two-level atomic ensemble: Topics by Science.gov

Sample records for two-level atomic ensemble

Enhancing optical nonreciprocity by an atomic ensemble in two coupled cavities

NASA Astrophysics Data System (ADS)

Song, L. N.; Wang, Z. H.; Li, Yong

2018-05-01

We study the optical nonreciprocal propagation in an optical molecule of two coupled cavities with one of them interacting with a two-level atomic ensemble. The effect of increasing the number of atoms on the optical isolation ratio of the system is studied. We demonstrate that the significant nonlinearity supplied by the coupling of the atomic ensemble with the cavity leads to the realization of greatly-enhanced optical nonreciprocity compared with the case of single atom.
Residue-level global and local ensemble-ensemble comparisons of protein domains.

PubMed

Clark, Sarah A; Tronrud, Dale E; Karplus, P Andrew

2015-09-01

Many methods of protein structure generation such as NMR-based solution structure determination and template-based modeling do not produce a single model, but an ensemble of models consistent with the available information. Current strategies for comparing ensembles lose information because they use only a single representative structure. Here, we describe the ENSEMBLATOR and its novel strategy to directly compare two ensembles containing the same atoms to identify significant global and local backbone differences between them on per-atom and per-residue levels, respectively. The ENSEMBLATOR has four components: eePREP (ee for ensemble-ensemble), which selects atoms common to all models; eeCORE, which identifies atoms belonging to a cutoff-distance dependent common core; eeGLOBAL, which globally superimposes all models using the defined core atoms and calculates for each atom the two intraensemble variations, the interensemble variation, and the closest approach of members of the two ensembles; and eeLOCAL, which performs a local overlay of each dipeptide and, using a novel measure of local backbone similarity, reports the same four variations as eeGLOBAL. The combination of eeGLOBAL and eeLOCAL analyses identifies the most significant differences between ensembles. We illustrate the ENSEMBLATOR's capabilities by showing how using it to analyze NMR ensembles and to compare NMR ensembles with crystal structures provides novel insights compared to published studies. One of these studies leads us to suggest that a "consistency check" of NMR-derived ensembles may be a useful analysis step for NMR-based structure determinations in general. The ENSEMBLATOR 1.0 is available as a first generation tool to carry out ensemble-ensemble comparisons. © 2015 The Protein Society.
Residue-level global and local ensemble-ensemble comparisons of protein domains

PubMed Central

Clark, Sarah A; Tronrud, Dale E; Andrew Karplus, P

2015-01-01

Many methods of protein structure generation such as NMR-based solution structure determination and template-based modeling do not produce a single model, but an ensemble of models consistent with the available information. Current strategies for comparing ensembles lose information because they use only a single representative structure. Here, we describe the ENSEMBLATOR and its novel strategy to directly compare two ensembles containing the same atoms to identify significant global and local backbone differences between them on per-atom and per-residue levels, respectively. The ENSEMBLATOR has four components: eePREP (ee for ensemble-ensemble), which selects atoms common to all models; eeCORE, which identifies atoms belonging to a cutoff-distance dependent common core; eeGLOBAL, which globally superimposes all models using the defined core atoms and calculates for each atom the two intraensemble variations, the interensemble variation, and the closest approach of members of the two ensembles; and eeLOCAL, which performs a local overlay of each dipeptide and, using a novel measure of local backbone similarity, reports the same four variations as eeGLOBAL. The combination of eeGLOBAL and eeLOCAL analyses identifies the most significant differences between ensembles. We illustrate the ENSEMBLATOR's capabilities by showing how using it to analyze NMR ensembles and to compare NMR ensembles with crystal structures provides novel insights compared to published studies. One of these studies leads us to suggest that a “consistency check” of NMR-derived ensembles may be a useful analysis step for NMR-based structure determinations in general. The ENSEMBLATOR 1.0 is available as a first generation tool to carry out ensemble-ensemble comparisons. PMID:26032515
Hong-Ou-Mandel Interference between Two Deterministic Collective Excitations in an Atomic Ensemble

NASA Astrophysics Data System (ADS)

Li, Jun; Zhou, Ming-Ti; Jing, Bo; Wang, Xu-Jie; Yang, Sheng-Jun; Jiang, Xiao; Mølmer, Klaus; Bao, Xiao-Hui; Pan, Jian-Wei

2016-10-01

We demonstrate deterministic generation of two distinct collective excitations in one atomic ensemble, and we realize the Hong-Ou-Mandel interference between them. Using Rydberg blockade we create single collective excitations in two different Zeeman levels, and we use stimulated Raman transitions to perform a beam-splitter operation between the excited atomic modes. By converting the atomic excitations into photons, the two-excitation interference is measured by photon coincidence detection with a visibility of 0.89(6). The Hong-Ou-Mandel interference witnesses an entangled NOON state of the collective atomic excitations, and we demonstrate its two times enhanced sensitivity to a magnetic field compared with a single excitation. Our work implements a minimal instance of boson sampling and paves the way for further multimode and multiexcitation studies with collective excitations of atomic ensembles.
Nonlinearities in reservoir engineering: Enhancing quantum correlations

NASA Astrophysics Data System (ADS)

Hu, Xiangming; Hu, Qingping; Li, Lingchao; Huang, Chen; Rao, Shi

2017-12-01

There are two decisive factors for quantum correlations in reservoir engineering, but they are strongly reversely dependent on the atom-field nonlinearities. One is the squeezing parameter for the Bogoliubov modes-mediated collective interactions, while the other is the dissipative rates for the engineered collective dissipations. Exemplifying two-level atomic ensembles, we show that the moderate nonlinearities can compromise these two factors and thus enhance remarkably two-mode squeezing and entanglement of different spin atomic ensembles or different optical fields. This suggests that the moderate nonlinearities of the two-level systems are more advantageous for applications in quantum networks associated with reservoir engineering.
Optical properties of an atomic ensemble coupled to a band edge of a photonic crystal waveguide

NASA Astrophysics Data System (ADS)

Munro, Ewan; Kwek, Leong Chuan; Chang, Darrick E.

2017-08-01

We study the optical properties of an ensemble of two-level atoms coupled to a 1D photonic crystal waveguide (PCW), which mediates long-range coherent dipole-dipole interactions between the atoms. We show that the long-range interactions can dramatically alter the linear and nonlinear optical behavior, as compared to a typical atomic ensemble. In particular, in the linear regime, we find that the transmission spectrum contains multiple transmission dips, whose properties we characterize. Moreover, we show how the linear spectrum may be used to infer the number of atoms present in the system, constituting an important experimental tool in a regime where techniques for conventional ensembles break down. We also show that some of the transmission dips are associated with an effective ‘two-level’ resonance that forms due to the long-range interactions. In particular, under strong global driving and appropriate conditions, we find that the atomic ensemble is only capable of absorbing and emitting single collective excitations at a time. Our results are of direct relevance to atom-PCW experiments that should soon be realizable.
Noise squeezing of fields that bichromatically excite atoms in a cavity.

PubMed

Li, Lingchao; Hu, Xiangming; Rao, Shi; Xu, Jun

2016-11-14

It is well known that bichromatic excitation on one common transition can tune the emission or absorption spectra of atoms due to the modulation frequency dependent non-linearities. However little attention has been focused on the quantum dynamics of fields under bichromatic excitation. Here we present dissipative effects on noise correlations of fields in bichromatic interactions with atoms in cavities. We first consider an ensemble of two-level atoms that interacts with the two cavity fields of different frequencies and considerable amplitudes. By transferring the atom-field nonlinearities to the dressed atoms we separate out the dissipative interactions of Bogoliubov modes with the dressed atoms. The Bogoliubov mode dissipation establishes stable two-photon processes of two involved fields and therefore leads to two-mode squeezing. As a generalization, we then consider an ensemble of three-level Λ atoms for cascade bichromatic interactions. We extract the Bogoliubov-like four-mode interactions, which establish a quadrilateral of the two-photon processes of four involved fields and thus result in four-mode squeezing.
Generation of entanglement and its decay in a noisy environment

NASA Astrophysics Data System (ADS)

Huang, Jiehui

Entanglement plays a central role in distinguishing quantum mechanics from classical physics. Due to its fantastic properties and many potential applications in quantum information science, entanglement is attracting more and more attention. This thesis focuses on the generation of entanglement and its decay in a noisy environment. In the first experimental scheme to entangle two thermal fields, an atomic ensemble, composed of many identical four-level atoms, is employed. In the first Raman scattering, this atomic ensemble emits write signal photons after the pumping by a weak write pulse, accompanied by the transfer from one lower level to the other for some atoms. Similarly, the atomic ensemble emits read signal photons after the driving by a strong read pulse, and the ensemble turns back to its ground state after the second Raman scattering. The coherence between the two lower atomic levels plays a key role in establishing the quantum correlation between two emission fields, which is verified through the violation of Cauchy-Schwarz inequality. In particular, the controllable time delay between the two emission fields actually means the storage time of photonic information in this system, which sheds light on some potential applications, such as quantum memory. In the second experimental scheme for the generation of spatially separated multiphoton entanglement, two or more identical optical cavities are aligned along a bee-line, and a four-level atom runs through these cavities sequentially. By appropriately adjusting the passage time of the atom in each cavity or the Rabi frequency of the classical pumping laser, a photon can be generated via the interaction between the excited atom and the cavity modes. This adiabatic passage model is an effective method to map atomic coherence to photonic state in cavity QED, thus all photons in different cavities quantum-mechanically correlate with the moving atom. When a final detection is made on this atom, a generalized n-photon GHZ entangled state will be generated with certainty. Environment-induced disentanglement is another important topic in quantum optics. Based on the Peres-Horodecki criterion for separability of bipartite states, we develop the principal minor method for the verification of two-qubit entanglement. Among the fifteen principal minors (seven effective ones) of a given two-qubit state's partial transpose, if the minimum one is negative, the two-qubit state is entangled, otherwise it is separable. By applying this method to a two-qubit system under amplitude and phase dampings, we have derived the necessary and sufficient conditions for the entanglement sudden death of an initially entangled two-qubit state. Keywords: entanglement generation, atomic ensemble, two-qubit, multiphoton entanglement, cavity QED, entanglement sudden death (ESD), amplitude damping, phase damping, principal minor.
Deterministically Entangling Two Remote Atomic Ensembles via Light-Atom Mixed Entanglement Swapping

PubMed Central

Liu, Yanhong; Yan, Zhihui; Jia, Xiaojun; Xie, Changde

2016-01-01

Entanglement of two distant macroscopic objects is a key element for implementing large-scale quantum networks consisting of quantum channels and quantum nodes. Entanglement swapping can entangle two spatially separated quantum systems without direct interaction. Here we propose a scheme of deterministically entangling two remote atomic ensembles via continuous-variable entanglement swapping between two independent quantum systems involving light and atoms. Each of two stationary atomic ensembles placed at two remote nodes in a quantum network is prepared to a mixed entangled state of light and atoms respectively. Then, the entanglement swapping is unconditionally implemented between the two prepared quantum systems by means of the balanced homodyne detection of light and the feedback of the measured results. Finally, the established entanglement between two macroscopic atomic ensembles is verified by the inseparability criterion of correlation variances between two anti-Stokes optical beams respectively coming from the two atomic ensembles. PMID:27165122
Dynamics of interacting Dicke model in a coupled-cavity array

NASA Astrophysics Data System (ADS)

Badshah, Fazal; Qamar, Shahid; Paternostro, Mauro

2014-09-01

We consider the dynamics of an array of mutually interacting cavities, each containing an ensemble of N two-level atoms. By exploring the possibilities offered by ensembles of various dimensions and a range of atom-light and photon-hopping values, we investigate the generation of multisite entanglement, as well as the performance of excitation transfer across the array, resulting from the competition between on-site nonlinearities of the matter-light interaction and intersite photon hopping. In particular, for a three-cavity interacting system it is observed that the initial excitation in the first cavity completely transfers to the ensemble in the third cavity through the hopping of photons between the adjacent cavities. Probabilities of the transfer of excitation of the cavity modes and ensembles exhibit characteristics of fast and slow oscillations governed by coupling and hopping parameters, respectively. In the large-hopping case, by seeding an initial excitation in the cavity at the center of the array, a tripartite W state, as well as a bipartite maximally entangled state, is obtained, depending on the interaction time. Population of the ensemble in a cavity has a positive impact on the rate of excitation transfer between the ensembles and their local cavity modes. In particular, for ensembles of five to seven atoms, tripartite W states can be produced even when the hopping rate is comparable to the cavity-atom coupling rate. A similar behavior of the transfer of excitation is observed for a four-coupled-cavity system with two initial excitations.
Implementation of a quantum metamaterial using superconducting qubits.

PubMed

Macha, Pascal; Oelsner, Gregor; Reiner, Jan-Michael; Marthaler, Michael; André, Stephan; Schön, Gerd; Hübner, Uwe; Meyer, Hans-Georg; Il'ichev, Evgeni; Ustinov, Alexey V

2014-10-14

The key issue for the implementation of a metamaterial is to demonstrate the existence of collective modes corresponding to coherent oscillations of the meta-atoms. Atoms of natural materials interact with electromagnetic fields as quantum two-level systems. Artificial quantum two-level systems can be made, for example, using superconducting nonlinear resonators cooled down to their ground state. Here we perform an experiment in which 20 of these quantum meta-atoms, so-called flux qubits, are embedded into a microwave resonator. We observe the dispersive shift of the resonator frequency imposed by the qubit metamaterial and the collective resonant coupling of eight qubits. The realized prototype represents a mesoscopic limit of naturally occurring spin ensembles and as such we demonstrate the AC-Zeeman shift of a resonant qubit ensemble. The studied system constitutes the implementation of a basic quantum metamaterial in the sense that many artificial atoms are coupled collectively to the quantized mode of a photon field.
Squeezing via two-photon transitions

NASA Astrophysics Data System (ADS)

Savage, C. M.; Walls, D. F.

1986-05-01

The squeezing spectrum for a cavity field mode interacting with an ensemble of three-level 'Lambda-configuration' atoms by an effective two-photon transition is calculated. The advantage of the three-level Lambda system as a squeezing medium, that is, optical nonlinearity without atomic saturation, has recently been pointed out by Reid, Walls, and Dalton. Perfect squeezing is predicted at the turning points for dispersive optical bistability and good squeezing for a range of other cases. Three-level ladder atoms interacting by an effective two-photon transition are also shown to give perfect squeezing in the dispersive limit.
Control of Goos-Hänchen shift via input probe field intensity

NASA Astrophysics Data System (ADS)

Ziauddin; Lee, Ray-Kuang; Qamar, Sajid

2016-11-01

We suggest a scheme to control Goos-Hänchen (GH) shift in an ensemble of strongly interacting Rydberg atoms, which act as super-atoms due to the dipole blockade mechanism. The ensemble of three-level cold Rydberg-dressed (87Rb) atoms follows a cascade configurations where two fields, i.e, a strong control and a weak field are employed [D. Petrosyan, J. Otterbach, and M. Fleischhauer, Phys. Rev. Lett. 107, 213601 (2011)]. The propagation of probe field is influenced by two-photon correlation within the blockade distance, which are damped due to the saturation of super-atoms. The amplitude of GH shift in the reflected light depends on the intensity of probe field. We observe large negative GH shift in the reflected light for small values of the probe field intensities.
Internal Spin Control, Squeezing and Decoherence in Ensembles of Alkali Atomic Spins

NASA Astrophysics Data System (ADS)

Norris, Leigh Morgan

Large atomic ensembles interacting with light are one of the most promising platforms for quantum information processing. In the past decade, novel applications for these systems have emerged in quantum communication, quantum computing, and metrology. Essential to all of these applications is the controllability of the atomic ensemble, which is facilitated by a strong coupling between the atoms and light. Non-classical spin squeezed states are a crucial step in attaining greater ensemble control. The degree of entanglement present in these states, furthermore, serves as a benchmark for the strength of the atom-light interaction. Outside the broader context of quantum information processing with atomic ensembles, spin squeezed states have applications in metrology, where their quantum correlations can be harnessed to improve the precision of magnetometers and atomic clocks. This dissertation focuses upon the production of spin squeezed states in large ensembles of cold trapped alkali atoms interacting with optical fields. While most treatments of spin squeezing consider only the case in which the ensemble is composed of two level systems or qubits, we utilize the entire ground manifold of an alkali atom with hyperfine spin f greater than or equal to 1/2, a qudit. Spin squeezing requires non-classical correlations between the constituent atomic spins, which are generated through the atoms' collective coupling to the light. Either through measurement or multiple interactions with the atoms, the light mediates an entangling interaction that produces quantum correlations. Because the spin squeezing treated in this dissertation ultimately originates from the coupling between the light and atoms, conventional approaches of improving this squeezing have focused on increasing the optical density of the ensemble. The greater number of internal degrees of freedom and the controllability of the spin-f ground hyperfine manifold enable novel methods of enhancing squeezing. In particular, we find that state preparation using control of the internal hyperfine spin increases the entangling power of squeezing protocols when f>1/2. Post-processing of the ensemble using additional internal spin control converts this entanglement into metrologically useful spin squeezing. By employing a variation of the Holstein-Primakoff approximation, in which the collective spin observables of the atomic ensemble are treated as quadratures of a bosonic mode, we model entanglement generation, spin squeezing and the effects of internal spin control. The Holstein-Primakoff formalism also enables us to take into account the decoherence of the ensemble due to optical pumping. While most works ignore or treat optical pumping phenomenologically, we employ a master equation derived from first principles. Our analysis shows that state preparation and the hyperfine spin size have a substantial impact upon both the generation of spin squeezing and the decoherence of the ensemble. Through a numerical search, we determine state preparations that enhance squeezing protocols while remaining robust to optical pumping. Finally, most work on spin squeezing in atomic ensembles has treated the light as a plane wave that couples identically to all atoms. In the final part of this dissertation, we go beyond the customary plane wave approximation on the light and employ focused paraxial beams, which are more efficiently mode matched to the radiation pattern of the atomic ensemble. The mathematical formalism and the internal spin control techniques that we applied in the plane wave case are generalized to accommodate the non-homogeneous paraxial probe. We find the optimal geometries of the atomic ensemble and the probe for mode matching and generation of spin squeezing.
Internal Spin Control, Squeezing and Decoherence in Ensembles of Alkali Atomic Spins

NASA Astrophysics Data System (ADS)

Norris, Leigh Morgan

Large atomic ensembles interacting with light are one of the most promising platforms for quantum information processing. In the past decade, novel applications for these systems have emerged in quantum communication, quantum computing, and metrology. Essential to all of these applications is the controllability of the atomic ensemble, which is facilitated by a strong coupling between the atoms and light. Non-classical spin squeezed states are a crucial step in attaining greater ensemble control. The degree of entanglement present in these states, furthermore, serves as a benchmark for the strength of the atom-light interaction. Outside the broader context of quantum information processing with atomic ensembles, spin squeezed states have applications in metrology, where their quantum correlations can be harnessed to improve the precision of magnetometers and atomic clocks. This dissertation focuses upon the production of spin squeezed states in large ensembles of cold trapped alkali atoms interacting with optical fields. While most treatments of spin squeezing consider only the case in which the ensemble is composed of two level systems or qubits, we utilize the entire ground manifold of an alkali atom with hyperfine spin f greater or equal to 1/2, a qudit. Spin squeezing requires non-classical correlations between the constituent atomic spins, which are generated through the atoms' collective coupling to the light. Either through measurement or multiple interactions with the atoms, the light mediates an entangling interaction that produces quantum correlations. Because the spin squeezing treated in this dissertation ultimately originates from the coupling between the light and atoms, conventional approaches of improving this squeezing have focused on increasing the optical density of the ensemble. The greater number of internal degrees of freedom and the controllability of the spin-f ground hyperfine manifold enable novel methods of enhancing squeezing. In particular, we find that state preparation using control of the internal hyperfine spin increases the entangling power of squeezing protocols when f >1/2. Post-processing of the ensemble using additional internal spin control converts this entanglement into metrologically useful spin squeezing. By employing a variation of the Holstein-Primakoff approximation, in which the collective spin observables of the atomic ensemble are treated as quadratures of a bosonic mode, we model entanglement generation, spin squeezing and the effects of internal spin control. The Holstein-Primakoff formalism also enables us to take into account the decoherence of the ensemble due to optical pumping. While most works ignore or treat optical pumping phenomenologically, we employ a master equation derived from first principles. Our analysis shows that state preparation and the hyperfine spin size have a substantial impact upon both the generation of spin squeezing and the decoherence of the ensemble. Through a numerical search, we determine state preparations that enhance squeezing protocols while remaining robust to optical pumping. Finally, most work on spin squeezing in atomic ensembles has treated the light as a plane wave that couples identically to all atoms. In the final part of this dissertation, we go beyond the customary plane wave approximation on the light and employ focused paraxial beams, which are more efficiently mode matched to the radiation pattern of the atomic ensemble. The mathematical formalism and the internal spin control techniques that we applied in the plane wave case are generalized to accommodate the non-homogeneous paraxial probe. We find the optimal geometries of the atomic ensemble and the probe for mode matching and generation of spin squeezing.
Dual-axis high-data-rate atom interferometer via cold ensemble exchange

DOE PAGES

Rakholia, Akash V.; McGuinness, Hayden J.; Biedermann, Grant W.

