reactive atoms are a result of photodissociation of diatomic oxygen molecules from solar photons having a wavelength less than or equal to 2430A. Spacecraft in low-Earth orbit collide with atomic oxygen in the 3P ground state at impact energies of approximately 4.2 to 4.5 eV. As a consequence, organic materials previously used for high altitude geosynchronous spacecraft are severely oxidized in the low-Earth orbital environment. The evaluation of materials durability to atomic oxygen requires ground simulation of this environment to cost effectively screen materials for durability. Directed broad beam oxygen sources are necessary to evaluate potential spacecraft materials performance before and after exposure to the simulated low-Earth orbital environment. This paper presents a description of a low energy, broad oxygen ion beam source used to simulate the low-Earth orbital atomic oxygen environment. The results of materials interaction with this beam and comparison with actual in-space tests of the same meterials will be discussed. Resulting surface morphologies appear to closely replicate those observed in space tests.

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.

PubMed

Keenan, Alexandra B; Jenkins, Sherry L; Jagodnik, Kathleen M; Koplev, Simon; He, Edward; Torre, Denis; Wang, Zichen; Dohlman, Anders B; Silverstein, Moshe C; Lachmann, Alexander; Kuleshov, Maxim V; Ma'ayan, Avi; Stathias, Vasileios; Terryn, Raymond; Cooper, Daniel; Forlin, Michele; Koleti, Amar; Vidovic, Dusica; Chung, Caty; Schürer, Stephan C; Vasiliauskas, Jouzas; Pilarczyk, Marcin; Shamsaei, Behrouz; Fazel, Mehdi; Ren, Yan; Niu, Wen; Clark, Nicholas A; White, Shana; Mahi, Naim; Zhang, Lixia; Kouril, Michal; Reichard, John F; Sivaganesan, Siva; Medvedovic, Mario; Meller, Jaroslaw; Koch, Rick J; Birtwistle, Marc R; Iyengar, Ravi; Sobie, Eric A; Azeloglu, Evren U; Kaye, Julia; Osterloh, Jeannette; Haston, Kelly; Kalra, Jaslin; Finkbiener, Steve; Li, Jonathan; Milani, Pamela; Adam, Miriam; Escalante-Chong, Renan; Sachs, Karen; Lenail, Alex; Ramamoorthy, Divya; Fraenkel, Ernest; Daigle, Gavin; Hussain, Uzma; Coye, Alyssa; Rothstein, Jeffrey; Sareen, Dhruv; Ornelas, Loren; Banuelos, Maria; Mandefro, Berhan; Ho, Ritchie; Svendsen, Clive N; Lim, Ryan G; Stocksdale, Jennifer; Casale, Malcolm S; Thompson, Terri G; Wu, Jie; Thompson, Leslie M; Dardov, Victoria; Venkatraman, Vidya; Matlock, Andrea; Van Eyk, Jennifer E; Jaffe, Jacob D; Papanastasiou, Malvina; Subramanian, Aravind; Golub, Todd R; Erickson, Sean D; Fallahi-Sichani, Mohammad; Hafner, Marc; Gray, Nathanael S; Lin, Jia-Ren; Mills, Caitlin E; Muhlich, Jeremy L; Niepel, Mario; Shamu, Caroline E; Williams, Elizabeth H; Wrobel, David; Sorger, Peter K; Heiser, Laura M; Gray, Joe W; Korkola, James E; Mills, Gordon B; LaBarge, Mark; Feiler, Heidi S; Dane, Mark A; Bucher, Elmar; Nederlof, Michel; Sudar, Damir; Gross, Sean; Kilburn, David F; Smith, Rebecca; Devlin, Kaylyn; Margolis, Ron; Derr, Leslie; Lee, Albert; Pillai, Ajay

2018-01-24

The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and signatures. By assembling an integrated picture of the range of responses of human cells exposed to many perturbations, the LINCS program aims to better understand human disease and to advance the development of new therapies. Perturbations under study include drugs, genetic perturbations, tissue micro-environments, antibodies, and disease-causing mutations. Responses to perturbations are measured by transcript profiling, mass spectrometry, cell imaging, and biochemical methods, among other assays. The LINCS program focuses on cellular physiology shared among tissues and cell types relevant to an array of diseases, including cancer, heart disease, and neurodegenerative disorders. This Perspective describes LINCS technologies, datasets, tools, and approaches to data accessibility and reusability. Copyright © 2017 Elsevier Inc. All rights reserved.

Proceedings of the NASA Workshop on Atomic Oxygen Effects. [low earth orbital environment

NASA Technical Reports Server (NTRS)

Brinza, David E. (Editor)

1987-01-01

A workshop was held to address the scientific issues concerning the effects of atomic oxygen on materials in the low Earth orbital (LEO) environment. The program included 18 invited speakers plus contributed posters covering topics such as LEO spaceflight experiments, interaction mechanisms, and atomic oxygen source development. Discussion sessions were also held to organize a test program to evaluate atomic oxygen exposure facilities. The key issues raised in the workshop were: (1) the need to develop a reliable predictive model of the effects of long-term exposure of materials to the LEO environment; (2) the ability of ground-based exposure facilities to provide useful data for development of durable materials; and (3) accurate determination of the composition of the LEO environment. These proceedings include the invited papers, the abstracts for the contributed posters, and an account of the test program discussion sessions.

Dissipative exciton transfer in donor-bridge-acceptor systems: numerical renormalization group calculation of equilibrium properties.

PubMed

Tornow, Sabine; Tong, Ning-Hua; Bulla, Ralf

2006-07-05

We present a detailed model study of exciton transfer processes in donor-bridge-acceptor (DBA) systems. Using a model which includes the intermolecular Coulomb interaction and the coupling to a dissipative environment we calculate the phase diagram, the absorption spectrum as well as dynamic equilibrium properties with the numerical renormalization group. This method is non-perturbative and therefore allows one to cover the full parameter space, especially the case when the intermolecular Coulomb interaction is of the same order as the coupling to the environment and perturbation theory cannot be applied. For DBA systems with up to six sites we found a transition to the localized phase (self-trapping) depending on the coupling to the dissipative environment. We discuss various criteria which favour delocalized exciton transfer.

Structural, spectroscopic and electronic properties of hydrogen-bonded water molecules in crystals. Ab initio calculations and experimental data of MC1 2· n(H,D) 2O, M = Sr or Ba

NASA Astrophysics Data System (ADS)

Möller, H.; Niu, J. E.; Lutz, H. D.; Schwarz, W. H. E.

1997-12-01

Structural, spectroscopic and electronic properties of (more or less deuterated) water molecules in the crystal fields of SrCl 2·2H 2O, SrCl 2·H 2O and BaCl 2·H 2O, previously investigated by experimental techniques, were calculated by ab initio SCF-MP methods. The H 2O molecules of each compound are asymmetrically surrounded by three adjacent chloride ions, one hydrogen atom being attached to a nearby Cl -, the other less perturbed hydrogen atom bridging the two less near Cl -. The diversity of structural and spectroscopic features found experimentally, for instance the trends from free H 2O to H 2O in BaCl 2·H 2OSrCl 2·H 2OSrCl 2·2H 2O, are well reproduced by the model calculations, which provide the correct assignment and physical interpretation. The differences between the compounds and the asymmetry of the hydrate water molecules can be rationalized with the help of crystal fields. The crystal environment expands the internuclear distances of H 2O by up to 3 pm. The change of vibrational frequencies can be explained qualitatively by only taking the coupling and anharmonicity of the free water molecule and its modified structure in the crystals into account. The infra-red intensities, however, are strongly influenced by the electronic polarization.

Gauge symmetry, chirality and parity effects in four-particle systems: Coulomb's law as a universal function for diatomic molecules.

PubMed

Van Hooydonk, G

2000-11-01

Following recent work in search for a universal function (Van Hooydonk, Eur. J. Inorg. Chem., (1999), 1617), we test four symmetric +/- a(n)Rn potentials for reproducing molecular potential energy curves (PECs). Classical gauge symmetry for 1/R-potentials results in generic left right asymmetric PECs. A pair of symmetric perturbed Coulomb potentials is quantitatively in accordance with observed PECs. For a bond, a four-particle system, charge inversion (a parity effect, atom chirality) is the key to explain this shape generically. A parity adapted Hamiltonian reduces from ten to two terms and to a soluble Bohr-like formula, a Kratzer (1 - Re/R)2 potential. The result is similar to the combined action of spin and wave function symmetry upon the Hamiltonian in Heitler-London theory. Analytical perturbed Coulomb functions varying with (1 - Re/R) scale attractive and repulsive branches of PECs for 13 bonds H2, HF, LiH, KH, AuH, Li2, LiF, KLi, NaCs, Rb2, RbCs, Cs2 and I2 in a single straight line. The 400 turning points for 13 bonds are reproduced with a deviation of 0.007 A at both branches. For 230 points at the repulsive side, the deviation is 0.003 A. The perturbed electrostatic Coulomb law is a universal molecular function. Ab initio zero molecular parameter functions give PECs of acceptable quality, just using atomic ionisation energies. The function can be used as a model potential for inverting levels and gives a first principle's comparison of short- and long-range interactions, important for the study of cold atoms. Wave-packet dynamics, femto-chemistry applied to the crossing of covalent and ionic curves, can provide evidence for this theory. We anticipate this scale/shape invariant scheme applies to smaller scales in nuclear and high-energy particle physics. For larger gravitational scales (Newton 1/R potentials), problems with super-unification are discussed. Reactions between hydrogen and antihydrogen, feasible in the near future, will probably produce normal H2.

Laser Assisted Free-Free Transition in Electron - Atom Collision

NASA Technical Reports Server (NTRS)

Sinha, C.; Bhatia, A. K.

2011-01-01

Free-free transition is studied for electron-Hydrogen atom system in ground state at very low incident energies in presence of an external homogeneous, monochromatic and linearly polarized laser field. The incident electron is considered to be dressed by the laser in a non perturbative manner by choosing the Volkov solutions in both the channels. The space part of the scattering wave function for the electron is solved numerically by taking into account the effect of electron exchange, short range as well as of the long range interactions. Laser assisted differential as well as elastic total cross sections are calculated for single photon absorption/emission in the soft photon limit, the laser intensity being much less than the atomic field intensity. A strong suppression is noted in the laser assisted cross sections as compared to the field free situations. Significant difference is noted in the singlet and the triplet cross sections.

Spontaneous light emission by atomic hydrogen: Fermi's golden rule without cheating

NASA Astrophysics Data System (ADS)

Debierre, V.; Durt, T.; Nicolet, A.; Zolla, F.

2015-10-01

Focusing on the 2 p- 1 s transition in atomic hydrogen, we investigate through first order perturbation theory the time evolution of the survival probability of an electron initially taken to be in the excited (2 p) state. We examine both the results yielded by the standard dipole approximation for the coupling between the atom and the electromagnetic field - for which we propose a cutoff-independent regularisation - and those yielded by the exact coupling function. In both cases, Fermi's golden rule is shown to be an excellent approximation for the system at hand: we found its maximal deviation from the exact behaviour of the system to be of order 10-8 /10-7. Our treatment also yields a rigorous prescription for the choice of the optimal cutoff frequency in the dipole approximation. With our cutoff, the predictions of the dipole approximation are almost indistinguishable at all times from the exact dynamics of the system.

Rayleigh scattering of twisted light by hydrogenlike ions

NASA Astrophysics Data System (ADS)

Peshkov, A. A.; Volotka, A. V.; Surzhykov, A.; Fritzsche, S.

2018-02-01

The elastic Rayleigh scattering of twisted light and, in particular, the polarization (transfer) of the scattered photons have been analyzed within the framework of second-order perturbation theory and Dirac's relativistic equation. Special attention was paid hereby to the scattering on three different atomic targets: single atoms, a mesoscopic (small) target, and a macroscopic (large) target, which are all centered with regard to the beam axis. Detailed calculations of the polarization Stokes parameters were performed for C5 + ions and for twisted Bessel beams. It is shown that the polarization of scattered photons is sensitive to the size of an atomic target and to the helicity, the opening angle, and the projection of the total angular momentum of the incident Bessel beam. These computations indicate more that the Stokes parameters of the (Rayleigh) scattered twisted light may significantly differ from their behavior for an incident plane-wave radiation.

Combining X-ray and neutron crystallography with spectroscopy.

PubMed

Kwon, Hanna; Smith, Oliver; Raven, Emma Lloyd; Moody, Peter C E

2017-02-01

X-ray protein crystallography has, through the determination of the three-dimensional structures of enzymes and their complexes, been essential to the understanding of biological chemistry. However, as X-rays are scattered by electrons, the technique has difficulty locating the presence and position of H atoms (and cannot locate H + ions), knowledge of which is often crucially important for the understanding of enzyme mechanism. Furthermore, X-ray irradiation, through photoelectronic effects, will perturb the redox state in the crystal. By using single-crystal spectrophotometry, reactions taking place in the crystal can be monitored, either to trap intermediates or follow photoreduction during X-ray data collection. By using neutron crystallography, the positions of H atoms can be located, as it is the nuclei rather than the electrons that scatter neutrons, and the scattering length is not determined by the atomic number. Combining the two techniques allows much greater insight into both reaction mechanism and X-ray-induced photoreduction.

Fine- and hyperfine structure investigations of the even-parity configuration system of the atomic holmium

NASA Astrophysics Data System (ADS)

Stefanska, D.; Ruczkowski, J.; Elantkowska, M.; Furmann, B.

2018-04-01

In this work new experimental results concerning the hyperfine structure (hfs) for the even-parity level system of the holmium atom (Ho I) were obtained; additionally, hfs data obtained recently as a by-product in investigations of the odd-parity level system were summarized. In the present work the values of the magnetic dipole and the electric quadrupole hfs constants A and B were determined for 24 even-parity levels, for 14 of them for the first time. On the basis of these results, as well as on available literature data, a parametric study of the fine structure and the hyperfine structure for the even-parity configurations of atomic holmium was performed. A multi-configuration fit of 7 configurations was carried out, taking into account second-order of the perturbation theory. For unknown electronic levels predicted values of the level energies and hfs constants are given, which can facilitate further experimental investigations.

Superradiance of cold atoms coupled to a superconducting circuit

NASA Astrophysics Data System (ADS)

Braun, Daniel; Hoffman, Jonathan; Tiesinga, Eite

2011-06-01

We investigate superradiance of an ensemble of atoms coupled to an integrated superconducting LC circuit. Particular attention is paid to the effect of inhomogeneous coupling constants. Combining perturbation theory in the inhomogeneity and numerical simulations, we show that inhomogeneous coupling constants can significantly affect the superradiant relaxation process. Incomplete relaxation terminating in “dark states” can occur, from which the only escape is through individual spontaneous emission on a much longer time scale. The relaxation dynamics can be significantly accelerated or retarded, depending on the distribution of the coupling constants. On the technical side, we also generalize the previously known propagator of superradiance for identical couplings in the completely symmetric sector to the full exponentially large Hilbert space.

Heavy atom vibrational modes and low-energy vibrational autodetachment in nitromethane anions

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

Thompson, Michael C.; Weber, J. Mathias, E-mail: weberjm@jila.colorado.edu; Department of Chemistry and Biochemistry, University of Colorado at Boulder, 215UCB, Boulder, Colorado 80309-0215

2015-06-21

We report infrared spectra of nitromethane anion, CH{sub 3}NO{sub 2}{sup −}, in the region 700–2150 cm{sup −1}, obtained by Ar predissociation spectroscopy and electron detachment spectroscopy. The data are interpreted in the framework of second-order vibrational perturbation theory based on coupled-cluster electronic structure calculations. The modes in the spectroscopic region studied here are mainly based on vibrations involving the heavier atoms; this work complements earlier studies on nitromethane anion that focused on the CH stretching region of the spectrum. Electron detachment begins at photon energies far below the adiabatic electron affinity due to thermal population of excited vibrational states.

Lattice-Assisted Spectroscopy: A Generalized Scanning Tunneling Microscope for Ultracold Atoms.

PubMed

Kantian, A; Schollwöck, U; Giamarchi, T

2015-10-16

We propose a scheme to measure the frequency-resolved local particle and hole spectra of any optical lattice-confined system of correlated ultracold atoms that offers single-site addressing and imaging, which is now an experimental reality. Combining perturbation theory and time-dependent density matrix renormalization group simulations, we quantitatively test and validate this approach of lattice-assisted spectroscopy on several one-dimensional example systems, such as the superfluid and Mott insulator, with and without a parabolic trap, and finally on edge states of the bosonic Su-Schrieffer-Heeger model. We highlight extensions of our basic scheme to obtain an even wider variety of interesting and important frequency resolved spectra.

Comments on atomic stabilization in intense fields and relativity

NASA Astrophysics Data System (ADS)

Faisal, F. H. M.

2000-07-01

We comment on the problem of atomic stabilization for non-relativistic intensities, Up≪mc2, and discuss how it might be affected at relativistic intensities, Up⩾mc2. Two concepts of stabilization, type I and type II, are distinguished in the present discussion. It is pointed out that in the relativistic case investigations in 3D become unavoidable for any reliable information on the problem. We also point out that for ponderomotive energies greater than 2mc2, the threshold of real pairs production, both the frameworks of classical relativistic simulation, as well as of one-particle Dirac wavefunction, break down. New thinking is needed to develop non-perturbative QED methods in that situation.

Experimental optimization of directed field ionization

NASA Astrophysics Data System (ADS)

Liu, Zhimin Cheryl; Gregoric, Vincent C.; Carroll, Thomas J.; Noel, Michael W.

2017-04-01

The state distribution of an ensemble of Rydberg atoms is commonly measured using selective field ionization. The resulting time resolved ionization signal from a single energy eigenstate tends to spread out due to the multiple avoided Stark level crossings atoms must traverse on the way to ionization. The shape of the ionization signal can be modified by adding a perturbation field to the main field ramp. Here, we present experimental results of the manipulation of the ionization signal using a genetic algorithm. We address how both the genetic algorithm and the experimental parameters were adjusted to achieve an optimized result. This work was supported by the National Science Foundation under Grants No. 1607335 and No. 1607377.

Electronic distributions within protein phenylalanine aromatic rings are reflected by the three-dimensional oxygen atom environments.

PubMed Central

Thomas, K A; Smith, G M; Thomas, T B; Feldmann, R J

1982-01-01

The atomic environments of 170 phenylalanine-residue aromatic rings from 28 protein crystal structures are transformed into a common orientation and combined to calculate an average three-dimensional environment. The spatial distribution of atom types in this environment reveals a preferred interaction between oxygen atoms and the edge of the planar aromatic rings. From the difference in frequency of interaction of oxygen atoms with the edge and the top of the ring, an apparent net free energy difference of interaction favoring the edge of the ring is estimated to be about -1 kcal/mol (1 cal = 4.184 J). Ab initio quantum mechanical calculations, performed on a model consisting of benzene and formamide, indicate that the observed geometry is stabilized by a favorable enthalpic interaction. Although benzene rings are considered to be nonpolar, the electron distribution is a complex multipole with no net dipole moment. The observed interaction orientation frequencies demonstrate that these multipolar electron distributions, when occurring at the short distances encountered in densely packed protein molecules, are significant determinants of internal packing geometries. PMID:6956896

Resonance dispersion interaction of alkali metal atoms in Rydberg states

NASA Astrophysics Data System (ADS)

Kamenski, A. A.; Mokhnenko, S. N.; Ovsyannikov, V. D.

2017-06-01

With the use of second-order perturbation theory in the long-range interatomic interaction for the degenerate states of two Rydberg atoms we have obtained a general formula for the dependence of atomic interaction energy on the interatomic distance R in the presence of the Förster resonance. Inside of the ‘Förster sphere’ (R < RF) this dependence transforms to the formula for electric dipole interaction energy ΔEd - d = C3/R3 and for R > RF it transforms to the formula for the van der Waals interaction energy ΔEVdW = -C6/R6. The van der Waals constant C6 is represented as an expansion in terms of irreducible components which define the dependence on the interatomic axis orientation relative to the quantisation axis of projections M of the total angular momentum J. The numerical values of the irreducible components of tensor C6 were calculated for rubidium atoms in the same Rydberg states |nlJM> with large quantum numbers n. We present the calculated resonance interaction energy of two rubidium atoms in the states |43D5/2M>, whose total energy exceeds by only 8 MHz the total energy of one of the atoms in the state |45P3/2M> and of the other in the state |41F7/2M>.

Compensatory dynamics stabilize aggregate community properties in response to multiple types of perturbations.

PubMed

Brown, Bryan L; Downing, Amy L; Leibold, Mathew A

2016-08-01

Compensatory dynamics are an important suite of mechanisms that can stabilize community and ecosystem attributes in systems subject to environmental fluctuations. However, few experimental investigations of compensatory dynamics have addressed these mechanisms in systems of real-world complexity, and existing evidence relies heavily on correlative analyses, retrospective examination, and experiments in simple systems. We investigated the potential for compensatory dynamics to stabilize plankton communities in plankton mesocosm systems of real-world complexity. We employed four types of perturbations including two types of nutrient pulses, shading, and acidification. To quantify how communities responded to these perturbations, we used a measure of community-wide synchrony combined with spectral analysis that allowed us to assess timescale-specific community dynamics, for example, whether dynamics were synchronous at some timescales but compensatory at others. The 150-d experiment produced 32-point time series of all zooplankton taxa in the mesocosms. We then used those time series to evaluate total zooplankton biomass as an aggregate property and to evaluate community dynamics. For three of our four perturbation types, total zooplankton biomass was significantly less variable in systems with environmental variation than in constant environments. For the same three perturbation types, community-wide synchrony was much lower in fluctuating environments than in the constant environment, particularly at longer timescales (periods ≈ 60 d). Additionally, there were strong negative correlations between population temporal variances and the level of community-wide synchrony. Taken together, these results strongly imply that compensatory interactions between species stabilized total biomass in response to perturbations. Diversity did not differ significantly across either treatments or perturbation types, thus ruling out several classes of mechanisms driven by changes in diversity. We also used several pieces of secondary evidence to evaluate the particular mechanism behind compensatory responses since a wide variety of mechanisms are hypothesized to produce compensatory dynamics. We concluded that fluctuation dependent endogenous cycles that occur as a consequence of consumer-resource interactions in competitive communities were the most likely explanation for the compensatory dynamics observed in our experiment. As with our previous work, scale-dependent dynamics were also a key to understanding compensatory dynamics in these experimental communities. © 2016 by the Ecological Society of America.

Impact-parameter dependence of the energy loss of fast molecular clusters in hydrogen

NASA Astrophysics Data System (ADS)

Fadanelli, R. C.; Grande, P. L.; Schiwietz, G.

2008-03-01

The electronic energy loss of molecular clusters as a function of impact parameter is far less understood than atomic energy losses. For instance, there are no analytical expressions for the energy loss as a function of impact parameter for cluster ions. In this work, we describe two procedures to evaluate the combined energy loss of molecules: Ab initio calculations within the semiclassical approximation and the coupled-channels method using atomic orbitals; and simplified models for the electronic cluster energy loss as a function of the impact parameter, namely the molecular perturbative convolution approximation (MPCA, an extension of the corresponding atomic model PCA) and the molecular unitary convolution approximation (MUCA, a molecular extension of the previous unitary convolution approximation UCA). In this work, an improved ansatz for MPCA is proposed, extending its validity for very compact clusters. For the simplified models, the physical inputs are the oscillators strengths of the target atoms and the target-electron density. The results from these models applied to an atomic hydrogen target yield remarkable agreement with their corresponding ab initio counterparts for different angles between cluster axis and velocity direction at specific energies of 150 and 300 keV/u.

Correlation between Geometrically Induced Oxygen Octahedral Tilts and Multiferroic Behaviors in BiFeO 3 Films

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

Lee, Sung Su; Kim, Young-Min; Lee, Hyun-Jae

The equilibrium position of atoms in a unit cell is directly connected to crystal functionalities, e.g., ferroelectricity, ferromagnetism, and piezoelectricity. The artificial tuning of the energy landscape can involve repositioning atoms as well as manipulating the functionalities of perovskites (ABO 3), which are good model systems to test this legacy. Mechanical energy from external sources accommodating various clamping substrates is utilized to perturb the energy state of perovskite materials fabricated on the substrates and consequently change their functionalities; however, this approach yields undesired complex behaviors of perovskite crystals, such as lattice distortion, displacement of B atoms, and/or tilting of oxygenmore » octahedra. Owing to complimentary collaborations between experimental and theoretical studies, the effects of both lattice distortion and displacement of B atoms are well understood so far, which leaves us a simple question: Can we exclusively control the positions of oxygen atoms in perovskites for functionality manipulation? Here the artificial manipulation of oxygen octahedral tilt angles within multiferroic BiFeO 3 thin films using strong oxygen octahedral coupling with bottom SrRuO 3 layers is reported, which opens up new possibilities of oxygen octahedral engineering.« less

Correlation between Geometrically Induced Oxygen Octahedral Tilts and Multiferroic Behaviors in BiFeO 3 Films

DOE PAGES

Lee, Sung Su; Kim, Young-Min; Lee, Hyun-Jae; ...

2018-03-26

The equilibrium position of atoms in a unit cell is directly connected to crystal functionalities, e.g., ferroelectricity, ferromagnetism, and piezoelectricity. The artificial tuning of the energy landscape can involve repositioning atoms as well as manipulating the functionalities of perovskites (ABO 3), which are good model systems to test this legacy. Mechanical energy from external sources accommodating various clamping substrates is utilized to perturb the energy state of perovskite materials fabricated on the substrates and consequently change their functionalities; however, this approach yields undesired complex behaviors of perovskite crystals, such as lattice distortion, displacement of B atoms, and/or tilting of oxygenmore » octahedra. Owing to complimentary collaborations between experimental and theoretical studies, the effects of both lattice distortion and displacement of B atoms are well understood so far, which leaves us a simple question: Can we exclusively control the positions of oxygen atoms in perovskites for functionality manipulation? Here the artificial manipulation of oxygen octahedral tilt angles within multiferroic BiFeO 3 thin films using strong oxygen octahedral coupling with bottom SrRuO 3 layers is reported, which opens up new possibilities of oxygen octahedral engineering.« less

Photoexcitation of atoms by Laguerre-Gaussian beams

NASA Astrophysics Data System (ADS)

Peshkov, A. A.; Seipt, D.; Surzhykov, A.; Fritzsche, S.

2017-08-01

In a recent experiment, Schmiegelow et al. [Nat. Commun. 7, 12998 (2016), 10.1038/ncomms12998] investigated the magnetic sublevel population of Ca+ ions in a Laguerre-Gaussian light beam if the target atoms were just centered along the beam axis. They demonstrated in this experiment that the sublevel population of the excited atoms is uniquely defined by the projection of the orbital angular momentum of the incident light. However, little attention has been paid so far to the question of how the magnetic sublevels are populated when atoms are displaced from the beam axis by some impact parameter b . Here, we analyze this sublevel population for different atomic impact parameters in first-order perturbation theory and by making use of the density-matrix formalism. Detailed calculations are performed especially for the 4 s 1/2 2S →3 d 5/2 2 transition in Ca+ ions and for the vector potential of a Laguerre-Gaussian beam in Coulomb gauge. It is shown that the magnetic sublevel population of the excited 5/2 2D level varies significantly with the impact parameter and is sensitive to the polarization, the radial index, as well as the orbital angular momentum of the incident light beam.

Resonance interaction energy between two entangled atoms in a photonic bandgap environment.

PubMed

Notararigo, Valentina; Passante, Roberto; Rizzuto, Lucia

2018-03-26

We consider the resonance interaction energy between two identical entangled atoms, where one is in the excited state and the other in the ground state. They interact with the quantum electromagnetic field in the vacuum state and are placed in a photonic-bandgap environment with a dispersion relation quadratic near the gap edge and linear for low frequencies, while the atomic transition frequency is assumed to be inside the photonic gap and near its lower edge. This problem is strictly related to the coherent resonant energy transfer between atoms in external environments. The analysis involves both an isotropic three-dimensional model and the one-dimensional case. The resonance interaction asymptotically decays faster with distance compared to the free-space case, specifically as 1/r 2 compared to the 1/r free-space dependence in the three-dimensional case, and as 1/r compared to the oscillatory dependence in free space for the one-dimensional case. Nonetheless, the interaction energy remains significant and much stronger than dispersion interactions between atoms. On the other hand, spontaneous emission is strongly suppressed by the environment and the correlated state is thus preserved by the spontaneous-decay decoherence effects. We conclude that our configuration is suitable for observing the elusive quantum resonance interaction between entangled atoms.

Toxicity of Graphene Shells, Graphene Oxide, and Graphene Oxide Paper Evaluated with Escherichia coli Biotests

PubMed Central

Efremova, Ludmila V.; Vasilchenko, Alexey S.; Rakov, Eduard G.; Deryabin, Dmitry G.

2015-01-01

The plate-like graphene shells (GS) produced by an original methane pyrolysis method and their derivatives graphene oxide (GO) and graphene oxide paper (GO-P) were evaluated with luminescent Escherichia coli biotests and additional bacterial-based assays which together revealed the graphene-family nanomaterials' toxicity and bioactivity mechanisms. Bioluminescence inhibition assay, fluorescent two-component staining to evaluate cell membrane permeability, and atomic force microscopy data showed GO expressed bioactivity in aqueous suspension, whereas GS suspensions and the GO-P surface were assessed as nontoxic materials. The mechanism of toxicity of GO was shown not to be associated with oxidative stress in the targeted soxS::lux and katG::lux reporter cells; also, GO did not lead to significant mechanical disruption of treated bacteria with the release of intracellular DNA contents into the environment. The well-coordinated time- and dose-dependent surface charge neutralization and transport and energetic disorders in the Escherichia coli cells suggest direct membrane interaction, internalization, and perturbation (i.e., “membrane stress”) as a clue to graphene oxide's mechanism of toxicity. PMID:26221608

Toxicity of Graphene Shells, Graphene Oxide, and Graphene Oxide Paper Evaluated with Escherichia coli Biotests.

PubMed

Efremova, Ludmila V; Vasilchenko, Alexey S; Rakov, Eduard G; Deryabin, Dmitry G

2015-01-01

The plate-like graphene shells (GS) produced by an original methane pyrolysis method and their derivatives graphene oxide (GO) and graphene oxide paper (GO-P) were evaluated with luminescent Escherichia coli biotests and additional bacterial-based assays which together revealed the graphene-family nanomaterials' toxicity and bioactivity mechanisms. Bioluminescence inhibition assay, fluorescent two-component staining to evaluate cell membrane permeability, and atomic force microscopy data showed GO expressed bioactivity in aqueous suspension, whereas GS suspensions and the GO-P surface were assessed as nontoxic materials. The mechanism of toxicity of GO was shown not to be associated with oxidative stress in the targeted soxS::lux and katG::lux reporter cells; also, GO did not lead to significant mechanical disruption of treated bacteria with the release of intracellular DNA contents into the environment. The well-coordinated time- and dose-dependent surface charge neutralization and transport and energetic disorders in the Escherichia coli cells suggest direct membrane interaction, internalization, and perturbation (i.e., "membrane stress") as a clue to graphene oxide's mechanism of toxicity.

Passive and active response of bacteria under mechanical compression

NASA Astrophysics Data System (ADS)

Garces, Renata; Miller, Samantha; Schmidt, Christoph F.; Byophysics Team; Institute of Medical Sciences Collaboration

Bacteria display simple but fascinating cellular structures and geometries. Their shapes are the result of the interplay between osmotic pressure and cell wall construction. Typically, bacteria maintain a high difference of osmotic pressure (on the order of 1 atm) to the environment. This pressure difference (turgor pressure) is supported by the cell envelope, a composite of lipid membranes and a rigid cell wall. The response of the cell envelope to mechanical perturbations such as geometrical confinements is important for the cells survival. Another key property of bacteria is the ability to regulate turgor pressure after abrupt changes of external osmotic conditions. This response relies on the activity of mechanosensitive (MS) channels: membrane proteins that release solutes in response to excessive stress in the cell envelope. We here present experimental data on the mechanical response of the cell envelope and on turgor regulation of bacteria subjected to compressive forces. We indent living cells with micron-sized beads attached to the cantilever of an atomic force microscope (AFM). This approach ensures global deformation of the cell. We show that such mechanical loading is sufficient to gate mechanosensitive channels in isosmotic conditions.

Controlling Directionality and Dimensionality of Radiation by Perturbing Separable Bound States in the Continuum

DOE PAGES

Rivera, Nicholas; Hsu, Chia Wei; Zhen, Bo; ...

2016-09-19

Here, a bound state in the continuum (BIC) is an unusual localized state that is embedded in a continuum of extended states. Here, we present the general condition for BICs to arise from wave equation separability. Then we show that by exploiting perturbations of certain symmetry such BICs can be turned into resonances that radiate with a tailorable directionality and dimensionality. Using this general framework, we construct new examples of separable BICs and resonances that can exist in optical potentials for ultracold atoms, photonic systems, and systems described by tight binding. Such resonances with easily reconfigurable radiation allow for applicationsmore » such as the storage and release of waves at a controllable rate and direction, as well systems that switch between different dimensions of confinement.« less

Universal formulation of second-order generalized Møller-Plesset perturbation theory for a spin-dependent two-component relativistic many-electron Hamiltonian

NASA Astrophysics Data System (ADS)

Nakano, Masahiko; Seino, Junji; Nakai, Hiromi

2017-05-01

We have derived and implemented a universal formulation of the second-order generalized Møller-Plesset perturbation theory (GMP2) for spin-dependent (SD) two-component relativistic many-electron Hamiltonians, such as the infinite-order Douglas-Kroll-Hess Hamiltonian for many-electron systems, which is denoted as IODKH/IODKH. Numerical assessments for He- and Ne-like atoms and 16 diatomic molecules show that the MP2 correlation energies with IODKH/IODKH agree well with those calculated with the four-component Dirac-Coulomb (DC) Hamiltonian, indicating a systematic improvement on the inclusion of relativistic two-electron terms. The present MP2 scheme for IODKH/IODKH is demonstrated to be computationally more efficient than that for DC.

Stark broadening parameter regularities and interpolation and critical evaluation of data for CP star atmospheres research: Stark line shifts

NASA Astrophysics Data System (ADS)

Dimitrijevic, M. S.; Tankosic, D.

1998-04-01

In order to find out if regularities and systematic trends found to be apparent among experimental Stark line shifts allow the accurate interpolation of new data and critical evaluation of experimental results, the exceptions to the established regularities are analysed on the basis of critical reviews of experimental data, and reasons for such exceptions are discussed. We found that such exceptions are mostly due to the situations when: (i) the energy gap between atomic energy levels within a supermultiplet is equal or comparable to the energy gap to the nearest perturbing levels; (ii) the most important perturbing level is embedded between the energy levels of the supermultiplet; (iii) the forbidden transitions have influence on Stark line shifts.