2014-11-24

We demonstrate a dual-axis accelerometer and gyroscope atom interferometer, which can form the building blocks of a six-axis inertial measurement unit. By recapturing the atoms after the interferometer sequence, we maintain a large atom number at high data rates of 50 to 100 measurements per second. Two cold ensembles are formed in trap zones located a few centimeters apart and are launched toward one another. During their ballistic trajectory, they are interrogated with a stimulated Raman sequence, detected, and recaptured in the opposing trap zone. As a result, we achieve sensitivities at μg/ √Hz and μrad/s/ √Hz levels, making thismore » a compelling prospect for expanding the use of atom interferometer inertial sensors beyond benign laboratory environments.« less
Atom Interferometry on Atom Chips - A Novel Approach Towards Precision Inertial Navigation System - PINS

DTIC Science & Technology

2010-06-01

Demonstration of an area-enclosing guided-atom interferometer for rotation sensing, Phys. Rev. Lett. 99, 173201 (2007). 4. Heralded Single- Magnon Quantum...excitations are quantized spin waves ( magnons ), such that transitions between its energy levels ( magnon number states) correspond to highly directional...polarization storage in the form of a single collective-spin excitation ( magnon ) that is shared between two spatially overlapped atomic ensembles
Dissipation induced asymmetric steering of distant atomic ensembles

NASA Astrophysics Data System (ADS)

Cheng, Guangling; Tan, Huatang; Chen, Aixi

2018-04-01

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

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

Mei Feng; Yu Yafei; Feng Mang

2009-10-15

We present a scheme for scalable quantum information processing with atomic ensembles and flying photons. Using the Rydberg blockade, we encode the qubits in the collective atomic states, which could be manipulated fast and easily due to the enhanced interaction in comparison to the single-atom case. We demonstrate that our proposed gating could be applied to generation of two-dimensional cluster states for measurement-based quantum computation. Moreover, the atomic ensembles also function as quantum repeaters useful for long-distance quantum state transfer. We show the possibility of our scheme to work in bad cavity or in weak coupling regime, which could muchmore » relax the experimental requirement. The efficient coherent operations on the ensemble qubits enable our scheme to be switchable between quantum computation and quantum communication using atomic ensembles.« less
Entanglement distillation for quantum communication network with atomic-ensemble memories.

PubMed

Li, Tao; Yang, Guo-Jian; Deng, Fu-Guo

2014-10-06

Atomic ensembles are effective memory nodes for quantum communication network due to the long coherence time and the collective enhancement effect for the nonlinear interaction between an ensemble and a photon. Here we investigate the possibility of achieving the entanglement distillation for nonlocal atomic ensembles by the input-output process of a single photon as a result of cavity quantum electrodynamics. We give an optimal entanglement concentration protocol (ECP) for two-atomic-ensemble systems in a partially entangled pure state with known parameters and an efficient ECP for the systems in an unknown partially entangled pure state with a nondestructive parity-check detector (PCD). For the systems in a mixed entangled state, we introduce an entanglement purification protocol with PCDs. These entanglement distillation protocols have high fidelity and efficiency with current experimental techniques, and they are useful for quantum communication network with atomic-ensemble memories.

Quantum-projection-noise-limited interferometry with coherent atoms in a Ramsey-type setup

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

Doering, D.; McDonald, G.; Debs, J. E.

2010-04-15

Every measurement of the population in an uncorrelated ensemble of two-level systems is limited by what is known as the quantum projection noise limit. Here, we present quantum-projection-noise-limited performance of a Ramsey-type interferometer using freely propagating coherent atoms. The experimental setup is based on an electro-optic modulator in an inherently stable Sagnac interferometer, optically coupling the two interfering atomic states via a two-photon Raman transition. Going beyond the quantum projection noise limit requires the use of reduced quantum uncertainty (squeezed) states. The experiment described demonstrates atom interferometry at the fundamental noise level and allows the observation of possible squeezing effectsmore » in an atom laser, potentially leading to improved sensitivity in atom interferometers.« less
Quasideterministic generation of maximally entangled states of two mesoscopic atomic ensembles by adiabatic quantum feedback

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

Di Lisi, Antonio; De Siena, Silvio; Illuminati, Fabrizio

2005-09-15

We introduce an efficient, quasideterministic scheme to generate maximally entangled states of two atomic ensembles. The scheme is based on quantum nondemolition measurements of total atomic populations and on adiabatic quantum feedback conditioned by the measurements outputs. The high efficiency of the scheme is tested and confirmed numerically for ideal photodetection as well as in the presence of losses.
Atomic entanglement purification and concentration using coherent state input-output process in low-Q cavity QED regime.

PubMed

Cao, Cong; Wang, Chuan; He, Ling-Yan; Zhang, Ru

2013-02-25

We investigate an atomic entanglement purification protocol based on the coherent state input-output process by working in low-Q cavity in the atom-cavity intermediate coupling region. The information of entangled states are encoded in three-level configured single atoms confined in separated one-side optical micro-cavities. Using the coherent state input-output process, we design a two-qubit parity check module (PCM), which allows the quantum nondemolition measurement for the atomic qubits, and show its use for remote parities to distill a high-fidelity atomic entangled ensemble from an initial mixed state ensemble nonlocally. The proposed scheme can further be used for unknown atomic states entanglement concentration. Also by exploiting the PCM, we describe a modified scheme for atomic entanglement concentration by introducing ancillary single atoms. As the coherent state input-output process is robust and scalable in realistic applications, and the detection in the PCM is based on the intensity of outgoing coherent state, the present protocols may be widely used in large-scaled and solid-based quantum repeater and quantum information processing.
Method and apparatus for quantum information processing using entangled neutral-atom qubits

DOEpatents

Jau, Yuan Yu; Biedermann, Grant; Deutsch, Ivan

2018-04-03

A method for preparing an entangled quantum state of an atomic ensemble is provided. The method includes loading each atom of the atomic ensemble into a respective optical trap; placing each atom of the atomic ensemble into a same first atomic quantum state by impingement of pump radiation; approaching the atoms of the atomic ensemble to within a dipole-dipole interaction length of each other; Rydberg-dressing the atomic ensemble; during the Rydberg-dressing operation, exciting the atomic ensemble with a Raman pulse tuned to stimulate a ground-state hyperfine transition from the first atomic quantum state to a second atomic quantum state; and separating the atoms of the atomic ensemble by more than a dipole-dipole interaction length.
Quantum Ensemble Classification: A Sampling-Based Learning Control Approach.

PubMed

Chen, Chunlin; Dong, Daoyi; Qi, Bo; Petersen, Ian R; Rabitz, Herschel

2017-06-01

Quantum ensemble classification (QEC) has significant applications in discrimination of atoms (or molecules), separation of isotopes, and quantum information extraction. However, quantum mechanics forbids deterministic discrimination among nonorthogonal states. The classification of inhomogeneous quantum ensembles is very challenging, since there exist variations in the parameters characterizing the members within different classes. In this paper, we recast QEC as a supervised quantum learning problem. A systematic classification methodology is presented by using a sampling-based learning control (SLC) approach for quantum discrimination. The classification task is accomplished via simultaneously steering members belonging to different classes to their corresponding target states (e.g., mutually orthogonal states). First, a new discrimination method is proposed for two similar quantum systems. Then, an SLC method is presented for QEC. Numerical results demonstrate the effectiveness of the proposed approach for the binary classification of two-level quantum ensembles and the multiclass classification of multilevel quantum ensembles.
Single-photon superradiant beating from a Doppler-broadened ladder-type atomic ensemble

NASA Astrophysics Data System (ADS)

Lee, Yoon-Seok; Lee, Sang Min; Kim, Heonoh; Moon, Han Seb

2017-12-01

We report on heralded-single-photon superradiant beating in the spontaneous four-wave mixing process of Doppler-broadened ladder-type 87Rb atoms. When Doppler-broadened atoms contribute to two-photon coherence, the detection probability amplitudes of the heralded single photons are coherently superposed despite inhomogeneous broadened atomic media. Single-photon superradiant beating is observed, which constitutes evidence for the coherent superposition of two-photon amplitudes from different velocity classes in the Doppler-broadened atomic ensemble. We present a theoretical model in which the single-photon superradiant beating originates from the interference between wavelength-separated two-photon amplitudes via the reabsorption filtering effect.
Cross Modulation of Two Laser Beams at the Individual-Photon Level

DTIC Science & Technology

2014-09-12

medium, such that the photons travel as slow-light polaritons [15,25,26], whose atomic excitation component can block the transmission of another light...through the ensemble, traveling in the medium as slow-light polaritons , a superposition of a photon and a collective atomic excitation to the state...unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 slow-light polariton , the polariton’s atomic component in state jci reduces
Quantum teleportation between remote atomic-ensemble quantum memories.

PubMed

Bao, Xiao-Hui; Xu, Xiao-Fan; Li, Che-Ming; Yuan, Zhen-Sheng; Lu, Chao-Yang; Pan, Jian-Wei

2012-12-11

Quantum teleportation and quantum memory are two crucial elements for large-scale quantum networks. With the help of prior distributed entanglement as a "quantum channel," quantum teleportation provides an intriguing means to faithfully transfer quantum states among distant locations without actual transmission of the physical carriers [Bennett CH, et al. (1993) Phys Rev Lett 70(13):1895-1899]. Quantum memory enables controlled storage and retrieval of fast-flying photonic quantum bits with stationary matter systems, which is essential to achieve the scalability required for large-scale quantum networks. Combining these two capabilities, here we realize quantum teleportation between two remote atomic-ensemble quantum memory nodes, each composed of ∼10(8) rubidium atoms and connected by a 150-m optical fiber. The spin wave state of one atomic ensemble is mapped to a propagating photon and subjected to Bell state measurements with another single photon that is entangled with the spin wave state of the other ensemble. Two-photon detection events herald the success of teleportation with an average fidelity of 88(7)%. Besides its fundamental interest as a teleportation between two remote macroscopic objects, our technique may be useful for quantum information transfer between different nodes in quantum networks and distributed quantum computing.
Precision bounds for gradient magnetometry with atomic ensembles

NASA Astrophysics Data System (ADS)

Apellaniz, Iagoba; Urizar-Lanz, Iñigo; Zimborás, Zoltán; Hyllus, Philipp; Tóth, Géza

2018-05-01

We study gradient magnetometry with an ensemble of atoms with arbitrary spin. We calculate precision bounds for estimating the gradient of the magnetic field based on the quantum Fisher information. For quantum states that are invariant under homogeneous magnetic fields, we need to measure a single observable to estimate the gradient. On the other hand, for states that are sensitive to homogeneous fields, a simultaneous measurement is needed, as the homogeneous field must also be estimated. We prove that for the cases studied in this paper, such a measurement is feasible. We present a method to calculate precision bounds for gradient estimation with a chain of atoms or with two spatially separated atomic ensembles. We also consider a single atomic ensemble with an arbitrary density profile, where the atoms cannot be addressed individually, and which is a very relevant case for experiments. Our model can take into account even correlations between particle positions. While in most of the discussion we consider an ensemble of localized particles that are classical with respect to their spatial degree of freedom, we also discuss the case of gradient metrology with a single Bose-Einstein condensate.
Continuous-variable controlled-Z gate using an atomic ensemble

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

Wang Mingfeng; Jiang Nianquan; Jin Qingli

2011-06-15

The continuous-variable controlled-Z gate is a canonical two-mode gate for universal continuous-variable quantum computation. It is considered as one of the most fundamental continuous-variable quantum gates. Here we present a scheme for realizing continuous-variable controlled-Z gate between two optical beams using an atomic ensemble. The gate is performed by simply sending the two beams propagating in two orthogonal directions twice through a spin-squeezed atomic medium. Its fidelity can run up to one if the input atomic state is infinitely squeezed. Considering the noise effects due to atomic decoherence and light losses, we show that the observed fidelities of the schememore » are still quite high within presently available techniques.« less
Coherent scattering of near-resonant light by a dense, microscopic cloud of cold two-level atoms: Experiment versus theory

NASA Astrophysics Data System (ADS)

Jennewein, Stephan; Brossard, Ludovic; Sortais, Yvan R. P.; Browaeys, Antoine; Cheinet, Patrick; Robert, Jacques; Pillet, Pierre

2018-05-01

We measure the coherent scattering of low-intensity, near-resonant light by a cloud of laser-cooled two-level rubidium atoms with a size comparable to the wavelength of light. We isolate a two-level atomic structure by applying a 300-G magnetic field. We measure both the temporal and the steady-state coherent optical response of the cloud for various detunings of the laser and for atom numbers ranging from 5 to 100. We compare our results to a microscopic coupled-dipole model and to a multimode, paraxial Maxwell-Bloch model. In the low-intensity regime, both models are in excellent agreement, thus validating the Maxwell-Bloch model. Comparing to the data, the models are found in very good agreement for relatively low densities (n /k3≲0.1 ), while significant deviations start to occur at higher density. This disagreement indicates that light scattering in dense, cold atomic ensembles is still not quantitatively understood, even in pristine experimental conditions.
Entanglement between two spatially separated atomic modes

NASA Astrophysics Data System (ADS)

Lange, Karsten; Peise, Jan; Lücke, Bernd; Kruse, Ilka; Vitagliano, Giuseppe; Apellaniz, Iagoba; Kleinmann, Matthias; Tóth, Géza; Klempt, Carsten

2018-04-01

Modern quantum technologies in the fields of quantum computing, quantum simulation, and quantum metrology require the creation and control of large ensembles of entangled particles. In ultracold ensembles of neutral atoms, nonclassical states have been generated with mutual entanglement among thousands of particles. The entanglement generation relies on the fundamental particle-exchange symmetry in ensembles of identical particles, which lacks the standard notion of entanglement between clearly definable subsystems. Here, we present the generation of entanglement between two spatially separated clouds by splitting an ensemble of ultracold identical particles prepared in a twin Fock state. Because the clouds can be addressed individually, our experiments open a path to exploit the available entangled states of indistinguishable particles for quantum information applications.
Quantum teleportation between remote atomic-ensemble quantum memories

PubMed Central

Bao, Xiao-Hui; Xu, Xiao-Fan; Li, Che-Ming; Yuan, Zhen-Sheng; Lu, Chao-Yang; Pan, Jian-Wei

2012-01-01

Quantum teleportation and quantum memory are two crucial elements for large-scale quantum networks. With the help of prior distributed entanglement as a “quantum channel,” quantum teleportation provides an intriguing means to faithfully transfer quantum states among distant locations without actual transmission of the physical carriers [Bennett CH, et al. (1993) Phys Rev Lett 70(13):1895–1899]. Quantum memory enables controlled storage and retrieval of fast-flying photonic quantum bits with stationary matter systems, which is essential to achieve the scalability required for large-scale quantum networks. Combining these two capabilities, here we realize quantum teleportation between two remote atomic-ensemble quantum memory nodes, each composed of ∼108 rubidium atoms and connected by a 150-m optical fiber. The spin wave state of one atomic ensemble is mapped to a propagating photon and subjected to Bell state measurements with another single photon that is entangled with the spin wave state of the other ensemble. Two-photon detection events herald the success of teleportation with an average fidelity of 88(7)%. Besides its fundamental interest as a teleportation between two remote macroscopic objects, our technique may be useful for quantum information transfer between different nodes in quantum networks and distributed quantum computing. PMID:23144222
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.
On the non-linear spectroscopy including saturated absorption and four-wave mixing in two and multi-level atoms: a computational study

NASA Astrophysics Data System (ADS)

Patel, M.; De Jager, G.; Nkosi, Z.; Wyngaard, A.; Govender, K.

2017-10-01

In this paper we report on the study of two and multi-level atoms interacting with multiple laser beams. The semi-classical approach is used to describe the system in which the atoms are treated quantum mechanically via the density matrix operator, while the laser beams are treated classically using Maxwells equations. We present results of a two level atom interacting with single and multiple laser beams and demonstrate Rabi oscillations between the levels. The effects of laser modulation on the dynamics of the atom (atomic populations and coherences) are examined by solving the optical Bloch equations. Plots of the density matrix elements as a function of time are presented for various parameters such as laser intensity, detuning, modulation etc. In addition, phase-space plots and Fourier analysis of the density matrix elements are provided. The atomic polarization, estimated from the coherence terms of the density matrix elements, is used in the numerical solution of Maxwells equations to determine the behaviour of the laser beams as they propagate through the atomic ensemble. The effects of saturation and hole-burning are demonstrated in the case of two counter propagating beams with one being a strong beam and the other being very weak. The above work is extended to include four-wave mixing in four level atoms in a diamond configuration. Two co-propagating beams of different wavelengths drive the atoms from a ground state |1〉 to an excited state |3〉 via an intermediate state |2〉. The atoms then move back to the ground state via another intermediate state |4〉, resulting in the generation of two additional correlated photon beams. The characteristics of these additional photons are studied.
Cavity electromagnetically induced transparency via spontaneously generated coherence

NASA Astrophysics Data System (ADS)

Tariq, Muhammad; Ziauddin, Bano, Tahira; Ahmad, Iftikhar; Lee, Ray-Kuang

2017-09-01

A four-level N-type atomic ensemble enclosed in a cavity is revisited to investigate the influence of spontaneous generated coherence (SGC) on transmission features of weak probe light field. A weak probe field is propagating through the cavity where each atom inside the cavity follows four-level N-type atom-field configuration of rubidium (?) atom. We use input-output theory and study the interaction of atomic ensemble and three cavity fields which are coupled to the same cavity mode. A SGC affects the transmission properties of weak probe light field due to which a transparency window (cavity EIT) appears. At resonance condition the transparency window increases with increasing the SGC in the system. We also studied the influence of the SGC on group delay and investigated magnitude enhancement of group delay for the maximum SGC in the system.
Quantum synchronization of many coupled atoms for an ultranarrow linewidth laser

NASA Astrophysics Data System (ADS)

He, Peiru; Xu, Minghui; Tieri, David; Zhu, Bihui; Rey, Ana Maria; Hazzard, Kaden; Holland, Murray

2014-05-01

We theoretically investigate the effect of quantum synchronization on many coupled two-level atoms acting as high quality oscillators. We show that quantum synchronization - the spontaneous alignment of the phase (of the two-level superposition) between different atoms - provides a potential approach to produce robust atomic coherences and coherent light with ultranarrow linewidth and extreme phase stability. The atoms may be coupled either through their direct dipole-dipole interactions or, as in a superradiant laser, through an optical cavity. We develop a variety of analytic and computational approaches for this problem, including exact open quantum system methods for small systems, semiclassical theories, and approaches that make use of the permutation symmetry of identically coupled ensembles. We investigate the first and second order coherence properties of both the optical and atomic degrees of freedom. We study synchronization in both the steady-state, as well as during the dynamically applied pulse sequences of Rabi and Ramsey interferometry. This work was supported by the DARPA QuASAR program, the NSF, and NIST.
Einstein-Podolsky-Rosen paradox and quantum steering in a three-mode optomechanical system

NASA Astrophysics Data System (ADS)

He, Qiongyi; Ficek, Zbigniew

2014-02-01

We study multipartite entanglement, the generation of Einstein-Podolsky-Rosen (EPR) states, and quantum steering in a three-mode optomechanical system composed of an atomic ensemble located inside a single-mode cavity with a movable mirror. The cavity mode is driven by a short laser pulse, has a nonlinear parametric-type interaction with the mirror and a linear beam-splitter-type interaction with the atomic ensemble. There is no direct interaction of the mirror with the atomic ensemble. A threshold effect for the dynamics of the system is found, above which the system works as an amplifier and below which as an attenuator of the output fields. The threshold is determined by the ratio of the coupling strengths of the cavity mode to the mirror and to the atomic ensemble. It is shown that above the threshold, the system effectively behaves as a two-mode system in which a perfect bipartite EPR state can be generated, while it is impossible below the threshold. Furthermore, a fully inseparable tripartite entanglement and even further a genuine tripartite entanglement can be produced above and below the threshold. In addition, we consider quantum steering and examine the monogamy relations that quantify the amount of bipartite steering that can be shared between different modes. It is found that the mirror is more capable for steering of entanglement than the cavity mode. The two-way steering is found between the mirror and the atomic ensemble despite the fact that they are not directly coupled to each other, while it is impossible between the output of cavity mode and the ensemble which are directly coupled to each other.
Electromagnetically induced grating with Rydberg atoms

NASA Astrophysics Data System (ADS)

Asghar, Sobia; Ziauddin, Qamar, Shahid; Qamar, Sajid

2016-09-01

We present a scheme to realize electromagnetically induced grating in an ensemble of strongly interacting Rydberg atoms, which act as superatoms due to the dipole blockade mechanism. The ensemble of three-level cold Rydberg-dressed (87Rb) atoms follows a cascade configuration where a strong standing-wave control field and a weak probe pulse are employed. The diffraction intensity is influenced by the strength of the probe intensity, the control field strength, and the van der Waals (vdW) interaction. It is noticed that relatively large first-order diffraction can be obtained for low-input intensity with a small vdW shift and a strong control field. The scheme can be considered as an amicable solution to realize the atomic grating at the microscopic level, which can provide background- and dark-current-free diffraction.
Mixing properties of the one-atom maser

NASA Astrophysics Data System (ADS)

Bruneau, Laurent

2014-06-01

We study the relaxation properties of the quantized electromagnetic field in a cavity under repeated interactions with single two-level atoms, so-called one-atom maser. We improve the ergodic results obtained in Bruneau and Pillet (J Stat Phys 134(5-6):1071-1095, 2009) and prove that, whenever the atoms are initially distributed according to the canonical ensemble at temperature , all the invariant states are mixing. Under some non-resonance condition this invariant state is known to be thermal equilibirum at some renormalized temperature and we prove that the mixing is then arbitrarily slow, in other words that there is no lower bound on the relaxation speed.

Measurement-induced entanglement for excitation stored in remote atomic ensembles.

PubMed

Chou, C W; de Riedmatten, H; Felinto, D; Polyakov, S V; van Enk, S J; Kimble, H J

2005-12-08

A critical requirement for diverse applications in quantum information science is the capability to disseminate quantum resources over complex quantum networks. For example, the coherent distribution of entangled quantum states together with quantum memory (for storing the states) can enable scalable architectures for quantum computation, communication and metrology. Here we report observations of entanglement between two atomic ensembles located in distinct, spatially separated set-ups. Quantum interference in the detection of a photon emitted by one of the samples projects the otherwise independent ensembles into an entangled state with one joint excitation stored remotely in 10(5) atoms at each site. After a programmable delay, we confirm entanglement by mapping the state of the atoms to optical fields and measuring mutual coherences and photon statistics for these fields. We thereby determine a quantitative lower bound for the entanglement of the joint state of the ensembles. Our observations represent significant progress in the ability to distribute and store entangled quantum states.
Single-bubble sonoluminescence as Dicke superradiance at finite temperature

NASA Astrophysics Data System (ADS)

Aparicio Alcalde, M.; Quevedo, H.; Svaiter, N. F.

2014-12-01

Sonoluminescence is a process in which a strong sound field is used to produce light in liquids. We explain sonoluminescence as a phase transition from ordinary fluorescence to a superradiant phase. We consider a spin-boson model composed of a single bosonic mode and an ensemble of N identical two-level atoms. We assume that the whole system is in thermal equilibrium with a reservoir at temperature β-1. We show that, in a ultrastrong-coupling regime, between the two-level atoms and the electromagnetic field it is possible to have a cooperative interaction of the molecules of the gas in the interior of the bubble with the field, generating sonoluminescence.
Repetitive Interrogation of 2-Level Quantum Systems

NASA Technical Reports Server (NTRS)

Prestage, John D.; Chung, Sang K.

2010-01-01

Trapped ion clocks derive information from a reference atomic transition by repetitive interrogations of the same quantum system, either a single ion or ionized gas of many millions of ions. Atomic beam frequency standards, by contrast, measure reference atomic transitions in a continuously replenished "flow through" configuration where initial ensemble atomic coherence is zero. We will describe some issues and problems that can arise when atomic state selection and preparation of the quantum atomic system is not completed, that is, optical pumping has not fully relaxed the coherence and also not fully transferred atoms to the initial state. We present a simple two-level density matrix analysis showing how frequency shifts during the state-selection process can cause frequency shifts of the measured clock transition. Such considerations are very important when a low intensity lamp light source is used for state selection, where there is relatively weak relaxation and re-pumping of ions to an initial state and much weaker 'environmental' relaxation of the atomic coherence set-up in the atomic sample.
Heterogeneous path ensembles for conformational transitions in semi–atomistic models of adenylate kinase

PubMed Central

Bhatt, Divesh; Zuckerman, Daniel M.

2010-01-01

We performed “weighted ensemble” path–sampling simulations of adenylate kinase, using several semi–atomistic protein models. The models have an all–atom backbone with various levels of residue interactions. The primary result is that full statistically rigorous path sampling required only a few weeks of single–processor computing time with these models, indicating the addition of further chemical detail should be readily feasible. Our semi–atomistic path ensembles are consistent with previous biophysical findings: the presence of two distinct pathways, identification of intermediates, and symmetry of forward and reverse pathways. PMID:21660120
Quantum iSWAP gate in optical cavities with a cyclic three-level system

NASA Astrophysics Data System (ADS)

Yan, Guo-an; Qiao, Hao-xue; Lu, Hua

2018-04-01

In this paper we present a scheme to directly implement the iSWAP gate by passing a cyclic three-level system across a two-mode cavity quantum electrodynamics. In the scheme, a three-level Δ -type atom ensemble prepared in its ground state mediates the interaction between the two-cavity modes. For this theoretical model, we also analyze its performance under practical noise, including spontaneous emission and the decay of the cavity modes. It is shown that our scheme may have a high fidelity under the practical noise.
Coherent Radiation in Atomic Systems

NASA Astrophysics Data System (ADS)

Sutherland, Robert Tyler

Over the last century, quantum mechanics has dramatically altered our understanding of light and matter. Impressively, exploring the relationship between the two continues to provide important insights into the physics of many-body systems. In this thesis, we add to this still growing field of study. Specifically, we discuss superradiant line-broadening and cooperative dipole-dipole interactions for cold atom clouds in the linear-optics regime. We then discuss how coherent radiation changes both the photon scattering properties and the excitation distribution of atomic arrays. After that, we explore the nature of superradiance in initially inverted clouds of multi-level atoms. Finally, we explore the physics of clouds with degenerate Zeeman ground states, and show that this creates quantum effects that fundamentally change the photon scattering of atomic ensembles.
Storing a single photon as a spin wave entangled with a flying photon in the telecommunication bandwidth

NASA Astrophysics Data System (ADS)

Zhang, Wei; Ding, Dong-Sheng; Shi, Shuai; Li, Yan; Zhou, Zhi-Yuan; Shi, Bao-Sen; Guo, Guang-Can

2016-02-01

Quantum memory is an essential building block for quantum communication and scalable linear quantum computation. Storing two-color entangled photons with one photon being at the telecommunication (telecom) wavelength while the other photon is compatible with quantum memory has great advantages toward the realization of the fiber-based long-distance quantum communication with the aid of quantum repeaters. Here, we report an experimental realization of storing a photon entangled with a telecom photon in polarization as an atomic spin wave in a cold atomic ensemble, thus establishing the entanglement between the telecom-band photon and the atomic-ensemble memory in a polarization degree of freedom. The reconstructed density matrix and the violation of the Clauser-Horne-Shimony-Holt inequality clearly show the preservation of quantum entanglement during storage. Our result is very promising for establishing a long-distance quantum network based on cold atomic ensembles.
Experimental realization of narrowband four-photon Greenberger-Horne-Zeilinger state in a single cold atomic ensemble.

PubMed

Dong, Ming-Xin; Zhang, Wei; Hou, Zhi-Bo; Yu, Yi-Chen; Shi, Shuai; Ding, Dong-Sheng; Shi, Bao-Sen

2017-11-15

Multi-photon entangled states not only play a crucial role in research on quantum physics but also have many applications in quantum information fields such as quantum computation, quantum communication, and quantum metrology. To fully exploit the multi-photon entangled states, it is important to establish the interaction between entangled photons and matter, which requires that photons have narrow bandwidth. Here, we report on the experimental generation of a narrowband four-photon Greenberger-Horne-Zeilinger state with a fidelity of 64.9% through multiplexing two spontaneous four-wave mixings in a cold Rb85 atomic ensemble. The full bandwidth of the generated GHZ state is about 19.5 MHz. Thus, the generated photons can effectively match the atoms, which are very suitable for building a quantum computation and quantum communication network based on atomic ensembles.
Operating Spin Echo in the Quantum Regime for an Atomic-Ensemble Quantum Memory

NASA Astrophysics Data System (ADS)

Rui, Jun; Jiang, Yan; Yang, Sheng-Jun; Zhao, Bo; Bao, Xiao-Hui; Pan, Jian-Wei

2015-09-01

Spin echo is a powerful technique to extend atomic or nuclear coherence times by overcoming the dephasing due to inhomogeneous broadenings. However, there are disputes about the feasibility of applying this technique to an ensemble-based quantum memory at the single-quanta level. In this experimental study, we find that noise due to imperfections of the rephasing pulses has both intense superradiant and weak isotropic parts. By properly arranging the beam directions and optimizing the pulse fidelities, we successfully manage to operate the spin echo technique in the quantum regime by observing nonclassical photon-photon correlations as well as the quantum behavior of retrieved photons. Our work for the first time demonstrates the feasibility of harnessing the spin echo method to extend the lifetime of ensemble-based quantum memories at the single-quanta level.
Superradiant phase transition in a model of three-level-Λ systems interacting with two bosonic modes

NASA Astrophysics Data System (ADS)

Hayn, Mathias; Emary, Clive; Brandes, Tobias

2012-12-01

We consider an ensemble of three-level particles in Lambda configuration interacting with two bosonic modes. The Hamiltonian has the form of a generalized Dicke model. We show that in the thermodynamic limit this model supports a superradiant quantum phase transition. Remarkably, this can be both a first- and a second-order phase transition. A connection of the phase diagram to the symmetries of the Hamiltonian is also given. In addition, we show that this model can describe atoms interacting with an electromagnetic field in which the microscopic Hamiltonian includes a diamagnetic contribution. Even though the parameters of the atomic system respect the Thomas-Reiche-Kuhn sum rule, the system still shows a superradiant phase transition.
A universal quantum frequency converter via four-wave-mixing processes

NASA Astrophysics Data System (ADS)

Cheng, Mingfei; Fang, Jinghuai

2016-06-01

We present a convenient and flexible way to realize a universal quantum frequency converter by using nondegenerate four-wave-mixing processes in the ladder-type three-level atomic system. It is shown that quantum state exchange between two fields with large frequency difference can be readily achieved, where one corresponds to the atomic resonant transition in the visible spectral region for quantum memory and the other to the telecommunication range wavelength (1550 nm) for long-distance transmission over optical fiber. This method would bring great facility in realistic quantum information processing protocols with atomic ensembles as quantum memory and low-loss optical fiber as transmission channel.
Universality and diversity of folding mechanics for three-helix bundle proteins.

PubMed

Yang, Jae Shick; Wallin, Stefan; Shakhnovich, Eugene I

2008-01-22

In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo folding simulations using a single transferable all-atom potential. Using these trajectories, we examine the relaxation behavior, secondary structure formation, and transition-state ensembles (TSEs) of the two proteins and compare our results with experimental data and previous computational studies. To obtain a detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Moreover, rigorous p(fold) analysis is used to obtain representative samples of the TSEs and a good quantitative agreement between experimental and simulated Phi values is obtained for protein A. Phi values for Villin also are obtained and left as predictions to be tested by future experiments. Our analysis shows that the two-helix hairpin is a common partially stable structural motif that gets formed before entering the TSE in the studied proteins. These results together with our earlier study of Engrailed Homeodomain and recent experimental studies provide a comprehensive, atomic-level picture of folding mechanics of three-helix bundle proteins.
Stimulated emission from ladder-type two-photon coherent atomic ensemble.

PubMed

Park, Jiho; Moon, Han Seb

2018-05-28

We investigated the stimulated emission from a ladder-type two-photon coherent atomic ensemble, for the 5S 1/2 - 5P 3/2 - 5D 5/2 transition of 87 Rb atoms. Under the ladder-type two-photon resonance condition obtained using pump and coupling lasers, we observed broad four-wave mixing (FWM) light stimulated from two-photon coherence induced by the seed laser coupled between the ground state of 5S 1/2 and the first excited state of 5P 3/2 . A dip in the FWM spectrum was obtained for three-photon resonance due to V-type two-photon coherence using the pump and seed lasers. From the FWM spectra obtained for varying frequency detuning and seed-laser power, we determined that the seed laser acts as a stimulator for FWM generation, but also acts as a disturber of FWM due to V-type two-photon coherence.
Generation, storage, and retrieval of nonclassical states of light using atomic ensembles

NASA Astrophysics Data System (ADS)

Eisaman, Matthew D.

This thesis presents the experimental demonstration of several novel methods for generating, storing, and retrieving nonclassical states of light using atomic ensembles, and describes applications of these methods to frequency-tunable single-photon generation, single-photon memory, quantum networks, and long-distance quantum communication. We first demonstrate emission of quantum-mechanically correlated pulses of light with a time delay between the pulses that is coherently controlled by utilizing 87Rb atoms. The experiment is based on Raman scattering, which produces correlated pairs of excited atoms and photons, followed by coherent conversion of the atomic states into a different photon field after a controllable delay. We then describe experiments demonstrating a novel approach for conditionally generating nonclassical pulses of light with controllable photon numbers, propagation direction, timing, and pulse shapes. We observe nonclassical correlations in relative photon number between correlated pairs of photons, and create few-photon light pulses with sub-Poissonian photon-number statistics via conditional detection on one field of the pair. Spatio-temporal control over the pulses is obtained by exploiting long-lived coherent memory for photon states and electromagnetically induced transparency (EIT) in an optically dense atomic medium. Finally, we demonstrate the use of EIT for the controllable generation, transmission, and storage of single photons with tunable frequency, timing, and bandwidth. To this end, we study the interaction of single photons produced in a "source" ensemble of 87Rb atoms at room temperature with another "target" ensemble. This allows us to simultaneously probe the spectral and quantum statistical properties of narrow-bandwidth single-photon pulses, revealing that their quantum nature is preserved under EIT propagation and storage. We measure the time delay associated with the reduced group velocity of the single-photon pulses and report observations of their storage and retrieval. Together these experiments utilize atomic ensembles to realize a narrow-bandwidth single-photon source, single-photon memory that preserves the quantum nature of the single photons, and a primitive quantum network comprised of two atomic-ensemble quantum memories connected by a single photon in an optical fiber. Each of these experimental demonstrations represents an essential element for the realization of long-distance quantum communication.
Manipulating mesoscopic multipartite entanglement with atom-light interfaces

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

Stasinska, J.; Rodo, C.; Paganelli, S.

2009-12-15

Entanglement between two macroscopic atomic ensembles induced by measurement on an ancillary light system has proven to be a powerful method for engineering quantum memories and quantum state transfer. Here we investigate the feasibility of such methods for generation, manipulation, and detection of genuine multipartite entanglement (Greenberger-Horne-Zeilinger and clusterlike states) between mesoscopic atomic ensembles without the need of individual addressing of the samples. Our results extend in a nontrivial way the Einstein-Podolsky-Rosen entanglement between two macroscopic gas samples reported experimentally in [B. Julsgaard, A. Kozhekin, and E. Polzik, Nature (London) 413, 400 (2001)]. We find that under realistic conditions, amore » second orthogonal light pulse interacting with the atomic samples, can modify and even reverse the entangling action of the first one leaving the samples in a separable state.« less
Phase-noise influence on coherent transients and hole burning

NASA Astrophysics Data System (ADS)

Shakhmuratov, R. N.; Szabo, Alex

1998-10-01

Resonant excitation of an inhomogeneously broadened ensemble of two-level atoms (TLA) by a stochastic field with phase noise is theoretically investigated. Free-induction decay (FID), hole burning (HB), and transient nutation (TN) are studied. We consider two kinds of driving fields, one with a free walking phase and another with the phase locked in a limited domain. It is shown that the resonant excitation behavior depends strongly on the noise property. Noise induced by a walking phase gives a simple contribution to the dephasing time, T2, of two-level atoms whereas phase locking qualitatively changes the laser-atom interaction. In the latter case, it is shown that even when the central part of the driving field spectrum is narrower than homogeneous absorption line of the TLA, the wide, low intensity wings of the spectrum (sidebands produced by the locked phase noise), have a strong effect on the FID, TN, and HB induced by the central, narrow part of the spectrum. The influence of sidebands on photon echoes is also discussed.
Electro-Optic Quantum Memory for Light Using Two-Level Atoms

NASA Astrophysics Data System (ADS)

Hétet, G.; Longdell, J. J.; Alexander, A. L.; Lam, P. K.; Sellars, M. J.