An exact solution of the van der Waals interaction between two ground-state hydrogen atoms

NASA Astrophysics Data System (ADS)

Koga, Toshikatsu; Matsumoto, Shinya

1985-06-01

A momentum space treatment shows that perturbation equations for the H(1s)-H(1s) van der Waals interaction can be exactly solved in their Schrödinger forms without invoking any variational methods. Using the Fock transformation, which projects the momentum vector of an electron from the three-dimensional hyperplane onto the four-dimensional hypersphere, we solve the third order integral-type perturbation equation with respect to the reciprocal of the internuclear distance R. An exact third order wave function is found as a linear combination of infinite number of four-dimensional spherical harmonics. The result allows us to evaluate the exact dispersion energy E6R-6, which is completely determined by the first three coefficients of the above linear combination.

Nuclear Physics Around the Unitarity Limit.

PubMed

König, Sebastian; Grießhammer, Harald W; Hammer, H-W; van Kolck, U

2017-05-19

We argue that many features of the structure of nuclei emerge from a strictly perturbative expansion around the unitarity limit, where the two-nucleon S waves have bound states at zero energy. In this limit, the gross features of states in the nuclear chart are correlated to only one dimensionful parameter, which is related to the breaking of scale invariance to a discrete scaling symmetry and set by the triton binding energy. Observables are moved to their physical values by small perturbative corrections, much like in descriptions of the fine structure of atomic spectra. We provide evidence in favor of the conjecture that light, and possibly heavier, nuclei are bound weakly enough to be insensitive to the details of the interactions but strongly enough to be insensitive to the exact size of the two-nucleon system.

The Materials Chemistry of Atomic Oxygen with Applications to Anisotropic Etching of Submicron Structures in Microelectronics and the Surface Chemistry Engineering of Porous Solids

NASA Technical Reports Server (NTRS)

Koontz, Steve L.; Leger, Lubert J.; Wu, Corina; Cross, Jon B.; Jurgensen, Charles W.

1994-01-01

Neutral atomic oxygen is the most abundant component of the ionospheric plasma in the low Earth orbit environment (LEO; 200 to 700 kilometers altitude) and can produce significant degradation of some spacecraft materials. In order to produce a more complete understanding of the materials chemistry of atomic oxygen, the chemistry and physics of O-atom interactions with materials were determined in three radically different environments: (1) The Space Shuttle cargo bay in low Earth orbit (the EOIM-3 space flight experiment), (2) a high-velocity neutral atom beam system (HVAB) at Los Alamos National Laboratory (LANL), and (3) a microwave-plasma flowing-discharge system at JSC. The Space Shuttle and the high velocity atom beam systems produce atom-surface collision energies ranging from 0.1 to 7 eV (hyperthermal atoms) under high-vacuum conditions, while the flowing discharge system produces a 0.065 eV surface collision energy at a total pressure of 2 Torr. Data obtained in the three different O-atom environments referred to above show that the rate of O-atom reaction with polymeric materials is strongly dependent on atom kinetic energy, obeying a reactive scattering law which suggests that atom kinetic energy is directly available for overcoming activation barriers in the reaction. General relationships between polymer reactivity with O atoms and polymer composition and molecular structure have been determined. In addition, vacuum ultraviolet photochemical effects have been shown to dominate the reaction of O atoms with fluorocarbon polymers. Finally, studies of the materials chemistry of O atoms have produced results which may be of interest to technologists outside the aerospace industry. Atomic oxygen 'spin-off' or 'dual use' technologies in the areas of anisotropic etching in microelectronic materials and device processing, as well as surface chemistry engineering of porous solid materials are described.

Spectral distribution of particle fluence in small field detectors and its implication on small field dosimetry.

PubMed

Benmakhlouf, Hamza; Andreo, Pedro

2017-02-01

Correction factors for the relative dosimetry of narrow megavoltage photon beams have recently been determined in several publications. These corrections are required because of the several small-field effects generally thought to be caused by the lack of lateral charged particle equilibrium (LCPE) in narrow beams. Correction factors for relative dosimetry are ultimately necessary to account for the fluence perturbation caused by the detector. For most small field detectors the perturbation depends on field size, resulting in large correction factors when the field size is decreased. In this work, electron and photon fluence differential in energy will be calculated within the radiation sensitive volume of a number of small field detectors for 6 MV linear accelerator beams. The calculated electron spectra will be used to determine electron fluence perturbation as a function of field size and its implication on small field dosimetry analyzed. Fluence spectra were calculated with the user code PenEasy, based on the PENELOPE Monte Carlo system. The detectors simulated were one liquid ionization chamber, two air ionization chambers, one diamond detector, and six silicon diodes, all manufactured either by PTW or IBA. The spectra were calculated for broad (10 cm × 10 cm) and narrow (0.5 cm × 0.5 cm) photon beams in order to investigate the field size influence on the fluence spectra and its resulting perturbation. The photon fluence spectra were used to analyze the impact of absorption and generation of photons. These will have a direct influence on the electrons generated in the detector radiation sensitive volume. The electron fluence spectra were used to quantify the perturbation effects and their relation to output correction factors. The photon fluence spectra obtained for all detectors were similar to the spectrum in water except for the shielded silicon diodes. The photon fluence in the latter group was strongly influenced, mostly in the low-energy region, by photoabsorption in the high-Z shielding material. For the ionization chambers and the diamond detector, the electron fluence spectra were found to be similar to that in water, for both field sizes. In contrast, electron spectra in the silicon diodes were much higher than that in water for both field sizes. The estimated perturbations of the fluence spectra for the silicon diodes were 11-21% for the large fields and 14-27% for the small fields. These perturbations are related to the atomic number, density and mean excitation energy (I-value) of silicon, as well as to the influence of the "extracameral"' components surrounding the detector sensitive volume. For most detectors the fluence perturbation was also found to increase when the field size was decreased, in consistency with the increased small-field effects observed for the smallest field sizes. The present work improves the understanding of small-field effects by relating output correction factors to spectral fluence perturbations in small field detectors. It is shown that the main reasons for the well-known small-field effects in silicon diodes are the high-Z and density of the "extracameral" detector components and the high I-value of silicon relative to that of water and diamond. Compared to these parameters, the density and atomic number of the radiation sensitive volume material play a less significant role. © 2016 American Association of Physicists in Medicine.

Sculling Compensation Algorithm for SINS Based on Two-Time Scale Perturbation Model of Inertial Measurements

PubMed Central

Wang, Lingling; Fu, Li

2018-01-01

In order to decrease the velocity sculling error under vibration environments, a new sculling error compensation algorithm for strapdown inertial navigation system (SINS) using angular rate and specific force measurements as inputs is proposed in this paper. First, the sculling error formula in incremental velocity update is analytically derived in terms of the angular rate and specific force. Next, two-time scale perturbation models of the angular rate and specific force are constructed. The new sculling correction term is derived and a gravitational search optimization method is used to determine the parameters in the two-time scale perturbation models. Finally, the performance of the proposed algorithm is evaluated in a stochastic real sculling environment, which is different from the conventional algorithms simulated in a pure sculling circumstance. A series of test results demonstrate that the new sculling compensation algorithm can achieve balanced real/pseudo sculling correction performance during velocity update with the advantage of less computation load compared with conventional algorithms. PMID:29346323

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.

Non-local electron transport through normal and topological ladder-like atomic systems

NASA Astrophysics Data System (ADS)

Kurzyna, Marcin; Kwapiński, Tomasz

2018-05-01

We propose a locally protected ladder-like atomic system (nanoconductor) on a substrate that is insensitive to external perturbations. The system corresponds to coupled atomic chains fabricated on different surfaces. Electron transport properties of such conductors are studied theoretically using the model tight-binding Su-Schriffer-Hegger (SSH) Hamiltonian and Green's function formalism. We have found that the conductance of the system is almost insensitive to single adatoms and oscillates as a function of the side chain length with very large periods. Non-local character of the electron transport was observed also for topological SSH chains where nontrivial end states survive in the presence of disturbances as well as for different substrates. We have found that the careful inspection of the density of states or charge waves can provide the information about the atom energy levels and hopping amplitudes. Moreover, the ladder-like geometry allows one to distinguish between normal and topological zero-energy states. It is important that topological chains do not reveal Friedel oscillations which are observed in non-topological chains.

Calculation of the atomic electric dipole moment of Pb2+ induced by nuclear Schiff moment

NASA Astrophysics Data System (ADS)

Ramachandran, S. M.; Latha, K. V. P.; Meenakshisundaram, N.

2017-07-01

We report the atomic electric dipole moment induced by the P, T violating interactions in the nuclear/sub-nuclear level, for 207Pb2+ and 207Pb, owing to the recent interest in the ferroelectric crystal PbTiO3 as one of the candidates for investigating macroscopic P, T-odd effects. In this paper, we calculate the atomic electric dipole moments of 207Pb and Pb2+, parametrized in terms of the P, T-odd coupling parameter, the nuclear Schiff moment (NSM), S, in the frame-work of the coupled-perturbed Hartree-Fock theory. We estimate the Schiff moment of Pb2+ using the experimental result of a system, which is electronically similar to the Pb2+ ion. We present the dominant contributions of the electric dipole moment (EDM) matrix elements and the important correlation effects contributing to the atomic EDM of Pb2+. Our results provide the first ever calculated EDM of the Pb2+ ion, and an estimate of its NSM from which the P, T-odd energy shift in a PbTiO3 crystal can be evaluated.

Relativistic calculation of correlational energy for a helium-like atom

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

Palchikov, V.G.

This paper presents an analytical method for calculating the firstorder correlational energy from the electron interaction, taking account of lag effects. Explicit analytical expressions are obtained for radial matrix elements. The nonrelativistic limit is investigated. The given method may be used to calculate correlation effects in higher orders of perturbation theory (second and higher orders with respect to 1/z) using the Strum expansion for the Coulomb Green's functions.

Tsunamis warning from space :Ionosphere seismology

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

Larmat, Carene

2012-09-04

Ionosphere is the layer of the atmosphere from about 85 to 600km containing electrons and electrically charged atoms that are produced by solar radiation. Perturbations - layering affected by day and night, X-rays and high-energy protons from the solar flares, geomagnetic storms, lightning, drivers-from-below. Strategic for radio-wave transmission. This project discusses the inversion of ionosphere signals, tsunami wave amplitude and coupling parameters, which improves tsunami warning systems.

Generalization and Parallelization of Messy Genetic Algorithms and Communication in Parallel Genetic Algorithms.

DTIC Science & Technology

1992-12-01

Dynamics and Free Energy Perturbation Methods." Reviews in Computational Chem- istry edited by Kenny B. Lipkowitz and Donald B. Boyd, chapter 8, 295-320...atomic motions during annealing, allows the search to probabilistically move in a locally non-optimal direction. The probability of doing so is...Network processors communicate via communication links. This type of communication is generally very slow relative to other processor activities

Atomic oxygen effects on spacecraft materials: The state of the art of our knowledge

NASA Technical Reports Server (NTRS)

Koontz, Steven L.

1989-01-01

In the flight materials exposure data base extensive quantitative data is available from limited exposures in a narrow range of orbital environments. More data is needed in a wider range of environments as well as longer exposure times. Synergistic effects with other environmental factors; polar orbit and higher altitude environments; and real time materials degradation data is needed to understand degradation kinetics and mechanism. Almost no laboratory data exists from high fidelity simulations of the LEO environment. Simulation and test system are under development, and the data base is scanty. Theoretical understanding of hyperthermal atom surface reactions in the LEO environment is not good enough to support development of reliable accelerated test methods. The laser sustained discharge, atom beam sources are the most promising high fidelity simulation-test systems at this time.

Nonperturbative Time Dependent Solution of a Simple Ionization Model

NASA Astrophysics Data System (ADS)

Costin, Ovidiu; Costin, Rodica D.; Lebowitz, Joel L.

2018-02-01

We present a non-perturbative solution of the Schrödinger equation {iψ_t(t,x)=-ψ_{xx}(t,x)-2(1 +α sinω t) δ(x)ψ(t,x)} , written in units in which \\hbar=2m=1, describing the ionization of a model atom by a parametric oscillating potential. This model has been studied extensively by many authors, including us. It has surprisingly many features in common with those observed in the ionization of real atoms and emission by solids, subjected to microwave or laser radiation. Here we use new mathematical methods to go beyond previous investigations and to provide a complete and rigorous analysis of this system. We obtain the Borel-resummed transseries (multi-instanton expansion) valid for all values of α, ω, t for the wave function, ionization probability, and energy distribution of the emitted electrons, the latter not studied previously for this model. We show that for large t and small α the energy distribution has sharp peaks at energies which are multiples of ω, corresponding to photon capture. We obtain small α expansions that converge for all t, unlike those of standard perturbation theory. We expect that our analysis will serve as a basis for treating more realistic systems revealing a form of universality in different emission processes.

Mechanical Characterization of Microengineered Epithelial Cysts by Using Atomic Force Microscopy.

PubMed

Shen, Yusheng; Guan, Dongshi; Serien, Daniela; Takeuchi, Shoji; Tong, Penger; Yobas, Levent; Huang, Pingbo

2017-01-24

Most organs contain interconnected tubular tissues that are one-cell-thick, polarized epithelial monolayers enclosing a fluid-filled lumen. Such tissue organization plays crucial roles in developmental and normal physiology, and the proper functioning of these tissues depends on their regulation by complex biochemical perturbations and equally important, but poorly understood, mechanical perturbations. In this study, by combining micropatterning techniques and atomic force microscopy, we developed a simple in vitro experimental platform for characterizing the mechanical properties of the MDCK II cyst, the simplest model of lumen-enclosing epithelial monolayers. By using this platform, we estimated the elasticity of the cyst monolayer and showed that the presence of a luminal space influences cyst mechanics substantially, which could be attributed to polarization and tissue-level coordination. More interestingly, the results from force-relaxation experiments showed that the cysts also displayed tissue-level poroelastic characteristics that differed slightly from those of single cells. Our study provides the first quantitative findings, to our knowledge, on the tissue-level mechanics of well-polarized epithelial cysts and offers new insights into the interplay between cyst mechanics and cyst physiology. Moreover, our simple platform is a potentially useful tool for enhancing the current understanding of cyst mechanics in health and disease. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Mechanically Assisted Self-Healing of Ultrathin Gold Nanowires.

PubMed

Wang, Binjun; Han, Ying; Xu, Shang; Qiu, Lu; Ding, Feng; Lou, Jun; Lu, Yang

2018-04-17

As the critical feature sizes of integrated circuits approaching sub-10 nm, ultrathin gold nanowires (diameter <10 nm) have emerged as one of the most promising candidates for next-generation interconnects in nanoelectronics. Also due to their ultrasmall dimensions, however, the structures and morphologies of ultrathin gold nanowires are more prone to be damaged during practical services, for example, Rayleigh instability can significantly alter their morphologies upon Joule heating, hindering their applications as interconnects. Here, it is shown that upon mechanical perturbations, predamaged, nonuniform ultrathin gold nanowires can quickly recover into uniform diameters and restore their smooth surfaces, via a simple mechanically assisted self-healing process. By examining the local self-healing process through in situ high-resolution transmission electron microscopy, the underlying mechanism is believed to be associated with surface atomic diffusion as evidenced by molecular dynamics simulations. In addition, mechanical manipulation can assist the atoms to overcome the diffusion barriers, as suggested by ab initio calculations, to activate more surface adatoms to diffuse and consequently speed up the self-healing process. This result can provide a facile method to repair ultrathin metallic nanowires directly in functional devices, and quickly restore their microstructures and morphologies by simple global mechanical perturbations. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enhancement of piezoelectric constants induced by cation-substitution and two-dimensional strain effects on ZnO predicted by density functional perturbation theory

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

Nakamura, Kaoru, E-mail: n-kaoru@criepi.denken.or.jp; Higuchi, Sadao; Ohnuma, Toshiharu

2016-03-21

Using density functional perturbation theory, we investigated the effect of various substitutional dopant elements and in-plane strain on the piezoelectric properties of ZnO. The piezoelectric stress constant e{sub 33} of doped ZnO was found to depend on the formal charge of the substitutional dopant. By decomposing the piezoelectric stress constant e{sub 33} into the individual atomic contributions, the change in the piezoelectric properties was found to originate from a change in the coupling between the atomic displacement and the strain. Furthermore, we found that in-plane tensile strain along the a axis, which is specific to the thin film, can enhancemore » the piezoelectric constant of ZnO. A phase transition from wurtzite to h-BN-type structure was found to occur with increasing in-plane tensile. The piezoelectric strain constant d{sub 33} was predicted to reach ∼200 pC/N for 2.78 at. % V-substituted ZnO at 5.5% in-plane strain, just before the phase transition. These theoretical results suggest that the piezoelectric constant of ZnO can be enhanced by controlling the in-plane strain via selection of the substrate material and dopant element.« less

Weak-field multiphoton femtosecond coherent control in the single-cycle regime.

PubMed

Chuntonov, Lev; Fleischer, Avner; Amitay, Zohar

2011-03-28

Weak-field coherent phase control of atomic non-resonant multiphoton excitation induced by shaped femtosecond pulses is studied theoretically in the single-cycle regime. The carrier-envelope phase (CEP) of the pulse, which in the multi-cycle regime does not play any control role, is shown here to be a new effective control parameter that its effect is highly sensitive to the spectral position of the ultrabroad spectrum. Rationally chosen position of the ultrabroadband spectrum coherently induces several groups of multiphoton transitions from the ground state to the excited state of the system: transitions involving only absorbed photons as well as Raman transitions involving both absorbed and emitted photons. The intra-group interference is controlled by the relative spectral phase of the different frequency components of the pulse, while the inter-group interference is controlled jointly by the CEP and the relative spectral phase. Specifically, non-resonant two- and three-photon excitation is studied in a simple model system within the perturbative frequency-domain framework. The developed intuition is then applied to weak-field multiphoton excitation of atomic cesium (Cs), where the simplified model is verified by non-perturbative numerical solution of the time-dependent Schrödinger equation. We expect this work to serve as a basis for a new line of femtosecond coherent control experiments.

Assessing the stability of free-energy perturbation calculations by performing variations in the method

NASA Astrophysics Data System (ADS)

Manzoni, Francesco; Ryde, Ulf

2018-03-01

We have calculated relative binding affinities for eight tetrafluorophenyl-triazole-thiogalactoside inhibitors of galectin-3 with the alchemical free-energy perturbation approach. We obtain a mean absolute deviation from experimental estimates of only 2-3 kJ/mol and a correlation coefficient (R 2) of 0.5-0.8 for seven relative affinities spanning a range of up to 11 kJ/mol. We also studied the effect of using different methods to calculate the charges of the inhibitor and different sizes of the perturbed group (the atoms that are described by soft-core potentials and are allowed to have differing coordinates). However, the various approaches gave rather similar results and it is not possible to point out one approach as consistently and significantly better than the others. Instead, we suggest that such small and reasonable variations in the computational method can be used to check how stable the calculated results are and to obtain a more accurate estimate of the uncertainty than if performing only one calculation with a single computational setup.

Hα3: an Hα imaging survey of HI selected galaxies from ALFALFA. II. Star formation properties of galaxies in the Virgo cluster and surroundings

NASA Astrophysics Data System (ADS)

Gavazzi, G.; Fumagalli, M.; Fossati, M.; Galardo, V.; Grossetti, F.; Boselli, A.; Giovanelli, R.; Haynes, M. P.

2013-05-01

Context. We present the analysis of Hα3, an Hα narrow-band imaging follow-up survey of 409 galaxies selected from the HI Arecibo Legacy Fast ALFA Survey (ALFALFA) in the Local Supercluster, including the Virgo cluster, in the region 11h < RA < 16h ; 4o < Dec < 16°; 350 < cz < 2000 km s-1. Aims: Taking advantage of Hα3, which provides the complete census of the recent massive star formation rate (SFR) in HI-rich galaxies in the local Universe and of ancillary optical data from SDSS we explore the relations between the stellar mass, the HI mass, and the current, massive SFR of nearby galaxies in the Virgo cluster. We compare these with those of isolated galaxies in the Local Supercluster, and we investigate the role of the environment in shaping the star formation properties of galaxies at the present cosmological epoch. Methods: By using the Hα hydrogen recombination line as a tracer of recent star formation, we investigated the relationships between atomic neutral gas and newly formed stars in different environments (cluster and field), for many morphological types (spirals and dwarfs), and over a wide range of stellar masses (107.5 to 1011.5 M⊙). To quantify the degree of environmental perturbation, we adopted an updated calibration of the HI deficiency parameter which we used to divide the sample into three classes: unperturbed galaxies (DefHI ≤ 0.3), perturbed galaxies (0.3 < DefHI < 0.9), and highly perturbed galaxies (DefHI ≥ 0.9). Results: Studying the mean properties of late-type galaxies in the Local Supercluster, we find that galaxies in increasing dense local galaxy conditions (or decreasing projected angular separation from M 87) show a significant decrease in the HI content and in the mean specific SFR, along with a progressive reddening of their stellar populations. The gradual quenching of the star formation occurs outside-in, consistently with the predictions of the ram pressure model. Once considered as a whole, the Virgo cluster is effective in removing neutral hydrogen from galaxies, and this perturbation is strong enough to appreciably reduce the SFR of its entire galaxy population. Conclusions: An estimate of the present infall rate of 300-400 galaxies per Gyr in the Virgo cluster is obtained from the number of existing HI-rich late-type systems, assuming 200-300 Myr as the time scale for HI ablation. If the infall process has been acting at a constant rate, this would imply that the Virgo cluster has formed approximately 2 Gyr ago, consistently with the idea that Virgo is in a young state of dynamical evolution. Based on observations taken at the observatory of San Pedro Martir (Baja California, Mexico), belonging to the Mexican Observatorio Astronómico Nacional.

Perturbed Communication in a Virtual Environment to Train Medical Team Leaders.

PubMed

Huguet, Lauriane; Lourdeaux, Domitile; Sabouret, Nicolas; Ferrer, Marie-Hélène

2016-01-01

The VICTEAMS project aims at designing a virtual environment for training medical team leaders to non-technical skills. The virtual environment is populated with autonomous virtual agents who are able to make mistakes (in action or communication) in order to train rescue team leaders and to make them adaptive with all kinds of situations or teams.

Camera pose estimation to improve accuracy and reliability of joint angles assessed with attitude and heading reference systems.

PubMed

Lebel, Karina; Hamel, Mathieu; Duval, Christian; Nguyen, Hung; Boissy, Patrick

2018-01-01

Joint kinematics can be assessed using orientation estimates from Attitude and Heading Reference Systems (AHRS). However, magnetically-perturbed environments affect the accuracy of the estimated orientations. This study investigates, both in controlled and human mobility conditions, a trial calibration technic based on a 2D photograph with a pose estimation algorithm to correct initial difference in AHRS Inertial reference frames and improve joint angle accuracy. In controlled conditions, two AHRS were solidly affixed onto a wooden stick and a series of static and dynamic trials were performed in varying environments. Mean accuracy of relative orientation between the two AHRS was improved from 24.4° to 2.9° using the proposed correction method. In human conditions, AHRS were placed on the shank and the foot of a participant who performed repeated trials of straight walking and walking while turning, varying the level of magnetic perturbation in the starting environment and the walking speed. Mean joint orientation accuracy went from 6.7° to 2.8° using the correction algorithm. The impact of starting environment was also greatly reduced, up to a point where one could consider it as non-significant from a clinical point of view (maximum mean difference went from 8° to 0.6°). The results obtained demonstrate that the proposed method improves significantly the mean accuracy of AHRS joint orientation estimations in magnetically-perturbed environments and can be implemented in post processing of AHRS data collected during biomechanical evaluation of motion. Copyright © 2017 Elsevier B.V. All rights reserved.

Wigner-Seitz local-environment study of the high-T/sub c/ superconductors

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

Melamud, M.; Bennett, L.H.; Watson, R.E.

The near-neighbor environments and the bonding of atoms in the high-T/sub c/ superconductors are studied using a Wigner-Seitz-cell contruction. Assuming metallic radii for the atoms, it is shown that the Ba, Y, and La atoms have large coordination numbers, implying a three-dimensional bonding scheme. The La-Cu-O type (approx. =40 K) and the Y-Ba-Cu-O type (approx. =90 K) superconductors both display the same bonding characteristics.

Fluorescence Modulation of Green Fluorescent Protein Using Fluorinated Unnatural Amino Acids.

PubMed

Villa, Jordan K; Tran, Hong-Anh; Vipani, Megha; Gianturco, Stephanie; Bhasin, Konark; Russell, Brent L; Harbron, Elizabeth J; Young, Douglas D

2017-07-16

The ability to modulate protein function through minimal perturbations to amino acid structure represents an ideal mechanism to engineer optimized proteins. Due to the novel spectroscopic properties of green fluorescent protein, it has found widespread application as a reporter protein throughout the fields of biology and chemistry. Using site-specific amino acid mutagenesis, we have incorporated various fluorotyrosine residues directly into the fluorophore of the protein, altering the fluorescence and shifting the pKa of the phenolic proton associated with the fluorophore. Relative to wild type GFP, the fluorescence spectrum of the protein is altered with each additional fluorine atom, and the mutant GFPs have the potential to be employed as pH sensors due to the altered electronic properties of the fluorine atoms.

FAST TRACK COMMUNICATION: Electronic structure of a graphene/hexagonal-BN heterostructure grown on Ru(0001) by chemical vapor deposition and atomic layer deposition: extrinsically doped graphene

NASA Astrophysics Data System (ADS)

Bjelkevig, Cameron; Mi, Zhou; Xiao, Jie; Dowben, P. A.; Wang, Lu; Mei, Wai-Ning; Kelber, Jeffry A.

2010-08-01

A significant BN-to-graphene charge donation is evident in the electronic structure of a graphene/h-BN(0001) heterojunction grown by chemical vapor deposition and atomic layer deposition directly on Ru(0001), consistent with density functional theory. This filling of the lowest unoccupied state near the Brillouin zone center has been characterized by combined photoemission/k vector resolved inverse photoemission spectroscopies, and Raman and scanning tunneling microscopy/spectroscopy. The unoccupied σ*(Γ1 +) band dispersion yields an effective mass of 0.05 me for graphene in the graphene/h-BN(0001) heterostructure, in spite of strong perturbations to the graphene conduction band edge placement.

Generation of long-living entanglement between two distant three-level atoms in non-Markovian environments.

PubMed

Li, Chuang; Yang, Sen; Song, Jie; Xia, Yan; Ding, Weiqiang

2017-05-15

In this paper, a scheme for the generation of long-living entanglement between two distant Λ-type three-level atoms separately trapped in two dissipative cavities is proposed. In this scheme, two dissipative cavities are coupled to their own non-Markovian environments and two three-level atoms are driven by the classical fields. The entangled state between the two atoms is produced by performing Bell state measurement (BSM) on photons leaving the dissipative cavities. Using the time-dependent Schördinger equation, we obtain the analytical results for the evolution of the entanglement. It is revealed that, by manipulating the detunings of classical field, the long-living stationary entanglement between two atoms can be generated in the presence of dissipation.

Localization of a small change in a multiple scattering environment without modeling of the actual medium.

PubMed

Rakotonarivo, S T; Walker, S C; Kuperman, W A; Roux, P

2011-12-01

A method to actively localize a small perturbation in a multiple scattering medium using a collection of remote acoustic sensors is presented. The approach requires only minimal modeling and no knowledge of the scatterer distribution and properties of the scattering medium and the perturbation. The medium is ensonified before and after a perturbation is introduced. The coherent difference between the measured signals then reveals all field components that have interacted with the perturbation. A simple single scatter filter (that ignores the presence of the medium scatterers) is matched to the earliest change of the coherent difference to localize the perturbation. Using a multi-source/receiver laboratory setup in air, the technique has been successfully tested with experimental data at frequencies varying from 30 to 60 kHz (wavelength ranging from 0.5 to 1 cm) for cm-scale scatterers in a scattering medium with a size two to five times bigger than its transport mean free path. © 2011 Acoustical Society of America

Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase.

PubMed

Woods, Christopher J; Shaw, Katherine E; Mulholland, Adrian J

2015-01-22

The applicability of combined quantum mechanics/molecular mechanics (QM/MM) methods for the calculation of absolute binding free energies of conserved water molecules in protein/ligand complexes is demonstrated. Here, we apply QM/MM Monte Carlo simulations to investigate binding of water molecules to influenza neuraminidase. We investigate five different complexes, including those with the drugs oseltamivir and peramivir. We investigate water molecules in two different environments, one more hydrophobic and one hydrophilic. We calculate the free-energy change for perturbation of a QM to MM representation of the bound water molecule. The calculations are performed at the BLYP/aVDZ (QM) and TIP4P (MM) levels of theory, which we have previously demonstrated to be consistent with one another for QM/MM modeling. The results show that the QM to MM perturbation is significant in both environments (greater than 1 kcal mol(-1)) and larger in the more hydrophilic site. Comparison with the same perturbation in bulk water shows that this makes a contribution to binding. The results quantify how electronic polarization differences in different environments affect binding affinity and also demonstrate that extensive, converged QM/MM free-energy simulations, with good levels of QM theory, are now practical for protein/ligand complexes.

Water quality assessment by means of HFNI valvometry and high-frequency data modeling.

PubMed

Sow, Mohamedou; Durrieu, Gilles; Briollais, Laurent; Ciret, Pierre; Massabuau, Jean-Charles

2011-11-01

The high-frequency measurements of valve activity in bivalves (e.g., valvometry) over a long period of time and in various environmental conditions allow a very accurate study of their behaviors as well as a global analysis of possible perturbations due to the environment. Valvometry uses the bivalve's ability to close its shell when exposed to a contaminant or other abnormal environmental conditions as an alarm to indicate possible perturbations in the environment. The modeling of such high-frequency serial valvometry data is statistically challenging, and here, a nonparametric approach based on kernel estimation is proposed. This method has the advantage of summarizing complex data into a simple density profile obtained from each animal at every 24-h period to ultimately make inference about time effect and external conditions on this profile. The statistical properties of the estimator are presented. Through an application to a sample of 16 oysters living in the Bay of Arcachon (France), we demonstrate that this method can be used to first estimate the normal biological rhythms of permanently immersed oysters and second to detect perturbations of these rhythms due to changes in their environment. We anticipate that this approach could have an important contribution to the survey of aquatic systems.

A multispacecraft event study of Pc5 ultralow-frequency waves in the magnetosphere and their external drivers

DOE PAGES

Wang, Chih-Ping; Thorne, Richard; Liu, Terry Z.; ...

2017-05-09

We investigate a quiet time event of magnetospheric Pc5 ultralow-frequency (ULF) waves and their likely external drivers using multiple spacecraft observations. Enhancements of electric and magnetic field perturbations in two narrow frequency bands, 1.5–2 mHz and 3.5–4 mHz, were observed over a large radial distance range from r ~ 5 to 11 RE. During the first half of this event, perturbations were mainly observed in the transverse components and only in the 3.5–4 mHz band. In comparison, enhancements were stronger during the second half in both transverse and compressional components and in both frequency bands. No indication of field linemore » resonances was found for these magnetic field perturbations. Perturbations in these two bands were also observed in the magnetosheath, but not in the solar wind dynamic pressure perturbations. For the first interval, good correlations between the flow perturbations in the magnetosphere and magnetosheath and an indirect signature for Kelvin-Helmholtz (K-H) vortices suggest K-H surface waves as the driver. For the second interval, good correlations are found between the magnetosheath dynamic pressure perturbations, magnetopause deformation, and magnetospheric waves, all in good correspondence to interplanetary magnetic field (IMF) discontinuities. The characteristics of these perturbations can be explained by being driven by foreshock perturbations resulting from these IMF discontinuities. This event shows that even during quiet periods, K-H-unstable magnetopause and ion foreshock perturbations can combine to create a highly dynamic magnetospheric ULF wave environment« less

A multispacecraft event study of Pc5 ultralow-frequency waves in the magnetosphere and their external drivers

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

Wang, Chih-Ping; Thorne, Richard; Liu, Terry Z.

We investigate a quiet time event of magnetospheric Pc5 ultralow-frequency (ULF) waves and their likely external drivers using multiple spacecraft observations. Enhancements of electric and magnetic field perturbations in two narrow frequency bands, 1.5–2 mHz and 3.5–4 mHz, were observed over a large radial distance range from r ~ 5 to 11 RE. During the first half of this event, perturbations were mainly observed in the transverse components and only in the 3.5–4 mHz band. In comparison, enhancements were stronger during the second half in both transverse and compressional components and in both frequency bands. No indication of field linemore » resonances was found for these magnetic field perturbations. Perturbations in these two bands were also observed in the magnetosheath, but not in the solar wind dynamic pressure perturbations. For the first interval, good correlations between the flow perturbations in the magnetosphere and magnetosheath and an indirect signature for Kelvin-Helmholtz (K-H) vortices suggest K-H surface waves as the driver. For the second interval, good correlations are found between the magnetosheath dynamic pressure perturbations, magnetopause deformation, and magnetospheric waves, all in good correspondence to interplanetary magnetic field (IMF) discontinuities. The characteristics of these perturbations can be explained by being driven by foreshock perturbations resulting from these IMF discontinuities. This event shows that even during quiet periods, K-H-unstable magnetopause and ion foreshock perturbations can combine to create a highly dynamic magnetospheric ULF wave environment« less

Post-Hartree-Fock studies of the He/Mg(0001) interaction: Anti-corrugation, screening, and pairwise additivity

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

Lara-Castells, María Pilar de, E-mail: Pilar.deLara.Castells@csic.es; Fernández-Perea, Ricardo; Madzharova, Fani

2016-06-28

The adsorption of noble gases on metallic surfaces represents a paradigmatic case of van-der-Waals (vdW) interaction due to the role of screening effects on the corrugation of the interaction potential [J. L. F. Da Silva et al., Phys. Rev. Lett. 90, 066104 (2003)]. The extremely small adsorption energy of He atoms on the Mg(0001) surface (below 3 meV) and the delocalized nature and mobility of the surface electrons make the He/Mg(0001) system particularly challenging, even for state-of-the-art vdW-corrected density functional-based (vdW-DFT) approaches [M. P. de Lara-Castells et al., J. Chem. Phys. 143, 194701 (2015)]. In this work, we meet thismore » challenge by applying two different procedures. First, the dispersion-corrected second-order Möller-Plesset perturbation theory (MP2C) approach is adopted, using bare metal clusters of increasing size. Second, the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)] is applied at coupled cluster singles and doubles and perturbative triples level, using embedded cluster models of the metal surface. Both approaches provide clear evidences of the anti-corrugation of the interaction potential: the He atom prefers on-top sites, instead of the expected hollow sites. This is interpreted as a signature of the screening of the He atom by the metal for the on-top configuration. The strong screening in the metal is clearly reflected in the relative contribution of successively deeper surface layers to the main dispersion contribution. Aimed to assist future dynamical simulations, a pairwise potential model for the He/surface interaction as a sum of effective He–Mg pair potentials is also presented, as an improvement of the approximation using isolated He–Mg pairs.« less

One Electron Atom in Special Relativity with de Sitter Space-Time Symmetry

NASA Astrophysics Data System (ADS)

Yan, Mu-Lin

2012-06-01

The de Sitter invariant Special Relativity (dS-SR) is SR with constant curvature, and a natural extension of usual Einstein SR (E-SR). In this paper, we solve the dS-SR Dirac equation of Hydrogen by means of the adiabatic approach and the quasi-stationary perturbation calculations of QM. Hydrogen atom is located in the light cone of the Universe. FRW metric and ΛCDM cosmological model are used to discuss this issue. To the atom, effects of de Sitter space-time geometry described by Beltrami metric are taken into account. The dS-SR Dirac equation turns out to be a time dependent quantum Hamiltonian system. We reveal that: (i) The fundamental physics constants me, ℏ, e variate adiabatically along with cosmologic time in dS-SR QM framework. But the fine-structure constant α ≡ e2/(ℏc) keeps to be invariant; (ii) (2s1/2-2p1/2)-splitting due to dS-SR QM effects: By means of perturbation theory, that splitting ΔE(z) are calculated analytically, which belongs to Script O(1/R2)-physics of dS-SR QM. Numerically, we find that when |R| ≃ {103 Gly, 104 Gly, 105 Gly}, and z ≃ {1, or 2}, the ΔE(z) ≫ 1 (Lamb shift). This indicates that for these cases the hyperfine structure effects due to QED could be ignored, and the dS-SR fine structure effects are dominant. This effect could be used to determine the universal constant R in dS-SR, and be thought as a new physics beyond E-SR.

Studies of Rotationally and Vibrationally Inelastic Collisions of NaK with Atomic Perturbers

NASA Astrophysics Data System (ADS)

Richter, Kara M.

This dissertation discusses investigations of vibrationally and rotationally inelastic collisions of NaK with argon, helium and potassium as collision partners. We have investigated collisions of NaK molecules in the 2(A) 1Sigma+, state with argon and helium collision partners in a laser-induced fluorescence (LIF) experiment. The pump laser prepares the molecules in particular ro-vibrational (v, J) levels in the 2(A) 1Sigma+, state. These excited molecules then emit fluorescence as they make transitions back to the ground [2(X)1Sigma +] state, and this fluorescence is collected by a Bomem Fourier-transform spectrometer. Weak collisional satellite lines appear flanking strong, direct lines in the recorded spectra. These satellite lines are due to collisions of the NaK molecule in the 2(A)1Sigma+, state with noble gas and alkali atom perturbers, which carry population to nearby rotational levels [(v, J) →(v, J + DeltaJ)] or to various rotational levels of nearby vibrational levels, [(v, J)→ (v + Deltav, J + DeltaJ)]. Ratios of the intensity of each collisional line to the intensity of the direct line then yields information pertaining to the transfer of population in the collision. Our results show a propensity for DeltaJ = even collisions of NaK with noble gas atoms, which is slightly more pronounced for collisions with helium than with argon. Such a DeltaJ = even propensity was not observed in the vibrationally inelastic collisions. Although it would be desirable to operate in the single collision regime, practical considerations make that difficult to achieve. Therefore, we have developed a method to estimate the effects of multiple collisions on our measured rate coefficients and have obtained approximate corrected values.

Electronic and optical properties of hexathiapentacene in the gas and crystal phases

NASA Astrophysics Data System (ADS)

Cardia, R.; Malloci, G.; Rignanese, G.-M.; Blase, X.; Molteni, E.; Cappellini, G.

2016-06-01

Using density functional theory (DFT) and its time-dependent (TD) extension, the electronic and optical properties of the hexathiapentacene (HTP) molecule, a derivative of pentacene (PNT) obtained by symmetric substitution of the six central H atoms with S atoms, are investigated for its gas and solid phases. For the molecular structure, all-electron calculations are performed using a Gaussian localized orbital basis set in conjunction with the Becke three-parameter Lee-Yang-Parr (B3LYP) hybrid exchange-correlation functional. Electron affinities, ionization energies, quasiparticle energy gaps, optical absorption spectra, and exciton binding energies are calculated and compared with the corresponding results for PNT, as well as with the available experimental data. The DFT and TDDFT results are also validated by performing many-body perturbation theory calculations within the G W and Bethe-Salpeter equation formalisms. The functionalization with S atoms induces an increase of both ionization energies and electron affinities, a sizable reduction of the fundamental electronic gap, and a redshift of the optical absorption onset. Notably, the intensity of the first absorption peak of HTP falling in the visible region is found to be nearly tripled with respect to the pure PNT molecule. For the crystal structures, pseudopotential calculations are adopted using a plane-wave basis set together with the Perdew-Burke-Ernzerhof exchange-correlation functional empirically corrected in order to take dispersive interactions into account. The electronic excitations are also obtained within a perturbative B3LYP scheme. A comparative analysis is carried out between the ground-state and excited-state properties of crystalline HTP and PNT linking to the findings obtained for the isolated molecules.

Post-Hartree-Fock studies of the He/Mg(0001) interaction: Anti-corrugation, screening, and pairwise additivity

NASA Astrophysics Data System (ADS)

de Lara-Castells, María Pilar; Fernández-Perea, Ricardo; Madzharova, Fani; Voloshina, Elena

2016-06-01

The adsorption of noble gases on metallic surfaces represents a paradigmatic case of van-der-Waals (vdW) interaction due to the role of screening effects on the corrugation of the interaction potential [J. L. F. Da Silva et al., Phys. Rev. Lett. 90, 066104 (2003)]. The extremely small adsorption energy of He atoms on the Mg(0001) surface (below 3 meV) and the delocalized nature and mobility of the surface electrons make the He/Mg(0001) system particularly challenging, even for state-of-the-art vdW-corrected density functional-based (vdW-DFT) approaches [M. P. de Lara-Castells et al., J. Chem. Phys. 143, 194701 (2015)]. In this work, we meet this challenge by applying two different procedures. First, the dispersion-corrected second-order Möller-Plesset perturbation theory (MP2C) approach is adopted, using bare metal clusters of increasing size. Second, the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)] is applied at coupled cluster singles and doubles and perturbative triples level, using embedded cluster models of the metal surface. Both approaches provide clear evidences of the anti-corrugation of the interaction potential: the He atom prefers on-top sites, instead of the expected hollow sites. This is interpreted as a signature of the screening of the He atom by the metal for the on-top configuration. The strong screening in the metal is clearly reflected in the relative contribution of successively deeper surface layers to the main dispersion contribution. Aimed to assist future dynamical simulations, a pairwise potential model for the He/surface interaction as a sum of effective He-Mg pair potentials is also presented, as an improvement of the approximation using isolated He-Mg pairs.

Effects of atomic oxygen on polymeric materials flown on EOIM-3

NASA Technical Reports Server (NTRS)

Kamenetzky, Rachel R.; Linton, Roger C.; Finckenor, Miria M.; Vaughn, Jason A.

1995-01-01

Diverse polymeric materials, including several variations of Kapton, were flown on STS-46 as part of the Evaluation of Oxygen Interaction with Materials Experiment (EOIM-3). These materials were flown in the cargo bay and exposed to the space environment July 31 - August 8, 1992, including 40 hours of direct atomic oxygen impingement. The atomic oxygen exposure was approximately 2.2 x 10(exp 20) atoms/sq cm. Polymeric materials flown on EOIM-3 include coated and uncoated Kapton, Tefzel ETFE, Lexan, FEP and TFE Teflon, bulk Halar and PEEK, S383 silicone and Viton elastomeric seal material. Analyses performed included thickness measurements using Dektak and eddy current methods, mass loss, resistance, permeability, hardness, and FTIR. The effects of stress and the space environment on Kapton were also evaluated. Previous EOIM missions on STS-5 and STS-8 and the Long Duration Exposure Facility also contained polymeric material samples. Data from these previous flights are shown for comparison, as well as ground simulation of space environment effects using both thermal energy flow tubes and 5 eV neutral atomic oxygen beam facilities. Reaction efficiencies for the various atomic oxygen exposure conditions are discussed.

Conductance maps of quantum rings due to a local potential perturbation.

PubMed

Petrović, M D; Peeters, F M; Chaves, A; Farias, G A

2013-12-11

We performed a numerical simulation of the dynamics of a Gaussian shaped wavepacket inside a small sized quantum ring, smoothly connected to two leads and exposed to a perturbing potential of a biased atomic force microscope tip. Using the Landauer formalism, we calculated conductance maps of this system in the case of single and two subband transport. We explain the main features in the conductance maps as due to the AFM tip influence on the wavepacket phase and amplitude. In the presence of an external magnetic field, the tip modifies the ϕ0 periodic Aharonov-Bohm oscillation pattern into a ϕ0/2 periodic Al'tshuler-Aronov-Spivak oscillation pattern. Our results in the case of multiband transport suggest tip selectivity to higher subbands, making them more observable in the total conductance map.

Perturbation-theory analysis of ionization by a chirped few-cycle attosecond pulse

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

Pronin, E. A.; Starace, Anthony F.; Peng Liangyou

2011-07-15

The angular distribution of electrons ionized from an atom by a chirped few-cycle attosecond pulse is analyzed using perturbation theory (PT), keeping terms in the transition amplitude up to second order in the pulse electric field. The dependence of the asymmetry in the ionized electron distributions on both the chirp and the carrier-envelope phase (CEP) of the pulse are explained using a simple analytical formula that approximates the exact PT result. This approximate formula (in which the chirp dependence is explicit) reproduces reasonably well the chirp-dependent oscillations of the electron angular distribution asymmetries found numerically by Peng et al. [Phys.more » Rev. A 80, 013407 (2009)]. It can also be used to determine the chirp rate of the attosecond pulse from the measured electron angular distribution asymmetry.« less

Electronic field emission models beyond the Fowler-Nordheim one

NASA Astrophysics Data System (ADS)

Lepetit, Bruno

2017-12-01

We propose several quantum mechanical models to describe electronic field emission from first principles. These models allow us to correlate quantitatively the electronic emission current with the electrode surface details at the atomic scale. They all rely on electronic potential energy surfaces obtained from three dimensional density functional theory calculations. They differ by the various quantum mechanical methods (exact or perturbative, time dependent or time independent), which are used to describe tunneling through the electronic potential energy barrier. Comparison of these models between them and with the standard Fowler-Nordheim one in the context of one dimensional tunneling allows us to assess the impact on the accuracy of the computed current of the approximations made in each model. Among these methods, the time dependent perturbative one provides a well-balanced trade-off between accuracy and computational cost.

Nuclear Physics Around the Unitarity Limit

DOE PAGES

König, Sebastian; Grießhammer, Harald W.; Hammer, H. -W.; ...

2017-05-15

We argue that many features of the structure of nuclei emerge from a strictly perturbative expansion around the unitarity limit, where the two-nucleon S waves have bound states at zero energy. In this limit, the gross features of states in the nuclear chart are correlated to only one dimensionful parameter, which is related to the breaking of scale invariance to a discrete scaling symmetry and set by the triton binding energy. Observables are moved to their physical values by small perturbative corrections, much like in descriptions of the fine structure of atomic spectra. We provide evidence in favor of themore » conjecture that light, and possibly heavier, nuclei are bound weakly enough to be insensitive to the details of the interactions but strongly enough to be insensitive to the exact size of the two-nucleon system.« less

Evolution of regulatory networks towards adaptability and stability in a changing environment

NASA Astrophysics Data System (ADS)

Lee, Deok-Sun

2014-11-01

Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which evolve by selectively rewiring links towards enhancing adaptability to a changing environment and stability against dynamical perturbations. We find that sparse and heterogeneous connectivity patterns emerge, which show qualitative agreement with real transcriptional regulatory networks and metabolic networks. The characteristic scaling behavior of stability reflects the balance between robustness and flexibility. The scaling of fluctuation in the perturbation spread shows a dynamic crossover, which is analyzed by investigating separately the stochasticity of internal dynamics and the network structure differences depending on the evolution pathways. Our study delineates how the ambivalent pressure of evolution shapes biological networks, which can be helpful for studying general complex systems interacting with environments.

The coherence lifetime-borrowing effect in vibronically coupled molecular aggregates under non-perturbative system-environment interactions.

NASA Astrophysics Data System (ADS)

Yeh, Shu-Hao; Engel, Gregory S.; Kais, Sabre

Recently it has been suggested that the long-lived coherences in some photosynthetic pigment-protein systems, such as the Fenna-Matthews-Olson complex, could be attributed to the mixing of the pigments' electronic and vibrational degrees of freedom. In order to verify whether this is the case and to understand its underlying mechanism, a theoretical model capable of including both the electronic excitations and intramolecular vibrational modes of the pigments is necessary. Our model simultaneously considers the electronic and vibrational degrees of freedom, treating the system-environment interactions non-perturbatively by implementing the hierarchical equations of motion approach. Here we report the simulated two-dimensional electronic spectra of vibronically coupled molecular dimers to demonstrate how the electronic coherence lifetimes can be extended by borrowing the lifetime from the vibrational coherences. Funded by Qatar National Research Fund and Qatar Environment and Energy Research Institute.

Infrared problem in quantum acoustodynamics

NASA Astrophysics Data System (ADS)

Clougherty, Dennis P.; Sengupta, Sanghita

2017-05-01

Quantum electrodynamics (QED) provides a highly accurate description of phenomena involving the interaction of atoms with light. We argue that the quantum theory describing the interaction of cold atoms with a vibrating membrane—quantum acoustodynamics (QAD)—shares many issues and features with QED. Specifically, the adsorption of an atom on a vibrating membrane can be viewed as the counterpart to QED radiative electron capture. A calculation of the adsorption rate to lowest order in the atom-phonon coupling is finite; however, higher-order contributions suffer from an infrared problem mimicking the case of radiative capture in QED. Terms in the perturbation series for the adsorption rate diverge as a result of massless particles in the model (flexural phonons of the membrane in QAD and photons in QED). We treat this infrared problem in QAD explicitly to obtain finite results by regularizing with a low-frequency cutoff that corresponds to the inverse size of the membrane. Using a coherent-state basis for the soft-phonon final state, we then sum the dominant contributions to derive a new formula for the multiphonon adsorption rate of atoms on the membrane that gives results that are finite, nonperturbative in the atom-phonon coupling, and consistent with the Kinoshita-Lee-Nauenberg theorem. For micromembranes, we predict a reduction with increasing membrane size for the low-energy adsorption rate. We discuss the relevance of this to the adsorption of a cold gas of atomic hydrogen on suspended graphene.

Exceptional points enhance sensing in an optical microcavity

NASA Astrophysics Data System (ADS)

Chen, Weijian; Kaya Özdemir, Şahin; Zhao, Guangming; Wiersig, Jan; Yang, Lan

2017-08-01

Sensors play an important part in many aspects of daily life such as infrared sensors in home security systems, particle sensors for environmental monitoring and motion sensors in mobile phones. High-quality optical microcavities are prime candidates for sensing applications because of their ability to enhance light-matter interactions in a very confined volume. Examples of such devices include mechanical transducers, magnetometers, single-particle absorption spectrometers, and microcavity sensors for sizing single particles and detecting nanometre-scale objects such as single nanoparticles and atomic ions. Traditionally, a very small perturbation near an optical microcavity introduces either a change in the linewidth or a frequency shift or splitting of a resonance that is proportional to the strength of the perturbation. Here we demonstrate an alternative sensing scheme, by which the sensitivity of microcavities can be enhanced when operated at non-Hermitian spectral degeneracies known as exceptional points. In our experiments, we use two nanoscale scatterers to tune a whispering-gallery-mode micro-toroid cavity, in which light propagates along a concave surface by continuous total internal reflection, in a precise and controlled manner to exceptional points. A target nanoscale object that subsequently enters the evanescent field of the cavity perturbs the system from its exceptional point, leading to frequency splitting. Owing to the complex-square-root topology near an exceptional point, this frequency splitting scales as the square root of the perturbation strength and is therefore larger (for sufficiently small perturbations) than the splitting observed in traditional non-exceptional-point sensing schemes. Our demonstration of exceptional-point-enhanced sensitivity paves the way for sensors with unprecedented sensitivity.

Use of Earth's magnetic field for mitigating gyroscope errors regardless of magnetic perturbation.

PubMed

Afzal, Muhammad Haris; Renaudin, Valérie; Lachapelle, Gérard

2011-01-01

Most portable systems like smart-phones are equipped with low cost consumer grade sensors, making them useful as Pedestrian Navigation Systems (PNS). Measurements of these sensors are severely contaminated by errors caused due to instrumentation and environmental issues rendering the unaided navigation solution with these sensors of limited use. The overall navigation error budget associated with pedestrian navigation can be categorized into position/displacement errors and attitude/orientation errors. Most of the research is conducted for tackling and reducing the displacement errors, which either utilize Pedestrian Dead Reckoning (PDR) or special constraints like Zero velocity UPdaTes (ZUPT) and Zero Angular Rate Updates (ZARU). This article targets the orientation/attitude errors encountered in pedestrian navigation and develops a novel sensor fusion technique to utilize the Earth's magnetic field, even perturbed, for attitude and rate gyroscope error estimation in pedestrian navigation environments where it is assumed that Global Navigation Satellite System (GNSS) navigation is denied. As the Earth's magnetic field undergoes severe degradations in pedestrian navigation environments, a novel Quasi-Static magnetic Field (QSF) based attitude and angular rate error estimation technique is developed to effectively use magnetic measurements in highly perturbed environments. The QSF scheme is then used for generating the desired measurements for the proposed Extended Kalman Filter (EKF) based attitude estimator. Results indicate that the QSF measurements are capable of effectively estimating attitude and gyroscope errors, reducing the overall navigation error budget by over 80% in urban canyon environment.

Use of Earth’s Magnetic Field for Mitigating Gyroscope Errors Regardless of Magnetic Perturbation

PubMed Central

Afzal, Muhammad Haris; Renaudin, Valérie; Lachapelle, Gérard

2011-01-01

Most portable systems like smart-phones are equipped with low cost consumer grade sensors, making them useful as Pedestrian Navigation Systems (PNS). Measurements of these sensors are severely contaminated by errors caused due to instrumentation and environmental issues rendering the unaided navigation solution with these sensors of limited use. The overall navigation error budget associated with pedestrian navigation can be categorized into position/displacement errors and attitude/orientation errors. Most of the research is conducted for tackling and reducing the displacement errors, which either utilize Pedestrian Dead Reckoning (PDR) or special constraints like Zero velocity UPdaTes (ZUPT) and Zero Angular Rate Updates (ZARU). This article targets the orientation/attitude errors encountered in pedestrian navigation and develops a novel sensor fusion technique to utilize the Earth’s magnetic field, even perturbed, for attitude and rate gyroscope error estimation in pedestrian navigation environments where it is assumed that Global Navigation Satellite System (GNSS) navigation is denied. As the Earth’s magnetic field undergoes severe degradations in pedestrian navigation environments, a novel Quasi-Static magnetic Field (QSF) based attitude and angular rate error estimation technique is developed to effectively use magnetic measurements in highly perturbed environments. The QSF scheme is then used for generating the desired measurements for the proposed Extended Kalman Filter (EKF) based attitude estimator. Results indicate that the QSF measurements are capable of effectively estimating attitude and gyroscope errors, reducing the overall navigation error budget by over 80% in urban canyon environment. PMID:22247672

Decoherence by spontaneous emission: A single-atom analog of superradiance

NASA Astrophysics Data System (ADS)

Souza, Reinaldo de Melo e.; Impens, François; Neto, Paulo A. Maia

2016-12-01

We show that the decoherence of the atomic center-of-mass induced by spontaneous emission involves interferences corresponding to a single-atom analog of superradiance. We use a decomposition of the stationary decoherence rate as a sum of local and nonlocal contributions obtained to second order in the interaction by the influence functional method. These terms are respectively related to the strength of the coupling between system and environment, and to the quality of the information about the system leaking into the environment. While the local contribution always yields a positive decoherence rate, the nonlocal one may lead to recoherence when only partial information about the system is obtained from the disturbed environment. The nonlocal contribution contains interferences between different quantum amplitudes leading to oscillations of the decoherence rate reminiscent of superradiance. These concepts, illustrated here in the framework of atom interferometry within a trap, may be applied to a variety of quantum systems.

Atom Probe Tomographic Mapping Directly Reveals the Atomic Distribution of Phosphorus in Resin Embedded Ferritin

NASA Astrophysics Data System (ADS)

Perea, Daniel E.; Liu, Jia; Bartrand, Jonah; Dicken, Quinten; Thevuthasan, S. Theva; Browning, Nigel D.; Evans, James E.

2016-02-01

Here we report the atomic-scale analysis of biological interfaces within the ferritin protein using atom probe tomography that is facilitated by an advanced specimen preparation approach. Embedding ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualise atomic distributions and distinguish the inorganic-organic interface of the ferrihydrite mineral core and protein shell, as well as the organic-organic interface between the ferritin protein shell and embedding resin. In addition, we definitively show the atomic-scale distribution of phosphorus as being at the surface of the ferrihydrite mineral with the distribution of sodium mapped within the protein shell environment with an enhanced distribution at the mineral/protein interface. The sample preparation method is robust and can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment.

Atom Probe Tomographic Mapping Directly Reveals the Atomic Distribution of Phosphorus in Resin Embedded Ferritin

PubMed Central

Perea, Daniel E.; Liu, Jia; Bartrand, Jonah; Dicken, Quinten; Thevuthasan, S. Theva; Browning, Nigel D.; Evans, James E.

2016-01-01

Here we report the atomic-scale analysis of biological interfaces within the ferritin protein using atom probe tomography that is facilitated by an advanced specimen preparation approach. Embedding ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualise atomic distributions and distinguish the inorganic-organic interface of the ferrihydrite mineral core and protein shell, as well as the organic-organic interface between the ferritin protein shell and embedding resin. In addition, we definitively show the atomic-scale distribution of phosphorus as being at the surface of the ferrihydrite mineral with the distribution of sodium mapped within the protein shell environment with an enhanced distribution at the mineral/protein interface. The sample preparation method is robust and can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment. PMID:26924804

Analog tree-organized multiplexer

NASA Technical Reports Server (NTRS)

Crabbe, J. S.; Smith, D. M.; Turner, W. R.

1971-01-01

An analog tree-organized multiplexer (ATOM) which is intended for use in the telemetry system of an interplanetary spacecraft is designed. The ATOM will be fabricated by a monolithic, dielectric isolation process, and will contain silicon junction field effect transistors (JFET) as the active elements. The effect of the radiation environment on the performance of the ATOM is analyzed. The result indicates that the expected radiation environment will cause only minor changes in the preradiation characteristics of ATOM. The JFET in the ATOM is designed to meet the electrical requirements when fabricated by either the double poly-dielectric isolation process or the raised dielectric isolation process. The effect of the heat treatment required for the dielectric isolation process on the diffusion profile of the JFET is described. The layout of the ATOM circuit for fabrication by either the double poly or raised dielectric isolation process is also given.

Sensitivity Analysis Applied to Atomic Data Used for X-ray Spectrum Synthesis

NASA Technical Reports Server (NTRS)

Kallman, Tim

2006-01-01

A great deal of work has been devoted to the accumulation of accurate quantities describing atomic processes for use in analysis of astrophysical spectra. But in many situations of interest the interpretation of a quantity which is observed, such as a line flux, depends on the results of a modeling- or spectrum synthesis code. The results of such a code depends in turn 011 many atomic rates or cross sections, and the sensitivity of the observable quantity on the various rates and cross sections may be non-linear and if so cannot easily be derived analytically. In such cases the most practical approach to understanding the sensitivity of observables to atomic cross sections is to perform numerical experiments, by calculating models with various rates perturbed by random (but known) factors. In addition, it is useful to compare the results of such experiments with some sample observations, in order to focus attention on the rates which are of the greatest relevance to real observations. In this paper I will present some attempts to carry out this program, focussing on two sample datasets taken with the Chandra HETG. I will discuss the sensitivity of synthetic spectra to atomic data affecting ionization balance, temperature, and line opacity or emissivity, and discuss the implications for the ultimate goal of inferring astrophysical parameters.

Sensitivity Analysis Applied to Atomic Data Used for X-ray Spectrum Synthesis

NASA Technical Reports Server (NTRS)

Kallman, Tim

2006-01-01

A great deal of work has been devoted to the accumulation of accurate quantities describing atomic processes for use in analysis of astrophysical spectra. But in many situations of interest the interpretation of a quantity which is observed, such as a line flux, depends on the results of a modeling- or spectrum synthesis code. The results of such a code depends in turn on many atomic rates or cross sections, and the sensitivity of the observable quantity on the various rates and cross sections may be non-linear and if so cannot easily be derived analytically. In such cases the most practical approach to understanding the sensitivity of observables to atomic cross sections is to perform numerical experiments, by calculating models with various rates perturbed by random (but known) factors. In addition, it is useful to compare the results of such experiments with some sample observations, in order to focus attention on the rates which are of the greatest relevance to real observations. In this paper I will present some attempts to carry out this program, focussing on two sample datasets taken with the Chandra HETG. I will discuss the sensitivity of synthetic spectra to atomic data affecting ionization balance, temperature, and line opacity or emissivity, and discuss the implications for the ultimate goal of inferring astrophysical parameters.

Sensitized and heavy atom induced production of acenaphthylene triplet: A laser flash photolysis study

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

Samanta, A.; Fessenden, R.W.

1989-07-27

The triplet state of acenaphthylene has been examined by nanosecond laser flash photolysis using sensitization and heavy atom perturbation techniques. Although acenaphthylene does not form any observable triplet upon direct flash excitation, a transient with microsecond lifetime ({lambda}{sub max} = 315 nm) is observable when a solution of the sample is excited by sensitizers (benzophenone, thioxanthone, benzil). This transient is ascribed to the triplet of acenaphthylene on the basis of its quenching behavior toward oxygen, ferrocene, azulene, and {beta}-carotene. Quantitative data concerning the triplet-triplet absorption and quenching constants are presented. The triplet energy is estimated to lie between 46 andmore » 47 kcal/mol. The triplet can also be produced by direct excitation in solvents containing heavy atoms (ethyl bromide, ethyl iodide). The triplet yield is found to increase with an increase of the amount of the heavy atom containing solvent. No saturation limit is obtained. These facts together with the effect of heavy atoms on the T{sub 1} {yields} S{sub 0} process allow the differing behavior of ethyl bromide and ethyl iodide on the photodimerization process of acenaphthylene to be explained. Triplet-state parameters (extinction coefficient and triplet yield) have been estimated in these solvents by the energy-transfer technique and actinometry.« less

An assessment of molecular pathways of obesity susceptible to nutrient, toxicant and genetically induced epigenetic perturbation

PubMed Central

Xue, Jing; Ideraabdullah, Folami Y.

2015-01-01

In recent years, the etiology of human disease has greatly improved with the inclusion of epigenetic mechanisms, in particular as a common link between environment and disease. However, for most diseases we lack a detailed interpretation of the epigenetic regulatory pathways perturbed by environment and causal mechanisms. Here, we focus on recent findings elucidating nutrient-related epigenetic changes linked to obesity. We highlight studies demonstrating that obesity is a complex disease linked to disruption of epigenetically regulated metabolic pathways in the brain, adipose tissue and liver. These pathways regulate (1) homeostatic and hedonic eating behaviors (2) adipocyte differentiation and fat accumulation, and (3) energy expenditure. By compiling these data we illustrate that obesity-related phenotypes are repeatedly linked to disruption of critical epigenetic mechanisms that regulate of key metabolic genes. These data are supported by genetic mutation of key epigenetic regulators and many of the diet induced epigenetic mechanisms of obesity are also perturbed by exposure to environmental toxicants. Identifying similarly perturbed epigenetic mechanisms in multiple experimental models of obesity strengthens the translational applications of these findings. We also discuss many of the ongoing challenges to understanding the role of environmentally-induced epigenetic pathways in obesity and suggest future studies to elucidate these roles. This assessment illustrates our current understanding of molecular pathways of obesity that are susceptible to environmental perturbation via epigenetic mechanisms. Thus, it lays the groundwork for dissecting the complex interactions between diet, genes, and toxicants that contribute to obesity and obesity-related phenotypes. PMID:27012616

UV-Visible Spectra of PAHs and Derivatives Seeded in Supersonic Jet. Astrophysical Implications

NASA Astrophysics Data System (ADS)

Salma, Bejaoui; Salama, Farid

2018-06-01

Laboratory absorption spectra of Polycyclic Aromatic Hydrocarbons (PAHs) and PAH derivatives measured under astrophysical relevant conditions are crucial to test the PAHs-DIBs hypothesis as well as the PAH model for the IR emission bands. Our dedicated experimental setup on the COsmic SImulation Chamber (COSmIC) provides an excellent platform to study neutral and ionized PAHs under the low temperature and pressure conditions that are representative of interstellar environments [1]. In this work, we study the effect of the substitution of CH bond(s) by a nitrogen atom(s) on the electronic spectra of phenanthrene. The electronic transitions associated with the lower excited states of neutral phenanthrene (C14H10) and phenanthridine (C13H9N) are measured in gas phase in the 315-345 nm region. Molecules are seeded in a supersonic expansion of argon gas and the absorption spectra are measured using the Cavity Ring Down Spectroscopy (CRDS) technique. Additional measurements of the absorption spectra of phenanthrene, phenantridine and 1,10-phenanthroline (C12H8N2) isolated in 10 K argon matrices are also performed. The comparison between the CRDS spectra with the absorption of the matrix-isolated molecules highlight the matrix-induced perturbations in band position, profiles and broadening and illustrates the need of gas phase measurements for more accurate comparisons with astronomical spectra.[1] Salama, F., Galazutdinov, G., Krelowski, et al. ApJ 728, 154[FS1] (2011).[2] A. Tielens, ApJ 526 Pt 1265–273 (2008),Acknowledgements: This research is supported by the APRA Program of NASA SMD

Stability enhancement of an atomic force microscope for long-term force measurement including cantilever modification for whole cell deformation

NASA Astrophysics Data System (ADS)

Weafer, P. P.; McGarry, J. P.; van Es, M. H.; Kilpatrick, J. I.; Ronan, W.; Nolan, D. R.; Jarvis, S. P.

2012-09-01

Atomic force microscopy (AFM) is widely used in the study of both morphology and mechanical properties of living cells under physiologically relevant conditions. However, quantitative experiments on timescales of minutes to hours are generally limited by thermal drift in the instrument, particularly in the vertical (z) direction. In addition, we demonstrate the necessity to remove all air-liquid interfaces within the system for measurements in liquid environments, which may otherwise result in perturbations in the measured deflection. These effects severely limit the use of AFM as a practical tool for the study of long-term cell behavior, where precise knowledge of the tip-sample distance is a crucial requirement. Here we present a readily implementable, cost effective method of minimizing z-drift and liquid instabilities by utilizing active temperature control combined with a customized fluid cell system. Long-term whole cell mechanical measurements were performed using this stabilized AFM by attaching a large sphere to a cantilever in order to approximate a parallel plate system. An extensive examination of the effects of sphere attachment on AFM data is presented. Profiling of cantilever bending during substrate indentation revealed that the optical lever assumption of free ended cantilevering is inappropriate when sphere constraining occurs, which applies an additional torque to the cantilevers "free" end. Here we present the steps required to accurately determine force-indentation measurements for such a scenario. Combining these readily implementable modifications, we demonstrate the ability to investigate long-term whole cell mechanics by performing strain controlled cyclic deformation of single osteoblasts.

Science Goals of the Primary Atomic Reference Clock in Space (PARCS) Experiment

NASA Technical Reports Server (NTRS)

Ashby, N.

2003-01-01

The PARCS (Primary Atomic Reference Clock in Space) experiment will use a laser-cooled Cesium atomic clock operating in the microgravity environment aboard the International Space Station (ISS) to provide both advanced tests of gravitational theory and to demonstrate a new cold-atom clock technology for space. PARCS is a joint project of the National Institute of Standards and Technology (NIST), NASA's Jet Propulsion Laboratory (JPL), and the University of Colorado (CU). This paper concentrates on the scientific goals of the PARCS mission. The microgravity space environment allows laser-cooled Cs atoms to have Ramsey times in excess of those feasible on Earth, resulting in improved clock performance. Clock stabilities of 5x10(exp -14) at one second, and accuracies better than 10(exp -16) are projected.

Digital lattice gauge theories

NASA Astrophysics Data System (ADS)

Zohar, Erez; Farace, Alessandro; Reznik, Benni; Cirac, J. Ignacio

2017-02-01

We propose a general scheme for a digital construction of lattice gauge theories with dynamical fermions. In this method, the four-body interactions arising in models with 2 +1 dimensions and higher are obtained stroboscopically, through a sequence of two-body interactions with ancillary degrees of freedom. This yields stronger interactions than the ones obtained through perturbative methods, as typically done in previous proposals, and removes an important bottleneck in the road towards experimental realizations. The scheme applies to generic gauge theories with Lie or finite symmetry groups, both Abelian and non-Abelian. As a concrete example, we present the construction of a digital quantum simulator for a Z3 lattice gauge theory with dynamical fermionic matter in 2 +1 dimensions, using ultracold atoms in optical lattices, involving three atomic species, representing the matter, gauge, and auxiliary degrees of freedom, that are separated in three different layers. By moving the ancilla atoms with a proper sequence of steps, we show how we can obtain the desired evolution in a clean, controlled way.

Analytical model for atomic resonant attosecond transient absorption

NASA Astrophysics Data System (ADS)

Cariker, C.; Kjellson, T.; Lindroth, E.; Argenti, L.

2017-04-01

Recent advancements in ultrafast laser technology have made it possible to probe electron dynamics in highly excited atomic states that autoionize on a femtosecond timescale, thus giving insight into the dynamics of Auger decay and its interference with the continuum. These experiments provide a stringent test for time-resolved analytical models of autoionization. Here we present a finite-pulse, multi-photon perturbative model which is used in conjunction with ab-initio structure calculations to predict the attosecond transient absorption spectrum (ATAS) of an atom above the ionization threshold. We apply this model to compute the ATAS of argon in the vicinity of the 3s-1 4 p resonance as a function of the time delay between an extreme ultraviolet (XUV) and an infrared (IR) pulse, as well as of the angle between their polarization. We show that by modulating the parameters of the IR pulse it is possible to control the dipolar coupling between neighboring states and hence the lineshape of the 3s-1 4 p resonance. NSF Grant No. 1607588.

Mechanism of Contact between a Droplet and an Atomically Smooth Substrate

NASA Astrophysics Data System (ADS)

Lo, Hau Yung; Liu, Yuan; Xu, Lei

2017-04-01

When a droplet gently lands on an atomically smooth substrate, it will most likely contact the underlying surface in about 0.1 s. However, theoretical estimation from fluid mechanics predicts a contact time of 10-100 s. What causes this large discrepancy, and how does nature speed up contact by 2 orders of magnitude? To probe this fundamental question, we prepare atomically smooth substrates by either coating a liquid film on glass or using a freshly cleaved mica surface, and visualize the droplet contact dynamics with 30-nm resolution. Interestingly, we discover two distinct speed-up approaches: (1) droplet skidding due to even minute perturbations breaks rotational symmetry and produces early contact at the thinnest gap location, and (2) for the unperturbed situation with rotational symmetry, a previously unnoticed boundary flow around only 0.1 mm /s expedites air drainage by over 1 order of magnitude. Together, these two mechanisms universally explain general contact phenomena on smooth substrates. The fundamental discoveries shed new light on contact and drainage research.

Search for domain wall dark matter with atomic clocks on board global positioning system satellites.