2008-01-01

We present a simple quantum memory scheme that allows for the storage of a light field in an ensemble of two-level atoms. The technique is analogous to the NMR gradient echo for which the imprinting and recalling of the input field are performed by controlling a linearly varying broadening. Our protocol is perfectly efficient in the limit of high optical depths and the output pulse is emitted in the forward direction. We provide a numerical analysis of the protocol together with an experiment performed in a solid state system. In close agreement with our model, the experiment shows a total efficiency of up to 15%, and a recall efficiency of 26%. We suggest simple realizable improvements for the experiment to surpass the no-cloning limit.
Electro-optic quantum memory for light using two-level atoms.

PubMed

Hétet, G; Longdell, J J; Alexander, A L; Lam, P K; Sellars, M J

2008-01-18

We present a simple quantum memory scheme that allows for the storage of a light field in an ensemble of two-level atoms. The technique is analogous to the NMR gradient echo for which the imprinting and recalling of the input field are performed by controlling a linearly varying broadening. Our protocol is perfectly efficient in the limit of high optical depths and the output pulse is emitted in the forward direction. We provide a numerical analysis of the protocol together with an experiment performed in a solid state system. In close agreement with our model, the experiment shows a total efficiency of up to 15%, and a recall efficiency of 26%. We suggest simple realizable improvements for the experiment to surpass the no-cloning limit.
Implementing the Deutsch-Jozsa algorithm with macroscopic ensembles

NASA Astrophysics Data System (ADS)

Semenenko, Henry; Byrnes, Tim

2016-05-01

Quantum computing implementations under consideration today typically deal with systems with microscopic degrees of freedom such as photons, ions, cold atoms, and superconducting circuits. The quantum information is stored typically in low-dimensional Hilbert spaces such as qubits, as quantum effects are strongest in such systems. It has, however, been demonstrated that quantum effects can be observed in mesoscopic and macroscopic systems, such as nanomechanical systems and gas ensembles. While few-qubit quantum information demonstrations have been performed with such macroscopic systems, a quantum algorithm showing exponential speedup over classical algorithms is yet to be shown. Here, we show that the Deutsch-Jozsa algorithm can be implemented with macroscopic ensembles. The encoding that we use avoids the detrimental effects of decoherence that normally plagues macroscopic implementations. We discuss two mapping procedures which can be chosen depending upon the constraints of the oracle and the experiment. Both methods have an exponential speedup over the classical case, and only require control of the ensembles at the level of the total spin of the ensembles. It is shown that both approaches reproduce the qubit Deutsch-Jozsa algorithm, and are robust under decoherence.
Integrated optical dipole trap for cold neutral atoms with an optical waveguide coupler

NASA Astrophysics Data System (ADS)

Lee, J.; Park, D. H.; Mittal, S.; Dagenais, M.; Rolston, S. L.

2013-04-01

An integrated optical dipole trap uses two-color (red and blue-detuned) traveling evanescent wave fields for trapping cold neutral atoms. To achieve longitudinal confinement, we propose using an integrated optical waveguide coupler, which provides a potential gradient along the beam propagation direction sufficient to confine atoms. This integrated optical dipole trap can support an atomic ensemble with a large optical depth due to its small mode area. Its quasi-TE0 waveguide mode has an advantage over the HE11 mode of a nanofiber, with little inhomogeneous Zeeman broadening at the trapping region. The longitudinal confinement eliminates the need for a one dimensional optical lattice, reducing collisional blockaded atomic loading, potentially producing larger ensembles. The waveguide trap allows for scalability and integrability with nano-fabrication technology. We analyze the potential performance of such integrated atom traps.

Towards an Einstein-Podolsky-Rosen paradox between two macroscopic atomic ensembles at room temperature

NASA Astrophysics Data System (ADS)

He, Q. Y.; Reid, M. D.

2013-06-01

Experiments have reported the entanglement of two spatially separated macroscopic atomic ensembles at room temperature (Krauter et al 2011 Phys. Rev. Lett. 107 080503; Julsgaard et al 2001 Nature 413 400). We show how an Einstein-Podolsky-Rosen (EPR) paradox is realizable with this experiment. Our proposed test involves violation of an inferred Heisenberg uncertainty principle, which is a sufficient condition for an EPR paradox. This is a stronger test of nonlocality than entanglement. Our proposal would enable the first definitive confirmation of quantum EPR paradox correlations between two macroscopic objects at room temperature. This is a necessary intermediate step towards a nonlocal experiment with causal measurement separations. As well as having fundamental significance, the realization of an atomic EPR paradox could provide a resource for novel applications in quantum technology.
Entanglement manipulation via Coulomb interaction in an optomechanical cavity assisted by two-level cold atoms

NASA Astrophysics Data System (ADS)

Wang, Jing; Tian, Xue-Dong; Liu, Yi-Mou; Cui, Cui-Li; Wu, Jin-Hui

2018-06-01

We investigate the stationary entanglement properties in a hybrid system consisting of an optical cavity, a mechanical resonator, a charged object, and an atomic ensemble. Numerical results show that this hybrid system exhibits three kinds of controllable bipartite entanglements in an experimentally accessible parameter regime with the help of the charged object. More importantly, it is viable to enhance on demand each bipartite entanglement at the expense of reducing others by modulating the Coulomb coupling strength. Last but not least, these bipartite entanglements seem more robust against on the environmental temperature for the positive Coulomb interaction.
Nanophotonic Optical Isolator Controlled by the Internal State of Cold Atoms

NASA Astrophysics Data System (ADS)

Sayrin, Clément; Junge, Christian; Mitsch, Rudolf; Albrecht, Bernhard; O'Shea, Danny; Schneeweiss, Philipp; Volz, Jürgen; Rauschenbeutel, Arno

2015-10-01

The realization of nanophotonic optical isolators with high optical isolation even at ultralow light levels and low optical losses is an open problem. Here, we employ the link between the local polarization of strongly confined light and its direction of propagation to realize low-loss nonreciprocal transmission through a silica nanofiber at the single-photon level. The direction of the resulting optical isolator is controlled by the spin state of cold atoms. We perform our experiment in two qualitatively different regimes, i.e., with an ensemble of cold atoms where each atom is weakly coupled to the waveguide and with a single atom strongly coupled to the waveguide mode. In both cases, we observe simultaneously high isolation and high forward transmission. The isolator concept constitutes a nanoscale quantum optical analog of microwave ferrite resonance isolators, can be implemented with all kinds of optical waveguides and emitters, and might enable novel integrated optical devices for fiber-based classical and quantum networks.
Experimental Demonstration of Quantum Stationary Light Pulses in an Atomic Ensemble

NASA Astrophysics Data System (ADS)

Park, Kwang-Kyoon; Cho, Young-Wook; Chough, Young-Tak; Kim, Yoon-Ho

2018-04-01

We report an experimental demonstration of the nonclassical stationary light pulse (SLP) in a cold atomic ensemble. A single collective atomic excitation is created and heralded by detecting a Stokes photon in the spontaneous Raman scattering process. The heralded single atomic excitation is converted into a single stationary optical excitation or the single-photon SLP, whose effective group velocity is zero, effectively forming a trapped single-photon pulse within the cold atomic ensemble. The single-photon SLP is then released from the atomic ensemble as an anti-Stokes photon after a specified trapping time. The second-order correlation measurement between the Stokes and anti-Stokes photons reveals the nonclassical nature of the single-photon SLP. Our work paves the way toward quantum nonlinear optics without a cavity.
Quantum Synchronization of Two Ensembles of Atoms

NASA Astrophysics Data System (ADS)

Xu, Minghui; Tieri, David; Fine, Effie; Thompson, James; Holland, Murray

2014-05-01

We present a system that exhibits quantum synchronization as a modern analogue of the Huygens experiment which is implemented using state-of-the-art neutral atom lattice clocks of the highest precision. In particular, we study the correlated phase dynamics of two mesoscopic ensembles of atoms through their collective coupling to an optical cavity. We find a dynamical quantum phase transition induced by pump noise and cavity output-coupling. The spectral properties of the superradiant light emitted from the cavity show that at a critical pump rate the system undergoes a transition from the independent behavior of two disparate oscillators to the phase-locking that is the signature of quantum synchronization. Besides being of fundamental importance in nonequilibrium quantum many-body physics, this work could have broad implications for many practical applications of ultrastable lasers and precision measurements. This work was supported by the DARPA QuASAR program, the NSF, and NIST.
Performance and Applications of an Ensemble of Atomic Fountains

DTIC Science & Technology

2012-01-01

continuous operation. At some institutions, only one fountain clock contributes to the ensemble at a given time, although two clocks at PTB and three at...at USNO is funded by SPAWAR. REFERENCES [1] A. Bauch, S. Weyers, D. Piester, E. Staliuniene, and W. Yang, “Generation of UTC( PTB ) as a fountain
Entanglement of 3000 atoms by detecting one photon

NASA Astrophysics Data System (ADS)

Vuletic, Vladan

2016-05-01

Quantum-mechanically correlated (entangled) states of many particles are of interest in quantum information, quantum computing and quantum metrology. In particular, entangled states of many particles can be used to overcome limits on measurements performed with ensembles of independent atoms (standard quantum limit). Metrologically useful entangled states of large atomic ensembles (spin squeezed states) have been experimentally realized. These states display Gaussian spin distribution functions with a non-negative Wigner quasiprobability distribution function. We report the generation of entanglement in a large atomic ensemble via an interaction with a very weak laser pulse; remarkably, the detection of a single photon prepares several thousand atoms in an entangled state. We reconstruct a negative-valued Wigner function, and verify an entanglement depth (the minimum number of mutually entangled atoms) that comprises 90% of the atomic ensemble containing 3100 atoms. Further technical improvement should allow the generation of more complex Schrödinger cat states, and of states the overcome the standard quantum limit.
Atom chips with free-standing two-dimensional electron gases: advantages and challenges

NASA Astrophysics Data System (ADS)

Sinuco-León, G. A.; Krüger, P.; Fromhold, T. M.

2018-03-01

In this work, we consider the advantages and challenges of using free-standing two-dimensional electron gases (2DEG) as active components in atom chips for manipulating ultracold ensembles of alkali atoms. We calculate trapping parameters achievable with typical high-mobility 2DEGs in an atom chip configuration and identify advantages of this system for trapping atoms at sub-micron distances from the atom chip. We show how the sensitivity of atomic gases to magnetic field inhomogeneity can be exploited for controlling the atoms with quantum electronic devices and, conversely, using the atoms to probe the structural and transport properties of semiconductor devices.
Master equation with quantized atomic motion including dipole-dipole interactions

NASA Astrophysics Data System (ADS)

Damanet, François; Braun, Daniel; Martin, John

2016-05-01

We derive a markovian master equation for the internal dynamics of an ensemble of two-level atoms including all effects related to the quantization of their motion. Our equation provides a unifying picture of the consequences of recoil and indistinguishability of atoms beyond the Lamb-Dicke regime on both their dissipative and conservative dynamics, and is relevant for experiments with ultracold trapped atoms. We give general expressions for the decay rates and the dipole-dipole shifts for any motional states, and we find analytical formulas for a number of relevant states (Gaussian states, Fock states and thermal states). In particular, we show that the dipole-dipole interactions and cooperative photon emission can be modulated through the external state of motion. The effects predicted should be experimentally observable with Rydberg atoms. FD would like to thank the F.R.S.-FNRS for financial support. FD is a FRIA Grant holder of the Fonds de la Recherche Scientifique-FNRS.
Entanglement with negative Wigner function of three thousand atoms heralded by one photon

NASA Astrophysics Data System (ADS)

McConnell, Robert; Zhang, Hao; Hu, Jiazhong; Ćuk, Senka; Vuletić, Vladan

2016-06-01

Quantum-mechanically correlated (entangled) states of many particles are of interest in quantum information, quantum computing and quantum metrology. Metrologically useful entangled states of large atomic ensembles have been experimentally realized [1, 2, 3, 4, 5, 6, 7, 8, 9, 10], but these states display Gaussian spin distribution functions with a non-negative Wigner function. Non-Gaussian entangled states have been produced in small ensembles of ions [11, 12], and very recently in large atomic ensembles [13, 14, 15]. Here, we generate entanglement in a large atomic ensemble via the interaction with a very weak laser pulse; remarkably, the detection of a single photon prepares several thousand atoms in an entangled state. We reconstruct a negative-valued Wigner function, an important hallmark of nonclassicality, and verify an entanglement depth (minimum number of mutually entangled atoms) of 2910 ± 190 out of 3100 atoms. Attaining such a negative Wigner function and the mutual entanglement of virtually all atoms is unprecedented for an ensemble containing more than a few particles. While the achieved purity of the state is slightly below the threshold for entanglement-induced metrological gain, further technical improvement should allow the generation of states that surpass this threshold, and of more complex Schrödinger cat states for quantum metrology and information processing.
Cavity electromagnetically induced transparency with Rydberg atoms

NASA Astrophysics Data System (ADS)

Bakar Ali, Abu; Ziauddin

2018-02-01

Cavity electromagnetically induced transparency (EIT) is revisited via the input probe field intensity. A strongly interacting Rydberg atomic medium ensemble is considered in a cavity, where atoms behave as superatoms (SAs) under the dipole blockade mechanism. Each atom in the strongly interacting Rydberg atomic medium (87 Rb) follows a three-level cascade atomic configuration. A strong control and weak probe field are employed in the cavity with the ensemble of Rydberg atoms. The features of the reflected and transmitted probe light are studied under the influence of the input probe field intensity. A transparency peak (cavity EIT) is revealed at a resonance condition for small values of input probe field intensity. The manipulation of the cavity EIT is reported by tuning the strength of the input probe field intensity. Further, the phase and group delay of the transmitted and reflected probe light are studied. It is found that group delay and phase in the reflected light are negative, while for the transmitted light they are positive. The magnitude control of group delay in the transmitted and reflected light is investigated via the input probe field intensity.
A density functional theory study on the acetylene cyclotrimerization on Pd-modified Au(111) surface

NASA Astrophysics Data System (ADS)

Ren, Bohua; Dong, Xiuqin; Yu, Yingzhe; Zhang, Minhua

2017-10-01

Calculations based on the first-principle density functional theory were carried out to study the possible acetylene cyclotrimerization reactions on Pd-Au(111) surface and to investigate the effect of Au atom alloying with Pd. The adsorption of C2H2, C4H4, C6H6 and the PDOS of 4d orbitals of surface Pd and Au atoms were studied. The comparison of d-band center of Pd and Au atom before and after C2H2 or C4H4 adsorption suggests that these molecules affect the activity of Pd-Au(111) surface to some degree due to the high binding energy of the adsorption. In our study, the second neighboring Pd ensembles on Pd-Au(111) surface can adsorb two acetylene molecules on parallel-bridge site of two Au atoms and one Pd atom, respectively. Csbnd C bonds are parallel to each other and two acetylenes are adsorbed face to face to produce four-membered ring C4H4 firstly. The geometric effect and electronic effect of Pd-Au(111) surface with the second neighboring Pd ensembles both help to reduce this activation barrier.
Size dependence of single-photon superradiance of cold and dilute atomic ensembles

NASA Astrophysics Data System (ADS)

Kuraptsev, A. S.; Sokolov, I. M.

2017-11-01

We report a theoretical investigation of angular distribution of a single-photon superradiance from cold and dilute atomic clouds. In the present work we focus our attention on the dependence of superradiance on the size and shape of the cloud. We analyze the dynamics of the afterglow of atomic ensemble excited by pulse radiation. Two theoretical approaches are used. The first is the quantum microscopic approach based on a coupled-dipole model. The second approach is random walk approximation. We show that the results obtained in both approaches coincide with a good accuracy for incoherent fluorescence excited by short resonant pulses. We also show that the superradiance decay rate changes with size differently for radiation emitted into different directions.
Correlation in photon pairs generated using four-wave mixing in a cold atomic ensemble

NASA Astrophysics Data System (ADS)

Ferdinand, Andrew Richard; Manjavacas, Alejandro; Becerra, Francisco Elohim

2017-04-01

Spontaneous four-wave mixing (FWM) in atomic ensembles can be used to generate narrowband entangled photon pairs at or near atomic resonances. While extensive research has been done to investigate the quantum correlations in the time and polarization of such photon pairs, the study and control of high dimensional quantum correlations contained in their spatial degrees of freedom has not been fully explored. In our work we experimentally investigate the generation of correlated light from FWM in a cold ensemble of cesium atoms as a function of the frequencies of the pump fields in the FWM process. In addition, we theoretically study the spatial correlations of the photon pairs generated in the FWM process, specifically the joint distribution of their orbital angular momentum (OAM). We investigate the width of the distribution of the OAM modes, known as the spiral bandwidth, and the purity of OAM correlations as a function of the properties of the pump fields, collected photons, and the atomic ensemble. These studies will guide experiments involving high dimensional entanglement of photons generated from this FWM process and OAM-based quantum communication with atomic ensembles. This work is supported by AFORS Grant FA9550-14-1-0300.
Coherence rephasing combined with spin-wave storage using chirped control pulses

NASA Astrophysics Data System (ADS)

Demeter, Gabor

2014-06-01

Photon-echo based optical quantum memory schemes often employ intermediate steps to transform optical coherences to spin coherences for longer storage times. We analyze a scheme that uses three identical chirped control pulses for coherence rephasing in an inhomogeneously broadened ensemble of three-level Λ systems. The pulses induce a cyclic permutation of the atomic populations in the adiabatic regime. Optical coherences created by a signal pulse are stored as spin coherences at an intermediate time interval, and are rephased for echo emission when the ensemble is returned to the initial state. Echo emission during a possible partial rephasing when the medium is inverted can be suppressed with an appropriate choice of control pulse wave vectors. We demonstrate that the scheme works in an optically dense ensemble, despite control pulse distortions during propagation. It integrates conveniently the spin-wave storage step into memory schemes based on a second rephasing of the atomic coherences.
Self-entanglement and the dissociation of homonuclear diatomic molecules

DOE PAGES

Gonis, A.; Zhang, X. -G.; Nicholson, D. M.; ...

2014-01-14

The concept of self-entanglement is introduced to describe a mixed state or ensemble density as a pure state in an augmented Hilbert space formed by the products of the individual states forming a mixed state (or ensemble). We use this representation of mixed states to show that upon dissociation a neutral homonuclear diatomic molecule will separate into two neutral atoms.
Encoding qubits into oscillators with atomic ensembles and squeezed light

NASA Astrophysics Data System (ADS)

Motes, Keith R.; Baragiola, Ben Q.; Gilchrist, Alexei; Menicucci, Nicolas C.

2017-05-01

The Gottesman-Kitaev-Preskill (GKP) encoding of a qubit within an oscillator provides a number of advantages when used in a fault-tolerant architecture for quantum computing, most notably that Gaussian operations suffice to implement all single- and two-qubit Clifford gates. The main drawback of the encoding is that the logical states themselves are challenging to produce. Here we present a method for generating optical GKP-encoded qubits by coupling an atomic ensemble to a squeezed state of light. Particular outcomes of a subsequent spin measurement of the ensemble herald successful generation of the resource state in the optical mode. We analyze the method in terms of the resources required (total spin and amount of squeezing) and the probability of success. We propose a physical implementation using a Faraday-based quantum nondemolition interaction.
Theory and modelling of light-matter interactions in photonic crystal cavity systems coupled to quantum dot ensembles

NASA Astrophysics Data System (ADS)

Cartar, William K.

Photonic crystal microcavity quantum dot lasers show promise as high quality-factor, low threshold lasers, that can be integrated on-chip, with tunable room temperature opera- tions. However, such semiconductor microcavity lasers are notoriously difficult to model in a self-consistent way and are primarily modelled by simplified rate equation approxima- tions, typically fit to experimental data, which limits investigations of their optimization and fundamental light-matter interaction processes. Moreover, simple cavity mode optical theory and rate equations have recently been shown to fail in explaining lasing threshold trends in triangular lattice photonic crystal cavities as a function of cavity size, and the potential impact of fabrication disorder is not well understood. In this thesis, we develop a simple but powerful numerical scheme for modelling the quantum dot active layer used for lasing in these photonic crystal cavity structures, as an ensemble of randomly posi- tioned artificial two-level atoms. Each two-level atom is defined by optical Bloch equations solved by a quantum master equation that includes phenomenological pure dephasing and an incoherent pump rate that effectively models a multi-level gain system. Light-matter in- teractions of both passive and lasing structures are analyzed using simulation defined tools and post-simulation Green function techniques. We implement an active layer ensemble of up to 24,000 statistically unique quantum dots in photonic crystal cavity simulations, using a self-consistent finite-difference time-domain method. This method has the distinct advantage of capturing effects such as dipole-dipole coupling and radiative decay, without the need for any phenomenological terms, since the time-domain solution self-consistently captures these effects. Our analysis demonstrates a powerful ability to connect with recent experimental trends, while remaining completely general in its set-up; for example, we do not invoke common approximations such as the rotating-wave or slowly-varying envelope approximations, and solve dynamics with zero a priori knowledge.
Single-photon-level quantum image memory based on cold atomic ensembles

PubMed Central

Ding, Dong-Sheng; Zhou, Zhi-Yuan; Shi, Bao-Sen; Guo, Guang-Can

2013-01-01

A quantum memory is a key component for quantum networks, which will enable the distribution of quantum information. Its successful development requires storage of single-photon light. Encoding photons with spatial shape through higher-dimensional states significantly increases their information-carrying capability and network capacity. However, constructing such quantum memories is challenging. Here we report the first experimental realization of a true single-photon-carrying orbital angular momentum stored via electromagnetically induced transparency in a cold atomic ensemble. Our experiments show that the non-classical pair correlation between trigger photon and retrieved photon is retained, and the spatial structure of input and retrieved photons exhibits strong similarity. More importantly, we demonstrate that single-photon coherence is preserved during storage. The ability to store spatial structure at the single-photon level opens the possibility for high-dimensional quantum memories. PMID:24084711
Integrated Optical Dipole Trap for Cold Neutral Atoms with an Optical Waveguide Coupler

NASA Astrophysics Data System (ADS)

Lee, J.; Park, D. H.; Mittal, S.; Meng, Y.; Dagenais, M.; Rolston, S. L.

2013-05-01

Using an optical waveguide, an integrated optical dipole trap uses two-color (red and blue-detuned) traveling evanescent wave fields for trapping cold neutral atoms. To achieve longitudinal confinement, we propose using an integrated optical waveguide coupler, which provides a potential gradient along the beam propagation direction sufficient to confine atoms. This integrated optical dipole trap can support an atomic ensemble with a large optical depth due to its small mode area. Its quasi-TE0 waveguide mode has an advantage over the HE11 mode of a nanofiber, with little inhomogeneous Zeeman broadening at the trapping region. The longitudinal confinement eliminates the need for a 1D optical lattice, reducing collisional blockaded atomic loading, potentially producing larger ensembles. The waveguide trap allows for scalability and integrability with nano-fabrication technology. We analyze the potential performance of such integrated atom traps and present current research progress towards a fiber-coupled silicon nitride optical waveguide integrable with atom chips. Work is supported by the ARO Atomtronics MURI. Work is supported by the ARO Atomtronics MURI.

Quantum Control of Open Systems and Dense Atomic Ensembles

NASA Astrophysics Data System (ADS)

DiLoreto, Christopher

Controlling the dynamics of open quantum systems; i.e. quantum systems that decohere because of interactions with the environment, is an active area of research with many applications in quantum optics and quantum computation. My thesis expands the scope of this inquiry by seeking to control open systems in proximity to an additional system. The latter could be a classical system such as metal nanoparticles, or a quantum system such as a cluster of similar atoms. By modelling the interactions between the systems, we are able to expand the accessible state space of the quantum system in question. For a single, three-level quantum system, I examine isolated systems that have only normal spontaneous emission. I then show that intensity-intensity correlation spectra, which depend directly on the density matrix of the system, can be used detect whether transitions share a common energy level. This detection is possible due to the presence of quantum interference effects between two transitions if they are connected. This effect allows one to asses energy level structure diagrams in complex atoms/molecules. By placing an open quantum system near a nanoparticle dimer, I show that the spontaneous emission rate of the system can be changed "on demand" by changing the polarization of an incident, driving field. In a three-level, Lambda system, this allows a qubit to both retain high qubit fidelity when it is operating, and to be rapidly initialized to a pure state once it is rendered unusable by decoherence. This type of behaviour is not possible in a single open quantum system; therefore adding a classical system nearby extends the overall control space of the quantum system. An open quantum system near identical neighbours in a dense ensemble is another example of how the accessible state space can be expanded. I show that a dense ensemble of atoms rapidly becomes disordered with states that are not directly excited by an incident field becoming significantly populated. This effect motivates the need for using multi-directional basis sets in theoretical analysis of dense quantum systems. My results demonstrate the shortcomings of short-pulse techniques used in many recent studies. Based on my numerical studies, I hypothesize that the dense ensemble can be modelled by an effective single quantum system that has a decoherence rate that changes over time. My effective single particle model provides a way in which computational time can be reduced, and also a model in which the underlying physical processes involved in the system's evolution are much easier to understand. I then use this model to provide an elegant theoretical explanation for an unusual experimental result called "transverse optical magnetism''. My effective single particle model's predictions match very well with experimental data.
A path integral approach to the full Dicke model with dipole-dipole interaction

NASA Astrophysics Data System (ADS)

Aparicio Alcalde, M.; Stephany, J.; Svaiter, N. F.

2011-12-01

We consider the full Dicke spin-boson model composed by a single bosonic mode and an ensemble of N identical two-level atoms with different couplings for the resonant and anti-resonant interaction terms, and incorporate a dipole-dipole interaction between the atoms. Assuming that the system is in thermal equilibrium with a reservoir at temperature β-1, we compute the free energy in the thermodynamic limit N → ∞ in the saddle-point approximation to the path integral and determine the critical temperature for the super-radiant phase transition. In the zero temperature limit, we recover the critical coupling of the quantum phase transition, presented in the literature.
Enhanced Spin Squeezing in Atomic Ensembles via Control of the Internal Spin States

NASA Astrophysics Data System (ADS)

Shojaee, Ezad; Norris, Leigh; Baragiola, Ben; Montano, Enrique; Hemmer, Daniel; Jessen, Poul; Deutsch, Ivan

2015-05-01

Abstract: We study the process by which the collective spin squeezing of an ensemble of Cesium atoms is enhanced by control of the internal spin state of the atoms. By increasing the initial atomic projection noise, one can enhance the Faraday interaction that entangles the atoms with a probe. The light acts as a quantum bus for creating atom-atom entanglement via measurement backaction. Further control can be used to transfer this entanglement to metrologically useful squeezing. We numerically simulate this protocol by a stochastic master equation, including QND measurement and optical pumping, which accounts for decoherence and transfer of coherences between magnetic sub-levels. We study the tradeoff between the enhanced entangling interaction and increased rates of decoherence for different initial state preparations. Under realistic conditions, we find that we can achieve squeezing with a ``CAT-State'' superpostion |F = 4, Mz = 4> + |F, Mz = -4> of ~ 9.9 dB and for the spin coherent state |F = 4, Mx = 4> of ~ 7.5 dB. The increased entanglement enabled by the CAT state preparation is partially, but not completely reduced by the increased fragility to decoherence. National Science Foundation.
Entanglement with negative Wigner function of almost 3,000 atoms heralded by one photon.

PubMed

McConnell, Robert; Zhang, Hao; Hu, Jiazhong; Ćuk, Senka; Vuletić, Vladan

2015-03-26

Quantum-mechanically correlated (entangled) states of many particles are of interest in quantum information, quantum computing and quantum metrology. Metrologically useful entangled states of large atomic ensembles have been experimentally realized, but these states display Gaussian spin distribution functions with a non-negative Wigner quasiprobability distribution function. Non-Gaussian entangled states have been produced in small ensembles of ions, and very recently in large atomic ensembles. Here we generate entanglement in a large atomic ensemble via an interaction with a very weak laser pulse; remarkably, the detection of a single photon prepares several thousand atoms in an entangled state. We reconstruct a negative-valued Wigner function--an important hallmark of non-classicality--and verify an entanglement depth (the minimum number of mutually entangled atoms) of 2,910 ± 190 out of 3,100 atoms. Attaining such a negative Wigner function and the mutual entanglement of virtually all atoms is unprecedented for an ensemble containing more than a few particles. Although the achieved purity of the state is slightly below the threshold for entanglement-induced metrological gain, further technical improvement should allow the generation of states that surpass this threshold, and of more complex Schrödinger cat states for quantum metrology and information processing. More generally, our results demonstrate the power of heralded methods for entanglement generation, and illustrate how the information contained in a single photon can drastically alter the quantum state of a large system.
Coherent Magnetic Response at Optical Frequencies Using Atomic Transitions

NASA Astrophysics Data System (ADS)

Brewer, Nicholas R.; Buckholtz, Zachary N.; Simmons, Zachary J.; Mueller, Eli A.; Yavuz, Deniz D.

2017-01-01

In optics, the interaction of atoms with the magnetic field of light is almost always ignored since its strength is many orders of magnitude weaker compared to the interaction with the electric field. In this article, by using a magnetic-dipole transition within the 4 f shell of europium ions, we show a strong interaction between a green laser and an ensemble of atomic ions. The electrons move coherently between the ground and excited ionic levels (Rabi flopping) by interacting with the magnetic field of the laser. By measuring the Rabi flopping frequency as the laser intensity is varied, we report the first direct measurement of a magnetic-dipole matrix element in the optical region of the spectrum. Using density-matrix simulations of the ensemble, we infer the generation of coherent magnetization with magnitude 5.5 ×10-3 A /m , which is capable of generating left-handed electromagnetic waves of intensity 1 nW /cm2 . These results open up the prospect of constructing left-handed materials using sharp transitions of atoms.
Interferometry with non-classical motional states of a Bose-Einstein condensate.

PubMed

van Frank, S; Negretti, A; Berrada, T; Bücker, R; Montangero, S; Schaff, J-F; Schumm, T; Calarco, T; Schmiedmayer, J

2014-05-30

The Ramsey interferometer is a prime example of precise control at the quantum level. It is usually implemented using internal states of atoms, molecules or ions, for which powerful manipulation procedures are now available. Whether it is possible to control external degrees of freedom of more complex, interacting many-body systems at this level remained an open question. Here we demonstrate a two-pulse Ramsey-type interferometer for non-classical motional states of a Bose-Einstein condensate in an anharmonic trap. The control sequences used to manipulate the condensate wavefunction are obtained from optimal control theory and are directly optimized to maximize the interferometric contrast. They permit a fast manipulation of the atomic ensemble compared to the intrinsic decay processes and many-body dephasing effects. This allows us to reach an interferometric contrast of 92% in the experimental implementation.
Controlling the delocalization-localization transition of light via electromagnetically induced transparency

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

Cheng Jing; Huang Guoxiang; State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062

2011-05-15

We propose a scheme to realize a transition from delocalization to localization of light waves via electromagnetically induced transparency. The system we suggested is a resonant cold atomic ensemble having N configuration, with a control field consisting of two pairs of laser beams with different cross angles, which produce an electromagnetically induced quasiperiodic waveguide (EIQPW) for the propagation of a signal field. By appropriately tuning the incommensurate rate or relative modulation strength between the two pairs of control-field components, the signal field can exhibit the delocalization-localization transition as it transports inside the atomic ensemble. The delocalization-localization transition point is determinedmore » and the propagation property of the signal field is studied in detail. Our work provides a way of realizing wave localization via atomic coherence, which is quite different from the conventional, off-resonant mechanism-based Aubry-Andre model, and the great controllability of the EIQPW also allows an easy manipulation of the delocalization-localization transition.« less
Photonic quantum state transfer between a cold atomic gas and a crystal.

PubMed

Maring, Nicolas; Farrera, Pau; Kutluer, Kutlu; Mazzera, Margherita; Heinze, Georg; de Riedmatten, Hugues

2017-11-22

Interfacing fundamentally different quantum systems is key to building future hybrid quantum networks. Such heterogeneous networks offer capabilities superior to those of their homogeneous counterparts, as they merge the individual advantages of disparate quantum nodes in a single network architecture. However, few investigations of optical hybrid interconnections have been carried out, owing to fundamental and technological challenges such as wavelength and bandwidth matching of the interfacing photons. Here we report optical quantum interconnection of two disparate matter quantum systems with photon storage capabilities. We show that a quantum state can be transferred faithfully between a cold atomic ensemble and a rare-earth-doped crystal by means of a single photon at 1,552 nanometre telecommunication wavelength, using cascaded quantum frequency conversion. We demonstrate that quantum correlations between a photon and a single collective spin excitation in the cold atomic ensemble can be transferred to the solid-state system. We also show that single-photon time-bin qubits generated in the cold atomic ensemble can be converted, stored and retrieved from the crystal with a conditional qubit fidelity of more than 85 per cent. Our results open up the prospect of optically connecting quantum nodes with different capabilities and represent an important step towards the realization of large-scale hybrid quantum networks.
Ensemble Pulsar Time Scale

NASA Astrophysics Data System (ADS)

Yin, Dong-shan; Gao, Yu-ping; Zhao, Shu-hong

2017-07-01

Millisecond pulsars can generate another type of time scale that is totally independent of the atomic time scale, because the physical mechanisms of the pulsar time scale and the atomic time scale are quite different from each other. Usually the pulsar timing observations are not evenly sampled, and the internals between two data points range from several hours to more than half a month. Further more, these data sets are sparse. All this makes it difficult to generate an ensemble pulsar time scale. Hence, a new algorithm to calculate the ensemble pulsar time scale is proposed. Firstly, a cubic spline interpolation is used to densify the data set, and make the intervals between data points uniform. Then, the Vondrak filter is employed to smooth the data set, and get rid of the high-frequency noises, and finally the weighted average method is adopted to generate the ensemble pulsar time scale. The newly released NANOGRAV (North American Nanohertz Observatory for Gravitational Waves) 9-year data set is used to generate the ensemble pulsar time scale. This data set includes the 9-year observational data of 37 millisecond pulsars observed by the 100-meter Green Bank telescope and the 305-meter Arecibo telescope. It is found that the algorithm used in this paper can reduce effectively the influence caused by the noises in pulsar timing residuals, and improve the long-term stability of the ensemble pulsar time scale. Results indicate that the long-term (> 1 yr) stability of the ensemble pulsar time scale is better than 3.4 × 10-15.
The Road to DLCZ Protocol in Rubidium Ensemble

NASA Astrophysics Data System (ADS)

Li, Chang; Pu, Yunfei; Jiang, Nan; Chang, Wei; Zhang, Sheng; CenterQuantum Information, InstituteInterdisciplinary Information Sciences, Tsinghua Univ Team

2017-04-01

Quantum communication is the powerful approach achieving a fully secure information transferal. The DLCZ protocol ensures that photon linearly decays with transferring distance increasing, which improves the success potential and shortens the time to build up an entangled channel. Apart from that, it provides an advanced idea that building up a quantum internet based on different nodes connected to different sites and themselves. In our laboratory, three sets of laser-cooled Rubidium 87 ensemble have been built. Two of them serve as the single photon emitter, which generate the entanglement between ensemble and photon. What's more, crossed AODs are equipped to multiplex and demultiplex optical circuit so that ensemble is divided into 2 hundred of 2D sub-memory cells. And the third ensemble is used as quantum telecommunication, which converts 780nm photon into telecom-wavelength one. And we have been building double-MOT system, which provides more atoms in ensemble and larger optical density.
Two-Dimensional Arrays of Neutral Atom Quantum Gates

DTIC Science & Technology

2012-10-20

Box 12211 Research Triangle Park, NC 27709-2211 15. SUBJECT TERMS quantum computing , Rydberg atoms, entanglement Mark Saffman University of...Nature Physics, (01 2009): 0. doi: 10.1038/nphys1178 10/19/2012 9.00 K. Mølmer, M. Saffman. Scaling the neutral-atom Rydberg gate quantum computer by...Saffman, E. Brion, K. Mølmer. Error Correction in Ensemble Registers for Quantum Repeaters and Quantum Computers , Physical Review Letters, (3 2008): 0
Atomic vapor quantum memory for a photonic polarization qubit.

PubMed

Cho, Young-Wook; Kim, Yoon-Ho

2010-12-06

We report an experimental realization of an atomic vapor quantum memory for the photonic polarization qubit. The performance of the quantum memory for the polarization qubit, realized with electromagnetically-induced transparency in two spatially separated ensembles of warm Rubidium atoms in a single vapor cell, has been characterized with quantum process tomography. The process fidelity better than 0.91 for up to 16 μs of storage time has been achieved.
Multiscale Macromolecular Simulation: Role of Evolving Ensembles

PubMed Central

Singharoy, A.; Joshi, H.; Ortoleva, P.J.

2013-01-01

Multiscale analysis provides an algorithm for the efficient simulation of macromolecular assemblies. This algorithm involves the coevolution of a quasiequilibrium probability density of atomic configurations and the Langevin dynamics of spatial coarse-grained variables denoted order parameters (OPs) characterizing nanoscale system features. In practice, implementation of the probability density involves the generation of constant OP ensembles of atomic configurations. Such ensembles are used to construct thermal forces and diffusion factors that mediate the stochastic OP dynamics. Generation of all-atom ensembles at every Langevin timestep is computationally expensive. Here, multiscale computation for macromolecular systems is made more efficient by a method that self-consistently folds in ensembles of all-atom configurations constructed in an earlier step, history, of the Langevin evolution. This procedure accounts for the temporal evolution of these ensembles, accurately providing thermal forces and diffusions. It is shown that efficiency and accuracy of the OP-based simulations is increased via the integration of this historical information. Accuracy improves with the square root of the number of historical timesteps included in the calculation. As a result, CPU usage can be decreased by a factor of 3-8 without loss of accuracy. The algorithm is implemented into our existing force-field based multiscale simulation platform and demonstrated via the structural dynamics of viral capsomers. PMID:22978601
Coherent Spin Control at the Quantum Level in an Ensemble-Based Optical Memory.