PubMed

Roberts, Benjamin M; Blewitt, Geoffrey; Dailey, Conner; Murphy, Mac; Pospelov, Maxim; Rollings, Alex; Sherman, Jeff; Williams, Wyatt; Derevianko, Andrei

2017-10-30

Cosmological observations indicate that dark matter makes up 85% of all matter in the universe yet its microscopic composition remains a mystery. Dark matter could arise from ultralight quantum fields that form macroscopic objects. Here we use the global positioning system as a ~ 50,000 km aperture dark matter detector to search for such objects in the form of domain walls. Global positioning system navigation relies on precision timing signals furnished by atomic clocks. As the Earth moves through the galactic dark matter halo, interactions with domain walls could cause a sequence of atomic clock perturbations that propagate through the satellite constellation at galactic velocities ~ 300 km s -1 . Mining 16 years of archival data, we find no evidence for domain walls at our current sensitivity level. This improves the limits on certain quadratic scalar couplings of domain wall dark matter to standard model particles by several orders of magnitude.

Measuring the internal energies of species emitted from hypervelocity nanoprojectile impacts on surfaces using recalibrated benzylpyridinium probe ions

NASA Astrophysics Data System (ADS)

DeBord, J. Daniel; Verkhoturov, Stanislav V.; Perez, Lisa M.; North, Simon W.; Hall, Michael B.; Schweikert, Emile A.

2013-06-01

We present herein a framework for measuring the internal energy distributions of vibrationally excited molecular ions emitted from hypervelocity nanoprojectile impacts on organic surfaces. The experimental portion of this framework is based on the measurement of lifetime distributions of "thermometer" benzylpyridinium ions dissociated within a time of flight mass spectrometer. The theoretical component comprises re-evaluation of the fragmentation energetics of benzylpyridinium ions at the coupled-cluster singles and doubles with perturbative triples level. Vibrational frequencies for the ground and transition states of select molecules are reported, allowing for a full description of vibrational excitations of these molecules via Rice-Ramsperger-Kassel-Marcus unimolecular fragmentation theory. Ultimately, this approach is used to evaluate the internal energy distributions from the measured lifetime distributions. The average internal energies of benzylpyridinium ions measured from 440 keV Au400+4 impacts are found to be relatively low (˜0.24 eV/atom) when compared with keV atomic bombardment of surfaces (1-2 eV/atom).

Nuclear Power and the Environment, Understanding the Atom Series.

ERIC Educational Resources Information Center

Atomic Energy Commission, Oak Ridge, TN. Div. of Technical Information.

This booklet is one of the booklets in the "Understanding the Atom Series" published by the U. S. Atomic Energy Commission for high school science teachers and their students. Discussion concentrates on the radiological and thermal aspects of the environmental effects of nuclear power plants; on the procedures followed by the Atomic Energy…

Densification and Devitrification of Fused Silica Induced by Ballistic Impact: A Computational Investigation

DTIC Science & Technology

2015-03-25

lime glass, the polyhedron -center atoms are all silicon and each silicon atom is surrounded by four oxygen atoms (while each oxygen atom is connected...of metallic force-field functions (in the pure metallic environment) within the force-field function database used in the present work. Consequently

Steady bipartite coherence induced by non-equilibrium environment

NASA Astrophysics Data System (ADS)

Huangfu, Yong; Jing, Jun

2018-01-01

We study the steady state of two coupled two-level atoms interacting with a non-equilibrium environment that consists of two heat baths at different temperatures. Specifically, we analyze four cases with respect to the configuration about the interactions between atoms and heat baths. Using secular approximation, the conventional master equation usually neglects steady-state coherence, even when the system is coupled with a non-equilibrium environment. When employing the master equation with no secular approximation, we find that the system coherence in our model, denoted by the off-diagonal terms in the reduced density matrix spanned by the eigenvectors of the system Hamiltonian, would survive after a long-time decoherence evolution. The absolute value of residual coherence in the system relies on different configurations of interaction channels between the system and the heat baths. We find that a large steady quantum coherence term can be achieved when the two atoms are resonant. The absolute value of quantum coherence decreases in the presence of additional atom-bath interaction channels. Our work sheds new light on the mechanism of steady-state coherence in microscopic quantum systems in non-equilibrium environments.

Searching for the Source of Salt Marsh Buried Mercury.

NASA Astrophysics Data System (ADS)

Brooke, C. G.; Nelson, D. C.; Fleming, E. J.

2016-12-01

Salt marshes provide a barrier between upstream mercury contamination and coastal ecosystems. Mercury is sorbed, transported, and deposited in estuarine systems. Once the upstream mercury source has been remediated, the downstream mercury contaminated salt marsh sediments should become "capped" or buried by uncontaminated sediments preventing further ecosystem contamination. Downstream from a remediated mercury mine, an estuarine intertidal marsh in Tomales Bay, CA, USA, scavengers/predators (e.g. Pachygrapsus crassipes, Lined Shore Crab) have leg mercury concentrations as high as 5.5 ppm (dry wt./dry wt.), which increase significantly with crab size, a surrogate for trophic level. These elevated mercury concentrations suggests that "buried" mercury is rereleased into the environment. To locate possible sources of mercury release in Walker Marsh, we sampled a transect across the marsh that included diverse micro-environments (e.g. rhizoshere, stratified sediments, faunal burrows). From each location we determined the sediment structure, sediment color, total sediment mercury, total sediment iron, and microbial composition (n = 28). Where flora or fauna had perturbed the sediment, mercury concentrations were 10% less than undisturbed stratified sediments (1025 ppb vs. 1164 ppb, respectively). High-throughput SSU rRNA gene sequencing and subsequent co-occurrence network analysis genera indicated that in flora- or fauna- perturbed sediments there was an increased likelihood that microbial genera contained mercury mobilizing genes (94% vs 57%; in perturbed vs stratified sediments, respectively). Our observations are consistent with findings by others that in perturbed sites mercury mobility increased. We did however identify a microbial and geochemical profile with increased mercury mobility. For future work we plan to quantify the role these micro-environments have on mercury-efflux from salt marshes.

Generalizing genetical genomics: getting added value from environmental perturbation.

PubMed

Li, Yang; Breitling, Rainer; Jansen, Ritsert C

2008-10-01

Genetical genomics is a useful approach for studying the effect of genetic perturbations on biological systems at the molecular level. However, molecular networks depend on the environmental conditions and, thus, a comprehensive understanding of biological systems requires studying them across multiple environments. We propose a generalization of genetical genomics, which combines genetic and sensibly chosen environmental perturbations, to study the plasticity of molecular networks. This strategy forms a crucial step toward understanding why individuals respond differently to drugs, toxins, pathogens, nutrients and other environmental influences. Here we outline a strategy for selecting and allocating individuals to particular treatments, and we discuss the promises and pitfalls of the generalized genetical genomics approach.

Thermal conductivity and phonon transport properties of silicon using perturbation theory and the environment-dependent interatomic potential

NASA Astrophysics Data System (ADS)

Pascual-Gutiérrez, José A.; Murthy, Jayathi Y.; Viskanta, Raymond

2009-09-01

Silicon thermal conductivities are obtained from the solution of the linearized phonon Boltzmann transport equation without the use of any parameter-fitting. Perturbation theory is used to compute the strength of three-phonon and isotope scattering mechanisms. Matrix elements based on Fermi's golden rule are computed exactly without assuming either average or mode-dependent Grüeisen parameters, and with no underlying assumptions of crystal isotropy. The environment-dependent interatomic potential is employed to describe the interatomic force constants and the perturbing Hamiltonians. A detailed methodology to accurately find three-phonon processes satisfying energy- and momentum-conservation rules is also described. Bulk silicon thermal conductivity values are computed across a range of temperatures and shown to match experimental data very well. It is found that about two-thirds of the heat transport in bulk silicon may be attributed to transverse acoustic modes. Effective relaxation times and mean free paths are computed in order to provide a more complete picture of the detailed transport mechanisms and for use with carrier transport models based on the Boltzmann transport equation.

Dynamics of solvation and desolvation of rubidium attached to He nanodroplets

NASA Astrophysics Data System (ADS)

von Vangerow, J.; John, O.; Stienkemeier, F.; Mudrich, M.

2015-07-01

The real-time dynamics of photoexcited and photoionized rubidium (Rb) atoms attached to helium (He) nanodroplets is studied by femtosecond pump-probe mass spectrometry. While excited Rb atoms in the perturbed 6p-state (Rb*) desorb off the He droplets, Rb+ photoions tend to sink into the droplet interior when created near the droplet surface. The transition from Rb+ solvation to full Rb* desorption is found to occur at a delay time τ ˜ 600 fs for Rb* in the 6pΣ-state and τ ˜ 1200 fs for the 6pΠ-state. Rb+He ions are found to be created by directly exciting bound Rb*He exciplex states as well as by populating bound Rb+He-states in a photoassociative ionization process.

Manipulating the magnetoelectric effect: Essence learned from Co4Nb2O9

NASA Astrophysics Data System (ADS)

Yanagi, Yuki; Hayami, Satoru; Kusunose, Hiroaki

2018-01-01

Recent experiments for linear magnetoelectric (ME) response in honeycomb antiferromagnet Co4Nb2O9 revealed that the electric polarization can be manipulated by the in-plane rotating magnetic field in a systematic way. We propose the minimal model by extracting essential ingredients of Co4Nb2O9 to exhibit such ME response. It is the three-orbital model with x y -type atomic spin-orbit coupling (SOC) on the single-layer honeycomb structure, and it is shown to reproduce qualitatively the observed field-angle dependence of the electric polarization. The obtained results can be understood by the perturbative calculation with respect to the atomic SOC. These findings could be useful to explore further ME materials having similar manipulability of the electric polarization.

A Hybrid Solution for Simultaneous Transfer of Ultrastable Optical Frequency, RF Frequency, and UTC Time-Tags Over Optical Fiber.

PubMed

Krehlik, Przemyslaw; Schnatz, Harald; Sliwczynski, Lukasz

2017-12-01

We describe a fiber-optic solution for simultaneous distribution of all signals generated at today's most advanced time and frequency laboratories, i.e., an ultrastable optical reference frequency derived from an optical atomic clock, a radio frequency precisely linked to a realization of the SI-Second, and a realization of an atomic timescale, being the local representation of the virtual, global UTC timescale. In our solution both the phase of the optical carrier and the delay of electrical signals (10-MHz frequency reference and one-pulse-per-second time tags) are stabilized against environmental perturbations influencing the fiber link instability and accuracy. We experimentally demonstrate optical transfer stabilities of and for 100 s averaging period, for optical carrier and 10-MHz signals, respectively.

Statics and dynamics of atomic dark-bright solitons in the presence of impurities

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

Achilleos, V.; Frantzeskakis, D. J.; Kevrekidis, P. G.

2011-11-15

Adopting a mean-field description for a two-component atomic Bose-Einstein condensate, we study the statics and dynamics of dark-bright solitons in the presence of localized impurities. We use adiabatic perturbation theory to derive an equation of motion for the dark-bright soliton center. We show that, counterintuitively, an attractive (repulsive) delta-like impurity, acting solely on the bright-soliton component, induces an effective localized barrier (well) in the effective potential felt by the soliton; this way, dark-bright solitons are reflected from (transmitted through) attractive (repulsive) impurities. Our analytical results for the small-amplitude oscillations of solitons are found to be in good agreement with resultsmore » obtained via a Bogoliubov-de Gennes analysis and direct numerical simulations.« less

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

Processes of energy deposition by heavy-particle and electron impact. Final progress report

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

Salop, A.; Smith, F.T.

1978-04-18

Progress is reported in three areas of reasearch during the present period: K-shell ionization in high energy collisions of heavy ions with light target atoms using the sudden (Magnus) approximation, K-L level matching phenomena associated with K-shell vacancy production in heavy-ion collisions, and studies of low energy collisions of electrons with molecules using semi-classical perturbation theory. A brief discussion of each of these activities is given.

Novel Infrared Dynamics of Cold Atoms on Hot Graphene

NASA Astrophysics Data System (ADS)

Sengupta, Sanghita; Kotov, Valeri; Clougherty, Dennis

The low-energy dynamics of cold atoms interacting with macroscopic graphene membranes exhibits severe infrared divergences when treated perturbatively. These infrared problems are even more pronounced at finite temperature due to the (infinitely) many flexural phonons excited in graphene. We have devised a technique to take account (resummation) of such processes in the spirit of the well-known exact solution of the independent boson model. Remarkably, there is also similarity to the infrared problems and their treatment (via the Bloch-Nordsieck scheme) in finite temperature ``hot'' quantum electrodynamics and chromodynamics due to the long-range, unscreened nature of gauge interactions. The method takes into account correctly the strong damping provided by the many emitted phonons at finite temperature. In our case, the inverse membrane size plays the role of an effective low-energy scale, and, unlike the above mentioned field theories, there remains an unusual, highly nontrivial dependence on that scale due to the 2D nature of the problem. We present detailed results for the sticking (atomic damping rate) rate of cold atomic hydrogen as a function of the membrane temperature and size. We find that the rate is very strongly dependent on both quantities.

Templated Atom-Precise Galvanic Synthesis and Structure Elucidation of a [Ag24Au(SR)18](-) Nanocluster.

PubMed

Bootharaju, Megalamane S; Joshi, Chakra P; Parida, Manas R; Mohammed, Omar F; Bakr, Osman M

2016-01-18

Synthesis of atom-precise alloy nanoclusters with uniform composition is challenging when the alloying atoms are similar in size (for example, Ag and Au). A galvanic exchange strategy has been devised to produce a compositionally uniform [Ag24Au(SR)18](-) cluster (SR: thiolate) using a pure [Ag25(SR)18](-) cluster as a template. Conversely, the direct synthesis of Ag24Au cluster leads to a mixture of [Ag(25-x)Au(x)(SR)18](-), x=1-8. Mass spectrometry and crystallography of [Ag24Au(SR)18](-) reveal the presence of the Au heteroatom at the Ag25 center, forming Ag24Au. The successful exchange of the central Ag of Ag25 with Au causes perturbations in the Ag25 crystal structure, which are reflected in the absorption, luminescence, and ambient stability of the particle. These properties are compared with those of Ag25 and Ag24Pd clusters with same ligand and structural framework, providing new insights into the modulation of cluster properties with dopants at the single-atom level. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

How different is the borazine-acetylene dimer from the benzene-acetylene dimer? A matrix isolation infrared and ab initio quantum chemical study

NASA Astrophysics Data System (ADS)

Verma, Kanupriya; Viswanathan, K. S.; Majumder, Moumita; Sathyamurthy, N.

2017-11-01

The 1:1 dimer of borazine-acetylene has been studied for the first time, both experimentally and computationally. The borazine-acetylene dimer was trapped in Ar and N2 matrices, and studied using infrared spectroscopy. Our experiments clearly revealed two isomers of the borazine-acetylene complex, one in which the N-H of borazine interacted with the carbon of acetylene, and another in which the C-H of acetylene formed a hydrogen bond with a nitrogen atom of borazine. The formation of both isomers in the matrix was evidenced by shifts in the vibrational frequencies of the appropriate modes. Reassuringly, the experimental observations were corroborated by our computations using the second-order Møller-Plesset perturbation theoretic method and coupled-cluster singles, doubles and perturbative triples method in conjunction with different Dunning basis sets, which indicated both these isomers to be stable minima, with the N-HṡṡṡC complex being the global minimum. Atoms-in-molecules and energy decomposition analysis were also carried out for the different isomers of the dimer. These studies reveal that replacing the three C-C linkages in benzene with three B-N linkages in borazine modifies the interaction in the dimer sufficiently, to result in a different potential energy landscape for the borazine-acetylene system when compared with the benzene-acetylene system.

An analysis of phonon emission as controlled by the combined interaction with the acoustic and piezoelectric phonons in a degenerate III-V compound semiconductor using an approximated Fermi-Dirac distribution at low lattice temperatures

NASA Astrophysics Data System (ADS)

Basu, A.; Das, B.; Middya, T. R.; Bhattacharya, D. P.

2018-03-01

Compound semiconductors being piezoelectric in nature, the intrinsic thermal vibration of the lattice atoms at any temperature gives rise to an additional potential field that perturbs the periodic potential field of the atoms. This is over and above the intrinsic deformation acoustic potential field which is always produced in every material. The scattering of the electrons through the piezoelectric perturbing potential is important in all compound semiconductors, particularly at the low lattice temperatures. Thus, the electrical transport in such materials is principally controlled by the combined interaction of the electrons with the deformation potential acoustic and piezoelectric phonons at low lattice temperatures. The study here, deals with the problem of phonon growth characteristics, considering the combined scattering of the non-equilibrium electrons in compound semiconductors, at low lattice temperatures. Beside degeneracy, other low temperature features, like the inelasticity of the electron-phonon collisions, and the full form of the phonon distribution have been duly considered. The distribution function of the degenerate ensemble of carriers, as given by the heated Fermi-Dirac function, has been approximated by a simplified, well-tested model. The model which has been proposed earlier, makes it much easier to carry out analytically the integrations without usual oversimplified approximations.

Prompt triggering of edge localized modes through lithium granule injection on EAST

NASA Astrophysics Data System (ADS)

Lunsford, Robert; Sun, Z.; Hu, J. S.; Xu, W.; Zuo, G. Z.; Gong, X. Z.; Wan, B. N.; Li, J. G.; Huang, M.; Maingi, R.; Diallo, A.; Tritz, K.; the EAST Team

2017-10-01

We report successful triggering of edge localized mode (ELMs) in EAST with Lithium (Li) micropellets, and the observed dependence of ELM triggering efficiency on granule size. ELM control is essential for successful ITER operation throughout the entire campaign, relying on magnetic perturbations for ELM suppression and ELM frequency enhancement via pellet injection. To separate the task of fueling from ELM pacing, we initiate the prompt generation of ELMs via impurity granule injection. Lithium granules ranging in size from 200 - 1000 microns are mechanically injected into upper-single null EAST long pulse H-mode discharges. The injections are monitored for their effect on high Z impurity accumulation and to assess the pressure perturbation required for reliable ELM triggering. We have determined that granules of diameter larger than 600 microns (corresponding to 5.2 x 1018 Li atoms) are successful at triggering ELMs more than 90% of the time. The triggering efficiency drops precipitously to less than 40% as the granule size is reduced to 400 microns (1.5 x 1018 Li atoms), indicating a triggering threshold has been crossed. Using this information an optimal impurity granule size which will regularly trigger a prompt ELM in these EAST discharges is determined. Coupling these results with alternate discharge scenarios on EAST and similar experiments performed on DIII-D provides the possibility of extrapolation to future devices.

MoS2 interactions with 1.5 eV atomic oxygen

NASA Technical Reports Server (NTRS)

Martin, J. A.; Cross, J. B.; Pope, L. E.

1989-01-01

Exposures of MoS2 to 1.5-eV atomic oxygen in an anhydrous environment reveal that the degree of oxidation is essentially independent of crystallite orientation, and that the surface-adsorbed reaction products are MoO3 and MoO2. A mixture of oxides and sulfide exists over a depth of about 90 A, and this layer has a low diffusion rate for oxygen. It is concluded that a protective oxide layer forms on MoS2 on exposure to the atomic-oxygen-rich environment of LEO.

Subsonic and Supersonic Effects in Bose-Einstein Condensate

NASA Technical Reports Server (NTRS)

Zak, Michail

2003-01-01

A paper presents a theoretical investigation of subsonic and supersonic effects in a Bose-Einstein condensate (BEC). The BEC is represented by a time-dependent, nonlinear Schroedinger equation that includes terms for an external confining potential term and a weak interatomic repulsive potential proportional to the number density of atoms. From this model are derived Madelung equations, which relate the quantum phase with the number density, and which are used to represent excitations propagating through the BEC. These equations are shown to be analogous to the classical equations of flow of an inviscid, compressible fluid characterized by a speed of sound (g/Po)1/2, where g is the coefficient of the repulsive potential and Po is the unperturbed mass density of the BEC. The equations are used to study the effects of a region of perturbation moving through the BEC. The excitations created by a perturbation moving at subsonic speed are found to be described by a Laplace equation and to propagate at infinite speed. For a supersonically moving perturbation, the excitations are found to be described by a wave equation and to propagate at finite speed inside a Mach cone.

Head stabilisation in fast running lizards.

PubMed

Goyens, Jana; Aerts, Peter

2018-04-01

The cyclic patterns of terrestrial animal locomotion are frequently perturbed in natural environments. The terrain can be complex or inclined, the substrate can move unexpectedly and animals can misjudge situations. Loosing stability due to perturbations increases the probability of capture by predators and decreases the chance of successful prey capture and winning intraspecific battles. When controlled corrective actions are necessary to negotiate perturbations, animals rely on their exteroceptive and proprioceptive senses to monitor the environment and their own body movements. The vestibular system in the inner ear perceives linear and angular accelerations. This information enables gaze stabilisation and the creation of a stable, world-bound reference frame for the integration of the information of other senses. During locomotion, both functions are known to be facilitated by head stabilisation in several animals with an erect posture. Animals with a sprawled body posture, however, undergo very large body undulations while running. Using high speed video recordings, we tested whether they nevertheless stabilise their head during running, and how this is influenced by perturbations. We found that running Acanthodactylus boskianus lizards strongly stabilise their head yaw rotations when running on a flat, straight runway: the head rotation amplitude is only 4.76±0.99°, while the adjacent trunk part rotates over 27.0±3.8°. Lateral head translations are not stabilised (average amplitude of 7.4±2.0mm). When the lizards are experimentally perturbed by a large and unexpected lateral substrate movement, lateral translations of both the head and the body decrease (on average by 1.52±0.81mm). At the same time, the rotations of the head and trunk also decrease (on average by 1.62°±7.21°). These results show that head stabilisation intensifies because of the perturbation, which emphasises the importance of vestibular perception and balance in these fast and manoeuvrable animals. Copyright © 2017 Elsevier GmbH. All rights reserved.

ARC: An open-source library for calculating properties of alkali Rydberg atoms

NASA Astrophysics Data System (ADS)

Šibalić, N.; Pritchard, J. D.; Adams, C. S.; Weatherill, K. J.

2017-11-01

We present an object-oriented Python library for the computation of properties of highly-excited Rydberg states of alkali atoms. These include single-body effects such as dipole matrix elements, excited-state lifetimes (radiative and black-body limited) and Stark maps of atoms in external electric fields, as well as two-atom interaction potentials accounting for dipole and quadrupole coupling effects valid at both long and short range for arbitrary placement of the atomic dipoles. The package is cross-referenced to precise measurements of atomic energy levels and features extensive documentation to facilitate rapid upgrade or expansion by users. This library has direct application in the field of quantum information and quantum optics which exploit the strong Rydberg dipolar interactions for two-qubit gates, robust atom-light interfaces and simulating quantum many-body physics, as well as the field of metrology using Rydberg atoms as precise microwave electrometers. Program Files doi:http://dx.doi.org/10.17632/hm5n8w628c.1 Licensing provisions: BSD-3-Clause Programming language: Python 2.7 or 3.5, with C extension External Routines: NumPy [1], SciPy [1], Matplotlib [2] Nature of problem: Calculating atomic properties of alkali atoms including lifetimes, energies, Stark shifts and dipole-dipole interaction strengths using matrix elements evaluated from radial wavefunctions. Solution method: Numerical integration of radial Schrödinger equation to obtain atomic wavefunctions, which are then used to evaluate dipole matrix elements. Properties are calculated using second order perturbation theory or exact diagonalisation of the interaction Hamiltonian, yielding results valid even at large external fields or small interatomic separation. Restrictions: External electric field fixed to be parallel to quantisation axis. Supplementary material: Detailed documentation (.html), and Jupyter notebook with examples and benchmarking runs (.html and .ipynb). [1] T.E. Oliphant, Comput. Sci. Eng. 9, 10 (2007). http://www.scipy.org/. [2] J.D. Hunter, Comput. Sci. Eng. 9, 90 (2007). http://matplotlib.org/.

Ab initio study of the molecular structure and vibrational spectrum of nitric acid and its protonated forms

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Rice, Julia E.

1992-01-01

The equilibrium structures, harmonic vibrational frequencies, IR intensities, and relative energetics of HNO3 and its protonated form H2NO3+ were investigated using double-zeta plus polarization and triple-zeta plus polarization basis sets in conjunction with high-level ab initio methods. The latter include second-order Moller-Plesset perturbation theory, the single and double excitation coupled cluster (CCSD) methods, a perturbational estimate of the effects of connected triple excitations (CCSD(T)), and the self-consistent field. To determine accurate energy differences CCSD(T) energies were computed using large atomic natural orbital basis sets. Four different isomers of H2NO3+ were considered. The lowest energy form of protonated nitric acid was found to correspond to a complex between H2O and NO2+, which is consistent with earlier theoretical and experimental studies.

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

Wang, Weizhou, E-mail: wzw@lynu.edu.cn, E-mail: ybw@gzu.edu.cn; Zhang, Yu; Sun, Tao

High-level coupled cluster singles, doubles, and perturbative triples [CCSD(T)] computations with up to the aug-cc-pVQZ basis set (1924 basis functions) and various extrapolations toward the complete basis set (CBS) limit are presented for the sandwich, T-shaped, and parallel-displaced benzene⋯naphthalene complex. Using the CCSD(T)/CBS interaction energies as a benchmark, the performance of some newly developed wave function and density functional theory methods has been evaluated. The best performing methods were found to be the dispersion-corrected PBE0 functional (PBE0-D3) and spin-component scaled zeroth-order symmetry-adapted perturbation theory (SCS-SAPT0). The success of SCS-SAPT0 is very encouraging because it provides one method for energy componentmore » analysis of π-stacked complexes with 200 atoms or more. Most newly developed methods do, however, overestimate the interaction energies. The results of energy component analysis show that interaction energies are overestimated mainly due to the overestimation of dispersion energy.« less

Impact of Adsorption on Gas Transport in Nanopores.

PubMed

Wu, Tianhao; Zhang, Dongxiao

2016-03-29

Given the complex nature of the interaction between gas and solid atoms, the development of nanoscale science and technology has engendered a need for further understanding of gas transport behavior through nanopores and more tractable models for large-scale simulations. In the present paper, we utilize molecular dynamic simulations to demonstrate the behavior of gas flow under the influence of adsorption in nano-channels consisting of illite and graphene, respectively. The results indicate that velocity oscillation exists along the cross-section of the nano-channel, and the total mass flow could be either enhanced or reduced depending on variations in adsorption under different conditions. The mechanisms can be explained by the extra average perturbation stress arising from density oscillation via the novel perturbation model for micro-scale simulation, and approximated via the novel dual-region model for macro-scale simulation, which leads to a more accurate permeability correction model for industrial applications than is currently available.

Spin-Flavor van der Waals Forces and NN interaction

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

Alvaro Calle Cordon, Enrique Ruiz Arriola

A major goal in Nuclear Physics is the derivation of the Nucleon-Nucleon (NN) interaction from Quantum Chromodynamics (QCD). In QCD the fundamental degrees of freedom are colored quarks and gluons which are confined to form colorless strongly interacting hadrons. Because of this the resulting nuclear forces at sufficiently large distances correspond to spin-flavor excitations, very much like the dipole excitations generating the van der Waals (vdW) forces acting between atoms. We study the Nucleon-Nucleon interaction in the Born-Oppenheimer approximation at second order in perturbation theory including the Delta resonance as an intermediate state. The potential resembles strongly chiral potentials computedmore » either via soliton models or chiral perturbation theory and has a van der Waals like singularity at short distances which is handled by means of renormalization techniques. Results for the deuteron are discussed.« less

Accelerating atomic structure search with cluster regularization

NASA Astrophysics Data System (ADS)

Sørensen, K. H.; Jørgensen, M. S.; Bruix, A.; Hammer, B.

2018-06-01

We present a method for accelerating the global structure optimization of atomic compounds. The method is demonstrated to speed up the finding of the anatase TiO2(001)-(1 × 4) surface reconstruction within a density functional tight-binding theory framework using an evolutionary algorithm. As a key element of the method, we use unsupervised machine learning techniques to categorize atoms present in a diverse set of partially disordered surface structures into clusters of atoms having similar local atomic environments. Analysis of more than 1000 different structures shows that the total energy of the structures correlates with the summed distances of the atomic environments to their respective cluster centers in feature space, where the sum runs over all atoms in each structure. Our method is formulated as a gradient based minimization of this summed cluster distance for a given structure and alternates with a standard gradient based energy minimization. While the latter minimization ensures local relaxation within a given energy basin, the former enables escapes from meta-stable basins and hence increases the overall performance of the global optimization.

Dipole-dipole interaction in cavity QED: The weak-coupling, nondegenerate regime

NASA Astrophysics Data System (ADS)

Donaire, M.; Muñoz-Castañeda, J. M.; Nieto, L. M.

2017-10-01

We compute the energies of the interaction between two atoms placed in the middle of a perfectly reflecting planar cavity, in the weak-coupling nondegenerate regime. Both inhibition and enhancement of the interactions can be obtained by varying the size of the cavity. We derive exact expressions for the dyadic Green's function of the cavity field which mediates the interactions and apply time-dependent quantum perturbation theory in the adiabatic approximation. We provide explicit expressions for the van der Waals potentials of two polarizable atomic dipoles and the electrostatic potential of two induced dipoles. We compute the van der Waals potentials in three different scenarios: two atoms in their ground states, two atoms excited, and two dissimilar atoms with one of them excited. In addition, we calculate the phase-shift rate of the two-atom wave function in each case. The effect of the two-dimensional confinement of the electromagnetic field on the dipole-dipole interactions is analyzed. This effect depends on the atomic polarization. For dipole moments oriented parallel to the cavity plates, both the electrostatic and the van der Waals interactions are exponentially suppressed for values of the cavity width much less than the interatomic distance, whereas for values of the width close to the interatomic distance, the strength of both interactions is higher than their values in the absence of cavity. For dipole moments perpendicular to the plates, the strength of the van der Waals interaction decreases for values of the cavity width close to the interatomic distance, while it increases for values of the width much less than the interatomic distance with respect to its strength in the absence of cavity. We illustrate these effects by computing the dipole-dipole interactions between two alkali atoms in circular Rydberg states.

Surface passivation for tight-binding calculations of covalent solids.

PubMed

Bernstein, N

2007-07-04

Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp(3) hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system.

Surface passivation for tight-binding calculations of covalent solids

NASA Astrophysics Data System (ADS)

Bernstein, N.

2007-07-01

Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp3 hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system.

Thomas-Fermi model electron density with correct boundary conditions: Application to atoms and ions

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

Patil, S.H.

1999-01-01

The author proposes an electron density in atoms and ions, which has the Thomas-Fermi-Dirac form in the intermediate region of r, satisfies the Kato condition for small r, and has the correct asymptotic behavior at large values of r, where r is the distance from the nucleus. He also analyzes the perturbation in the density produced by multipolar fields. He uses these densities in the Poisson equation to deduce average values of r{sup m}, multipolar polarizabilities, and dispersion coefficients of atoms and ions. The predictions are in good agreement with experimental and other theoretical values, generally within about 20%. Hemore » tabulates here the coefficient A in the asymptotic density; radial expectation values (r{sup m}) for m = 2, 4, 6; multipolar polarizabilities {alpha}{sub 1}, {alpha}{sub 2}, {alpha}{sub 3}; expectation values {l_angle}r{sup 0}{r_angle} and {l_angle}r{sup 2}{r_angle} of the asymptotic electron density; and the van der Waals coefficient C{sub 6} for atoms and ions with 2 {le} Z {le} 92. Many of the results, particularly the multipolar polarizabilities and the higher order dispersion coefficients, are the only ones available in the literature. The variation of these properties also provides interesting insight into the shell structure of atoms and ions. Overall, the Thomas-Fermi-Dirac model with the correct boundary conditions provides a good global description of atoms and ions.« less

Optoelectronic Properties of X-Doped (X = O, S, Te) Photovoltaic CSe with Puckered Structure.

PubMed

Zhang, Qiang; Xin, Tianyuan; Lu, Xiaoke; Wang, Yuexia

2018-03-16

We exploited novel two-dimensional (2D) carbon selenide (CSe) with a structure analogous to phosphorene, and probed its electronics and optoelectronics. Calculating phonon spectra using the density functional perturbation theory (DFPT) method indicated that 2D CSe possesses dynamic stability, which made it possible to tune and equip CSe with outstanding properties by way of X-doping (X = O, S, Te), i.e., X substituting Se atoms. Then systematic investigation on the structural, electronic, and optical properties of pristine and X-doped monolayer CSe was carried out using the density functional theory (DFT) method. It was found that the bonding feature of C-X is intimately associated with the electronegativity and radius of the doping atoms, which leads to diverse electronic and optical properties for doping different group VI elements. All the systems possess direct gaps, except for O-doping. Substituting O for Se atoms in monolayer CSe brings about a transition from a direct Γ-Γ band gap to an indirect Γ-Y band gap. Moreover, the value of the band gap decreases with increased doping concentration and radius of doping atoms. A red shift in absorption spectra occurs toward the visible range of radiation after doping, and the red-shift phenomenon becomes more obvious with increased radius and concentration of doping atoms. The results can be useful for filtering doping atoms according to their radius or electronegativity in order to tailor optical spectra efficiently.

Optoelectronic Properties of X-Doped (X = O, S, Te) Photovoltaic CSe with Puckered Structure

PubMed Central

Zhang, Qiang; Xin, Tianyuan; Lu, Xiaoke; Wang, Yuexia

2018-01-01

We exploited novel two-dimensional (2D) carbon selenide (CSe) with a structure analogous to phosphorene, and probed its electronics and optoelectronics. Calculating phonon spectra using the density functional perturbation theory (DFPT) method indicated that 2D CSe possesses dynamic stability, which made it possible to tune and equip CSe with outstanding properties by way of X-doping (X = O, S, Te), i.e., X substituting Se atoms. Then systematic investigation on the structural, electronic, and optical properties of pristine and X-doped monolayer CSe was carried out using the density functional theory (DFT) method. It was found that the bonding feature of C-X is intimately associated with the electronegativity and radius of the doping atoms, which leads to diverse electronic and optical properties for doping different group VI elements. All the systems possess direct gaps, except for O-doping. Substituting O for Se atoms in monolayer CSe brings about a transition from a direct Γ-Γ band gap to an indirect Γ-Y band gap. Moreover, the value of the band gap decreases with increased doping concentration and radius of doping atoms. A red shift in absorption spectra occurs toward the visible range of radiation after doping, and the red-shift phenomenon becomes more obvious with increased radius and concentration of doping atoms. The results can be useful for filtering doping atoms according to their radius or electronegativity in order to tailor optical spectra efficiently. PMID:29547504

Application of the Interacting Quantum Atoms Approach to the S66 and Ionic-Hydrogen-Bond Datasets for Noncovalent Interactions.