PubMed

Jobez, Pierre; Laplane, Cyril; Timoney, Nuala; Gisin, Nicolas; Ferrier, Alban; Goldner, Philippe; Afzelius, Mikael

2015-06-12

Long-lived quantum memories are essential components of a long-standing goal of remote distribution of entanglement in quantum networks. These can be realized by storing the quantum states of light as single-spin excitations in atomic ensembles. However, spin states are often subjected to different dephasing processes that limit the storage time, which in principle could be overcome using spin-echo techniques. Theoretical studies suggest this to be challenging due to unavoidable spontaneous emission noise in ensemble-based quantum memories. Here, we demonstrate spin-echo manipulation of a mean spin excitation of 1 in a large solid-state ensemble, generated through storage of a weak optical pulse. After a storage time of about 1 ms we optically read-out the spin excitation with a high signal-to-noise ratio. Our results pave the way for long-duration optical quantum storage using spin-echo techniques for any ensemble-based memory.
Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.

PubMed

Salmon, Loïc; Giambaşu, George M; Nikolova, Evgenia N; Petzold, Katja; Bhattacharya, Akash; Case, David A; Al-Hashimi, Hashim M

2015-10-14

Approaches that combine experimental data and computational molecular dynamics (MD) to determine atomic resolution ensembles of biomolecules require the measurement of abundant experimental data. NMR residual dipolar couplings (RDCs) carry rich dynamics information, however, difficulties in modulating overall alignment of nucleic acids have limited the ability to fully extract this information. We present a strategy for modulating RNA alignment that is based on introducing variable dynamic kinks in terminal helices. With this strategy, we measured seven sets of RDCs in a cUUCGg apical loop and used this rich data set to test the accuracy of an 0.8 μs MD simulation computed using the Amber ff10 force field as well as to determine an atomic resolution ensemble. The MD-generated ensemble quantitatively reproduces the measured RDCs, but selection of a sub-ensemble was required to satisfy the RDCs within error. The largest discrepancies between the RDC-selected and MD-generated ensembles are observed for the most flexible loop residues and backbone angles connecting the loop to the helix, with the RDC-selected ensemble resulting in more uniform dynamics. Comparison of the RDC-selected ensemble with NMR spin relaxation data suggests that the dynamics occurs on the ps-ns time scales as verified by measurements of R(1ρ) relaxation-dispersion data. The RDC-satisfying ensemble samples many conformations adopted by the hairpin in crystal structures indicating that intrinsic plasticity may play important roles in conformational adaptation. The approach presented here can be applied to test nucleic acid force fields and to characterize dynamics in diverse RNA motifs at atomic resolution.
Counterfactual Rydberg gate for photons

NASA Astrophysics Data System (ADS)

Garcia-Escartin, Juan Carlos; Chamorro-Posada, Pedro

2012-03-01

Quantum computation with photons requires efficient two-photon gates. We put forward a two-photon entangling gate which uses an intermediate atomic system. The system includes a single Rydberg atom which can switch on and off photon absorption in an ensemble using the dipole blockade. The gate is based in a counterfactual protocol. The mere possibility of an absorption that can only occur with a vanishing probability steers the photons to the desired final state.
Adiabatic passage in photon-echo quantum memories

NASA Astrophysics Data System (ADS)

Demeter, Gabor

2013-11-01

Photon-echo-based quantum memories use inhomogeneously broadened, optically thick ensembles of absorbers to store a weak optical signal and employ various protocols to rephase the atomic coherences for information retrieval. We study the application of two consecutive, frequency-chirped control pulses for coherence rephasing in an ensemble with a “natural” inhomogeneous broadening. Although propagation effects distort the two control pulses differently, chirped pulses that drive adiabatic passage can rephase atomic coherences in an optically thick storage medium. Combined with spatial phase-mismatching techniques to prevent primary echo emission, coherences can be rephased around the ground state to achieve secondary echo emission with close to unit efficiency. Potential advantages over similar schemes working with π pulses include greater potential signal fidelity, reduced noise due to spontaneous emission, and better capability for the storage of multiple memory channels.
Atom-chip based quantum gravimetry for the precise determination of absolute local gravity

NASA Astrophysics Data System (ADS)

Abend, S.

2015-12-01

We present a novel technique for the precise measurement of absolute local gravity based on cold atom interferometry. Atom interferometry utilizes the interference of matter waves interrogated by laser light to read out inertial forces. Today's generation of these devices typically operate with test mass samples, that consists of ensembles of laser cooled atoms. Their performance is limited by the velocity spread and finite-size of the test masses that impose systematic uncertainties at the level of a few μGal. Rather than laser cooled atoms we employ quantum degenerate ensembles, so called Bose-Einstein condensates, as ultra-sensitive probes for gravity. These sources offer unique properties in temperature as well as in ensemble size that will allow to overcome the current limitations with the next generation of sensors. Furthermore, atom-chip technologies offer the possibility to generate Bose-Einstein condensates in a fast and reliable way. We show a lab-based prototype that uses the atom-chip itself to retro-reflect the interrogation laser and thus serving as inertial reference inside the vacuum. With this setup it is possible to demonstrate all necessary steps to measure gravity, including the preparation of the source, spanning an interferometer as well as the detection of the output signal, within an area of 1 cm3 right below the atom-chip and to analyze relevant systematic effects. In the framework of the center of excellence geoQ a next generation device is under construction at the Institut für Quantenoptik, that will allow for in-field measurements. This device will feature a state-of-the-art atom-chip source with a high-flux of ultra-cold atoms at a repetition rate of 1-2 Hz. In cooperation with the Müller group at the Institut für Erdmessung the sensor will be characterized in the laboratory first, to be ultimately employed in campaigns to measure the Fennoscandian uplift at the level of 1 μGal. The presented work is part of the center of excellence geoQ (SFB 1128), funded by the Deutsche Forschungsgemeinschaft (DFG). This work is supported by the German Space Agency (DLR) with funds provided by the Federal Ministry for Economic Affairs and Energy (BMWi) due to an enactment of the German Bundestag under grant numbers DLR 50 1131-1137 (QUANTUS-III).
A molecular mechanism of chaperone-client recognition

PubMed Central

He, Lichun; Sharpe, Timothy; Mazur, Adam; Hiller, Sebastian

2016-01-01

Molecular chaperones are essential in aiding client proteins to fold into their native structure and in maintaining cellular protein homeostasis. However, mechanistic aspects of chaperone function are still not well understood at the atomic level. We use nuclear magnetic resonance spectroscopy to elucidate the mechanism underlying client recognition by the adenosine triphosphate-independent chaperone Spy at the atomic level and derive a structural model for the chaperone-client complex. Spy interacts with its partially folded client Im7 by selective recognition of flexible, locally frustrated regions in a dynamic fashion. The interaction with Spy destabilizes a partially folded client but spatially compacts an unfolded client conformational ensemble. By increasing client backbone dynamics, the chaperone facilitates the search for the native structure. A comparison of the interaction of Im7 with two other chaperones suggests that the underlying principle of recognizing frustrated segments is of a fundamental nature. PMID:28138538
Robust Deterministic Controlled Phase-Flip Gate and Controlled-Not Gate Based on Atomic Ensembles Embedded in Double-Sided Optical Cavities

NASA Astrophysics Data System (ADS)

Liu, A.-Peng; Cheng, Liu-Yong; Guo, Qi; Zhang, Shou

2018-02-01

We first propose a scheme for controlled phase-flip gate between a flying photon qubit and the collective spin wave (magnon) of an atomic ensemble assisted by double-sided cavity quantum systems. Then we propose a deterministic controlled-not gate on magnon qubits with parity-check building blocks. Both the gates can be accomplished with 100% success probability in principle. Atomic ensemble is employed so that light-matter coupling is remarkably improved by collective enhancement. We assess the performance of the gates and the results show that they can be faithfully constituted with current experimental techniques.

Atomic clock ensemble in space (ACES) data analysis

NASA Astrophysics Data System (ADS)

Meynadier, F.; Delva, P.; le Poncin-Lafitte, C.; Guerlin, C.; Wolf, P.

2018-02-01

The Atomic Clocks Ensemble in Space (ACES/PHARAO mission, ESA & CNES) will be installed on board the International Space Station (ISS) next year. A crucial part of this experiment is its two-way microwave link (MWL), which will compare the timescale generated on board with those provided by several ground stations disseminated on the Earth. A dedicated data analysis center is being implemented at SYRTE—Observatoire de Paris, where our team currently develops theoretical modelling, numerical simulations and the data analysis software itself. In this paper, we present some key aspects of the MWL measurement method and the associated algorithms for simulations and data analysis. We show the results of tests using simulated data with fully realistic effects such as fundamental measurement noise, Doppler, atmospheric delays, or cycle ambiguities. We demonstrate satisfactory performance of the software with respect to the specifications of the ACES mission. The main scientific product of our analysis is the clock desynchronisation between ground and space clocks, i.e. the difference of proper times between the space clocks and ground clocks at participating institutes. While in flight, this measurement will allow for tests of general relativity and Lorentz invariance at unprecedented levels, e.g. measurement of the gravitational redshift at the 3×10-6 level. As a specific example, we use real ISS orbit data with estimated errors at the 10 m level to study the effect of such errors on the clock desynchronisation obtained from MWL data. We demonstrate that the resulting effects are totally negligible.
A report on the gravitational redshift test for non-metric theories of gravitation

NASA Technical Reports Server (NTRS)

1980-01-01

The frequencies of two atomic hydrogen masers and of three superconducting cavity stabilized oscillators were compared as the ensemble of oscillators was moved in the Sun's gravitational field by the rotation and orbital motion of the Earth. Metric gravitation theories predict that the gravitational redshifts of the two types of oscillators are identical, and that there should be no relative frequency shift between the oscillators; nonmetric theories, in contrast, predict a frequency shift between masers and SCSOs that is proportional to the change in solar gravitational potential experienced by the oscillators. The results are consistent with metric theories of gravitation at a level of 2%.
ACES microwave link requirements.

PubMed

Uhrich, P M; Guillernot, P; Aubry, P; Gonzalez, F; Salomon, C

2000-01-01

Atomic Clock Ensemble in Space (ACES) is a project of the European Space Agency on-board the future International Space Station (ISS). The payload consists mainly of two atomic frequency standards, one space hydrogen maser (SHM) prepared by the Observatoire de Neuchatel (Switzerland), and one cold atom caesium clock called PHARAO prepared by the CNES (France), with the participation of the BNM-LPTF, the ENS-LKB, and the CNRS-LHA. Because of the anticipated performances of these clocks on-board the ISS, the requirements of the links between the payload and the clocks on the Earth are at the limits of the known potential of the optical or microwave techniques. The microwave link (MWL) requirements are described in this paper. Taking into account the characteristics of the ISS orbit, and fixing an arbitrary limit to the additional noise brought to the clock readings by the MWL, the computation of the required stability leads to two kinds of requirements: the first one at the subpicosecond level over each single continuous pass of the ISS above any Earth station, and the second one at the level of one part in 10(16) and below over a one day or more averaging period. Moreover, the ISS orbit parameters should lead to a knowledge of the ACES clock position at the m level, and of the ACES clock speed at the mm/s level.
Few-Photon Nonlinearity with an Atomic Ensemble in an Optical Cavity

NASA Astrophysics Data System (ADS)

Tanji, Haruka

2011-12-01

This thesis investigates the effect of the cavity vacuum field on the dispersive properties of an atomic ensemble in a strongly coupled high-finesse cavity. In particular, we demonstrate vacuum-induced transparency (VIT). The light absorption by the ensemble is suppressed by up to 40% in the presence of a cavity vacuum field. The sharp transparency peak is accompanied by the reduction in the group velocity of a light pulse, measured to be as low as 1800 m/s. This observation is a large step towards the realization of photon number-state filters, recently proposed by Nikoghosyan et al. Furthermore, we demonstrate few-photon optical nonlinearity, where the transparency is increased from 40% to 80% with ˜12 photons in the cavity mode. The result may be viewed as all-optical switching, where the transmission of photons in one mode may be controlled by 12 photons in another. These studies point to the possibility of nonlinear interaction between photons in different free-space modes, a scheme that circumvents cavity-coupling losses that plague cavity-based quantum information processing. Potential applications include advanced quantum devices such as photonic quantum gates, photon-number resolving detectors, and single-photon transistors. In the efforts leading up to these results, we investigate the collective enhancement of atomic coupling to a single mode of a low-finesse cavity. With the strong collective coupling, we obtain exquisite control of quantum states in the atom-photon coupled system. In this system, we demonstrate a heralded single-photon source with 84% conditional efficiency, a quantum bus for deterministic entanglement of two remote ensembles, and heralded polarization-state quantum memory with fidelity above 90%.
Optical Precursor with Four-Wave Mixing and Storage Based on a Cold-Atom Ensemble

NASA Astrophysics Data System (ADS)

Ding, Dong-Sheng; Jiang, Yun Kun; Zhang, Wei; Zhou, Zhi-Yuan; Shi, Bao-Sen; Guo, Guang-Can

2015-03-01

We observed optical precursors in four-wave mixing based on a cold-atom gas. Optical precursors appear at the edges of pulses of the generated optical field, and propagate through the atomic medium without absorption. Theoretical analysis suggests that these precursors correspond to high-frequency components of the signal pulse, which means the atoms cannot respond quickly to rapid changes in the electromagnetic field. In contrast, the low-frequency signal components are absorbed by the atoms during transmission. We also showed experimentally that the backward precursor can be stored using a Raman transition of the atomic ensemble and retrieved later.
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.
Interfacing broadband photonic qubits to on-chip cavity-protected rare-earth ensembles

NASA Astrophysics Data System (ADS)

Zhong, Tian; Kindem, Jonathan M.; Rochman, Jake; Faraon, Andrei

2017-01-01

Ensembles of solid-state optical emitters enable broadband quantum storage and transduction of photonic qubits, with applications in high-rate quantum networks for secure communications and interconnecting future quantum computers. To transfer quantum states using ensembles, rephasing techniques are used to mitigate fast decoherence resulting from inhomogeneous broadening, but these techniques generally limit the bandwidth, efficiency and active times of the quantum interface. Here, we use a dense ensemble of neodymium rare-earth ions strongly coupled to a nanophotonic resonator to demonstrate a significant cavity protection effect at the single-photon level--a technique to suppress ensemble decoherence due to inhomogeneous broadening. The protected Rabi oscillations between the cavity field and the atomic super-radiant state enable ultra-fast transfer of photonic frequency qubits to the ions (~50 GHz bandwidth) followed by retrieval with 98.7% fidelity. With the prospect of coupling to other long-lived rare-earth spin states, this technique opens the possibilities for broadband, always-ready quantum memories and fast optical-to-microwave transducers.
Tunable ion-photon entanglement in an optical cavity.

PubMed

Stute, A; Casabone, B; Schindler, P; Monz, T; Schmidt, P O; Brandstätter, B; Northup, T E; Blatt, R

2012-05-23

Proposed quantum networks require both a quantum interface between light and matter and the coherent control of quantum states. A quantum interface can be realized by entangling the state of a single photon with the state of an atomic or solid-state quantum memory, as demonstrated in recent experiments with trapped ions, neutral atoms, atomic ensembles and nitrogen-vacancy spins. The entangling interaction couples an initial quantum memory state to two possible light-matter states, and the atomic level structure of the memory determines the available coupling paths. In previous work, the transition parameters of these paths determined the phase and amplitude of the final entangled state, unless the memory was initially prepared in a superposition state (a step that requires coherent control). Here we report fully tunable entanglement between a single (40)Ca(+) ion and the polarization state of a single photon within an optical resonator. Our method, based on a bichromatic, cavity-mediated Raman transition, allows us to select two coupling paths and adjust their relative phase and amplitude. The cavity setting enables intrinsically deterministic, high-fidelity generation of any two-qubit entangled state. This approach is applicable to a broad range of candidate systems and thus is a promising method for distributing information within quantum networks.
An ensemble pulsar time

NASA Technical Reports Server (NTRS)

Petit, Gerard; Thomas, Claudine; Tavella, Patrizia

1993-01-01

Millisecond pulsars are galactic objects that exhibit a very stable spinning period. Several tens of these celestial clocks have now been discovered, which opens the possibility that an average time scale may be deduced through a long-term stability algorithm. Such an ensemble average makes it possible to reduce the level of the instabilities originating from the pulsars or from other sources of noise, which are unknown but independent. The basis for such an algorithm is presented and applied to real pulsar data. It is shown that pulsar time could shortly become more stable than the present atomic time, for averaging times of a few years. Pulsar time can also be used as a flywheel to maintain the accuracy of atomic time in case of temporary failure of the primary standards, or to transfer the improved accuracy of future standards back to the present.
Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles.

PubMed

Snyder, David A; Montelione, Gaetano T

2005-06-01

An important open question in the field of NMR-based biomolecular structure determination is how best to characterize the precision of the resulting ensemble of structures. Typically, the RMSD, as minimized in superimposing the ensemble of structures, is the preferred measure of precision. However, the presence of poorly determined atomic coordinates and multiple "RMSD-stable domains"--locally well-defined regions that are not aligned in global superimpositions--complicate RMSD calculations. In this paper, we present a method, based on a novel, structurally defined order parameter, for identifying a set of core atoms to use in determining superimpositions for RMSD calculations. In addition we present a method for deciding whether to partition that core atom set into "RMSD-stable domains" and, if so, how to determine partitioning of the core atom set. We demonstrate our algorithm and its application in calculating statistically sound RMSD values by applying it to a set of NMR-derived structural ensembles, superimposing each RMSD-stable domain (or the entire core atom set, where appropriate) found in each protein structure under consideration. A parameter calculated by our algorithm using a novel, kurtosis-based criterion, the epsilon-value, is a measure of precision of the superimposition that complements the RMSD. In addition, we compare our algorithm with previously described algorithms for determining core atom sets. The methods presented in this paper for biomolecular structure superimposition are quite general, and have application in many areas of structural bioinformatics and structural biology.
Quantum teleportation of four-dimensional qudits

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

Al-Amri, M.; Max-Planck-Institut fuer Kernphysik, Saupfercheckweg 1, D-69117 Heidelberg; Evers, Joerg

2010-08-15

A protocol for the teleportation of arbitrary quantum states of four-dimensional qudits is presented. The qudit to be teleported is encoded in the combined state of two ensembles of atoms placed in a cavity at the sender's side. The receiver uses a similar setup, with his atoms prepared in a particular initial state. The teleportation protocol then consists of adiabatic mapping of the ensemble states onto photonic degrees of freedom, which are then directed onto a specific beam splitter and detection setup. For part of the measurement outcome, the qudit state is fully transferred to the receiver. Other detection eventsmore » lead to partial teleportation or failed teleportation attempts. The interpretation of the different detection outcomes and possible ways of improving the full teleportation probability are discussed.« less
Error assessment in molecular dynamics trajectories using computed NMR chemical shifts.

PubMed

Koes, David R; Vries, John K

2017-01-01

Accurate chemical shifts for the atoms in molecular mechanics (MD) trajectories can be obtained from quantum mechanical (QM) calculations that depend solely on the coordinates of the atoms in the localized regions surrounding atoms of interest. If these coordinates are correct and the sample size is adequate, the ensemble average of these chemical shifts should be equal to the chemical shifts obtained from NMR spectroscopy. If this is not the case, the coordinates must be incorrect. We have utilized this fact to quantify the errors associated with the backbone atoms in MD simulations of proteins. A library of regional conformers containing 169,499 members was constructed from 6 model proteins. The chemical shifts associated with the backbone atoms in each of these conformers was obtained from QM calculations using density functional theory at the B3LYP level with a 6-311+G(2d,p) basis set. Chemical shifts were assigned to each backbone atom in each MD simulation frame using a template matching approach. The ensemble average of these chemical shifts was compared to chemical shifts from NMR spectroscopy. A large systematic error was identified that affected the 1 H atoms of the peptide bonds involved in hydrogen bonding with water molecules or peptide backbone atoms. This error was highly sensitive to changes in electrostatic parameters. Smaller errors affecting the 13 C a and 15 N atoms were also detected. We believe these errors could be useful as metrics for comparing the force-fields and parameter sets used in MD simulation because they are directly tied to errors in atomic coordinates.
Optical beams with embedded vortices: building blocks for atom optics and quantum information

NASA Astrophysics Data System (ADS)

Chattrapiban, N.; Arakelyan, I.; Mitra, S.; Hill, W. T., III

2006-05-01

Laser beams with embedded vortices, Bessel or Laguerre-Gaussian modes, provide a unique opportunity for creating elements for atom optics, entangling photons and, potentially, mediating novel quantum interconnects between photons and matter. High-order Bessel modes, for example, contain intensity voids and propagate nearly diffraction-free for tens of meters. These vortices can be exploited to produce dark channels oriented longitudinally (hollow beams) or transversely to the laser propagation direction. Such channels are ideal for generating networks or circuits to guide and manipulate cold neutral atoms, an essential requirement for realizing future applications associated with atom interferometry, atom lithography and even some neutral atom-based quantum computing architectures. Recently, we divided a thermal cloud of neutral atoms moving within a blue-detuned beam into two clouds with two different momenta by crossing two hollow beams. In this presentation, we will describe these results and discuss the prospects for extending the process to coherent ensembles of matter.
From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum

DOE PAGES

Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.; ...

2016-08-31

Researcher feedback has indicated that in Urzhumtsevet al.[(2015)Acta Cryst.D71, 1668–1683] clarification of key parts of the algorithm for interpretation of TLS matrices in terms of elemental atomic motions and corresponding ensembles of atomic models is required. Also, it has been brought to the attention of the authors that the incorrect PDB code was reported for one of test models. Lastly, these issues are addressed in this article.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Y.; Sun, C.P.

We study the propagation of a probe light in an ensemble of {lambda}-type atoms, utilizing the dynamic symmetry as recently discovered when the atoms are coupled to a classical control field and a quantum probe field [Sun et al., Phys. Rev. Lett. 91, 147903 (2003)]. Under two-photon resonance, we calculate the group velocity of the probe light with collective atomic excitations. Our result gives the dependence of the group velocity on the common one-photon detuning, and can be compared with the recent experiment of E. E. Mikhailov, Y. V. Rostovtsev, and G. R. Welch, e-print quant-ph/0309173.
Heralded high-efficiency quantum repeater with atomic ensembles assisted by faithful single-photon transmission

NASA Astrophysics Data System (ADS)

Li, Tao; Deng, Fu-Guo

2015-10-01

Quantum repeater is one of the important building blocks for long distance quantum communication network. The previous quantum repeaters based on atomic ensembles and linear optical elements can only be performed with a maximal success probability of 1/2 during the entanglement creation and entanglement swapping procedures. Meanwhile, the polarization noise during the entanglement distribution process is harmful to the entangled channel created. Here we introduce a general interface between a polarized photon and an atomic ensemble trapped in a single-sided optical cavity, and with which we propose a high-efficiency quantum repeater protocol in which the robust entanglement distribution is accomplished by the stable spatial-temporal entanglement and it can in principle create the deterministic entanglement between neighboring atomic ensembles in a heralded way as a result of cavity quantum electrodynamics. Meanwhile, the simplified parity-check gate makes the entanglement swapping be completed with unity efficiency, other than 1/2 with linear optics. We detail the performance of our protocol with current experimental parameters and show its robustness to the imperfections, i.e., detuning and coupling variation, involved in the reflection process. These good features make it a useful building block in long distance quantum communication.
Heralded high-efficiency quantum repeater with atomic ensembles assisted by faithful single-photon transmission.

PubMed

Li, Tao; Deng, Fu-Guo

2015-10-27

Quantum repeater is one of the important building blocks for long distance quantum communication network. The previous quantum repeaters based on atomic ensembles and linear optical elements can only be performed with a maximal success probability of 1/2 during the entanglement creation and entanglement swapping procedures. Meanwhile, the polarization noise during the entanglement distribution process is harmful to the entangled channel created. Here we introduce a general interface between a polarized photon and an atomic ensemble trapped in a single-sided optical cavity, and with which we propose a high-efficiency quantum repeater protocol in which the robust entanglement distribution is accomplished by the stable spatial-temporal entanglement and it can in principle create the deterministic entanglement between neighboring atomic ensembles in a heralded way as a result of cavity quantum electrodynamics. Meanwhile, the simplified parity-check gate makes the entanglement swapping be completed with unity efficiency, other than 1/2 with linear optics. We detail the performance of our protocol with current experimental parameters and show its robustness to the imperfections, i.e., detuning and coupling variation, involved in the reflection process. These good features make it a useful building block in long distance quantum communication.
Heralded high-efficiency quantum repeater with atomic ensembles assisted by faithful single-photon transmission

PubMed Central

Li, Tao; Deng, Fu-Guo

2015-01-01

Quantum repeater is one of the important building blocks for long distance quantum communication network. The previous quantum repeaters based on atomic ensembles and linear optical elements can only be performed with a maximal success probability of 1/2 during the entanglement creation and entanglement swapping procedures. Meanwhile, the polarization noise during the entanglement distribution process is harmful to the entangled channel created. Here we introduce a general interface between a polarized photon and an atomic ensemble trapped in a single-sided optical cavity, and with which we propose a high-efficiency quantum repeater protocol in which the robust entanglement distribution is accomplished by the stable spatial-temporal entanglement and it can in principle create the deterministic entanglement between neighboring atomic ensembles in a heralded way as a result of cavity quantum electrodynamics. Meanwhile, the simplified parity-check gate makes the entanglement swapping be completed with unity efficiency, other than 1/2 with linear optics. We detail the performance of our protocol with current experimental parameters and show its robustness to the imperfections, i.e., detuning and coupling variation, involved in the reflection process. These good features make it a useful building block in long distance quantum communication. PMID:26502993
Interfacial hydration, dynamics and electron transfer: multi-scale ET modeling of the transient [myoglobin, cytochrome b5] complex.

PubMed

Keinan, Shahar; Nocek, Judith M; Hoffman, Brian M; Beratan, David N

2012-10-28

Formation of a transient [myoglobin (Mb), cytochrome b(5) (cyt b(5))] complex is required for the reductive repair of inactive ferri-Mb to its functional ferro-Mb state. The [Mb, cyt b(5)] complex exhibits dynamic docking (DD), with its cyt b(5) partner in rapid exchange at multiple sites on the Mb surface. A triple mutant (Mb(3M)) was designed as part of efforts to shift the electron-transfer process to the simple docking (SD) regime, in which reactive binding occurs at a restricted, reactive region on the Mb surface that dominates the docked ensemble. An electrostatically-guided brownian dynamics (BD) docking protocol was used to generate an initial ensemble of reactive configurations of the complex between unrelaxed partners. This ensemble samples a broad and diverse array of heme-heme distances and orientations. These configurations seeded all-atom constrained molecular dynamics simulations (MD) to generate relaxed complexes for the calculation of electron tunneling matrix elements (T(DA)) through tunneling-pathway analysis. This procedure for generating an ensemble of relaxed complexes combines the ability of BD calculations to sample the large variety of available conformations and interprotein distances, with the ability of MD to generate the atomic level information, especially regarding the structure of water molecules at the protein-protein interface, that defines electron-tunneling pathways. We used the calculated T(DA) values to compute ET rates for the [Mb(wt), cyt b(5)] complex and for the complex with a mutant that has a binding free energy strengthened by three D/E → K charge-reversal mutations, [Mb(3M), cyt b(5)]. The calculated rate constants are in agreement with the measured values, and the mutant complex ensemble has many more geometries with higher T(DA) values than does the wild-type Mb complex. Interestingly, water plays a double role in this electron-transfer system, lowering the tunneling barrier as well as inducing protein interface remodeling that screens the repulsion between the negatively-charged propionates of the two hemes.
Counterfactual quantum-information transfer without transmitting any physical particles

NASA Astrophysics Data System (ADS)

Guo, Qi; Cheng, Liu-Yong; Chen, Li; Wang, Hong-Fu; Zhang, Shou

2015-02-01

We demonstrate quantum information can be transferred between two distant participants without any physical particles traveling between them. The key procedure of the counterfactual scheme is to entangle two nonlocal qubits with each other without interaction, so the scheme can also be used to generate nonlocal entanglement counterfactually. We here illustrate the scheme by using flying photon qubits and Rydberg atom qubits assisted by a mesoscopic atomic ensemble. Unlike the typical teleportation, the present scheme can transport an unknown qubit in a nondeterministic manner without prior entanglement sharing or classical communication between the two distant participants.

Counterfactual quantum-information transfer without transmitting any physical particles.

PubMed

Guo, Qi; Cheng, Liu-Yong; Chen, Li; Wang, Hong-Fu; Zhang, Shou

2015-02-12

We demonstrate quantum information can be transferred between two distant participants without any physical particles traveling between them. The key procedure of the counterfactual scheme is to entangle two nonlocal qubits with each other without interaction, so the scheme can also be used to generate nonlocal entanglement counterfactually. We here illustrate the scheme by using flying photon qubits and Rydberg atom qubits assisted by a mesoscopic atomic ensemble. Unlike the typical teleportation, the present scheme can transport an unknown qubit in a nondeterministic manner without prior entanglement sharing or classical communication between the two distant participants.
Robust entanglement between a movable mirror and atomic ensemble and entanglement transfer in coupled optomechanical system

PubMed Central

Bai, Cheng-Hua; Wang, Dong-Yang; Wang, Hong-Fu; Zhu, Ai-Dong; Zhang, Shou

2016-01-01

We propose a scheme for the creation of robust entanglement between a movable mirror and atomic ensemble at the macroscopic level in coupled optomechanical system. We numerically simulate the degree of entanglement of the bipartite macroscopic entanglement and show that it depends on the coupling strength between the cavities and is robust with respect to the certain environment temperature. Inspiringly and surprisingly, according to the reported relation between the mechanical damping rate and the mechanical frequency of the movable mirror, the numerical simulation result shows that such bipartite macroscopic entanglement persists for environment temperature up to 170 K, which breaks the liquid nitrogen cooling and liquid helium cooling and largely lowers down the experiment cost. We also investigate the entanglement transfer based on this coupled system. The scheme can be used for the realization of quantum memories for continuous variable quantum information processing and quantum-limited displacement measurements. PMID:27624534
Forces and stress in second order Møller-Plesset perturbation theory for condensed phase systems within the resolution-of-identity Gaussian and plane waves approach

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

Del Ben, Mauro, E-mail: mauro.delben@chem.uzh.ch; Hutter, Jürg, E-mail: hutter@chem.uzh.ch; VandeVondele, Joost, E-mail: Joost.VandeVondele@mat.ethz.ch

The forces acting on the atoms as well as the stress tensor are crucial ingredients for calculating the structural and dynamical properties of systems in the condensed phase. Here, these derivatives of the total energy are evaluated for the second-order Møller-Plesset perturbation energy (MP2) in the framework of the resolution of identity Gaussian and plane waves method, in a way that is fully consistent with how the total energy is computed. This consistency is non-trivial, given the different ways employed to compute Coulomb, exchange, and canonical four center integrals, and allows, for example, for energy conserving dynamics in various ensembles.more » Based on this formalism, a massively parallel algorithm has been developed for finite and extended system. The designed parallel algorithm displays, with respect to the system size, cubic, quartic, and quintic requirements, respectively, for the memory, communication, and computation. All these requirements are reduced with an increasing number of processes, and the measured performance shows excellent parallel scalability and efficiency up to thousands of nodes. Additionally, the computationally more demanding quintic scaling steps can be accelerated by employing graphics processing units (GPU’s) showing, for large systems, a gain of almost a factor two compared to the standard central processing unit-only case. In this way, the evaluation of the derivatives of the RI-MP2 energy can be performed within a few minutes for systems containing hundreds of atoms and thousands of basis functions. With good time to solution, the implementation thus opens the possibility to perform molecular dynamics (MD) simulations in various ensembles (microcanonical ensemble and isobaric-isothermal ensemble) at the MP2 level of theory. Geometry optimization, full cell relaxation, and energy conserving MD simulations have been performed for a variety of molecular crystals including NH{sub 3}, CO{sub 2}, formic acid, and benzene.« less
Experimental demonstration of a BDCZ quantum repeater node.

PubMed

Yuan, Zhen-Sheng; Chen, Yu-Ao; Zhao, Bo; Chen, Shuai; Schmiedmayer, Jörg; Pan, Jian-Wei

2008-08-28

Quantum communication is a method that offers efficient and secure ways for the exchange of information in a network. Large-scale quantum communication (of the order of 100 km) has been achieved; however, serious problems occur beyond this distance scale, mainly due to inevitable photon loss in the transmission channel. Quantum communication eventually fails when the probability of a dark count in the photon detectors becomes comparable to the probability that a photon is correctly detected. To overcome this problem, Briegel, Dür, Cirac and Zoller (BDCZ) introduced the concept of quantum repeaters, combining entanglement swapping and quantum memory to efficiently extend the achievable distances. Although entanglement swapping has been experimentally demonstrated, the implementation of BDCZ quantum repeaters has proved challenging owing to the difficulty of integrating a quantum memory. Here we realize entanglement swapping with storage and retrieval of light, a building block of the BDCZ quantum repeater. We follow a scheme that incorporates the strategy of BDCZ with atomic quantum memories. Two atomic ensembles, each originally entangled with a single emitted photon, are projected into an entangled state by performing a joint Bell state measurement on the two single photons after they have passed through a 300-m fibre-based communication channel. The entanglement is stored in the atomic ensembles and later verified by converting the atomic excitations into photons. Our method is intrinsically phase insensitive and establishes the essential element needed to realize quantum repeaters with stationary atomic qubits as quantum memories and flying photonic qubits as quantum messengers.
Establishing and storing of deterministic quantum entanglement among three distant atomic ensembles.

PubMed

Yan, Zhihui; Wu, Liang; Jia, Xiaojun; Liu, Yanhong; Deng, Ruijie; Li, Shujing; Wang, Hai; Xie, Changde; Peng, Kunchi

2017-09-28

It is crucial for the physical realization of quantum information networks to first establish entanglement among multiple space-separated quantum memories and then, at a user-controlled moment, to transfer the stored entanglement to quantum channels for distribution and conveyance of information. Here we present an experimental demonstration on generation, storage, and transfer of deterministic quantum entanglement among three spatially separated atomic ensembles. The off-line prepared multipartite entanglement of optical modes is mapped into three distant atomic ensembles to establish entanglement of atomic spin waves via electromagnetically induced transparency light-matter interaction. Then the stored atomic entanglement is transferred into a tripartite quadrature entangled state of light, which is space-separated and can be dynamically allocated to three quantum channels for conveying quantum information. The existence of entanglement among three released optical modes verifies that the system has the capacity to preserve multipartite entanglement. The presented protocol can be directly extended to larger quantum networks with more nodes.Continuous-variable encoding is a promising approach for quantum information and communication networks. Here, the authors show how to map entanglement from three spatial optical modes to three separated atomic samples via electromagnetically induced transparency, releasing it later on demand.
Polarization insensitive frequency conversion for an atom-photon entanglement distribution via a telecom network.

PubMed

Ikuta, Rikizo; Kobayashi, Toshiki; Kawakami, Tetsuo; Miki, Shigehito; Yabuno, Masahiro; Yamashita, Taro; Terai, Hirotaka; Koashi, Masato; Mukai, Tetsuya; Yamamoto, Takashi; Imoto, Nobuyuki

2018-05-21

Long-lifetime quantum storages accessible to the telecom photonic infrastructure are essential to long-distance quantum communication. Atomic quantum storages have achieved subsecond storage time corresponding to 1000 km transmission time for a telecom photon through a quantum repeater algorithm. However, the telecom photon cannot be directly interfaced to typical atomic storages. Solid-state quantum frequency conversions fill this wavelength gap. Here we report on the experimental demonstration of a polarization-insensitive solid-state quantum frequency conversion to a telecom photon from a short-wavelength photon entangled with an atomic ensemble. Atom-photon entanglement has been generated with a Rb atomic ensemble and the photon has been translated to telecom range while retaining the entanglement by our nonlinear-crystal-based frequency converter in a Sagnac interferometer.
Relevance of Bose-Einstein condensation to the interference of two independent Bose gases

NASA Astrophysics Data System (ADS)

Iazzi, Mauro; Yuasa, Kazuya

2011-03-01

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

NASA Astrophysics Data System (ADS)

Mahadeswaraswamy, Chetan

First ever mobile gravity gradient measurement based on Atom Interferometric sensors has been demonstrated. Mobile gravity gradiometers play a significant role in high accuracy inertial navigation systems in order to distinguish inertial acceleration and acceleration due to gravity. The gravity gradiometer consists of two atom interferometric accelerometers. In each of the accelerometer an ensemble of laser cooled Cesium atoms is dropped and using counter propagating Raman pulses (pi/2-pi-pi/2) the ensemble is split into two states for carrying out atom interferometry. The interferometer phase is proportional to the specific force experienced by the atoms which is a combination of inertial acceleration and acceleration due to gravity. The difference in phase between the two atom interferometric sensors is proportional to gravity gradient if the platform does not undergo any rotational motion. However, any rotational motion of the platform induces spurious gravity gradient measurements. This apparent gravity gradient due to platform rotation is considerably different for an atom interferometric sensor compared to a conventional force rebalance type sensor. The atoms are in free fall and are not influenced by the motion of the case except at the instants of Raman pulses. A model for determining apparent gravity gradient due to rotation of platform was developed and experimentally verified for different frequencies. This transfer function measurement also lead to the development of a new technique for aligning the Raman laser beams with the atom clusters to within 20 mu rad. This gravity gradiometer is situated in a truck for the purpose of undertaking mobile surveys. A disturbance compensation system was designed and built in order to compensate for the rotational disturbances experienced on the floor of a truck. An electric drive system was also designed specifically to be able to move the truck in a uniform motion at very low speeds of about 1cm/s. A 250 x10-9 s-2 gravity gradient signature due to an underground void at Hansen Experimental Physics Building at Stanford was successfully measured using this mobile gradiometer.
Controlled dipole-dipole interactions between K Rydberg atoms in a laser-chopped effusive beam

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

Kutteruf, M. R.; Jones, R. R.