PubMed

Suárez, Dimas; Díaz, Natalia; Francisco, Evelio; Martín Pendás, Angel

2018-04-17

The interacting quantum atoms (IQA) method can assess, systematically and in great detail, the strength and physics of both covalent and noncovalent interactions. The lack of a pair density in density functional theory (DFT), which precludes the direct IQA decomposition of the characteristic exchange-correlation energy, has been recently overcome by means of a scaling technique, which can largely expand the applicability of the method. To better assess the utility of the augmented IQA methodology to derive quantum chemical decompositions at the atomic and molecular levels, we report the results of Hartree-Fock (HF) and DFT calculations on the complexes included in the S66 and the ionic H-bond databases of benchmark geometry and binding energies. For all structures, we perform single-point and geometry optimizations using HF and selected DFT methods with triple-ζ basis sets followed by full IQA calculations. Pairwise dispersion energies are accounted for by the D3 method. We analyze the goodness of the HF-D3 and DFT-D3 binding energies, the magnitude of numerical errors, the fragment and atomic distribution of formation energies, etc. It is shown that fragment-based IQA decomposes the formation energies in comparable terms to those of perturbative approaches and that the atomic IQA energies hold the promise of rigorously quantifying atomic and group energy contributions in larger biomolecular systems. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Coupled-cluster based basis sets for valence correlation calculations

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

Claudino, Daniel; Bartlett, Rodney J., E-mail: bartlett@qtp.ufl.edu; Gargano, Ricardo

Novel basis sets are generated that target the description of valence correlation in atoms H through Ar. The new contraction coefficients are obtained according to the Atomic Natural Orbital (ANO) procedure from CCSD(T) (coupled-cluster singles and doubles with perturbative triples correction) density matrices starting from the primitive functions of Dunning et al. [J. Chem. Phys. 90, 1007 (1989); ibid. 98, 1358 (1993); ibid. 100, 2975 (1993)] (correlation consistent polarized valence X-tuple zeta, cc-pVXZ). The exponents of the primitive Gaussian functions are subject to uniform scaling in order to ensure satisfaction of the virial theorem for the corresponding atoms. These newmore » sets, named ANO-VT-XZ (Atomic Natural Orbital Virial Theorem X-tuple Zeta), have the same number of contracted functions as their cc-pVXZ counterparts in each subshell. The performance of these basis sets is assessed by the evaluation of the contraction errors in four distinct computations: correlation energies in atoms, probing the density in different regions of space via 〈r{sup n}〉 (−3 ≤ n ≤ 3) in atoms, correlation energies in diatomic molecules, and the quality of fitting potential energy curves as measured by spectroscopic constants. All energy calculations with ANO-VT-QZ have contraction errors within “chemical accuracy” of 1 kcal/mol, which is not true for cc-pVQZ, suggesting some improvement compared to the correlation consistent series of Dunning and co-workers.« less

Reactivity of amino acid anions with nitrogen and oxygen atoms.

PubMed

Wang, Zhe-Chen; Li, Ya-Ke; He, Sheng-Gui; Bierbaum, Veronica M

2018-02-14

For many decades, astronomers have searched for biological molecules, including amino acids, in the interstellar medium; this endeavor is important for investigating the hypothesis of the origin of life from space. The space environment is complex and atomic species, such as nitrogen and oxygen atoms, are widely distributed. In this work, the reactions of eight typical deprotonated amino acids (glycine, alanine, cysteine, proline, aspartic acid, histidine, tyrosine, and tryptophan) with ground state nitrogen and oxygen atoms are studied by experiment and theory. These amino acid anions do not react with nitrogen atoms. However, the reactions of these ions with oxygen atoms show an intriguing variety of ionic products and the reaction rate constants are of the order of 10 -10 cm 3 s -1 . Density functional calculations provide detailed mechanisms of the reactions, and demonstrate that spin conversion is essential for some processes. Our study provides important data and insights for understanding the kinetic and dynamic behavior of amino acids in space environments.

Method and apparatus for atomic imaging

DOEpatents

Saldin, Dilano K.; de Andres Rodriquez, Pedro L.

1993-01-01

A method and apparatus for three dimensional imaging of the atomic environment of disordered adsorbate atoms are disclosed. The method includes detecting and measuring the intensity of a diffuse low energy electron diffraction pattern formed by directing a beam of low energy electrons against the surface of a crystal. Data corresponding to reconstructed amplitudes of a wave form is generated by operating on the intensity data. The data corresponding to the reconstructed amplitudes is capable of being displayed as a three dimensional image of an adsorbate atom. The apparatus includes a source of a beam of low energy electrons and a detector for detecting the intensity distribution of a DLEED pattern formed at the detector when the beam of low energy electrons is directed onto the surface of a crystal. A device responsive to the intensity distribution generates a signal corresponding to the distribution which represents a reconstructed amplitude of a wave form and is capable of being converted into a three dimensional image of the atomic environment of an adsorbate atom on the crystal surface.

Atomic oxygen durability of solar concentrator materials for Space Station Freedom

NASA Technical Reports Server (NTRS)

Degroh, Kim K.; Terlep, Judith A.; Dever, Therese M.

1990-01-01

The findings are reviewed of atomic oxygen exposure testing of candidate solar concentrator materials containing SiO2 and Al2O3 protective coatings for use on Space Station Freedom solar dynamic power modules. Both continuous and iterative atomic oxygen exposure tests were conducted. Iterative air plasma ashing resulted in larger specular reflectance decreases and solar absorptance increases than continuous ashing to the same fluence, and appears to provide a more severe environment than the continuous atomic oxygen exposure that would occur in the low Earth orbit environment. First generation concentrator fabrication techniques produced surface defects including scratches, macroscopic bumps, dendritic regions, porosity, haziness, and pin hole defects. Several of these defects appear to be preferential sites for atomic oxygen attack leading to erosive undercutting. Extensive undercutting and flaking of reflective and protective coatings were found to be promoted through an undercutting tearing propagation process. Atomic oxygen erosion processes and effects on optical performance is presented.

Atom probe tomographic mapping directly reveals the atomic distribution of phosphorus in resin embedded ferritin

DOE PAGES

Perea, Daniel E.; Liu, Jia; Bartrand, Jonah A. G.; ...

2016-02-29

In this study, we report the atomic-scale analysis of biological interfaces using atom probe tomography. Embedding the protein ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualize atomic distributions and distinguish organic-organic and organic-inorganic interfaces. The sample preparation method can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment.

Atoms in molecules, an axiomatic approach. I. Maximum transferability

NASA Astrophysics Data System (ADS)

Ayers, Paul W.

2000-12-01

Central to chemistry is the concept of transferability: the idea that atoms and functional groups retain certain characteristic properties in a wide variety of environments. Providing a completely satisfactory mathematical basis for the concept of atoms in molecules, however, has proved difficult. The present article pursues an axiomatic basis for the concept of an atom within a molecule, with particular emphasis devoted to the definition of transferability and the atomic description of Hirshfeld.

a Study of the Interaction of Atoms with Strong Laser Fields.

NASA Astrophysics Data System (ADS)

Edwards, Mark

1984-02-01

In this thesis three aspects of the interactions of atoms with high intensity laser fields were treated. All three were motivated by experiment. The first investigation was prompted by a recent experiment (Kruit et al. 1983) involving multiphoton ionization of Xe. In this experiment it was found that the photoelectron energy spectrum contained peaks which corresponded to the absorption of more than the minimum number of photons required to ionize the atom. The effective orders of nonlinearity, furthermore, showed a striking uniformity. These effects were investigated using a model approximation consisting of a single bound state and m continua. Simple analytic expressions were obtained for the quantities measured in the experiment and the limit m (--->) (INFIN) was obtained. The results showed good qualitative agreement with experiment. An experiment (Grove et al. 1977) designed to test a theoretical calculation of the dynamical Stark effect stimulated the second part of this thesis. When experimental conditions were varied slightly, strong field turn-on effects were observed in the resonance fluorescence spectrum from a two-level atom (TLA). This experimental result led to the present study of how an adiabatically and near-adiabatically changing field intensity affects the resonance fluorescence spectrum of a TLA. It was found that there is an asymmetry in the spectrum for off-resonance excitation produced because the field turn-on repopulates the dressed state that is depopulated by spontaneous emission. The experimental result was not explained by this result, however. The third part of this thesis was based on an experiment (Granneman and Van der Wiel 1976) which attempted to verify a perturbation calculation of the two-photon ionization cross section of Cs. A discrepancy of four orders of magnitude near a minimum in the cross section was found between theory and experiment. To explain this discrepancy it was suggested (Armstrong and Beers 1977) that the effective order of nonlinearity (k) for this process varied significantly around the minimum. The present study involves a perturbation calculation of k. It was found that k varies rapidly around the minimum, and that this variation should be experimentally observable for laser intensities of the order of tens of GW cm('-2).

Products of Dissociative Recombination in the Ionosphere

NASA Technical Reports Server (NTRS)

Cosby, Philip

1996-01-01

SRI International undertook a novel experimental measurement of the product states formed by dissociative recombination (DR) of O2(+), NO(+), and N2(+) as a function of both electron energy and reactant ion vibrational level. For these measurements we used a recently developed experimental technique for measuring dissociation product distributions that allows both the branching ratios to be accurately determined and the electronic and rovibrational state composition of the reactant ions to be specified. DR is the dominant electron loss mechanism in all regions of the ionosphere. In this process, electron attachment to the molecular ion produces an unstable neutral molecule that rapidly dissociates. For a molecular ion such as O2(+), the dissociation recombination reaction is (1) O2(+) + e yields O + O + W. The atomic products of this reaction, in this case two oxygen atoms, can be produced in a variety of excited states and with a variety of kinetic energies, as represented by W in Eq. (1). These atoms are not only active in the neutral chemistry of the ionosphere, but are also especially important because their optical emissions are often used to infer in situ concentrations of the parent molecular ion and ambient electron densities. Many laboratory measurements have been made of DR reaction rates under a wide range of electron temperatures, but very little is known about the actual distributions among the final states of the atomic products. This lack of knowledge seriously limits the validity and effectiveness of efforts to model both natural and man-made ionospheric disturbances. Bates recently identified major deficiencies in the currently accepted branching ratios for O2(+) as they relate to blue and green line emission measurements in the nocturnal F-region. During our two-year effort, we partially satisfied our ambitious goals. We constructed and operated a variable pressure, electron-impact ion source and a high pressure, hollow-cathode discharge ion source for O2(+), NO(+), and N2(+) beams. Translational spectroscopy of the products of dissociative charge transfer in Cs vapor was used to accurately assay the composition of the O2(+) and NO(+) beams and to develop a methodology for the vibrationally controlled preparation of the ground state ion beams. Attempts to assay the N2(+) beam revealed a novel two-electron process in the charge transfer reactions. A coaxial electron gun for the DR measurements was constructed following an extensive numerical design of the fields. Tests of the gun, however, found substantial perturbations of the magnetic fields by the soft iron (CMI-C) assembly containing the Langmuir probe that locates the electron beam. Hydrogen annealing of the iron failed to eliminate the field perturbations, necessitating the removal of the probe assembly. During this work on the coaxial electron gun, we discovered that predissociated high Rydberg states of O2 could be produced by subjecting the molecules to a sudden perturbation by an electromagnetic field. This technique allowed a measurement of the product branching to the atomic limits for the lowest seven vibrational levels of O2(+).

Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. II. Confined fluids and vapor-liquid interfaces

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

Ghobadi, Ahmadreza F.; Elliott, J. Richard, E-mail: elliot1@uakron.edu

2014-07-14

In this work, a new classical density functional theory is developed for group-contribution equations of state (EOS). Details of implementation are demonstrated for the recently-developed SAFT-γ WCA EOS and selective applications are studied for confined fluids and vapor-liquid interfaces. The acronym WCA (Weeks-Chandler-Andersen) refers to the characterization of the reference part of the third-order thermodynamic perturbation theory applied in formulating the EOS. SAFT-γ refers to the particular form of “statistical associating fluid theory” that is applied to the fused-sphere, heteronuclear, united-atom molecular models of interest. For the monomer term, the modified fundamental measure theory is extended to WCA-spheres. A newmore » chain functional is also introduced for fused and soft heteronuclear chains. The attractive interactions are taken into account by considering the structure of the fluid, thus elevating the theory beyond the mean field approximation. The fluctuations of energy are also included via a non-local third-order perturbation theory. The theory includes resolution of the density profiles of individual groups such as CH{sub 2} and CH{sub 3} and satisfies stoichiometric constraints for the density profiles. New molecular simulations are conducted to demonstrate the accuracy of each Helmholtz free energy contribution in reproducing the microstructure of inhomogeneous systems at the united-atom level of coarse graining. At each stage, comparisons are made to assess where the present theory stands relative to the current state of the art for studying inhomogeneous fluids. Overall, it is shown that the characteristic features of real molecular fluids are captured both qualitatively and quantitatively. For example, the average pore density deviates ∼2% from simulation data for attractive pentadecane in a 2-nm slit pore. Another example is the surface tension of ethane/heptane mixture, which deviates ∼1% from simulation data while the theory reproduces the excess accumulation of ethane at the interface.« less

Oxidation and protection of fiberglass-epoxy composite masts for photovoltaic arrays in the low Earth orbital environment

NASA Technical Reports Server (NTRS)

Rutledge, Sharon K.; Paulsen, Phillip E.; Brady, Joyce A.; Ciancone, Michael L.

1988-01-01

Fiberglass-epoxy composites are considered for use as structural members for the mast of the space station solar array panel. The low Earth orbital environment in which space station is to operate is composed mainly of atomic oxygen, which has been shown to cause erosion of many organic materials and some metals. Ground based testing in a plasma asher was performed to determine the extent of degradation of fiberglass-epoxy composites when exposed to a simulated atomic oxygen environment. During exposure, the epoxy at the surface of the composite was oxidized, exposing individual glass fibers which could easily be removed. Several methods of protecting the composite were evaluated in an atomic oxygen environment and with thermal cycling and flexing. The protection techniques evaluated to date include an aluminum braid covering, an indium-tin eutectic and a silicone based paint. The open aluminum braid offered little protection while the CV-1144 coating offered some initial protection against atomic oxygen, but appears to develop cracks which accelerate degradation when flexed. Coatings such as the In-Sn eutectic may provide adequate protection by containing the glass fibers even though mass loss still occurs.

Synthesis and structural characterization of two half-sandwich nickel(II) complexes with the scorpionate ligands

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

Wang, G.-F., E-mail: wgf1979@126.com, E-mail: s-shuwen@163.com; Zhang, X., E-mail: zhangx@hit.edu.cn; Sun, S.-W.

The synthesis and characterization of two new halfsandwich mononuclear nickel(II) complexes with the scorpionate ligands, [k{sup 3}-N, N',N''-Tp{sup t-Bu}, {sup Me}NiI] (1) and [k{sup 3}-N,N',N''-Tp{sup t-Bu}, {sup Me}NiNO{sub 3}] (2), are reported. These complexes have been fully characterized by elemental analyses and infrared spectra. Their molecular structures were determined by single crystal X-ray diffraction. The nickel(II) ion of complex 1 is in a four-coordinate environment, in which the donor atoms are provided by three nitrogen atoms of a hydrotris(pyrazolyl) borate ligand and one iodide atom, while that of complex 2 is in a five-coordinate environment with three nitrogen atoms frommore » a hydrotris(pyrazolyl)borate ligand and two oxygen atoms from a nitrate ion.« less

A spectral study of a radio-frequency plasma-generated flux of atomic oxygen

NASA Technical Reports Server (NTRS)

Batten, Carmen E.; Brown, Kenneth G.; Lewis, Beverley W.

1994-01-01

The active environment of a radio-frequency (RF) plasma generator, with and without low-pressure oxygen, has been characterized through the identification of emission lines in the spectral region from 250 to 900 nm. The environment is shown to be dependent on the partial pressure of oxygen and the power applied to the RF generator. Atomic oxygen has been found in significant amounts as well as atomic hydrogen and the molecular oxygen species O2((sup 1)Sigma). The only charged species observed was the singly charged molecular ion O2(+). With a polymer specimen in the plasma chamber, carbon monoxide was also observed. The significance of these observations with respect to previous studies using this type of generator to stimulate material degradation in space is discussed. The possibility of using these generators as atomic oxygen sources in the development of oxygen atom fluorescence sensors is explored.

Sensitive Technique Developed Using Atomic Force Microscopy to Measure the Low-Earth-Orbit Atomic Oxygen Erosion of Polymers

NASA Technical Reports Server (NTRS)

deGroh, Kim D.; Banks, Bruce A.; Clark, Gregory W.; Hammerstrom, Anne; Youngstrom, Erica; Kaminski, Carolyn; Fine, Elizabeth; Marx, Laura

2001-01-01

A recession measurement technique has been developed at the NASA Glenn Research Center to determine the atomic oxygen durability of polymers exposed to the space environment for short durations. Polymers such as polyimide Kapton and Teflon FEP (fluorinated ethylene propylene, DuPont) are commonly used in spacecraft because of their desirable properties, such as flexibility, low density, and in the case of FEP, low solar absorptance and high thermal emittance. Polymers on the exterior of spacecraft in the low- Earth-orbit environment are exposed to energetic atomic oxygen, resulting in erosion and potential structural loss. It is, therefore, important to understand the atomic oxygen erosion yield (E, the volume loss per incident oxygen atom) of polymers being considered in spacecraft design. Because long-term space exposure data are rare and very costly, short-term exposures, such as on the space shuttles, are often relied on for atomic oxygen erosion determination. The most common technique for determining E is through mass-loss measurements. For limited-duration exposure experiments, such as shuttle flight experiments, the atomic oxygen fluence is often so small that mass-loss measurements are not sensitive enough. Therefore, a recession measurement technique has been developed at Glenn to obtain accurate erosion yields of polymers exposed to low atomic oxygen fluences.

Oxidation and crystal field effects in uranium

NASA Astrophysics Data System (ADS)

Tobin, J. G.; Yu, S.-W.; Booth, C. H.; Tyliszczak, T.; Shuh, D. K.; van der Laan, G.; Sokaras, D.; Nordlund, D.; Weng, T.-C.; Bagus, P. S.

2015-07-01

An extensive investigation of oxidation in uranium has been pursued. This includes the utilization of soft x-ray absorption spectroscopy, hard x-ray absorption near-edge structure, resonant (hard) x-ray emission spectroscopy, cluster calculations, and a branching ratio analysis founded on atomic theory. The samples utilized were uranium dioxide (U O2) , uranium trioxide (U O3) , and uranium tetrafluoride (U F4) . A discussion of the role of nonspherical perturbations, i.e., crystal or ligand field effects, will be presented.

Strong Interaction Studies with PANDA at FAIR

NASA Astrophysics Data System (ADS)

Schönning, Karin

2016-10-01

The Facility for Antiproton and Ion Research (FAIR) in Darmstadt, Germany, provides unique possibilities for a new generation of nuclear-, hadron- and atomic physics experiments. The future PANDA experiment at FAIR will offer a broad physics programme with emphasis on different aspects of hadron physics. Understanding the strong interaction in the perturbative regime remains one of the greatest challenges in contemporary physics and hadrons provide several important keys. In these proceedings, PANDA will be presented along with some high-lights of the planned physics programme.

Properties of solid and gaseous hydrogen, based upon anisotropic pair interactions

NASA Technical Reports Server (NTRS)

Etters, R. D.; Danilowicz, R.; England, W.

1975-01-01

Properties of H2 are studied on the basis of an analytic anisotropic potential deduced from atomic orbital and perturbation calculations. The low-pressure solid results are based on a spherical average of the anisotropic potential. The ground state energy and the pressure-volume relation are calculated. The metal-insulator phase transition pressure is predicted. Second virial coefficients are calculated for H2 and D2, as is the difference in second virial coefficients between ortho and para H2 and D2.

Random Walk on a Perturbation of the Infinitely-Fast Mixing Interchange Process

NASA Astrophysics Data System (ADS)

Salvi, Michele; Simenhaus, François

2018-05-01

We consider a random walk in dimension d≥ 1 in a dynamic random environment evolving as an interchange process with rate γ >0. We prove that, if we choose γ large enough, almost surely the empirical velocity of the walker X_t/t eventually lies in an arbitrary small ball around the annealed drift. This statement is thus a perturbation of the case γ =+∞ where the environment is refreshed between each step of the walker. We extend three-way part of the results of Huveneers and Simenhaus (Electron J Probab 20(105):42, 2015), where the environment was given by the 1-dimensional exclusion process: (i) We deal with any dimension d≥1; (ii) We treat the much more general interchange process, where each particle carries a transition vector chosen according to an arbitrary law μ ; (iii) We show that X_t/t is not only in the same direction of the annealed drift, but that it is also close to it.

Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory

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

Wang, Hao; Yang, Weitao, E-mail: weitao.yang@duke.edu; Department of Physics, Duke University, Durham, North Carolina 27708

We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniformmore » external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics’ force fields and nontransferable molecule-specific atomic polarizabilities.« less

HM{sup +}–RG complexes (M = group 2 metal; RG = rare gas): Physical vs. chemical interactions

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

Harris, Joe P.; Dodson, Hannah; Wright, Timothy G., E-mail: Tim.Wright@nottingham.ac.uk

2015-04-21

Previous work on the HM{sup +}–He complexes (M = Be–Ra) has been extended to the cases of the heavier rare gas atoms, HM{sup +}–RG (RG = Ne–Rn). Optimized geometries and harmonic vibrational frequencies have been calculated using MP2 theory and quadruple-ζ quality basis sets. Dissociation energies for the loss of the rare gas atom have been calculated at these optimized geometries using coupled cluster with single and double excitations and perturbative triples, CCSD(T)theory, extrapolating interaction energies to the basis set limit. Comparisons are made between the present data and the previously obtained helium results, as well as to those ofmore » the bare HM{sup +} molecules; furthermore, comparisons are made to the related M{sup +}–RG and M{sup 2+}–RG complexes. Partial atomic charge analyses have also been undertaken, and these used to test a simple charge-induced dipole model. Molecular orbital diagrams are presented together with contour plots of the natural orbitals from the quadratic configuration with single and double excitations (QCISD) density. The conclusion is that the majority of these complexes are physically bound, with very little sharing of electron density; however, for M = Be, and to a lesser extent M = Mg, some evidence for chemical effects is seen in HM{sup +}–RG complexes involving RG atoms with the higher atomic numbers.« less

Voronoi analysis of the short–range atomic structure in iron and iron–carbon melts

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

Sobolev, Andrey; Mirzoev, Alexander

2015-08-17

In this work, we simulated the atomic structure of liquid iron and iron–carbon alloys by means of ab initio molecular dynamics. Voronoi analysis was used to highlight changes in the close environments of Fe atoms as carbon concentration in the melt increases. We have found, that even high concentrations of carbon do not affect short–range atomic order of iron atoms — it remains effectively the same as in pure iron melts.

Changes in charge density vs changes in formal oxidation states: The case of Sn halide perovskites and their ordered vacancy analogues

NASA Astrophysics Data System (ADS)

Dalpian, Gustavo M.; Liu, Qihang; Stoumpos, Constantinos C.; Douvalis, Alexios P.; Balasubramanian, Mahalingam; Kanatzidis, Mercouri G.; Zunger, Alex

2017-07-01

Shifting the Fermi energy in solids by doping, defect formation, or gating generally results in changes in the charge density distribution, which reflect the ability of the bonding pattern in solids to adjust to such external perturbations. In the traditional chemistry textbook, such changes are often described by the formal oxidation states (FOS) whereby a single atom type is presumed to absorb the full burden of the perturbation (change in charge) of the whole compound. In the present paper, we analyze the changes in the position-dependence charge density due to shifts of the Fermi energy on a general physical basis, comparing with the view of the FOS picture. We use the halide perovskites CsSn X3 (X =F , Cl, Br, I) as examples for studying the general principle. When the solar absorber CsSn I3 (termed 113) loses 50 % of its Sn atoms, thereby forming the ordered vacancy compound C s2Sn I6 (termed 216), the Sn is said in the FOS picture to change from Sn(II) to Sn(IV). To understand the electronic properties of these two groups we studied the 113 and 216 compound pairs CsSnC l3 and C s2SnC l6 , CsSnB r3 and C s2SnB r6 , and CsSn I3 and C s2Sn I6 , complementing them by CsSn F3 and C s2Sn F6 in the hypothetical cubic structure for completing the chemical trends. These materials were also synthesized by chemical routes and characterized by x-ray diffraction, 119Sn-Mössbauer spectroscopy, and K -edge x-ray absorption spectroscopy. We find that indeed in going from 113 to 216 (equivalent to the introduction of two holes per unit) there is a decrease in the s charge on Sn, in agreement with the FOS picture. However, at the same time, we observe an increase of the p charge via downshift of the otherwise unoccupied p level, an effect that tends to replenish much of the lost s charge. At the end, the change in the charge on the Sn site as a result of adding two holes to the unit cell is rather small. This effect is theoretically explained as a "self-regulating response" [Raebiger, Lany, and Zunger, Nature (London) 453, 763 (2008), 10.1038/nature07009] whereby the system rehybridizes to minimize the effect of the charge perturbation created by vacancy formation. Rather than having a single preselected atom (here Sn) absorb the full brunt of the perturbation producing two holes, we find that the holes are distributed in a complex pattern throughout the octahedral systems of X6 ligands, forming hole orbitals with some specific symmetries. This clarifies the relation between FOS and charge transfer that can be applied to a wide variety of materials.

Changes in charge density vs changes in formal oxidation states: The case of Sn halide perovskites and their ordered vacancy analogues

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

Dalpian, Gustavo M.; Liu, Qihang; Stoumpos, Constantinos C.

Shifting the Fermi energy in solids by doping, defect formation, or gating generally results in changes in the charge density distribution, which reflect the ability of the bonding pattern in solids to adjust to such external perturbations. In the traditional chemistry textbook, such changes are often described by the formal oxidation states (FOS) whereby a single atom type is presumed to absorb the full burden of the perturbation (change in charge) of the whole compound. In the present paper, we analyze the changes in the position-dependence charge density due to shifts of the Fermi energy on a general physical basis,more » comparing with the view of the FOS picture. We use the halide perovskites CsSnX3 (X = F, Cl, Br, I) as examples for studying the general principle. When the solar absorber CsSnI3 (termed 113) loses 50% of its Sn atoms, thereby forming the ordered vacancy compound Cs2SnI6 (termed 216), the Sn is said in the FOS picture to change from Sn(II) to Sn(IV). To understand the electronic properties of these two groups we studied the 113 and 216 compound pairs CsSnCl3 and Cs2SnCl6, CsSnBr3 and Cs2SnBr6, and CsSnI3 and Cs2SnI6, complementing them by CsSnF3 and Cs2SnF6 in the hypothetical cubic structure for completing the chemical trends. These materials were also synthesized by chemical routes and characterized by x-ray diffraction, 119Sn-Mössbauer spectroscopy, and K-edge x-ray absorption spectroscopy. We find that indeed in going from 113 to 216 (equivalent to the introduction of two holes per unit) there is a decrease in the s charge on Sn, in agreement with the FOS picture. However, at the same time, we observe an increase of the p charge via downshift of the otherwise unoccupied p level, an effect that tends to replenish much of the lost s charge. At the end, the change in the charge on the Sn site as a result of adding two holes to the unit cell is rather small. This effect is theoretically explained as a “self-regulating response” [Raebiger, Lany, and Zunger, Nature (London) 453, 763 (2008)] whereby the system rehybridizes to minimize the effect of the charge perturbation created by vacancy formation. Rather than having a single preselected atom (here Sn) absorb the full brunt of the perturbation producing two holes, we find that the holes are distributed in a complex pattern throughout the octahedral systems of X6 ligands, forming hole orbitals with some specific symmetries. This clarifies the relation between FOS and charge transfer that can be applied to a wide variety of materials.« less

Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways

PubMed Central

Jo, Kyuri; Jung, Inuk; Moon, Ji Hwan; Kim, Sun

2016-01-01

Motivation: To understand the dynamic nature of the biological process, it is crucial to identify perturbed pathways in an altered environment and also to infer regulators that trigger the response. Current time-series analysis methods, however, are not powerful enough to identify perturbed pathways and regulators simultaneously. Widely used methods include methods to determine gene sets such as differentially expressed genes or gene clusters and these genes sets need to be further interpreted in terms of biological pathways using other tools. Most pathway analysis methods are not designed for time series data and they do not consider gene-gene influence on the time dimension. Results: In this article, we propose a novel time-series analysis method TimeTP for determining transcription factors (TFs) regulating pathway perturbation, which narrows the focus to perturbed sub-pathways and utilizes the gene regulatory network and protein–protein interaction network to locate TFs triggering the perturbation. TimeTP first identifies perturbed sub-pathways that propagate the expression changes along the time. Starting points of the perturbed sub-pathways are mapped into the network and the most influential TFs are determined by influence maximization technique. The analysis result is visually summarized in TF-Pathway map in time clock. TimeTP was applied to PIK3CA knock-in dataset and found significant sub-pathways and their regulators relevant to the PIP3 signaling pathway. Availability and Implementation: TimeTP is implemented in Python and available at http://biohealth.snu.ac.kr/software/TimeTP/. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: sunkim.bioinfo@snu.ac.kr PMID:27307609

Changes in Head Stability Control in Response to a Lateral Perturbation while Walking in Older Adults

NASA Technical Reports Server (NTRS)

Buccello, Regina R.; Cromwell, Ronita L.; Bloomberg, Jacob J.

2008-01-01

Falling is a main contributor of injury in older adults. The decline in sensory systems associated with aging limits information needed to successfully compensate for unexpected perturbations. Therefore, sensory changes result in older adults having problems maintaining balance stability when experiencing an unexpected lateral perturbation (e.g. slip) in the environment. The goal of this study was to determine head stability movement strategies used by older adults when experiencing an unexpected lateral perturbation during walking. A total of 16 healthy adults, aged 66-81 years, walked across a foam pathway 6 times. One piece of the foam pathway covered a movable platform that translated to the left when the subject stepped on the foam. Three trials were randomized in which the platform shifted. Angular rate sensors were placed on the center of mass for the head and trunk segments to collect head and trunk movement in all three planes of motion. The predominant movement strategies for maintaining head stability were determined from the results of the cross-correlation analyses between the head and trunk segments. The Chi square test of independence was used to evaluate the movement pattern distributions of head-trunk coordination during perturbed and non-perturbed walking. When perturbed, head stabilization was significantly challenged in the yaw and roll planes of motion. Subjects demonstrated a movement pattern of the head leading the trunk in an effort to stabilize the head. The older adult subjects used this head stabilization movement pattern to compensate for sensory changes when experiencing the unexpected lateral perturbation.

Generalized nonlinear Schrödinger equation and ultraslow optical solitons in a cold four-state atomic system.

PubMed

Hang, Chao; Huang, Guoxiang; Deng, L

2006-03-01

We investigate the influence of high-order dispersion and nonlinearity on the propagation of ultraslow optical solitons in a lifetime broadened four-state atomic system under a Raman excitation. Using a standard method of multiple-scales we derive a generalized nonlinear Schrödinger equation and show that for realistic physical parameters and at the pulse duration of 10(-6)s, the effects of third-order linear dispersion, nonlinear dispersion, and delay in nonlinear refractive index can be significant and may not be considered as perturbations. We provide exact soliton solutions for the generalized nonlinear Schrödinger equation and demonstrate that optical solitons obtained may still have ultraslow propagating velocity. Numerical simulations on the stability and interaction of these ultraslow optical solitons in the presence of linear and differential absorptions are also presented.

Quantum coherent control of the photoelectron angular distribution in bichromatic-field ionization of atomic neon

NASA Astrophysics Data System (ADS)

Gryzlova, E. V.; Grum-Grzhimailo, A. N.; Staroselskaya, E. I.; Douguet, N.; Bartschat, K.

2018-01-01

We investigate the coherent control of the photoelectron angular distribution in bichromatic atomic ionization. Neon is selected as target since it is one of the most popular systems in current gas-phase experiments with free-electron lasers (FELSs). In particular, we tackle practical questions, such as the role of the fine-structure splitting, the pulse length, and the intensity. Time-dependent and stationary perturbation theory are employed, and we also solve the time-dependent Schrödinger equation in a single-active electron model. We consider neon ionized by a FEL pulse whose fundamental frequency is in resonance with either 2 p -3 s or 2 p -4 s excitation. The contribution of the nonresonant two-photon process and its potential constructive or destructive role for quantum coherent control is investigated.

Into rude air: hummingbird flight performance in variable aerial environments.

PubMed

Ortega-Jimenez, V M; Badger, M; Wang, H; Dudley, R

2016-09-26

Hummingbirds are well known for their ability to sustain hovering flight, but many other remarkable features of manoeuvrability characterize the more than 330 species of trochilid. Most research on hummingbird flight has been focused on either forward flight or hovering in otherwise non-perturbed air. In nature, however, hummingbirds fly through and must compensate for substantial environmental perturbation, including heavy rain, unpredictable updraughts and turbulent eddies. Here, we review recent studies on hummingbirds flying within challenging aerial environments, and discuss both the direct and indirect effects of unsteady environmental flows such as rain and von Kármán vortex streets. Both perturbation intensity and the spatio-temporal scale of disturbance (expressed with respect to characteristic body size) will influence mechanical responses of volant taxa. Most features of hummingbird manoeuvrability remain undescribed, as do evolutionary patterns of flight-related adaptation within the lineage. Trochilid flight performance under natural conditions far exceeds that of microair vehicles at similar scales, and the group as a whole presents many research opportunities for understanding aerial manoeuvrability.This article is part of the themed issue 'Moving in a moving medium: new perspectives on flight'. © 2016 The Author(s).

Into rude air: hummingbird flight performance in variable aerial environments

PubMed Central

Ortega-Jimenez, V. M.; Badger, M.; Wang, H.; Dudley, R.

2016-01-01

Hummingbirds are well known for their ability to sustain hovering flight, but many other remarkable features of manoeuvrability characterize the more than 330 species of trochilid. Most research on hummingbird flight has been focused on either forward flight or hovering in otherwise non-perturbed air. In nature, however, hummingbirds fly through and must compensate for substantial environmental perturbation, including heavy rain, unpredictable updraughts and turbulent eddies. Here, we review recent studies on hummingbirds flying within challenging aerial environments, and discuss both the direct and indirect effects of unsteady environmental flows such as rain and von Kármán vortex streets. Both perturbation intensity and the spatio-temporal scale of disturbance (expressed with respect to characteristic body size) will influence mechanical responses of volant taxa. Most features of hummingbird manoeuvrability remain undescribed, as do evolutionary patterns of flight-related adaptation within the lineage. Trochilid flight performance under natural conditions far exceeds that of microair vehicles at similar scales, and the group as a whole presents many research opportunities for understanding aerial manoeuvrability. This article is part of the themed issue ‘Moving in a moving medium: new perspectives on flight’. PMID:27528777

A High-Sensitivity Flexible Eddy Current Array Sensor for Crack Monitoring of Welded Structures under Varying Environment.

PubMed

Chen, Tao; He, Yuting; Du, Jinqiang

2018-06-01

This paper develops a high-sensitivity flexible eddy current array (HS-FECA) sensor for crack monitoring of welded structures under varying environment. Firstly, effects of stress, temperature and crack on output signals of the traditional flexible eddy current array (FECA) sensor were investigated by experiments that show both stress and temperature have great influences on the crack monitoring performance of the sensor. A 3-D finite element model was established using Comsol AC/DC module to analyze the perturbation effects of crack on eddy currents and output signals of the sensor, which showed perturbation effect of cracks on eddy currents is reduced by the current loop when crack propagates. Then, the HS-FECA sensor was proposed to boost the sensitivity to cracks. Simulation results show that perturbation effect of cracks on eddy currents excited by the HS-FECA sensor gradually grows stronger when the crack propagates, resulting in much higher sensitivity to cracks. Experimental result further shows that the sensitivity of the new sensor is at least 19 times that of the original one. In addition, both stress and temperature variations have little effect on signals of the new sensor.

Traffic information computing platform for big data

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

Duan, Zongtao, E-mail: ztduan@chd.edu.cn; Li, Ying, E-mail: ztduan@chd.edu.cn; Zheng, Xibin, E-mail: ztduan@chd.edu.cn

Big data environment create data conditions for improving the quality of traffic information service. The target of this article is to construct a traffic information computing platform for big data environment. Through in-depth analysis the connotation and technology characteristics of big data and traffic information service, a distributed traffic atomic information computing platform architecture is proposed. Under the big data environment, this type of traffic atomic information computing architecture helps to guarantee the traffic safety and efficient operation, more intelligent and personalized traffic information service can be used for the traffic information users.

Chemical crosslinking and mass spectrometry studies of the structure and dynamics of membrane proteins and receptors.

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

Haskins, William E.; Leavell, Michael D.; Lane, Pamela

2005-03-01

Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurementmore » using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.« less

Calculating constants of the rates of the reactions of excitation, ionization, and atomic exchange: A model of a shock oscillator with a change of the Hamiltonian of the system

NASA Astrophysics Data System (ADS)

Tsyganov, D. L.

2017-11-01

A new model for calculating the rates of reactions of excitation, ionization, and atomic exchange is proposed. Diatomic molecule AB is an unstructured particle M upon the exchange of elastic-vibrational (VT) energy, i.e., a model of a shock forceful oscillator with a change in Hamiltonian (SFOH). The SFOH model is based on the quantum theory of strong perturbations. The SFOH model allows generalization in simulating the rates of the reactions of excitation, ionization, and atomic exchange in the vibrational-vibrational (VV) energy exchange of diatomic molecules, and the exchange of VV- and VT-energy of polyatomic molecules. The rate constants of the excitation of metastables A 3Σ u +, B 3Π g , W 3Δ u , B'3Σ u -, a'3Σ u -, and the ionization of a nitrogen molecules from ground state X2Σ g + upon a collision with a heavy structureless particle (a nitrogen molecule), are found as examples.

Two-Photon Emission of a Hydrogenlike Atom with Photon Polarization and Electron Spin States Taken into Account

NASA Astrophysics Data System (ADS)

Skobelev, V. V.

2017-02-01

The process of two-photon emission ( Ze)* → ( Ze) + 2 γ of a hydrogenlike atom is considered with spin states of the electron and polarization of the photons taken into account, which had not been done before. A general expression for the probability of the process per unit time has been obtained for different polarization states of the photons with a formulation of hard and soft selection rules for the quantum numbers m and l. It is shown that by virtue of the established specifics of the properties of the two-photon emission process (absence of a Zeeman effect and dependence of the probability on the polarization states of the photons), it can in principle be identified against the background of single-photon emission ( Ze)* → ( Ze) + γ, despite the presence of additional small factors: 1) α = e 2/ ћc ≈ 1/137 of the perturbation theory in e, and 2) the square of the atomic expansion parameter ( Zα)2 in the expression for the probability.

High Speed Video Measurements of a Magneto-optical Trap

NASA Astrophysics Data System (ADS)

Horstman, Luke; Graber, Curtis; Erickson, Seth; Slattery, Anna; Hoyt, Chad

2016-05-01

We present a video method to observe the mechanical properties of a lithium magneto-optical trap. A sinusoidally amplitude-modulated laser beam perturbed a collection of trapped ce7 Li atoms and the oscillatory response was recorded with a NAC Memrecam GX-8 high speed camera at 10,000 frames per second. We characterized the trap by modeling the oscillating cold atoms as a damped, driven, harmonic oscillator. Matlab scripts tracked the atomic cloud movement and relative phase directly from the captured high speed video frames. The trap spring constant, with magnetic field gradient bz = 36 G/cm, was measured to be 4 . 5 +/- . 5 ×10-19 N/m, which implies a trap resonant frequency of 988 +/- 55 Hz. Additionally, at bz = 27 G/cm the spring constant was measured to be 2 . 3 +/- . 2 ×10-19 N/m, which corresponds to a resonant frequency of 707 +/- 30 Hz. These properties at bz = 18 G/cm were found to be 8 . 8 +/- . 5 ×10-20 N/m, and 438 +/- 13 Hz. NSF #1245573.

Properties of NiO thin films deposited by intermittent spray pyrolysis process

NASA Astrophysics Data System (ADS)

Reguig, B. A.; Khelil, A.; Cattin, L.; Morsli, M.; Bernède, J. C.

2007-02-01

NiO thin films have been grown on glass substrates by intermittent spray pyrolysis deposition of NiCl 2·6H 2O diluted in distilled water, using a simple "perfume atomizer". The effect of the solution molarity on their properties was studied and compared to those of NiO thin films deposited with a classical spray system. It is shown that NiO thin films crystallized in the NiO structure are achieved after deposition. Whatever the precursor molarity, the grain size is around 25-30 nm. The crystallites are preferentially oriented along the (1 1 1) direction. All the films are p-type. However, the thickness and the conductivity of the NiO films depend on the precursor contraction. By comparison with the properties of films deposited by classical spray technique, it is shown that the critical precursor concentration, which induces strong thin films properties perturbations, is higher when a perfume atomizer is used. This broader stability domain can be attributed to better chlorides decomposition during the rest time used in the perfume atomizer technique.

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.

AtomPy: an open atomic-data curation environment

NASA Astrophysics Data System (ADS)

Bautista, Manuel; Mendoza, Claudio; Boswell, Josiah S; Ajoku, Chukwuemeka

2014-06-01

We present a cloud-computing environment for atomic data curation, networking among atomic data providers and users, teaching-and-learning, and interfacing with spectral modeling software. The system is based on Google-Drive Sheets, Pandas (Python Data Analysis Library) DataFrames, and IPython Notebooks for open community-driven curation of atomic data for scientific and technological applications. The atomic model for each ionic species is contained in a multi-sheet Google-Drive workbook, where the atomic parameters from all known public sources are progressively stored. Metadata (provenance, community discussion, etc.) accompanying every entry in the database are stored through Notebooks. Education tools on the physics of atomic processes as well as their relevance to plasma and spectral modeling are based on IPython Notebooks that integrate written material, images, videos, and active computer-tool workflows. Data processing workflows and collaborative software developments are encouraged and managed through the GitHub social network. Relevant issues this platform intends to address are: (i) data quality by allowing open access to both data producers and users in order to attain completeness, accuracy, consistency, provenance and currentness; (ii) comparisons of different datasets to facilitate accuracy assessment; (iii) downloading to local data structures (i.e. Pandas DataFrames) for further manipulation and analysis by prospective users; and (iv) data preservation by avoiding the discard of outdated sets.

Estimating the Error of an Analog Quantum Simulator by Additional Measurements

NASA Astrophysics Data System (ADS)

Schwenk, Iris; Zanker, Sebastian; Reiner, Jan-Michael; Leppäkangas, Juha; Marthaler, Michael

2017-12-01

We study an analog quantum simulator coupled to a reservoir with a known spectral density. The reservoir perturbs the quantum simulation by causing decoherence. The simulator is used to measure an operator average, which cannot be calculated using any classical means. Since we cannot predict the result, it is difficult to estimate the effect of the environment. Especially, it is difficult to resolve whether the perturbation is small or if the actual result of the simulation is in fact very different from the ideal system we intend to study. Here, we show that in specific systems a measurement of additional correlators can be used to verify the reliability of the quantum simulation. The procedure only requires additional measurements on the quantum simulator itself. We demonstrate the method theoretically in the case of a single spin connected to a bosonic environment.

Novel Hybrid Adaptive Controller for Manipulation in Complex Perturbation Environments

PubMed Central

Smith, Alex M. C.; Yang, Chenguang; Ma, Hongbin; Culverhouse, Phil; Cangelosi, Angelo; Burdet, Etienne

2015-01-01

In this paper we present a hybrid control scheme, combining the advantages of task-space and joint-space control. The controller is based on a human-like adaptive design, which minimises both control effort and tracking error. Our novel hybrid adaptive controller has been tested in extensive simulations, in a scenario where a Baxter robot manipulator is affected by external disturbances in the form of interaction with the environment and tool-like end-effector perturbations. The results demonstrated improved performance in the hybrid controller over both of its component parts. In addition, we introduce a novel method for online adaptation of learning parameters, using the fuzzy control formalism to utilise expert knowledge from the experimenter. This mechanism of meta-learning induces further improvement in performance and avoids the need for tuning through trial testing. PMID:26029916

In utero undernourishment perturbs the adult sperm methylome and is linked to metabolic disease transmission

PubMed Central

Radford, Elizabeth J.; Corish, Jennifer A.; Seisenberger, Stefanie; Hore, Timothy A.; Reik, Wolf; Erkek, Serap; Peters, Antoine H. F. M.; Patti, Mary-Elizabeth; Ferguson-Smith, Anne C.

2015-01-01

Adverse prenatal environments can promote metabolic disease in offspring and subsequent generations. Animal models and epidemiological data implicate epigenetic inheritance but mechanisms remain unknown. In an intergenerational developmental programming model affecting F2 metabolism, we demonstrate that the in utero nutritional environment of F1 embryos alters the germline DNA methylome of F1 adult males in a locus-specific manner. Differentially methylated regions are hypomethylated and enriched in nucleosome-retaining regions. A substantial fraction is resistant to early embryo methylation reprogramming, potentially impacting F2 development. Importantly, differential methylation is not maintained in F2 tissues, yet locus-specific expression is perturbed. Thus, in utero nutritional exposures during critical windows of germ cell development can impact the male germline methylome, associated with metabolic disease in offspring. PMID:25011554

Testing Photoionization Calculations Using Chandra X-ray Spectra

NASA Technical Reports Server (NTRS)

Kallman, Tim

2008-01-01

A great deal of work has been devoted to the accumulation of accurate quantities describing atomic processes for use in analysis of astrophysical spectra. But in many situations of interest the interpretation of a quantity which is observed, such as a line flux, depends on the results of a modeling- or spectrum synthesis code. The results of such a code depends in turn on many atomic rates or cross sections, and the sensitivity of the observable quantity on the various rates and cross sections may be non-linear and if so cannot easily be derived analytically. In such cases the most practical approach to understanding the sensitivity of observables to atomic cross sections is to perform numerical experiments, by calculating models with various rates perturbed by random (but known) factors. In addition, it is useful to compare the results of such experiments with some sample observations, in order to focus attention on the rates which are of the greatest relevance to real observations. In this paper I will present some attempts to carry out this program, focussing on two sample datasets taken with the Chandra HETG. I will discuss the sensitivity of synthetic spectra to atomic data affecting ionization balance, temperature, and line opacity or emissivity, and discuss the implications for the ultimate goal of inferring astrophysical parameters.

Quantum Analogies in the Interaction between Acoustic Waves and Bubble Clouds

NASA Astrophysics Data System (ADS)

Parrales, Miguel A.; Rodriguez-Rodriguez, Javier

2014-11-01

Analogies between quantum mechanical and acoustical propagation phenomena have a great interest in academic research due to their ability to shed light on some complex quantum effects, which are impossible to visualize directly in the macroscopic world. In this talk, we describe a number of these analogies concerning the acoustic behavior of bubble clouds. Firstly, we show that the structure of the collective oscillation modes of a spherical bubble cloud resembles that of the atomic orbitals of a hydrogen atom. Secondly, we present an analogy between some perturbation methods used in quantum-electrodynamics and the computation of the acoustic response of the randomly distributed bubble cloud by considering the contribution to the total scattered pressure of the multiple scattering paths that take place inside the clouds. As an application of this analogy, we obtain the scattering cross-section of a diluted cloud, which remarkably mimics the quantum scattering of an neutron wave when passing through an atomic nucleus. Finally, we numerically reproduce the behavior of an electron in a covalent bond between two hydrogen atoms by simulating the acoustic wave propagation through two neighboring spherical bubble assemblages. Funded by the Spanish Ministry of Economy and Competitiveness through Grants DPI2011-28356-C03-01 and DPI2011-28356-C03-02.

A review of atomic clock technology, the performance capability of present spaceborne and terrestrial atomic clocks, and a look toward the future

NASA Technical Reports Server (NTRS)

Vessot, Robert F. C.

1989-01-01

Clocks have played a strong role in the development of general relativity. The concept of the proper clock is presently best realized by atomic clocks, whose development as precision instruments has evolved very rapidly in the last decades. To put a historical prospective on this progress since the year AD 1000, the time stability of various clocks expressed in terms of seconds of time error over one day of operation is shown. This stability of operation must not be confused with accuracy. Stability refers to the constancy of a clock operation as compared to that of some other clocks that serve as time references. Accuracy, on the other hand, is the ability to reproduce a previously defined frequency. The issues are outlined that must be considered when accuracy and stability of clocks and oscillators are studied. In general, the most widely used resonances result from the hyperfine interaction of the nuclear magnetic dipole moment and that of the outermost electron, which is characteristic of hydrogen and the alkali atoms. During the past decade hyperfine resonances of ions have also been used. The principal reason for both the accuracy and the stability of atomic clocks is the ability of obtaining very narrow hyperfine transition resonances by isolating the atom in some way so that only the applied stimulating microwave magnetic field is a significant source of perturbation. It is also important to make resonance transitions among hyperfine magnetic sublevels where separation is independent, at least to first order, of the magnetic field. In the case of ions stored in traps operating at high magnetic fields, one selects the trapping field to be consistent with a field-independent transition of the trapped atoms.

Black hole quantum spectrum

NASA Astrophysics Data System (ADS)

Corda, Christian

2013-12-01

Introducing a black hole (BH) effective temperature, which takes into account both the non-strictly thermal character of Hawking radiation and the countable behavior of emissions of subsequent Hawking quanta, we recently re-analysed BH quasi-normal modes (QNMs) and interpreted them naturally in terms of quantum levels. In this work we improve such an analysis removing some approximations that have been implicitly used in our previous works and obtaining the corrected expressions for the formulas of the horizon's area quantization and the number of quanta of area and hence also for Bekenstein-Hawking entropy, its subleading corrections and the number of micro-states, i.e. quantities which are fundamental to realize the underlying quantum gravity theory, like functions of the QNMs quantum "overtone" number n and, in turn, of the BH quantum excited level. An approximation concerning the maximum value of n is also corrected. On the other hand, our previous results were strictly corrected only for scalar and gravitational perturbations. Here we show that the discussion holds also for vector perturbations. The analysis is totally consistent with the general conviction that BHs result in highly excited states representing both the "hydrogen atom" and the "quasi-thermal emission" in quantum gravity. Our BH model is somewhat similar to the semi-classical Bohr's model of the structure of a hydrogen atom. The thermal approximation of previous results in the literature is consistent with the results in this paper. In principle, such results could also have important implications for the BH information paradox.

Atomic research

NASA Technical Reports Server (NTRS)

Hadaway, James B.; Connatser, Robert; Cothren, Bobby; Johnson, R. B.

1993-01-01

Work performed by the University of Alabama in Huntsville's (UAH) Center for Applied Optics (CAO) entitled Atomic Research is documented. Atomic oxygen (AO) effects on materials have long been a critical concern in designing spacecraft to withstand exposure to the Low Earth Orbit (LEO) environment. The objective of this research effort was to provide technical expertise in the design of instrumentation and experimental techniques for analyzing materials exposed to atomic oxygen in accelerated testing at NASA/MSFC. Such testing was required to answer fundamental questions concerning Space Station Freedom (SSF) candidate materials and materials exposed to atomic oxygen aboard the Long-Duration Exposure Facility (LDEF). The primary UAH task was to provide technical design, review, and analysis to MSFC in the development of a state-of-the-art 5eV atomic oxygen beam facility required to simulate the RAM-induced low earth orbit (LEO) AO environment. This development was to be accomplished primarily at NASA/MSFC. In support of this task, contamination effects and ultraviolet (UV) simulation testing was also to be carried out using NASA/MSFC facilities. Any materials analysis of LDEF samples was to be accomplished at UAH.

Neutral atom imaging at Mercury

NASA Astrophysics Data System (ADS)

Mura, A.; Orsini, S.; Milillo, A.; Di Lellis, A. M.; De Angelis, E.

2006-02-01

The feasibility of neutral atom detection and imaging in the Hermean environment is discussed in this study. In particular, we consider those energetic neutral atoms (ENA) whose emission is directly related to solar wind entrance into Mercury's magnetosphere. In fact, this environment is characterised by a weak magnetic field; thus, cusp regions are extremely large if compared to the Earth's ones, and intense proton fluxes are expected there. Our study includes a model of H + distribution in space, energy and pitch angle, simulated by means of a single-particle, Monte-Carlo simulation. Among processes that could generate neutral atom emission, we focus our attention on charge-exchange and ion sputtering, which, in principle, are able to produce directional ENA fluxes. Simulated neutral atom images are investigated in the frame of the neutral particle analyser-ion spectrometer (NPA-IS) SERENA experiment, proposed to fly on board the ESA mission BepiColombo/MPO. The ELENA (emitted low-energy neutral atoms) unit, which is part of this experiment, will be able to detect such fluxes; instrumental details and predicted count rates are given.

Scattering from Marine Sediments in a Very Shallow Water Environment

DTIC Science & Technology

2015-12-28

taking into account only large-scale changes of the environment. Keywords: Reciprocity , integral equations, volume and roughness scattering...for Public Release, Distribution Unlimited A. Ivakin: Scattering in range-dependent waveguides 5 II. VOLUME PERTURBATIONS: RECIPROCITY THEOREM...6], i.e. with the same υ , and therefore same Q , which, along with following discussion of reciprocity , explains the choice of this parameter

Genotype * environment interaction: a case study for Douglas-fir in western Oregon.

Treesearch

Robert K. Campbell

1992-01-01

Unrecognized genotype x environment interactions (g,e) can bias genetic-gain predictions and models for predicting growth dynamics or species perturbations by global climate change. This study tested six sets of families in 10 plantation sites in a 78-thousand-hectare breeding zone. Plantation differences accounted for 71 percent of sums of squares (15-year heights),...

Interaction of Rydberg atoms in circular states with the alkaline-earth Ca(4s{sup 2}) and Sr(5s{sup 2}) atoms

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

Mironchuk, E. S.; Narits, A. A.; Lebedev, V. S., E-mail: vlebedev@sci.lebedev.ru

2015-11-15

The resonant mechanism of interaction of alkaline-earth atoms having a low electron affinity to Rydberg atoms in circular (l = vertical bar m vertical bar = n–1) and near-circular states has been studied. To describe the dynamics of resonant processes accompanied by nonadiabatic transitions between ionic and Rydberg covalent terms of a quasimolecule, an approach based on the integration of coupled equations for the probability amplitudes has been developed taking into account the possibility of the decay of an anion in the Coulomb field of the positive ionic core of a highly excited atom. The approach involves the specific featuresmore » of the problem associated with the structure of the wavefunction of a Rydberg electron in states with high orbital angular momenta l ∼ n–1. This approach provides a much more accurate description of the dynamics of electronic transitions at collisions between atoms than that within the modified semiclassical Landau–Zener model. In addition, this approach makes it possible to effectively take into account many channels of the problem. The cross sections for resonant quenching of Rydberg states of the Li(nlm) atom with given principal n, orbital l = n–1, and magnetic m quantum numbers at thermal collisions with the Ca(4s{sup 2}) and Sr(5s{sup 2}) atoms have been calculated. The dependences of the results on n, m, and angle α between the relative velocity of the atoms and the normal to the plane of the orbit of the Rydberg electron have been obtained. The influence of orientational effects on the efficiency of the collisional destruction of circular and near-circular states has been studied. The results indicate a higher stability of such states to their perturbations by neutral particles as compared to usually studied nl states with low values of l (l ≪ n)« less

Calculations of long-range three-body interactions for He(n0λS )-He(n0λS )-He(n0'λL )

NASA Astrophysics Data System (ADS)

Yan, Pei-Gen; Tang, Li-Yan; Yan, Zong-Chao; Babb, James F.

2018-04-01

We theoretically investigate long-range interactions between an excited L -state He atom and two identical S -state He atoms for the cases of the three atoms all in spin-singlet states or all in spin-triplet states, denoted by He(n0λS )-He(n0λS )-He(n0'λL ), with n0 and n0' principal quantum numbers, λ =1 or 3 the spin multiplicity, and L the orbital angular momentum of a He atom. Using degenerate perturbation theory for the energies up to second-order, we evaluate the coefficients C3 of the first-order dipolar interactions and the coefficients C6 and C8 of the second-order additive and nonadditive interactions. Both the dipolar and dispersion interaction coefficients, for these three-body degenerate systems, show dependences on the geometrical configurations of the three atoms. The nonadditive interactions start to appear in second-order. To demonstrate the results and for applications, the obtained coefficients Cn are evaluated with highly accurate variationally generated nonrelativistic wave functions in Hylleraas coordinates for He(1 1S ) -He(1 1S ) -He(2 1S ) , He(1 1S ) -He(1 1S ) -He(2 1P ) , He(2 1S ) -He(2 1S ) -He(2 1P ) , and He(2 3S ) -He(2 3S ) -He(2 3P ) . The calculations are given for three like nuclei for the cases of hypothetical infinite mass He nuclei, and of real finite mass 4He or 3He nuclei. The special cases of the three atoms in equilateral triangle configurations are explored in detail, and for the cases in which one of the atoms is in a P state, we also present results for the atoms in an isosceles right triangle configuration or in an equally spaced collinear configuration. The results can be applied to construct potential energy surfaces for three helium atom systems.

Frequency modulation detection atomic force microscopy in the liquid environment

NASA Astrophysics Data System (ADS)

Jarvis, S. P.; Ishida, T.; Uchihashi, T.; Nakayama, Y.; Tokumoto, H.

True atomic resolution imaging using frequency modulation detection is already well established in ultra-high vacuum. In this paper we demonstrate that it also has great potential in the liquid environment. Using a combination of magnetic activation and high-aspect-ratio carbon nanotube probes, we show that imaging can be readily combined with point spectroscopy, revealing both the tip-sample interaction and the structure of the intermediate liquid.

Two-Dimensional Description of Potential Perturbations to the Ozone Layer Due to NOx and H2O Aircraft Emissions,

DTIC Science & Technology

1984-01-01

Perturbations to the Ozone 01aparUNM fe"MAWLayer Due to NOX and H20Arrf Emissions20Araf Office of Environment and Energy Washington, D.C. 20591 uTI LEOU George F...and Energy 14. Sponsorng Agency Code Washington, D.C. 20591 15. Supplementary Notes 1 . Abstroct . This report is divided into two parts. Part I is an...obtained from the work of Louis, et al. (1974), who calculated the circulation patterns by solving the continuity and energy equations using compiled

Effectiveness of Modal Decomposition for Tapping Atomic Force Microscopy Microcantilevers in Liquid Environment.

PubMed

Kim, Il Kwang; Lee, Soo Il

2016-05-01

The modal decomposition of tapping mode atomic force microscopy microcantilevers in liquid environments was studied experimentally. Microcantilevers with different lengths and stiffnesses and two sample surfaces with different elastic moduli were used in the experiment. The response modes of the microcantilevers were extracted as proper orthogonal modes through proper orthogonal decomposition. Smooth orthogonal decomposition was used to estimate the resonance frequency directly. The effects of the tapping setpoint and the elastic modulus of the sample under test were examined in terms of their multi-mode responses with proper orthogonal modes, proper orthogonal values, smooth orthogonal modes and smooth orthogonal values. Regardless of the stiffness of the microcantilever under test, the first mode was dominant in tapping mode atomic force microscopy under normal operating conditions. However, at lower tapping setpoints, the flexible microcantilever showed modal distortion and noise near the tip when tapping on a hard sample. The stiff microcantilever had a higher mode effect on a soft sample at lower tapping setpoints. Modal decomposition for tapping mode atomic force microscopy can thus be used to estimate the characteristics of samples in liquid environments.

Local structures in mixed Li{sub x}Fe{sub 1−y}M{sub y}PO{sub 4} (M=Co, Ni) electrode materials

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

Jalkanen, K.; Lindén, J.; Karppinen, M., E-mail: maarit.karppinen@aalto.fi

We employ {sup 57}Fe Mössbauer spectroscopy as a local tool to probe electrical environments of Fe{sup 2+} and Fe{sup 3+} at different lithiation (x) and cation-substitution (y) levels in Li{sub x}Fe{sub 1−y}M{sub y}PO{sub 4}/C (M=Co, Ni) Li-ion battery electrode materials. Upon delithiation the local environment of Fe{sup 3+} remains unaffected for the parent y=0 system due to the LiFePO{sub 4}/FePO{sub 4} phase separation, whereas for y>0 changes in the electrical environment are seen for Fe{sup 3+}. When the Fe{sup 2+}/Fe{sup 3+} redox couple is partially-delithiated, a decreasing quadrupole splitting value is observed for Fe{sup 3+} with increasing y, implying amore » more symmetric electrical environment. The increasing concentration of the Co{sup 2+}/Ni{sup 2+} substituent introduces increasing amounts of Li atoms in the Fe{sup 3+}-containing phase, and these nearest-neighbor Li atoms are suspected to cause the changes seen in the local environment of Fe{sup 3+}. - Graphical abstract: Local environment of iron in Li{sub x}Fe{sub 1−y}(Co/Ni){sub y}PO{sub 4} is studied by {sup 57}Fe Mössbauer spectroscopy at different lithiation (x) and cation-substitution (y) levels. - Highlights: • Local Fe environment in Li{sub x}Fe{sub 1−y}(Co/Ni){sub y}PO{sub 4} is studied by {sup 57}Fe Mössbauer spectroscopy. • Co/Ni-for-Fe substitution results in a more symmetric electrical environment for Fe{sup 3+}. • Due to presence of Co{sup 2+}/Ni{sup 2+}, Li atoms are introduced into the Fe{sup 3+}-containing phase. • These nearest-neighbor Li atoms are suggested to change the local Fe{sup 3+} environment.« less

Convergent Close-Coupling Approach to Electron-Atom Collisions

NASA Technical Reports Server (NTRS)

Bray, Igor; Stelbovics, Andris

2007-01-01

It was with great pleasure and honour to accept the invitation to make a presentation at the symposium celebrating the life-long work of Aaron Temkin and Richard Drachman. The work of Aaron Temkin was particularly influential on our own during the development of the CCC method for electron-atom collisions. There are a number of key problems that need to be dealt with when developing a general computational approach to such collisions. Traditionally, the electron energy range was subdivided into the low, intermediate, and high energies. At the low energies only a finite number of channels are open and variational or close-coupling techniques could be used to obtain accurate results. At high energies an infinite number of discrete channels and the target continuum are open, but perturbative techniques are able to yield accurate results. However, at the intermediate energies perturbative techniques fail and computational approaches need to be found for treating the infinite number of open channels. In addition, there are also problems associated with the identical nature of electrons and the difficulty of implementing the boundary conditions for ionization processes. The beauty of the Temkin-Poet model of electron-hydrogen scattering is that it simplifies the full computational problem by neglecting any non-zero orbital angular momenta in the partial-wave expansion, without loosing the complexity associated with the above-mentioned problems. The unique nature of the problem allowed for accurate solution leading to benchmark results which could then be used to test the much more general approaches to electron-atom collision problems. The immense value of the Temkin-Poet model is readily summarised by the fact that the initial papers of Temkin and Poet have been collectively cited around 250 times to date and are still being cited in present times. Many of the citations came from our own work during the course of the development of the CCC method, which we now describe.

SparseMaps—A systematic infrastructure for reduced-scaling electronic structure methods. III. Linear-scaling multireference domain-based pair natural orbital N-electron valence perturbation theory

NASA Astrophysics Data System (ADS)

Guo, Yang; Sivalingam, Kantharuban; Valeev, Edward F.; Neese, Frank

2016-03-01

Multi-reference (MR) electronic structure methods, such as MR configuration interaction or MR perturbation theory, can provide reliable energies and properties for many molecular phenomena like bond breaking, excited states, transition states or magnetic properties of transition metal complexes and clusters. However, owing to their inherent complexity, most MR methods are still too computationally expensive for large systems. Therefore the development of more computationally attractive MR approaches is necessary to enable routine application for large-scale chemical systems. Among the state-of-the-art MR methods, second-order N-electron valence state perturbation theory (NEVPT2) is an efficient, size-consistent, and intruder-state-free method. However, there are still two important bottlenecks in practical applications of NEVPT2 to large systems: (a) the high computational cost of NEVPT2 for large molecules, even with moderate active spaces and (b) the prohibitive cost for treating large active spaces. In this work, we address problem (a) by developing a linear scaling "partially contracted" NEVPT2 method. This development uses the idea of domain-based local pair natural orbitals (DLPNOs) to form a highly efficient algorithm. As shown previously in the framework of single-reference methods, the DLPNO concept leads to an enormous reduction in computational effort while at the same time providing high accuracy (approaching 99.9% of the correlation energy), robustness, and black-box character. In the DLPNO approach, the virtual space is spanned by pair natural orbitals that are expanded in terms of projected atomic orbitals in large orbital domains, while the inactive space is spanned by localized orbitals. The active orbitals are left untouched. Our implementation features a highly efficient "electron pair prescreening" that skips the negligible inactive pairs. The surviving pairs are treated using the partially contracted NEVPT2 formalism. A detailed comparison between the partial and strong contraction schemes is made, with conclusions that discourage the strong contraction scheme as a basis for local correlation methods due to its non-invariance with respect to rotations in the inactive and external subspaces. A minimal set of conservatively chosen truncation thresholds controls the accuracy of the method. With the default thresholds, about 99.9% of the canonical partially contracted NEVPT2 correlation energy is recovered while the crossover of the computational cost with the already very efficient canonical method occurs reasonably early; in linear chain type compounds at a chain length of around 80 atoms. Calculations are reported for systems with more than 300 atoms and 5400 basis functions.

Observation of correlated electronic decay in expanding clusters triggered by near-infrared fields

PubMed Central

Schütte, B.; Arbeiter, M.; Fennel, T.; Jabbari, G.; Kuleff, A.I.; Vrakking, M.J.J.; Rouzée, A.

2015-01-01

When an excited atom is embedded into an environment, novel relaxation pathways can emerge that are absent for isolated atoms. A well-known example is interatomic Coulombic decay, where an excited atom relaxes by transferring its excess energy to another atom in the environment, leading to its ionization. Such processes have been observed in clusters ionized by extreme-ultraviolet and X-ray lasers. Here, we report on a correlated electronic decay process that occurs following nanoplasma formation and Rydberg atom generation in the ionization of clusters by intense, non-resonant infrared laser fields. Relaxation of the Rydberg states and transfer of the available electronic energy to adjacent electrons in Rydberg states or quasifree electrons in the expanding nanoplasma leaves a distinct signature in the electron kinetic energy spectrum. These so far unobserved electron-correlation-driven energy transfer processes may play a significant role in the response of any nano-scale system to intense laser light. PMID:26469997

Influence of the plasma environment on atomic structure using an ion-sphere model

DOE PAGES

Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

2015-09-03

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe 22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less

Influence of the plasma environment on atomic structure using an ion-sphere model

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

Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe 22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less

O-atom degradation mechanisms of materials

NASA Technical Reports Server (NTRS)

Coulter, Daniel R.; Liang, Ranty H.; Chung, Shirley Y.; Smith, Keri Oda; Gupta, Amitava

1987-01-01

The low Earth orbit environment is described and the critical issues relating to oxygen atom degradation are discussed. Some analytic techniques for studying the problem and preliminary results on the underlying degradation mechanisms are presented.

Structured crowding and its effects on enzyme catalysis.

PubMed

Ma, Buyong; Nussinov, Ruth

2013-01-01

Macromolecular crowding decreases the diffusion rate, shifts the equilibrium of protein-protein and protein-substrate interactions, and changes protein conformational dynamics. Collectively, these effects contribute to enzyme catalysis. Here we describe how crowding may bias the conformational change and dynamics of enzyme populations and in this way affect catalysis. Crowding effects have been studied using artificial crowding agents and in vivo-like environments. These studies revealed a correlation between protein dynamics and function in the crowded environment. We suggest that crowded environments be classified into uniform crowding and structured crowding. Uniform crowding represents random crowding conditions created by synthetic particles with a narrow size distribution. Structured crowding refers to the highly coordinated cellular environment, where proteins and other macromolecules are clustered and organized. In structured crowded environments the perturbation of protein thermal stability may be lower; however, it may still be able to modulate functions effectively and dynamically. Dynamic, allosteric enzymes could be more sensitive to cellular perturbations if their free energy landscape is flatter around the native state; on the other hand, if their free energy landscape is rougher, with high kinetic barriers separating deep minima, they could be more robust. Above all, cells are structured; and this holds both for the cytosol and for the membrane environment. The crowded environment is organized, which limits the search, and the crowders are not necessarily inert. More likely, they too transmit allosteric effects, and as such play important functional roles. Overall, structured cellular crowding may lead to higher enzyme efficiency and specificity.

Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics.

PubMed

Abriata, Luciano A; Spiga, Enrico; Peraro, Matteo Dal

2016-08-23

Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and atomic levels. Here, NMR and molecular dynamics investigations on ubiquitin disclose variable interactions with concentrated solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chemical properties. Most strikingly, small polar uncharged molecules are sticky on the protein surface, whereas charged small molecules are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromolecular crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromolecular crowders do not exert such strong perturbation. Finally, molecular dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the physical chemistry of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Copper-silver-titanium filler metal for direct brazing of structural ceramics

DOEpatents

Moorhead, Arthur J.

1987-01-01

A method of joining ceramics and metals to themselves and to one another is described using a brazing filler metal consisting essentially of 35 to 50 atomic percent copper, 15 to 50 atomic percent silver and 10 to 45 atomic percent titanium. This method produces strong joints that can withstand high service temperatures and oxidizing environments.

40 CFR Appendix C to Part 136 - Inductively Coupled Plasma-Atomic Emission Spectrometric Method for Trace Element Analysis of...

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false Inductively Coupled Plasma-Atomic... to Part 136—Inductively Coupled Plasma—Atomic Emission Spectrometric Method for Trace Element... technique. Samples are nebulized and the aerosol that is produced is transported to the plasma torch where...

40 CFR Appendix C to Part 136 - Inductively Coupled Plasma-Atomic Emission Spectrometric Method for Trace Element Analysis of...

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false Inductively Coupled Plasma-Atomic... to Part 136—Inductively Coupled Plasma—Atomic Emission Spectrometric Method for Trace Element... technique. Samples are nebulized and the aerosol that is produced is transported to the plasma torch where...

Noncontact atomic force microscopy in liquid environment with quartz tuning fork and carbon nanotube probe

NASA Astrophysics Data System (ADS)

Kageshima, Masami; Jensenius, Henriette; Dienwiebel, Martin; Nakayama, Yoshikazu; Tokumoto, Hiroshi; Jarvis, Suzanne P.; Oosterkamp, Tjerk H.

2002-03-01

A force sensor for noncontact atomic force microscopy in liquid environment was developed by combining a multiwalled carbon nanotube (MWNT) probe with a quartz tuning fork. Solvation shells of octamethylcyclotetrasiloxane on a graphite surface were detected both in the frequency shift and dissipation. Due to the high aspect ratio of the CNT probe, the long-range background force was barely detectable in the solvation region.

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

Dutta, S.; Saha, J. K.; Chandra, R.

The Rayleigh-Ritz variational technique with a Hylleraas basis set is being tested for the first time to estimate the structural modifications of a lithium atom embedded in a weakly coupled plasma environment. The Debye-Huckel potential is used to mimic the weakly coupled plasma environment. The wave functions for both the helium-like lithium ion and the lithium atom are expanded in the explicitly correlated Hylleraas type basis set which fully takes care of the electron-electron correlation effect. Due to the continuum lowering under plasma environment, the ionization potential of the system gradually decreases leading to the destabilization of the atom. Themore » excited states destabilize at a lower value of the plasma density. The estimated ionization potential agrees fairly well with the few available theoretical estimates. The variation of one and two particle moments, dielectric susceptibility and magnetic shielding constant, with respect to plasma density is also been discussed in detail.« less

Tuning the electronic and optical properties of hexagonal boron-nitride nanosheet by inserting graphene quantum dots

NASA Astrophysics Data System (ADS)

Ding, Yi-Min; Shi, Jun-Jie; Zhang, Min; Wu, Meng; Wang, Hui; Cen, Yu-Lang; Pan, Shu-Hang; Guo, Wen-Hui

2018-02-01

It is difficult to integrate two-dimensional (2D) graphene and hexagonal boron-nitride (h-BN) in optoelectronic nanodevices, due to the semi-metal and insulator characteristic of graphene and h-BN, respectively. Using the state-of-the-art first-principles calculations based on many-body perturbation theory, we investigate the electronic and optical properties of h-BN nanosheet embedded with graphene dots. We find that C atom impurities doped in h-BN nanosheet tend to phase-separate into graphene quantum dots (QD), and BNC hybrid structure, i.e. a graphene dot within a h-BN background, can be formed. The band gaps of BNC hybrid structures have an inverse relationship with the size of graphene dot. The calculated optical band gaps for BNC structures vary from 4.71 eV to 3.77 eV, which are much smaller than that of h-BN nanosheet. Furthermore, the valence band maximum is located in C atoms bonded to B atoms and conduction band minimum is located in C atoms bonded to N atoms, which means the electron and hole wave functions are closely distributed around the graphene dot. The bound excitons, localized around the graphene dot, determine the optical spectra of the BNC hybrid structures, in which the exciton binding energies decrease with increase in the size of graphene dots. Our results provide an important theoretical basis for the design and development of BNC-based optoelectronic nanodevices.

Angular-momentum couplings in ultra-long-range giant dipole molecules

NASA Astrophysics Data System (ADS)

Stielow, Thomas; Scheel, Stefan; Kurz, Markus

2018-02-01

In this article we extend the theory of ultra-long-range giant dipole molecules, formed by an atom in a giant dipole state and a ground-state alkali-metal atom, by angular-momentum couplings known from recent works on Rydberg molecules. In addition to s -wave scattering, the next higher order of p -wave scattering in the Fermi pseudopotential describing the binding mechanism is considered. Furthermore, the singlet and triplet channels of the scattering interaction as well as angular-momentum couplings such as hyperfine interaction and Zeeman interactions are included. Within the framework of Born-Oppenheimer theory, potential energy surfaces are calculated in both first-order perturbation theory and exact diagonalization. Besides the known pure triplet states, mixed-spin character states are obtained, opening up a whole new landscape of molecular potentials. We determine exact binding energies and wave functions of the nuclear rotational and vibrational motion numerically from the various potential energy surfaces.

Theoretical investigations of plasma processes in the ion bombardment thruster

NASA Technical Reports Server (NTRS)

Wilhelm, H. E.

1975-01-01

A physical model for a thruster discharge was developed, consisting of a spatially diverging plasma sustained electrically between a small ring cathode and a larger ring anode in a cylindrical chamber with an axial magnetic field. The associated boundary-value problem for the coupled partial differential equations with mixed boundary conditions, which describe the electric potential and the plasma velocity fields, was solved in closed form. By means of quantum-mechanical perturbation theory, a formula for the number S(E) of atoms sputtered on the average by an ion of energy E was derived from first principles. The boundary-value problem describing the diffusion of the sputtered atoms through the surrounding rarefied electron-ion plasma to the system surfaces of ion propulsion systems was formulated and treated analytically. It is shown that outer boundary-value problems of this type lead to a complex integral equation, which requires numerical resolution.

Plasma-screening effects on the electron-impact excitation of hydrogenic ions in dense plasmas

NASA Technical Reports Server (NTRS)

Jung, Young-Dae

1993-01-01

Plasma-screening effects are investigated on electron-impact excitation of hydrogenic ions in dense plasmas. Scaled cross sections Z(exp 4) sigma for 1s yields 2s and 1s yields 2p are obtained for a Debye-Hueckel model of the screened Coulomb interaction. Ground and excited bound wave functions are modified in the screened Coulomb potential (Debye-Hueckel model) using the Ritz variation method. The resulting atomic wave functions and their eigenenergies agree well with the numerical and high-order perturbation theory calculations for the interesting domain of the Debye length not less than 10. The Born approximation is used to describe the continuum states of the projectile electron. Plasma screening effects on the atomic electrons cannot be neglected in the high-density cases. Including these effects, the cross sections are appreciably increased for 1s yields 2s transitions and decreased for 1s yields 2p transitions.

Embedded-cluster calculations in a numeric atomic orbital density-functional theory framework.

PubMed

Berger, Daniel; Logsdail, Andrew J; Oberhofer, Harald; Farrow, Matthew R; Catlow, C Richard A; Sherwood, Paul; Sokol, Alexey A; Blum, Volker; Reuter, Karsten

2014-07-14

We integrate the all-electron electronic structure code FHI-aims into the general ChemShell package for solid-state embedding quantum and molecular mechanical (QM/MM) calculations. A major undertaking in this integration is the implementation of pseudopotential functionality into FHI-aims to describe cations at the QM/MM boundary through effective core potentials and therewith prevent spurious overpolarization of the electronic density. Based on numeric atomic orbital basis sets, FHI-aims offers particularly efficient access to exact exchange and second order perturbation theory, rendering the established QM/MM setup an ideal tool for hybrid and double-hybrid level density functional theory calculations of solid systems. We illustrate this capability by calculating the reduction potential of Fe in the Fe-substituted ZSM-5 zeolitic framework and the reaction energy profile for (photo-)catalytic water oxidation at TiO2(110).

Embedded-cluster calculations in a numeric atomic orbital density-functional theory framework

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

Berger, Daniel, E-mail: daniel.berger@ch.tum.de; Oberhofer, Harald; Reuter, Karsten

2014-07-14

We integrate the all-electron electronic structure code FHI-aims into the general ChemShell package for solid-state embedding quantum and molecular mechanical (QM/MM) calculations. A major undertaking in this integration is the implementation of pseudopotential functionality into FHI-aims to describe cations at the QM/MM boundary through effective core potentials and therewith prevent spurious overpolarization of the electronic density. Based on numeric atomic orbital basis sets, FHI-aims offers particularly efficient access to exact exchange and second order perturbation theory, rendering the established QM/MM setup an ideal tool for hybrid and double-hybrid level density functional theory calculations of solid systems. We illustrate this capabilitymore » by calculating the reduction potential of Fe in the Fe-substituted ZSM-5 zeolitic framework and the reaction energy profile for (photo-)catalytic water oxidation at TiO{sub 2}(110)« less

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

Vidmer, Alexandre, E-mail: alexandre@vidmer.com; Sclauzero, Gabriele; Pasquarello, Alfredo

The infrared absorption spectra of jennite, tobermorite 14 Å, anomalous tobermorite 11 Å, and normal tobermorite 11 Å are simulated within a density-functional-theory scheme. The atomic coordinates and the cell parameters are optimized resulting in structures which agree with previous studies. The vibrational frequencies and modes are obtained for each mineral. The vibrational density of states is analyzed through extensive projections on silicon tetrahedra, oxygen atoms, OH groups, and water molecules. The coupling with the electric field is achieved through the use of density functional perturbation theory, which yields Born effective charges and dielectric constants. The simulated absorption spectra reproducemore » well the experimental spectra, thereby allowing for a detailed interpretation of the spectral features in terms of the underlying vibrational modes. In the far-infrared part of the absorption spectra, the interplay between Ca and Si related vibrations leads to differences which are sensitive to the calcium/silicon ratio of the mineral.« less

Singly and Doubly Excited States of the D-Dimensional Helium Atom(Supported by DOD-ONR N00014-94-1-0998)

NASA Astrophysics Data System (ADS)

Carzoli, J.; Dunn, M.; Watson, D. K.

1998-05-01

Large order dimensional perturbation theory (DPT) has been used to study the ground and a number of excited states of two-electron atoms for the case L=0. Here we present the first application of recent work generalizing DPT to higher angular momentum.(M. Dunn, D.K. Watson, Ann. Phys. 251 (1996) 266)^,(M. Dunn, D.K. Watson, The Large Dimension Limit of Higher Angular Momentum States. Phys. Rev. A. (accepted for publication)) In this work we begin the investigation of P^o states, presenting results for the energies of some of the lowest lying states and discuss the analytic structure of these energies as functions of 1/D. We also obtain energies of corresponding D^o states with almost no additional effort by making use of interdimensional degeneracies with the P^o states.

Asymptotic Energies and QED Shifts for Rydberg States of Helium

NASA Technical Reports Server (NTRS)

Drake, G.W.F.

2007-01-01

This paper reviews progress that has been made in obtaining essentially exact solutions to the nonrelativistic three-body problem for helium by a combination of variational and asymptotic expansion methods. The calculation of relativistic and quantum electrodynamic corrections by perturbation theory is discussed, and in particular, methods for the accurate calculation of the Bethe logarithm part of the electron self energy are presented. As an example, the results are applied to the calculation of isotope shifts for the short-lived 'halo' nucleus He-6 relative to He-4 in order to determine the nuclear charge radius of He-6 from high precision spectroscopic measurements carried out at the Argonne National Laboratory. The results demonstrate that the high precision that is now available from atomic theory is creating new opportunities to create novel measurement tools, and helium, along with hydrogen, can be regarded as a fundamental atomic system whose spectrum is well understood for all practical purposes.

Long-Range Adiabatic Corrections to the Ground Molecular State of Alkali-Metal Dimers.

NASA Astrophysics Data System (ADS)

Marinescu, M.; Dalgarno, A.

1997-04-01

The structure of the long-range limit of the diagonal adiabatic corrections to the ground molecular state of diatomic molecules, may be expressed as a series of inverse powers of internuclear distance, R. The coefficients of this expansion are proportional to the inverse of the nuclear mass. Thus, they may be interpreted as a nuclear mass-dependent corrections to the dispersion coefficients. Using perturbation theory we have calculated the long-range coefficients of the diagonal adiabatic corrections up to the order of R-10. The final expressions are in terms of integrals over imaginary frequencies of products of atomic matrix elements involving Green's functions of complex energy. Thus, in our approach the molecular problem is reduced to an atomic one. Numerical evaluations have been done for all alkali-metal dimers. We acknowledge the support of the U.S. Dept. of Energy.

Thermodynamics and kinetics of graphene chemistry: a graphene hydrogenation prototype study.

PubMed

Pham, Buu Q; Gordon, Mark S

2016-12-07

The thermodynamic and kinetic controls of graphene chemistry are studied computationally using a graphene hydrogenation reaction and polyaromatic hydrocarbons to represent the graphene surface. Hydrogen atoms are concertedly chemisorped onto the surface of graphene models of different shapes (i.e., all-zigzag, all-armchair, zigzag-armchair mixed edges) and sizes (i.e., from 16-42 carbon atoms). The second-order Z-averaged perturbation theory (ZAPT2) method combined with Pople double and triple zeta basis sets are used for all calculations. It is found that both the net enthalpy change and the barrier height of graphene hydrogenation at graphene edges are lower than at their interior surfaces. While the thermodynamic product distribution is mainly determined by the remaining π-islands of functionalized graphenes (Phys. Chem. Chem. Phys., 2013, 15, 3725-3735), the kinetics of the reaction is primarily correlated with the localization of the electrostatic potential of the graphene surface.

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.

An NMR study of microvoids in polymers

NASA Technical Reports Server (NTRS)

Toy, James; Mattix, Larry

1995-01-01

An understanding of polymer defect structures, like microvoids in polymeric matrices, is crucial to their fabrication and application potential. In this project guest atoms are introduced into the microvoids in PMR-15 and NMR is used to determine microvoid sizes and locations. Xenon is a relatively inert probe that would normally be found naturally in polymer or in NMR probe materials. There are two NMR active xenon isotopes, Xe-129 and Xe-131. The Xe atom has a very high polarizability, which makes it sensitive to the intracrystalline environment of polymers. Interactions between the Xe atoms and the host matrix perturb the Xe electron cloud, deshielding the nuclei, and thereby expanding the range of the observed NMR chemical shifts. This chemical shift range which may be as large as 5000 ppm, permits subtle structural and chemical effects to be studied with high sensitivity. The Xe(129)-NMR line shape has been found to vary in response to changes in the pore symmetry of the framework hosts line Zeolites and Clathrasil compounds. Before exposure to Xe gas, the PMR-15 samples were dried in a vacuum oven at 150 C for 48 hours. The samples were then exposed to Xe gas at 30 psi for 72 hours and sealed in glass tubes with 1 atmosphere of xenon gas. Xenon gas at 1 atmosphere was used to tune up the spectrometer and to set up the appropriate NMR parameters. A single Xe-129 line at 83.003498 Mhz (with protons at 300 Mhz) was observed for the gas. With the xenon charged PMR-15 samples, a second broader line is observed 190 ppm downfield from the gas line (also observed). The width of the NMR line from the Xe-129 absorbed in the polymer is at least partially due to the distribution of microvoid sizes. From the chemical shift (relative to the gas line) and the line width, we estimate the average void sizes to be 2.74 +/- 0.20 angstroms. Since Xe-129 has such a large chemical shift range (approximately 5000 ppm), we expect the chemical shift anisotropy to contribute to the line width (delta upsilon = 2.5 kHz).

Towards scalable quantum communication and computation: Novel approaches and realizations

NASA Astrophysics Data System (ADS)

Jiang, Liang

Quantum information science involves exploration of fundamental laws of quantum mechanics for information processing tasks. This thesis presents several new approaches towards scalable quantum information processing. First, we consider a hybrid approach to scalable quantum computation, based on an optically connected network of few-qubit quantum registers. Specifically, we develop a novel scheme for scalable quantum computation that is robust against various imperfections. To justify that nitrogen-vacancy (NV) color centers in diamond can be a promising realization of the few-qubit quantum register, we show how to isolate a few proximal nuclear spins from the rest of the environment and use them for the quantum register. We also demonstrate experimentally that the nuclear spin coherence is only weakly perturbed under optical illumination, which allows us to implement quantum logical operations that use the nuclear spins to assist the repetitive-readout of the electronic spin. Using this technique, we demonstrate more than two-fold improvement in signal-to-noise ratio. Apart from direct application to enhance the sensitivity of the NV-based nano-magnetometer, this experiment represents an important step towards the realization of robust quantum information processors using electronic and nuclear spin qubits. We then study realizations of quantum repeaters for long distance quantum communication. Specifically, we develop an efficient scheme for quantum repeaters based on atomic ensembles. We use dynamic programming to optimize various quantum repeater protocols. In addition, we propose a new protocol of quantum repeater with encoding, which efficiently uses local resources (about 100 qubits) to identify and correct errors, to achieve fast one-way quantum communication over long distances. Finally, we explore quantum systems with topological order. Such systems can exhibit remarkable phenomena such as quasiparticles with anyonic statistics and have been proposed as candidates for naturally error-free quantum computation. We propose a scheme to unambiguously detect the anyonic statistics in spin lattice realizations using ultra-cold atoms in an optical lattice. We show how to reliably read and write topologically protected quantum memory using an atomic or photonic qubit.

Inhibition of quantum transport due to 'scars' of unstable periodic orbits

NASA Technical Reports Server (NTRS)

Jensen, R. V.; Sanders, M. M.; Saraceno, M.; Sundaram, B.

1989-01-01

A new quantum mechanism for the suppression of chaotic ionization of highly excited hydrogen atoms explains the appearance of anomalously stable states in the microwave ionization experiments of Koch et al. A novel phase-space representation of the perturbed wave functions reveals that the inhibition of quantum transport is due to the selective excitation of wave functions that are highly localized near unstable periodic orbits in the chaotic classical phase space. The 'scarred' wave functions provide a new basis for the quantum description of a variety of classically chaotic systems.

Direct solution of the H(1s)-H + long-range interaction problem in momentum space

NASA Astrophysics Data System (ADS)

Koga, Toshikatsu

1985-02-01

Perturbation equations for the H(1s)-H+ long-range interaction are solved directly in momentum space up to the fourth order with respect to the reciprocal of the internuclear distance. As in the hydrogen atom problem, the Fock transformation is used which projects the momentum vector of an electron from the three-dimensional hyperplane onto the four-dimensional hypersphere. Solutions are given as linear combinations of several four-dimensional spherical harmonics. The present results add an example to the momentum-space solution of the nonspherical potential problem.

Extended Lindhard-Scharf-Schiott Theory for Ion Implantation Profiles Expressed with Pearson Function

NASA Astrophysics Data System (ADS)

Suzuki, Kunihiro

2009-04-01

Ion implantation profiles are expressed by the Pearson function with first, second, third, and fourth moment parameters of Rp, ΔRp, γ, and β. We derived an analytical model for these profile moments by solving a Lindhard-Scharf-Schiott (LSS) integration equation using perturbation approximation. This analytical model reproduces Monte Carlo data that were well calibrated to reproduce a vast experimental database. The extended LSS theory is vital for instantaneously predicting ion implantation profiles with any combination of incident ions and substrate atoms including their energy dependence.

Periodic surface instabilities in stressed polymer solids

NASA Astrophysics Data System (ADS)

Tsukruk, Vladimir V.; Reneker, Darrell H.

1995-03-01

The surface morphology of isothermally grown polymer single crystals of polypropylene is observed by atomic force microscopy. The distinguishing features of the polymer single crystals studied are periodic undulations and transverse fractures (cracks) across the single crystal laths. Up to 20 wrinkles are observed near the edges of the cracks. The periodicity of these surface perturbations is 400+/-100 nm and the amplitude is 6+/-3 nm. The formation of the periodic modulations and transverse fractures is attributed to surface stress relief caused by the uniaxial thermal contraction of polymer solids.

Method for producing an atomic oxygen beam

NASA Technical Reports Server (NTRS)

Outlaw, Ronald A. (Inventor)

1989-01-01

A method for producing an atomic oxygen beam is provided by the present invention. First, a material 10' is provided which dissociates molecular oxygen and dissolves atomic oxygen into its bulk. Next, molecular oxygen is exposed to entrance surface 11' of material 10'. Next, material 10' is heated by heater 17' to facilitate the permeation of atomic oxygen through material 10' to the UHV side 12'. UHV side 12' is interfaced with an ultra-high vacuum (UHV) environment provided by UHV pump 15'. The atomic oxygen on the UHV side 12' is excited to a non-binding state by exciter 14' thus producing the release of atomic oxygen to form an atomic oxygen beam 35'.

Applying systems biology methods to the study of human physiology in extreme environments

PubMed Central

2013-01-01

Systems biology is defined in this review as ‘an iterative process of computational model building and experimental model revision with the aim of understanding or simulating complex biological systems’. We propose that, in practice, systems biology rests on three pillars: computation, the omics disciplines and repeated experimental perturbation of the system of interest. The number of ethical and physiologically relevant perturbations that can be used in experiments on healthy humans is extremely limited and principally comprises exercise, nutrition, infusions (e.g. Intralipid), some drugs and altered environment. Thus, we argue that systems biology and environmental physiology are natural symbionts for those interested in a system-level understanding of human biology. However, despite excellent progress in high-altitude genetics and several proteomics studies, systems biology research into human adaptation to extreme environments is in its infancy. A brief description and overview of systems biology in its current guise is given, followed by a mini review of computational methods used for modelling biological systems. Special attention is given to high-altitude research, metabolic network reconstruction and constraint-based modelling. PMID:23849719

Electrokinetic detection for X-ray spectra of weakly interacting liquids: n-decane and n-nonane.

PubMed

Lam, Royce K; Shih, Orion; Smith, Jacob W; Sheardy, Alex T; Rizzuto, Anthony M; Prendergast, David; Saykally, Richard J

2014-06-21

The introduction of liquid microjets into soft X-ray absorption spectroscopy enabled the windowless study of liquids by this powerful atom-selective high vacuum methodology. However, weakly interacting liquids produce large vapor backgrounds that strongly perturb the liquid signal. Consequently, solvents (e.g., hydrocarbons, ethers, ketones, etc.) and solutions of central importance in chemistry and biology have been inaccessible by this technology. Here we describe a new detection method, upstream detection, which greatly reduces the vapor phase contribution to the X-ray absorption signal while retaining important advantages of liquid microjet sample introduction (e.g., minimal radiation damage). The effectiveness of the upstream detection method is demonstrated in this first study of room temperature liquid hydrocarbons: n-nonane and n-decane. Good agreement with first principles' calculations indicates that the eXcited electron and Core Hole theory adequately describes the subtle interactions in these liquids that perturb the electronic structure of the unoccupied states probed in core-level experiments.

Non-perturbative calculation of orbital and spin effects in molecules subject to non-uniform magnetic fields

NASA Astrophysics Data System (ADS)

Sen, Sangita; Tellgren, Erik I.

2018-05-01

External non-uniform magnetic fields acting on molecules induce non-collinear spin densities and spin-symmetry breaking. This necessitates a general two-component Pauli spinor representation. In this paper, we report the implementation of a general Hartree-Fock method, without any spin constraints, for non-perturbative calculations with finite non-uniform fields. London atomic orbitals are used to ensure faster basis convergence as well as invariance under constant gauge shifts of the magnetic vector potential. The implementation has been applied to investigate the joint orbital and spin response to a field gradient—quantified through the anapole moments—of a set of small molecules. The relative contributions of orbital and spin-Zeeman interaction terms have been studied both theoretically and computationally. Spin effects are stronger and show a general paramagnetic behavior for closed shell molecules while orbital effects can have either direction. Basis set convergence and size effects of anapole susceptibility tensors have been reported. The relation of the mixed anapole susceptibility tensor to chirality is also demonstrated.

Magnetocrystalline anisotropy in cobalt based magnets: a choice of correlation parameters and the relativistic effects

DOE PAGES

Nguyen, Manh Cuong; Yao, Yongxin; Wang, Cai-Zhuang; ...

2018-05-16

The dependence of the magnetocrystalline anisotropy energy (MAE) in MCo 5 (M = Y, La, Ce, Gd) and CoPt on the Coulomb correlations and strength of spin orbit (SO) interaction within the GGA + U scheme is investigated. A range of parameters suitable for the satisfactory description of key magnetic properties is determined. We show that for a large variation of SO interaction the MAE in these materials can be well described by the traditional second order perturbation theory. We also show that in these materials the MAE can be both proportional and negatively proportional to the orbital moment anisotropymore » (OMA) of Co atoms. Dependence of relativistic effects on Coulomb correlations, applicability of the second order perturbation theory for the description of MAE, and effective screening of the SO interaction in these systems are discussed using a generalized virial theorem. Finally, such determined sets of parameters of Coulomb correlations can be used in much needed large scale atomistic simulations.« less

GTC Turbulence Simulations near H-mode Pedestal with Resonant Magnetic Perturbations

NASA Astrophysics Data System (ADS)

Shi, Lei; Ferraro, Nathaniel; Taimourzadeh, Sam; Fu, Jingyuan; Lin, Zhihong; Nazikian, Raffi

2017-10-01

Full plasma responses to Resonant Magnetic Perturbations (RMPs) as provided by the resistive MHD code M3D-C1 are implemented into Gyrokinetic Toroidal Code (GTC) to study the effect of magnetic islands and stochastic field regions on microturbulence in realistic DIII-D geometry. Electrostatic turbulence simulations with adiabatic electrons show no significant increase of the saturated ion heat conductivity in the presence of RMP-induced islands. However, electron response to zonal flow in the presence of magnetic islands and stochastic fields can drastically increase zonal flow dielectric constant for long wavelength fluctuations. Zonal flow generation can then be reduced and the microturbulence can be enhanced greatly. Furthermore, because the RMP magnetic island size is comparable to the ion banana width, electron and ion responses to these islands may be fundamentally different, which could drive non-ambipolar particles fluxes leading to changes of the radial electric field shear. This work is supported by General Atomics subcontract.

Magnetocrystalline anisotropy in cobalt based magnets: a choice of correlation parameters and the relativistic effects

NASA Astrophysics Data System (ADS)

Nguyen, Manh Cuong; Yao, Yongxin; Wang, Cai-Zhuang; Ho, Kai-Ming; Antropov, Vladimir P.

2018-05-01

The dependence of the magnetocrystalline anisotropy energy (MAE) in MCo5 (M  =  Y, La, Ce, Gd) and CoPt on the Coulomb correlations and strength of spin orbit (SO) interaction within the GGA  +  U scheme is investigated. A range of parameters suitable for the satisfactory description of key magnetic properties is determined. We show that for a large variation of SO interaction the MAE in these materials can be well described by the traditional second order perturbation theory. We also show that in these materials the MAE can be both proportional and negatively proportional to the orbital moment anisotropy (OMA) of Co atoms. Dependence of relativistic effects on Coulomb correlations, applicability of the second order perturbation theory for the description of MAE, and effective screening of the SO interaction in these systems are discussed using a generalized virial theorem. Such determined sets of parameters of Coulomb correlations can be used in much needed large scale atomistic simulations.

Recent Progress in the Development of a Multi-Layer Green's Function Code for Ion Beam Transport

NASA Technical Reports Server (NTRS)

Tweed, John; Walker, Steven A.; Wilson, John W.; Tripathi, Ram K.

2008-01-01

To meet the challenge of future deep space programs, an accurate and efficient engineering code for analyzing the shielding requirements against high-energy galactic heavy radiation is needed. To address this need, a new Green's function code capable of simulating high charge and energy ions with either laboratory or space boundary conditions is currently under development. The computational model consists of combinations of physical perturbation expansions based on the scales of atomic interaction, multiple scattering, and nuclear reactive processes with use of the Neumann-asymptotic expansions with non-perturbative corrections. The code contains energy loss due to straggling, nuclear attenuation, nuclear fragmentation with energy dispersion and downshifts. Previous reports show that the new code accurately models the transport of ion beams through a single slab of material. Current research efforts are focused on enabling the code to handle multiple layers of material and the present paper reports on progress made towards that end.

The stark effect on the spectrum energy of tritium in first excited state with relativistic condition

NASA Astrophysics Data System (ADS)

Prastowo, S. H. B.; Supriadi, B.; Bahri, S.; Ridlo, Z. R.

2018-04-01

This research discussed about the correction of Stark Effect on Tritium atoms in the first excited state with relativistic conditions. The approach used to solve this Stark Effect correction was the perturbation theory which was from time independent degenerate perturbation theory to second-order correction. The Stark Effect on the excited state made the spectrum energy polarization of Tritium which was included in the isotope of hydrogen with an electron moving around the nucleus with high velocity. Hence, the relativistic correction affected the spectrum energy shift. Tritium was a radioactive material having half-time 12,3 years and relatively safe. The Tritium application was a material for the manufacture of nuclear battery. The most effective external electric field that should give to Tritium was 108 V/mith the total correction energy that was 0,97398557 × 10-21 Joule. Therefore, its effect reduced the binding energy between electron and nucleus, and increased the power of Tritium Betavoltaics Battery.

Realization of a quantum gate using gravitational search algorithm by perturbing three-dimensional harmonic oscillator with an electromagnetic field

NASA Astrophysics Data System (ADS)

Sharma, Navneet; Rawat, Tarun Kumar; Parthasarathy, Harish; Gautam, Kumar

2016-06-01

The aim of this paper is to design a current source obtained as a representation of p information symbols \\{I_k\\} so that the electromagnetic (EM) field generated interacts with a quantum atomic system producing after a fixed duration T a unitary gate U( T) that is as close as possible to a given unitary gate U_g. The design procedure involves calculating the EM field produced by \\{I_k\\} and hence the perturbing Hamiltonian produced by \\{I_k\\} finally resulting in the evolution operator produced by \\{I_k\\} up to cubic order based on the Dyson series expansion. The gate error energy is thus obtained as a cubic polynomial in \\{I_k\\} which is minimized using gravitational search algorithm. The signal to noise ratio (SNR) in the designed gate is higher as compared to that using quadratic Dyson series expansion. The SNR is calculated as the ratio of the Frobenius norm square of the desired gate to that of the desired gate error.

Magnetocrystalline anisotropy in cobalt based magnets: a choice of correlation parameters and the relativistic effects

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

Nguyen, Manh Cuong; Yao, Yongxin; Wang, Cai-Zhuang

The dependence of the magnetocrystalline anisotropy energy (MAE) in MCo 5 (M = Y, La, Ce, Gd) and CoPt on the Coulomb correlations and strength of spin orbit (SO) interaction within the GGA + U scheme is investigated. A range of parameters suitable for the satisfactory description of key magnetic properties is determined. We show that for a large variation of SO interaction the MAE in these materials can be well described by the traditional second order perturbation theory. We also show that in these materials the MAE can be both proportional and negatively proportional to the orbital moment anisotropymore » (OMA) of Co atoms. Dependence of relativistic effects on Coulomb correlations, applicability of the second order perturbation theory for the description of MAE, and effective screening of the SO interaction in these systems are discussed using a generalized virial theorem. Finally, such determined sets of parameters of Coulomb correlations can be used in much needed large scale atomistic simulations.« less

Force modulation and electrochemical gating of conductance in a cytochrome

NASA Astrophysics Data System (ADS)

Davis, Jason J.; Peters, Ben; Xi, Wang

2008-09-01

Scanning probe methods have been used to measure the effect of electrochemical potential and applied force on the tunnelling conductance of the redox metalloprotein yeast iso-1-cytochrome c (YCC) at a molecular level. The interaction of a proximal probe with any sample under test will, at this scale, be inherently perturbative. This is demonstrated with conductive probe atomic force microscopy (CP-AFM) current-voltage spectroscopy in which YCC, chemically adsorbed onto pristine Au(111) via its surface cysteine residue, is observed to become increasingly compressed as applied load is increased, with concomitant decrease in junction resistance. Electrical contact at minimal perturbation, where probe-molecule coupling is comparable to that in scanning tunnelling microscopy, brings with it the observation of negative differential resistance, assigned to redox-assisted probe-substrate tunnelling. The role of the redox centre in conductance is also resolved in electrochemical scanning tunnelling microscopy assays where molecular conductance is electrochemically gateable through more than an order of magnitude.

Mutations of Electrons as Constituents of Hadrons

NASA Astrophysics Data System (ADS)

Driscoll, R. B.

1997-04-01

Conjecture (C) 1: Coulomb-charged constituents of electron (e) are attracted to its barycentre by lepto-strong force F=K/r^2+f; f is stably perturbative for r < the "radius" of e. An exterior magnetic field (MF) with gradient (G) secularly perturbs the eccentricities but not the energies of the constituents' orbits, changing the spin (s) and magnetic moment (μ) of e. (C) 2: F coheres two or more e's dynamically with r approximately equal to the "radius" of e. The resulting MF and G at each e oscillate. Stable values of s and μ result for each e which differs from the atomic values. Binding energies change the masses of the e's. A hadron results. (C) 3: An e similarly may bind to a proton to form a Rutherford- Santilli neutron. The proton is negligibly mutated.(References: H. Dehmelt, Science 247, 539 (1990); T.E. Phipps, Jr., Heretical Verities (Classic Non-fiction Library, Urbana, 1986); R.M. Santilli, Hadronic Mechanics (Ukrainian Academy of Sciences, Kiev, 1995 and 1996), 3 volumes.)

Electron-hydrogen collisions in a laser field. (Reannouncement with new availability information)

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

Smith, P.H.; Flannery, M.R.

1991-12-31

The Floquet treatment has already been successfully employed (Chu, Potvliege and Shakeshaft) in calculations of laser-induced multiphoton ionizations, where it provides dressed states for an atom in a laser field. The (perturbative) dressing of target states can have important consequences in laser-assisted scattering was illustrated by Byron and Joachain. These dressed states are useful, not only for laser-induced phenomena, but also as a collisional basis set for laser-assisted collisions. In this role they are in fact very appealing, since the Floquet treatment naturally lends itself to a time-independent analysis, and hence are compatible with present field-free scattering theories. Despite themore » apparent applicability of this approach, work along these lines has only just recently appeared (Sharma and Mohan, Smith and Flannery, Burke et al). Byron and Joachain have illustrated that perturbative dressing of the target states can have important consequences in laser-assisted scattering. Floquet dressing however provides a more complete description (Smith and Flannery).« less

Range of validity for perturbative treatments of relativistic sum rules

NASA Astrophysics Data System (ADS)

Cohen, Scott M.

2003-10-01

The range of validity of perturbative calculations of relativistic sum rules is investigated by calculating the second-order relativistic corrections to the Bethe sum rule and its small momentum limit, the Thomas-Reiche-Kuhn (TRK) sum rule. For the TRK sum rule and atomic systems, the second-order correction is found to be less than 0.5% up to about Z=70. The total relativistic corrections should then be accurate at least through this range of Z, and probably beyond this range if the second-order terms are included. For Rn (Z=86), however, the second-order corrections are nearly 1%. The total corrections to the Bethe sum rule are largest at small momentum, never being significantly larger than the corresponding corrections to the TRK sum rule. The first-order corrections to the Bethe sum rule also give better than 0.5% accuracy for Z<70, and inclusion of the second-order corrections should extend this range, as well.

On One Possible Generalization of the Regression Theorem

NASA Astrophysics Data System (ADS)

Bogolubov, N. N.; Soldatov, A. V.

2018-03-01

A general approach to derivation of formally exact closed time-local or time-nonlocal evolution equations for non-equilibrium multi-time correlations functions made of observables of an open quantum system interacting simultaneously with external time-dependent classical fields and dissipative environment is discussed. The approach allows for the subsequent treatment of these equations within a perturbative scheme assuming that the system-environment interaction is weak.

In utero effects. In utero undernourishment perturbs the adult sperm methylome and intergenerational metabolism.

PubMed

Radford, Elizabeth J; Ito, Mitsuteru; Shi, Hui; Corish, Jennifer A; Yamazawa, Kazuki; Isganaitis, Elvira; Seisenberger, Stefanie; Hore, Timothy A; Reik, Wolf; Erkek, Serap; Peters, Antoine H F M; Patti, Mary-Elizabeth; Ferguson-Smith, Anne C

2014-08-15

Adverse prenatal environments can promote metabolic disease in offspring and subsequent generations. Animal models and epidemiological data implicate epigenetic inheritance, but the mechanisms remain unknown. In an intergenerational developmental programming model affecting F2 mouse metabolism, we demonstrate that the in utero nutritional environment of F1 embryos alters the germline DNA methylome of F1 adult males in a locus-specific manner. Differentially methylated regions are hypomethylated and enriched in nucleosome-retaining regions. A substantial fraction is resistant to early embryo methylation reprogramming, which may have an impact on F2 development. Differential methylation is not maintained in F2 tissues, yet locus-specific expression is perturbed. Thus, in utero nutritional exposures during critical windows of germ cell development can impact the male germline methylome, associated with metabolic disease in offspring. Copyright © 2014, American Association for the Advancement of Science.

Catching What We Can't See: Manual Interception of Occluded Fly-Ball Trajectories

PubMed Central

Bosco, Gianfranco; Delle Monache, Sergio; Lacquaniti, Francesco

2012-01-01

Control of interceptive actions may involve fine interplay between feedback-based and predictive mechanisms. These processes rely heavily on target motion information available when the target is visible. However, short-term visual memory signals as well as implicit knowledge about the environment may also contribute to elaborate a predictive representation of the target trajectory, especially when visual feedback is partially unavailable because other objects occlude the visual target. To determine how different processes and information sources are integrated in the control of the interceptive action, we manipulated a computer-generated visual environment representing a baseball game. Twenty-four subjects intercepted fly-ball trajectories by moving a mouse cursor and by indicating the interception with a button press. In two separate sessions, fly-ball trajectories were either fully visible or occluded for 750, 1000 or 1250 ms before ball landing. Natural ball motion was perturbed during the descending trajectory with effects of either weightlessness (0 g) or increased gravity (2 g) at times such that, for occluded trajectories, 500 ms of perturbed motion were visible before ball disappearance. To examine the contribution of previous visual experience with the perturbed trajectories to the interception of invisible targets, the order of visible and occluded sessions was permuted among subjects. Under these experimental conditions, we showed that, with fully visible targets, subjects combined servo-control and predictive strategies. Instead, when intercepting occluded targets, subjects relied mostly on predictive mechanisms based, however, on different type of information depending on previous visual experience. In fact, subjects without prior experience of the perturbed trajectories showed interceptive errors consistent with predictive estimates of the ball trajectory based on a-priori knowledge of gravity. Conversely, the interceptive responses of subjects previously exposed to fully visible trajectories were compatible with the fact that implicit knowledge of the perturbed motion was also taken into account for the extrapolation of occluded trajectories. PMID:23166653

Catching what we can't see: manual interception of occluded fly-ball trajectories.

PubMed

Bosco, Gianfranco; Delle Monache, Sergio; Lacquaniti, Francesco

2012-01-01

Control of interceptive actions may involve fine interplay between feedback-based and predictive mechanisms. These processes rely heavily on target motion information available when the target is visible. However, short-term visual memory signals as well as implicit knowledge about the environment may also contribute to elaborate a predictive representation of the target trajectory, especially when visual feedback is partially unavailable because other objects occlude the visual target. To determine how different processes and information sources are integrated in the control of the interceptive action, we manipulated a computer-generated visual environment representing a baseball game. Twenty-four subjects intercepted fly-ball trajectories by moving a mouse cursor and by indicating the interception with a button press. In two separate sessions, fly-ball trajectories were either fully visible or occluded for 750, 1000 or 1250 ms before ball landing. Natural ball motion was perturbed during the descending trajectory with effects of either weightlessness (0 g) or increased gravity (2 g) at times such that, for occluded trajectories, 500 ms of perturbed motion were visible before ball disappearance. To examine the contribution of previous visual experience with the perturbed trajectories to the interception of invisible targets, the order of visible and occluded sessions was permuted among subjects. Under these experimental conditions, we showed that, with fully visible targets, subjects combined servo-control and predictive strategies. Instead, when intercepting occluded targets, subjects relied mostly on predictive mechanisms based, however, on different type of information depending on previous visual experience. In fact, subjects without prior experience of the perturbed trajectories showed interceptive errors consistent with predictive estimates of the ball trajectory based on a-priori knowledge of gravity. Conversely, the interceptive responses of subjects previously exposed to fully visible trajectories were compatible with the fact that implicit knowledge of the perturbed motion was also taken into account for the extrapolation of occluded trajectories.

Influence of Plasma Environment on K-Line Emission in Highly Ionized Iron Atoms Evaluated Using a Debye-Huckel Model

NASA Technical Reports Server (NTRS)

Deprince, J.; Fritzsche, S.; Kallman, T. R.; Palmeri, P.; Quinet, P.

2017-01-01

The influence of plasma environment on the atomic parameters associated with the K-vacancy states has been investigated theoretically for several iron ions. To do this, a time-averaged Debye-Huckel potential for both the electron-nucleus and electron-electron interactions has been considered in the framework of relativistic multiconfiguration Dirac-Fock computations. More particularly, the plasma screening effects on ionization potentials, K-thresholds, transition energies, and radiative rates have been estimated in the astrophysical context of accretion disks around black holes. In the present paper, we describe the behavior of those atomic parameters for Ne-, Na-, Ar-, and K-like iron ions.

Optical Measurements of Strong Radio-Frequency Fields Using Rydberg Atoms

NASA Astrophysics Data System (ADS)

Miller, Stephanie Anne

There has recently been an initiative toward establishing atomic measurement standards for field quantities, including radio-frequency, millimeter-wave, and micro-wave electric fields. Current measurement standards are obtained using dipole antennas, which are fundamentally limited in frequency bandwidth (set by the physical size of the antenna) and accuracy (due to the metal perturbing the field during the measurement). Establishing an atomic standard rectifies these problems. My thesis work contributes to an ongoing effort towards establishing the viability of using Rydberg electromagnetically induced transparency (EIT) to perform atom-based measurements of radio-frequency (RF) fields over a wide range of frequencies and field strengths, focusing on strong-field measurements. Rydberg atoms are atoms with an electron excited to a high principal quantum number, resulting in a high sensitivity to an applied field. A model based on Floquet theory is implemented to accurately describe the observed atomic energy level shifts from which information about the field is extracted. Additionally, the effects due to the different electric field domains within the measurement volume are accurately modeled. Absolute atomic measurements of fields up to 296 V/m within a +/-0.35% relative uncertainty are demonstrated. This is the strongest field measured at the time of data publication. Moreover, the uncertainty is over an order of magnitude better than that of current standards. A vacuum chamber setup that I implemented during my graduate studies is presented and its unique components are detailed. In this chamber, cold-atom samples are generated and Rydberg atoms are optically excited within the ground-state sample. The Rydberg ion detection and imaging procedure are discussed, particularly the high magnification that the system provides. By analyzing the position of the ions, the spatial correlation g(2) (r) of Rydberg-atom distributions can be extracted. Aside from ion detection, EIT is implemented in the cold-atom samples. By measuring the timing of the probe photons exiting the EIT medium, the temporal correlation function g(2)(tau) can be extracted, yielding information about the timing between two different arbitrary photons. An experimental goal using this setup is to look at g(2)(tau) in conjunction with g(2)(r) for Rydberg atoms. Progress and preliminary measurements of ion detection and EIT spectra are presented including observed qualitative behaviors.

Extended X-ray absorption fine structure investigation of Sn local environment in strained and relaxed epitaxial Ge{sub 1−x}Sn{sub x} films

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

Gencarelli, F., E-mail: federica.gencarelli@imec.be; Heyns, M.; Department of Metallurgy and Materials Engineering, KU Leuven, Kasteelpark Arenberg 44, B-3001 Leuven

2015-03-07

We present an extended X-ray absorption fine structure investigation of the local environment of Sn atoms in strained and relaxed Ge{sub 1−x}Sn{sub x} layers with different compositions. We show that the preferred configuration for the incorporation of Sn atoms in these Ge{sub 1−x}Sn{sub x} layers is that of a α-Sn defect, with each Sn atom covalently bonded to four Ge atoms in a classic tetrahedral configuration. Sn interstitials, Sn-split vacancy complexes, or Sn dimers, if present at all, are not expected to involve more than 2.5% of the total Sn atoms. This finding, along with a relative increase of Snmore » atoms in the second atomic shell around a central Sn atom in Ge{sub 1−x}Sn{sub x} layers with increasing Sn concentrations, suggests that the investigated materials are homogeneous random substitutional alloys. Within the accuracy of the measurements, the degree of strain relaxation of the Ge{sub 1−x}Sn{sub x} layers does not have a significant impact on the local atomic surrounding of the Sn atoms. Finally, the calculated topological rigidity parameter a** = 0.69 ± 0.29 indicates that the strain due to alloying in Ge{sub 1−x}Sn{sub x} is accommodated via bond stretching and bond bending, with a slight predominance of the latter, in agreement with ab initio calculations reported in literature.« less

Addressing Issues for Land Change Science

NASA Astrophysics Data System (ADS)

Braimoh, Ademola; Huang, He Qing

2009-09-01

Workshop on Vulnerability and Resilience of Land Systems in Asia; Beijing, China, 15-17 June 2009; There is a growing international community of scholars who work within the interdisciplinary field of land change science, a scientific domain that seeks to understand the dynamics of the land system as a coupled human-environment system. A coupled human-environment system is one in which the social and biophysical subsystems are intertwined so that the system's condition and responses to external forcing are based on the synergy of the two subsystems. Research on land system vulnerability, defined as a function of exposure and sensitivity to natural and anthropogenic perturbations, such as climate variability and sudden changes in macroeconomic conditions and the ability to cope with the impacts of those perturbations, is a fundamental component of land change science. To address issues related to land system vulnerability, the Global Land Project (GLP; http://www.glp-beijing.org.cn/index.php and http://www.glp.hokudai.ac.jp) brought together an interdisciplinary group of researchers with backgrounds ranging from environmental to social sciences. Participants came from both developed and developing countries. The workshop sought to (1) improve knowledge of the causal processes that affect a system's vulnerability and capacity to cope with different perturbations and (2) identify factors that hinder the integration of vulnerability assessment into policies and decision making.

Atomistic material behavior at extreme pressures

DOE PAGES

Beland, Laurent K.; Osetskiy, Yury N.; Stoller, Roger E.

2016-08-05

Computer simulations are routinely performed to model the response of materials to extreme environments, such as neutron (or ion) irradiation. The latter involves high-energy collisions from which a recoiling atom creates a so-called atomic displacement cascade. These cascades involve coordinated motion of atoms in the form of supersonic shockwaves. These shockwaves are characterized by local atomic pressures >15 GPa and interatomic distances <2 Å. Similar pressures and interatomic distances are observed in other extreme environment, including short-pulse laser ablation, high-impact ballistic collisions and diamond anvil cells. Displacement cascade simulations using four different force fields, with initial kinetic energies ranging frommore » 1 to 40 keV, show that there is a direct relationship between these high-pressure states and stable defect production. An important shortcoming in the modeling of interatomic interactions at these short distances, which in turn determines final defect production, is brought to light.« less

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

Perea, Daniel E.; Liu, Jia; Bartrand, Jonah A. G.

In this study, we report the atomic-scale analysis of biological interfaces using atom probe tomography. Embedding the protein ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualize atomic distributions and distinguish organic-organic and organic-inorganic interfaces. The sample preparation method can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment.

Effect of Atomic Charges on Octanol-Water Partition Coefficient Using Alchemical Free Energy Calculation.

PubMed

Ogata, Koji; Hatakeyama, Makoto; Nakamura, Shinichiro

2018-02-15

The octanol-water partition coefficient (log P ow ) is an important index for measuring solubility, membrane permeability, and bioavailability in the drug discovery field. In this paper, the log P ow values of 58 compounds were predicted by alchemical free energy calculation using molecular dynamics simulation. In free energy calculations, the atomic charges of the compounds are always fixed. However, they must be recalculated for each solvent. Therefore, three different sets of atomic charges were tested using quantum chemical calculations, taking into account vacuum, octanol, and water environments. The calculated atomic charges in the different environments do not necessarily influence the correlation between calculated and experimentally measured ∆ G water values. The largest correlation coefficient values of the solvation free energy in water and octanol were 0.93 and 0.90, respectively. On the other hand, the correlation coefficient of log P ow values calculated from free energies, the largest of which was 0.92, was sensitive to the combination of the solvation free energies calculated from the calculated atomic charges. These results reveal that the solvent assumed in the atomic charge calculation is an important factor determining the accuracy of predicted log P ow values.

Origin of the periodic structure in the conductance curve of gold nanojunctions in hydrogen environment

NASA Astrophysics Data System (ADS)

Jiang, Zhuoling; Wang, Hao; Sanvito, Stefano; Hou, Shimin

2016-03-01

The evolution of the atomic structure and the vibrational and electronic transport properties of gold atomic junctions incorporating molecular and atomic hydrogen upon elongation have been investigated with the nonequilibrium Green's function formalism combined with density functional theory. Our calculations show that for the case of gold junctions doped with a single H2 molecule the low-bias conductance drops rapidly with the electrodes' separation, while it remains almost constant if a single H atom replaces the molecule. In contrast, when one considers two H atoms adsorbed on a gold monatomic chain forming an Au-H-Au-H-Au double-bridge structure, the low-bias conductance increases first and then shows a plateau upon stretching the junction, in perfect agreement with experiments on gold nanocontacts in hydrogen environment. Furthermore, also the distribution of the calculated vibrational energies of the two H atoms is consistent with the experimental result in the low-conductance region, demonstrating clear evidence that hydrogen molecules can dissociate on stretched gold monatomic chains. These findings are helpful to improve our understanding of the structure-property relation of gold nanocontacts and also provide a new prospect for gold nanowires being used as chemical sensors and catalysts.

Importance of chlorine atom oxidation to tropospheric chemistry in an urban, coastal environment

NASA Astrophysics Data System (ADS)

Young, C. J.; Washenfelder, R. A.; Edwards, P.; Gilman, J. B.; Kuster, W. C.; Brown, S. S.

2012-12-01

Chlorine atom contribution to tropospheric chemistry is considered to be small on a global scale. It has been demonstrated to be significant in a few areas, such as the Arctic, using ratios of volatile organic compounds (VOCs) as tracers. During the CalNex campaign in Los Angeles, CA, Cl was shown to be a significant contributor to the primary radical budget. However, ratios of VOCs during this time period show no evidence of Cl atom oxidation. Using the Master Chemical Mechanism model, we investigate this discrepancy. We observe that the VOC ratios are highly dependent on the presence of secondary radicals through radical propagation, which are dependent on NOx levels. Thus, we suggest that in a high-NOx urban environment, VOC ratios are an unsuitable tracer of the importance of Cl chemistry. During the CalNex campaign, Cl atom reactivity is approximately an order of magnitude larger than OH radical reactivity. Further, Cl atoms react preferentially with unsaturated compounds for which OH reaction rates are small. Using the model, we determine the amount of additional ozone that can be expected in Los Angeles as a result of the presence of Cl atom reactivity.

A universal strategy for the creation of machine learning-based atomistic force fields

NASA Astrophysics Data System (ADS)

Huan, Tran Doan; Batra, Rohit; Chapman, James; Krishnan, Sridevi; Chen, Lihua; Ramprasad, Rampi

2017-09-01

Emerging machine learning (ML)-based approaches provide powerful and novel tools to study a variety of physical and chemical problems. In this contribution, we outline a universal strategy to create ML-based atomistic force fields, which can be used to perform high-fidelity molecular dynamics simulations. This scheme involves (1) preparing a big reference dataset of atomic environments and forces with sufficiently low noise, e.g., using density functional theory or higher-level methods, (2) utilizing a generalizable class of structural fingerprints for representing atomic environments, (3) optimally selecting diverse and non-redundant training datasets from the reference data, and (4) proposing various learning approaches to predict atomic forces directly (and rapidly) from atomic configurations. From the atomistic forces, accurate potential energies can then be obtained by appropriate integration along a reaction coordinate or along a molecular dynamics trajectory. Based on this strategy, we have created model ML force fields for six elemental bulk solids, including Al, Cu, Ti, W, Si, and C, and show that all of them can reach chemical accuracy. The proposed procedure is general and universal, in that it can potentially be used to generate ML force fields for any material using the same unified workflow with little human intervention. Moreover, the force fields can be systematically improved by adding new training data progressively to represent atomic environments not encountered previously.

Stability of Local Quantum Dissipative Systems

NASA Astrophysics Data System (ADS)

Cubitt, Toby S.; Lucia, Angelo; Michalakis, Spyridon; Perez-Garcia, David

2015-08-01

Open quantum systems weakly coupled to the environment are modeled by completely positive, trace preserving semigroups of linear maps. The generators of such evolutions are called Lindbladians. In the setting of quantum many-body systems on a lattice it is natural to consider Lindbladians that decompose into a sum of local interactions with decreasing strength with respect to the size of their support. For both practical and theoretical reasons, it is crucial to estimate the impact that perturbations in the generating Lindbladian, arising as noise or errors, can have on the evolution. These local perturbations are potentially unbounded, but constrained to respect the underlying lattice structure. We show that even for polynomially decaying errors in the Lindbladian, local observables and correlation functions are stable if the unperturbed Lindbladian has a unique fixed point and a mixing time that scales logarithmically with the system size. The proof relies on Lieb-Robinson bounds, which describe a finite group velocity for propagation of information in local systems. As a main example, we prove that classical Glauber dynamics is stable under local perturbations, including perturbations in the transition rates, which may not preserve detailed balance.

Keldysh meets Lindblad: Correlated Gain and Loss in Higher Order Perturbation Theory

NASA Astrophysics Data System (ADS)

Stace, Tom; Mueller, Clemens

Motivated by correlated decay processes driving gain, loss and lasing in driven artificial quantum systems, we develop a theoretical technique using Keldysh diagrammatic perturbation theory to derive a Lindblad master equation that goes beyond the usual second order perturbation theory. We demonstrate the method on the driven dissipative Rabi model, including terms up to fourth order in the interaction between the qubit and both the resonator and environment. This results in a large class of Lindblad dissipators and associated rates which go beyond the terms that have previously been proposed to describe similar systems. All of the additional terms contribute to the system behaviour at the same order of perturbation theory. We then apply these results to analyse the phonon-assisted steady-state gain of a microwave field driving a double quantum-dot in a resonator. We show that resonator gain and loss are substantially affected by dephasing- assisted dissipative processes in the quantum-dot system. These additional processes, which go beyond recently proposed polaronic theories, are in good quantitative agreement with experimental observations.

Adaptation in locomotor stability, cognition, and metabolic cost during sensory discordance.

PubMed

Peters, Brian T; Brady, Rachel A; Batson, Crystal D; Guined, Jamie R; Ploutz-Snyder, Robert J; Mulavara, Ajitkumar P; Bloomberg, Jacob J

2013-06-01

Locomotor instability may affect planetary extravehicular activities during the initial adaptation to the new gravitational environment. The goal of this study was to quantify the locomotor, cognitive, and metabolic effects of exposure to a discordant sensory environment. A treadmill mounted on a 6-degree-of-freedom motion base was used to present 15 healthy subjects with a destabilizing support surface while they walked. Dependent measures of locomotor stability, cognitive load, and metabolic cost were stride frequency (SF), reaction time (RT), and the volume of oxygen consumed (Vo2), respectively. Subjects completed an 8-min baseline walk followed by 20 min of walking with a continuous, sinusoidal, laterally oscillating support-surface perturbation. Data for minutes 1, 7, 13, and 20 of the support-surface perturbation period were compared with the baseline. SF, RT, and Vo2 were significantly greater during support-surface motion than during the baseline walking condition and showed a trend toward recovery to baseline levels during the perturbation period. Results demonstrated that adaptation to walking in a discordant sensory environment has quantifiable and significant costs in SF, RT, and Vo2 as shown by mean increases of 9%, 20%, and 4%, respectively, collected during the first minute of exposure. By the fourth minute of exposure, mean Vo2 consumption had increased to 20% over its baseline. We believe that preflight sensorimotor adaptation training paradigms will impart gains in stability and the ability to multitask, and might increase productive mission time by extending work time in extravehicular activity suits where metabolic expenditure is a limiting factor.

Rotationally inelastic collisions of excited NaK and NaCs molecules with noble gas and alkali atom perturbers.

PubMed

Jones, J; Richter, K; Price, T J; Ross, A J; Crozet, P; Faust, C; Malenda, R F; Carlus, S; Hickman, A P; Huennekens, J

2017-10-14

We report measurements of rate coefficients at T ≈ 600 K for rotationally inelastic collisions of NaK molecules in the 2(A) 1 Σ + electronic state with helium, argon, and potassium atom perturbers. Several initial rotational levels J between 14 and 44 were investigated. Collisions involving molecules in low-lying vibrational levels (v = 0, 1, and 2) of the 2(A) 1 Σ + state were studied using Fourier-transform spectroscopy. Collisions involving molecules in a higher vibrational level, v = 16, were studied using pump/probe, optical-optical double resonance spectroscopy. In addition, polarization spectroscopy measurements were carried out to study the transfer of orientation in these collisions. Many, but not all, of the measurements were carried out in the "single-collision regime" where more than one collision is unlikely to occur within the lifetime of the excited molecule. The analysis of the experimental data, which is described in detail, includes an estimate of effects of multiple collisions on the reported rate coefficients. The most significant result of these experiments is the observation of a strong propensity for ΔJ = even transitions in collisions involving either helium or argon atoms; the propensity is much stronger for helium than for argon. For the initial rotational levels studied experimentally, almost all initial orientation is preserved in collisions of NaK 2(A) 1 Σ + molecules with helium. Roughly between 1/3 and 2/3 of the orientation is preserved in collisions with argon, and almost all orientation is destroyed in collisions with potassium atoms. Complementary measurements on rotationally inelastic collisions of NaCs 2(A) 1 Σ + with argon do not show a ΔJ = even propensity. The experimental results are compared with new theoretical calculations of collisions of NaK 2(A) 1 Σ + with helium and argon. The calculations are in good agreement with the absolute magnitudes of the experimentally determined rate coefficients and accurately reproduce the very strong propensity for ΔJ = even transitions in helium collisions and the less strong propensity for ΔJ = even transitions in argon collisions. The calculations also show that collisions with helium are less likely to destroy orientation than collisions with argon, in agreement with the experimental results.

Rotationally inelastic collisions of excited NaK and NaCs molecules with noble gas and alkali atom perturbers

NASA Astrophysics Data System (ADS)

Jones, J.; Richter, K.; Price, T. J.; Ross, A. J.; Crozet, P.; Faust, C.; Malenda, R. F.; Carlus, S.; Hickman, A. P.; Huennekens, J.

2017-10-01

We report measurements of rate coefficients at T ≈ 600 K for rotationally inelastic collisions of NaK molecules in the 2(A)1Σ+ electronic state with helium, argon, and potassium atom perturbers. Several initial rotational levels J between 14 and 44 were investigated. Collisions involving molecules in low-lying vibrational levels (v = 0, 1, and 2) of the 2(A)1Σ+ state were studied using Fourier-transform spectroscopy. Collisions involving molecules in a higher vibrational level, v = 16, were studied using pump/probe, optical-optical double resonance spectroscopy. In addition, polarization spectroscopy measurements were carried out to study the transfer of orientation in these collisions. Many, but not all, of the measurements were carried out in the "single-collision regime" where more than one collision is unlikely to occur within the lifetime of the excited molecule. The analysis of the experimental data, which is described in detail, includes an estimate of effects of multiple collisions on the reported rate coefficients. The most significant result of these experiments is the observation of a strong propensity for ΔJ = even transitions in collisions involving either helium or argon atoms; the propensity is much stronger for helium than for argon. For the initial rotational levels studied experimentally, almost all initial orientation is preserved in collisions of NaK 2(A)1Σ+ molecules with helium. Roughly between 1/3 and 2/3 of the orientation is preserved in collisions with argon, and almost all orientation is destroyed in collisions with potassium atoms. Complementary measurements on rotationally inelastic collisions of NaCs 2(A)1Σ+ with argon do not show a ΔJ = even propensity. The experimental results are compared with new theoretical calculations of collisions of NaK 2(A)1Σ+ with helium and argon. The calculations are in good agreement with the absolute magnitudes of the experimentally determined rate coefficients and accurately reproduce the very strong propensity for ΔJ = even transitions in helium collisions and the less strong propensity for ΔJ = even transitions in argon collisions. The calculations also show that collisions with helium are less likely to destroy orientation than collisions with argon, in agreement with the experimental results.

Comparison of High-Performance Fiber Materials Properties in Simulated and Actual Space Environments

NASA Technical Reports Server (NTRS)

Finckernor, M. M.

2017-01-01

A variety of high-performance fibers, including Kevlar, Nomex, Vectran, and Spectra, have been tested for durability in the space environment, mostly the low Earth orbital environment. These materials have been tested in yarn, tether/cable, and fabric forms. Some material samples were tested in a simulated space environment, such as the Atomic Oxygen Beam Facility and solar simulators in the laboratory. Other samples were flown on the International Space Station as part of the Materials on International Space Station Experiment. Mass loss due to atomic oxygen erosion and optical property changes due to ultraviolet radiation degradation are given. Tensile test results are also presented, including where moisture loss in a vacuum had an impact on tensile strength.

Local Chemical Ordering and Negative Thermal Expansion in PtNi Alloy Nanoparticles.

PubMed

Li, Qiang; Zhu, He; Zheng, Lirong; Fan, Longlong; Wang, Na; Rong, Yangchun; Ren, Yang; Chen, Jun; Deng, Jinxia; Xing, Xianran

2017-12-13

An atomic insight into the local chemical ordering and lattice strain is particular interesting to recent emerging bimetallic nanocatalysts such as PtNi alloys. Here, we reported the atomic distribution, chemical environment, and lattice thermal evolution in full-scale structural description of PtNi alloy nanoparticles (NPs). The different segregation of elements in the well-faceted PtNi nanoparticles is convinced by extended X-ray absorption fine structure (EXAFS). Atomic pair distribution function (PDF) study evidences the coexistence of the face-centered cubic and tetragonal ordering parts in the local environment of PtNi nanoparticles. Further reverse Monte Carlo (RMC) simulation with PDF data obviously exposed the segregation as Ni and Pt in the centers of {111} and {001} facets, respectively. Layer-by-layer statistical analysis up to 6 nm for the local atomic pairs revealed the distribution of local tetragonal ordering on the surface. This local coordination environment facilitates the distribution of heteroatomic Pt-Ni pairs, which plays an important role in the negative thermal expansion of Pt 41 Ni 59 NPs. The present study on PtNi alloy NPs from local short-range coordination to long-range average lattice provides a new perspective on tailoring physical properties in nanomaterials.

Electron-phonon coupling and thermal transport in the thermoelectric compound Mo 3Sb 7–xTe x

DOE PAGES

Bansal, Dipanshu; Li, Chen W.; Said, Ayman H.; ...

2015-12-07

Phonon properties of Mo 3Sb 7–xTe x (x = 0, 1.5, 1.7), a potential high-temperature thermoelectric material, have been studied with inelastic neutron and x-ray scattering, and with first-principles simulations. The substitution of Te for Sb leads to pronounced changes in the electronic struc- ture, local bonding, phonon density of states (DOS), dispersions, and phonon lifetimes. Alloying with tellurium shifts the Fermi level upward, near the top of the valence band, resulting in a strong suppression of electron-phonon screening, and a large overall stiffening of interatomic force- constants. The suppression in electron-phonon coupling concomitantly increases group velocities and suppresses phononmore » scattering rates, surpassing the effects of alloy-disorder scattering, and re- sulting in a surprising increased lattice thermal conductivity in the alloy. We also identify that the local bonding environment changes non-uniformly around different atoms, leading to variable perturbation strengths for different optical phonon branches. The respective roles of changes in phonon group velocities and phonon lifetimes on the lattice thermal conductivity are quantified. Lastly, our results highlight the importance of the electron-phonon coupling on phonon mean-free-paths in this compound, and also estimates the contributions from boundary scattering, umklapp scattering, and point-defect scattering.« less

Elucidation of the binding mechanism of renin using a wide array of computational techniques and biological assays.

PubMed

Tzoupis, Haralambos; Leonis, Georgios; Avramopoulos, Aggelos; Reis, Heribert; Czyżnikowska, Żaneta; Zerva, Sofia; Vergadou, Niki; Peristeras, Loukas D; Papavasileiou, Konstantinos D; Alexis, Michael N; Mavromoustakos, Thomas; Papadopoulos, Manthos G

2015-11-01

We investigate the binding mechanism in renin complexes, involving three drugs (remikiren, zankiren and enalkiren) and one lead compound, which was selected after screening the ZINC database. For this purpose, we used ab initio methods (the effective fragment potential, the variational perturbation theory, the energy decomposition analysis, the atoms-in-molecules), docking, molecular dynamics, and the MM-PBSA method. A biological assay for the lead compound has been performed to validate the theoretical findings. Importantly, binding free energy calculations for the three drug complexes are within 3 kcal/mol of the experimental values, thus further justifying our computational protocol, which has been validated through previous studies on 11 drug-protein systems. The main elements of the discovered mechanism are: (i) minor changes are induced to renin upon drug binding, (ii) the three drugs form an extensive network of hydrogen bonds with renin, whilst the lead compound presented diminished interactions, (iii) ligand binding in all complexes is driven by favorable van der Waals interactions and the nonpolar contribution to solvation, while the lead compound is associated with diminished van der Waals interactions compared to the drug-bound forms of renin, and (iv) the environment (H2O/Na(+)) has a small effect on the renin-remikiren interaction. Copyright © 2015 Elsevier Inc. All rights reserved.

Simulation of the synergistic low Earth orbit effects of vacuum thermal cycling, vacuum UV radiation, and atomic oxygen

NASA Technical Reports Server (NTRS)

Dever, Joyce A.; Degroh, Kim K.; Stidham, Curtis R.; Stueber, Thomas J.; Dever, Therese M.; Rodriguez, Elvin; Terlep, Judith A.

1992-01-01

In order to assess the low Earth orbit (LEO) durability of candidate space materials, it is necessary to use ground laboratory facilities which provide LEO environmental effects. A facility combining vacuum thermal cycling and vacuum ultraviolet (VUV) radiation has been designed and constructed at NASA Lewis Research Center for this purpose. This facility can also be operated without the VUV lamps. An additional facility can be used to provide VUV exposure only. By utilizing these facilities, followed by atomic oxygen exposure in an RF plasma asher, the effects of the individual vacuum thermal cycling and VUV environments can be compared to the effect of the combined vacuum thermal cycling/VUV environment on the atomic oxygen durability of materials. The synergistic effects of simulated LEO environmental conditions on materials were evaluated by first exposing materials to vacuum thermal cycling, VUV, and vacuum thermal cycling/VUV environments followed by exposure to atomic oxygen in an RP plasma asher. Candidate space power materials such as atomic oxygen protected polyimides and solar concentrator mirrors were evaluated using these facilities. Characteristics of the Vacuum Thermal Cycling/VUV Exposure Facility which simulates the temperature sequences and solar ultraviolet radiation exposure that would be experienced by a spacecraft surface in LEO are discussed. Results of durability evaluations of some candidate space power materials to the simulated LEO environmental conditions will also be discussed. Such results have indicated that for some materials, atomic oxygen durability is affected by previous exposure to thermal cycling and/or VUV exposure.

Probability theory for 3-layer remote sensing in ideal gas law environment.

PubMed

Ben-David, Avishai; Davidson, Charles E

2013-08-26

We extend the probability model for 3-layer radiative transfer [Opt. Express 20, 10004 (2012)] to ideal gas conditions where a correlation exists between transmission and temperature of each of the 3 layers. The effect on the probability density function for the at-sensor radiances is surprisingly small, and thus the added complexity of addressing the correlation can be avoided. The small overall effect is due to (a) small perturbations by the correlation on variance population parameters and (b) cancellation of perturbation terms that appear with opposite signs in the model moment expressions.

Toggling Bistable Atoms via Mechanical Switching of Bond Angle

NASA Astrophysics Data System (ADS)

Sweetman, Adam; Jarvis, Sam; Danza, Rosanna; Bamidele, Joseph; Gangopadhyay, Subhashis; Shaw, Gordon A.; Kantorovich, Lev; Moriarty, Philip

2011-04-01

We reversibly switch the state of a bistable atom by direct mechanical manipulation of bond angle using a dynamic force microscope. Individual buckled dimers at the Si(100) surface are flipped via the formation of a single covalent bond, actuating the smallest conceivable in-plane toggle switch (two atoms) via chemical force alone. The response of a given dimer to a flip event depends critically on both the local and nonlocal environment of the target atom—an important consideration for future atomic scale fabrication strategies.

Influence of Atomic Oxygen Exposure on Friction Behavior of 321 Stainless Steel

NASA Astrophysics Data System (ADS)

Liu, Y.; Yang, J.; Ye, Z.; Dong, S.; Zhang, L.; Zhang, Z.

Atomic oxygen (AO) exposure testing has been conducted on a 321 stainless steel rolled 1 mm thick sheet to simulate the effect of AO environment on steel in low Earth orbit (LEO). An atomic oxygen exposure facility was employed to carry out AO experiments with the fluence up to ~1021 atom/cm2. The AO exposed specimens were evaluated in air at room temperature using a nanoindenter and a tribological system. The exposed surfaces were analyzed usign XPS technique.

Electronegativity determination of individual surface atoms by atomic force microscopy.

PubMed

Onoda, Jo; Ondráček, Martin; Jelínek, Pavel; Sugimoto, Yoshiaki

2017-04-26

Electronegativity is a fundamental concept in chemistry. Despite its importance, the experimental determination has been limited only to ensemble-averaged techniques. Here, we report a methodology to evaluate the electronegativity of individual surface atoms by atomic force microscopy. By measuring bond energies on the surface atoms using different tips, we find characteristic linear relations between the bond energies of different chemical species. We show that the linear relation can be rationalized by Pauling's equation for polar covalent bonds. This opens the possibility to characterize the electronegativity of individual surface atoms. Moreover, we demonstrate that the method is sensitive to variation of the electronegativity of given atomic species on a surface due to different chemical environments. Our findings open up ways of analysing surface chemical reactivity at the atomic scale.

Electronegativity determination of individual surface atoms by atomic force microscopy

PubMed Central

Onoda, Jo; Ondráček, Martin; Jelínek, Pavel; Sugimoto, Yoshiaki

2017-01-01

Electronegativity is a fundamental concept in chemistry. Despite its importance, the experimental determination has been limited only to ensemble-averaged techniques. Here, we report a methodology to evaluate the electronegativity of individual surface atoms by atomic force microscopy. By measuring bond energies on the surface atoms using different tips, we find characteristic linear relations between the bond energies of different chemical species. We show that the linear relation can be rationalized by Pauling's equation for polar covalent bonds. This opens the possibility to characterize the electronegativity of individual surface atoms. Moreover, we demonstrate that the method is sensitive to variation of the electronegativity of given atomic species on a surface due to different chemical environments. Our findings open up ways of analysing surface chemical reactivity at the atomic scale. PMID:28443645