2010-12-15

We explore pulsed-field control of resonant dipole-dipole interactions between K Rydberg atoms. A laser-based atomic beam chopper is used to reduce the relative velocities of Rydberg atoms excited from an effusive thermal source. Resonant energy transfer (RET) between pairs of atoms is controlled via Stark tuning of the relevant Rydberg energy levels. Resonance line shapes in the electric field dependence of the RET probability are used to determine the effective temperature of the sample. We demonstrate that the relative atom velocities can be reduced to the point where the duration of the electric-field tuning pulses, and not the motion ofmore » neighboring atoms, defines the interaction time for each pair within the ensemble. Coherent, transform-limited broadening of the resonance line shape is observed as the tuning pulse duration is reduced below the natural time scale for collisions.« less
Controlled rephasing of single spin-waves in a quantum memory based on cold atoms

NASA Astrophysics Data System (ADS)

Farrera, Pau; Albrecht, Boris; Heinze, Georg; Cristiani, Matteo; de Riedmatten, Hugues; Quantum Photonics With Solids; Atoms Team

2015-05-01

Quantum memories for light allow a reversible transfer of quantum information between photons and long lived matter quantum bits. In atomic ensembles, this information is commonly stored in the form of single collective spin excitations (spin-waves). In this work we demonstrate that we can actively control the dephasing of the spin-waves created in a quantum memory based on a cold Rb87 atomic ensemble. The control is provided by an external magnetic field gradient, which induces an inhomogeneous broadening of the atomic hyperfine levels. We show that acting on this gradient allows to control the dephasing of individual spin-waves and to induce later a rephasing. The spin-waves are then mapped into single photons, and we demonstrate experimentally that the active rephasing preserves the sub-Poissonian statistics of the retrieved photons. Finally we show that this rephasing control enables the creation and storage of multiple spin-waves in different temporal modes, which can be selectively readout. This is an important step towards the implementation of a functional temporally multiplexed quantum memory for quantum repeaters. We acknowledge support from the ERC starting grant, the Spanish Ministry of Economy and Competitiveness, the Fondo Europeo de Desarrollo Regional, and the International PhD- fellowship program ``la Caixa''-Severo Ochoa @ICFO.
Velocity selection in a Doppler-broadened ensemble of atoms interacting with a monochromatic laser beam

NASA Astrophysics Data System (ADS)

Hughes, Ifan G.

2018-03-01

There is extensive use of monochromatic lasers to select atoms with a narrow range of velocities in many atomic physics experiments. For the commonplace situation of the inhomogeneous Doppler-broadened (Gaussian) linewidth exceeding the homogeneous (Lorentzian) natural linewidth by typically two orders of magnitude, a substantial narrowing of the velocity class of atoms interacting with the light can be achieved. However, this is not always the case, and here we show that for a certain parameter regime there is essentially no selection - all of the atoms interact with the light in accordance with the velocity probability density. An explanation of this effect is provided, emphasizing the importance of the long tail of the constituent Lorentzian distribution in a Voigt profile.
Single-shot imaging of trapped Fermi gas

NASA Astrophysics Data System (ADS)

Gajda, Mariusz; Mostowski, Jan; Sowiński, Tomasz; Załuska-Kotur, Magdalena

2016-07-01

Recently developed techniques allow for simultaneous measurements of the positions of all ultra-cold atoms in a trap with high resolution. Each such single-shot experiment detects one element of the quantum ensemble formed by the cloud of atoms. Repeated single-shot measurements can be used to determine all correlations between particle positions as opposed to standard measurements that determine particle density or two-particle correlations only. In this paper we discuss the possible outcomes of such single-shot measurements in the case of cloud of ultra-cold noninteracting Fermi atoms. We show that the Pauli exclusion principle alone leads to correlations between particle positions that originate from unexpected spatial structures formed by the atoms.
Optimally Squeezed Spin States

NASA Astrophysics Data System (ADS)

Rojo, Alberto

2004-03-01

We consider optimally spin-squeezed states that maximize the sensitivity of the Ramsey spectroscopy, and for which the signal to noise ratio scales as the number of particles N. Using the variational principle we prove that these states are eigensolutions of the Hamiltonian H(λ)=λ S_z^2-S_x, and that, for large N, the states become equivalent to the quadrature squeezed states of the harmonic oscillator. We present numerical results that illustrate the validity of the equivalence. We also present results of spin squeezing via atom-field interactions within the context of the Tavis-Cummings model. An ensemble of N two-level atoms interacts with a quantized cavity field. For all the atoms initially in their ground states, it is shown that spin squeezing of both the atoms and the field can be achieved provided the initial state of the cavity field has coherence between number states differing by 2. Most of the discussion is restricted to the case of a cavity field initially in a coherent state, but initial squeezed states for the field are also discussed. An analytic solution is found that is valid in the limit that the number of atoms is much greater than unity. References: A. G. Rojo, Phys. Rev A, 68, 013807 (2003); Claudiu Genes, P. R. Berman, and A. G. Rojo Phys. Rev. A 68, 043809 (2003).
Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations

PubMed Central

Budday, Dominik; Leyendecker, Sigrid; van den Bedem, Henry

2015-01-01

Proteins operate and interact with partners by dynamically exchanging between functional substates of a conformational ensemble on a rugged free energy landscape. Understanding how these substates are linked by coordinated, collective motions requires exploring a high-dimensional space, which remains a tremendous challenge. While molecular dynamics simulations can provide atomically detailed insight into the dynamics, computational demands to adequately sample conformational ensembles of large biomolecules and their complexes often require tremendous resources. Kinematic models can provide high-level insights into conformational ensembles and molecular rigidity beyond the reach of molecular dynamics by reducing the dimensionality of the search space. Here, we model a protein as a kinematic linkage and present a new geometric method to characterize molecular rigidity from the constraint manifold Q and its tangent space Q at the current configuration q. In contrast to methods based on combinatorial constraint counting, our method is valid for both generic and non-generic, e.g., singular configurations. Importantly, our geometric approach provides an explicit basis for collective motions along floppy modes, resulting in an efficient procedure to probe conformational space. An atomically detailed structural characterization of coordinated, collective motions would allow us to engineer or allosterically modulate biomolecules by selectively stabilizing conformations that enhance or inhibit function with broad implications for human health. PMID:26213417
Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations

NASA Astrophysics Data System (ADS)

Budday, Dominik; Leyendecker, Sigrid; van den Bedem, Henry

2015-10-01

Proteins operate and interact with partners by dynamically exchanging between functional substates of a conformational ensemble on a rugged free energy landscape. Understanding how these substates are linked by coordinated, collective motions requires exploring a high-dimensional space, which remains a tremendous challenge. While molecular dynamics simulations can provide atomically detailed insight into the dynamics, computational demands to adequately sample conformational ensembles of large biomolecules and their complexes often require tremendous resources. Kinematic models can provide high-level insights into conformational ensembles and molecular rigidity beyond the reach of molecular dynamics by reducing the dimensionality of the search space. Here, we model a protein as a kinematic linkage and present a new geometric method to characterize molecular rigidity from the constraint manifold Q and its tangent space Tq Q at the current configuration q. In contrast to methods based on combinatorial constraint counting, our method is valid for both generic and non-generic, e.g., singular configurations. Importantly, our geometric approach provides an explicit basis for collective motions along floppy modes, resulting in an efficient procedure to probe conformational space. An atomically detailed structural characterization of coordinated, collective motions would allow us to engineer or allosterically modulate biomolecules by selectively stabilizing conformations that enhance or inhibit function with broad implications for human health.
Highly-efficient quantum memory for polarization qubits in a spatially-multiplexed cold atomic ensemble.

PubMed

Vernaz-Gris, Pierre; Huang, Kun; Cao, Mingtao; Sheremet, Alexandra S; Laurat, Julien

2018-01-25

Quantum memory for flying optical qubits is a key enabler for a wide range of applications in quantum information. A critical figure of merit is the overall storage and retrieval efficiency. So far, despite the recent achievements of efficient memories for light pulses, the storage of qubits has suffered from limited efficiency. Here we report on a quantum memory for polarization qubits that combines an average conditional fidelity above 99% and efficiency around 68%, thereby demonstrating a reversible qubit mapping where more information is retrieved than lost. The qubits are encoded with weak coherent states at the single-photon level and the memory is based on electromagnetically-induced transparency in an elongated laser-cooled ensemble of cesium atoms, spatially multiplexed for dual-rail storage. This implementation preserves high optical depth on both rails, without compromise between multiplexing and storage efficiency. Our work provides an efficient node for future tests of quantum network functionalities and advanced photonic circuits.
Orthopositronium decay form factors and two-photon correlations

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

Adkins, Gregory S.; Droz, Daniel R.; Rastawicki, Dominik

2010-04-15

We give results for the orthopositronium decay form factors through one-loop order. We use the form factors to calculate momentum correlations of the final-state photons and , including one-loop corrections, for ensembles of initial orthopositronium atoms having arbitrary polarization.
Ensemble averaged structure–function relationship for nanocrystals: effective superparamagnetic Fe clusters with catalytically active Pt skin [Ensemble averaged structure-function relationship for composite nanocrystals: magnetic bcc Fe clusters with catalytically active fcc Pt skin

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

Petkov, Valeri; Prasai, Binay; Shastri, Sarvjit

Practical applications require the production and usage of metallic nanocrystals (NCs) in large ensembles. Besides, due to their cluster-bulk solid duality, metallic NCs exhibit a large degree of structural diversity. This poses the question as to what atomic-scale basis is to be used when the structure–function relationship for metallic NCs is to be quantified precisely. In this paper, we address the question by studying bi-functional Fe core-Pt skin type NCs optimized for practical applications. In particular, the cluster-like Fe core and skin-like Pt surface of the NCs exhibit superparamagnetic properties and a superb catalytic activity for the oxygen reduction reaction,more » respectively. We determine the atomic-scale structure of the NCs by non-traditional resonant high-energy X-ray diffraction coupled to atomic pair distribution function analysis. Using the experimental structure data we explain the observed magnetic and catalytic behavior of the NCs in a quantitative manner. Lastly, we demonstrate that NC ensemble-averaged 3D positions of atoms obtained by advanced X-ray scattering techniques are a very proper basis for not only establishing but also quantifying the structure–function relationship for the increasingly complex metallic NCs explored for practical applications.« less
Mobile quantum gravity sensor with unprecedented stability

NASA Astrophysics Data System (ADS)

Leykauf, Bastian; Freier, Christian; Schkolnik, Vladimir; Krutzik, Markus; Peters, Achim

2017-04-01

The gravimetric atom interferometer GAIN is based on interfering ensembles of laser-cooled 87Rb atoms in a fountain setup, using stimulated Raman transitions. GAIN's rugged design allows for transports to sites of geodetic and geophysical interest while maintaining a high accuracy compatible with the best classical instruments. We compared our instrument's performance with falling corner-cube and superconducting gravimeters in two measurement campaigns at geodetic observatories in Wettzell, Germany and Onsala, Sweden. Our instrument's long-term stability of 0.5 nm/s2 is the best value for absolute gravimeters reported to date [1]. Our measured gravity value agrees with other state-of-the-art gravimeters on the 10-9 level in g, demonstrating effective control over systematics including wavefront distortions of the Raman beams [2]. By using the juggling technique [3], we are able to perform gravity measurements on two atomic clouds simultaneously. Advantages include the suppression of common mode phase noise, enabling differential phase shift extraction without the need for vibration isolation. We will present the results of our first gravity gradient measurements. [1] Freier, Hauth, Schkolnik, Leykauf, Schilling, Wziontek, Scherneck, Müller and Peters (2016). Mobile quantum gravity sensor with unprecedented stability. Journal of Physics: Conference Series, 8th Symposium on Frequency Standards and Metrology 2015, 723, 12050. [2] Schkolnik, Leykauf, Hauth, Freier and Peters (2015). The effect of wavefront aberrations in atom interferometry. Applied Physics B, 120(2), 311 - 316. [3] Legere and Gibble (1998). Quantum Scattering in a Juggling Atomic Fountain. Physical Review Letters, 81(1), 5780 - 5783.
Ensemble modeling of very small ZnO nanoparticles.

PubMed

Niederdraenk, Franziska; Seufert, Knud; Stahl, Andreas; Bhalerao-Panajkar, Rohini S; Marathe, Sonali; Kulkarni, Sulabha K; Neder, Reinhard B; Kumpf, Christian

2011-01-14

The detailed structural characterization of nanoparticles is a very important issue since it enables a precise understanding of their electronic, optical and magnetic properties. Here we introduce a new method for modeling the structure of very small particles by means of powder X-ray diffraction. Using thioglycerol-capped ZnO nanoparticles with a diameter of less than 3 nm as an example we demonstrate that our ensemble modeling method is superior to standard XRD methods like, e.g., Rietveld refinement. Besides fundamental properties (size, anisotropic shape and atomic structure) more sophisticated properties like imperfections in the lattice, a size distribution as well as strain and relaxation effects in the particles and-in particular-at their surface (surface relaxation effects) can be obtained. Ensemble properties, i.e., distributions of the particle size and other properties, can also be investigated which makes this method superior to imaging techniques like (high resolution) transmission electron microscopy or atomic force microscopy, in particular for very small nanoparticles. For the particles under study an excellent agreement of calculated and experimental X-ray diffraction patterns could be obtained with an ensemble of anisotropic polyhedral particles of three dominant sizes, wurtzite structure and a significant relaxation of Zn atoms close to the surface.

0.75 atoms improve the clock signal of 10,000 atoms

NASA Astrophysics Data System (ADS)

Kruse, I.; Lange, K.; Peise, J.; Lücke, B.; Pezzè, L.; Arlt, J.; Ertmer, W.; Lisdat, C.; Santos, L.; Smerzi, A.; Klempt, C.

2017-02-01

Since the pioneering work of Ramsey, atom interferometers are employed for precision metrology, in particular to measure time and to realize the second. In a classical interferometer, an ensemble of atoms is prepared in one of the two input states, whereas the second one is left empty. In this case, the vacuum noise restricts the precision of the interferometer to the standard quantum limit (SQL). Here, we propose and experimentally demonstrate a novel clock configuration that surpasses the SQL by squeezing the vacuum in the empty input state. We create a squeezed vacuum state containing an average of 0.75 atoms to improve the clock sensitivity of 10,000 atoms by 2.05 dB. The SQL poses a significant limitation for today's microwave fountain clocks, which serve as the main time reference. We evaluate the major technical limitations and challenges for devising a next generation of fountain clocks based on atomic squeezed vacuum.
Evaluation of protective ensemble thermal characteristics through sweating hot plate, sweating thermal manikin, and human tests.

PubMed

Kim, Jung-Hyun; Powell, Jeffery B; Roberge, Raymond J; Shepherd, Angie; Coca, Aitor

2014-01-01

The purpose of this study was to evaluate the predictive capability of fabric Total Heat Loss (THL) values on thermal stress that Personal Protective Equipment (PPE) ensemble wearers may encounter while performing work. A series of three tests, consisting of the Sweating Hot Plate (SHP) test on two sample fabrics and the Sweating Thermal Manikin (STM) and human performance tests on two single-layer encapsulating ensembles (fabric/ensemble A = low THL and B = high THL), was conducted to compare THL values between SHP and STM methods along with human thermophysiological responses to wearing the ensembles. In human testing, ten male subjects performed a treadmill exercise at 4.8 km and 3% incline for 60 min in two environmental conditions (mild = 22°C, 50% relative humidity (RH) and hot/humid = 35°C, 65% RH). The thermal and evaporative resistances were significantly higher on a fabric level as measured in the SHP test than on the ensemble level as measured in the STM test. Consequently the THL values were also significantly different for both fabric types (SHP vs. STM: 191.3 vs. 81.5 W/m(2) in fabric/ensemble A, and 909.3 vs. 149.9 W/m(2) in fabric/ensemble B (p < 0.001). Body temperature and heart rate response between ensembles A and B were consistently different in both environmental conditions (p < 0.001), which is attributed to significantly higher sweat evaporation in ensemble B than in A (p < 0.05), despite a greater sweat production in ensemble A (p < 0.001) in both environmental conditions. Further, elevation of microclimate temperature (p < 0.001) and humidity (p < 0.01) was significantly greater in ensemble A than in B. It was concluded that: (1) SHP test determined THL values are significantly different from the actual THL potential of the PPE ensemble tested on STM, (2) physiological benefits from wearing a more breathable PPE ensemble may not be feasible with incremental THL values (SHP test) less than approximately 150-200 W·m(2), and (3) the effects of thermal environments on a level of heat stress in PPE ensemble wearers are greater than ensemble thermal characteristics.
Coherence properties of nanofiber-trapped cesium atoms.

PubMed

Reitz, D; Sayrin, C; Mitsch, R; Schneeweiss, P; Rauschenbeutel, A

2013-06-14

We experimentally study the ground state coherence properties of cesium atoms in a nanofiber-based two-color dipole trap, localized ∼ 200 nm away from the fiber surface. Using microwave radiation to coherently drive the clock transition, we record Ramsey fringes as well as spin echo signals and infer a reversible dephasing time of T(2)(*) = 0.6 ms and an irreversible dephasing time of T(2)(') = 3.7 ms. By modeling the signals, we find that, for our experimental parameters, T(2)(*) and T(2)(') are limited by the finite initial temperature of the atomic ensemble and the heating rate, respectively. Our results represent a fundamental step towards establishing nanofiber-based traps for cold atoms as a building block in an optical fiber quantum network.
Coherent and dynamic beam splitting based on light storage in cold atoms

PubMed Central

Park, Kwang-Kyoon; Zhao, Tian-Ming; Lee, Jong-Chan; Chough, Young-Tak; Kim, Yoon-Ho

2016-01-01

We demonstrate a coherent and dynamic beam splitter based on light storage in cold atoms. An input weak laser pulse is first stored in a cold atom ensemble via electromagnetically-induced transparency (EIT). A set of counter-propagating control fields, applied at a later time, retrieves the stored pulse into two output spatial modes. The high visibility interference between the two output pulses clearly demonstrates that the beam splitting process is coherent. Furthermore, by manipulating the control lasers, it is possible to dynamically control the storage time, the power splitting ratio, the relative phase, and the optical frequencies of the output pulses. With further improvements, the active beam splitter demonstrated in this work might have applications in photonic photonic quantum information and in all-optical information processing. PMID:27677457
Biased Metropolis Sampling for Rugged Free Energy Landscapes

NASA Astrophysics Data System (ADS)

Berg, Bernd A.

2003-11-01

Metropolis simulations of all-atom models of peptides (i.e. small proteins) are considered. Inspired by the funnel picture of Bryngelson and Wolyness, a transformation of the updating probabilities of the dihedral angles is defined, which uses probability densities from a higher temperature to improve the algorithmic performance at a lower temperature. The method is suitable for canonical as well as for generalized ensemble simulations. A simple approximation to the full transformation is tested at room temperature for Met-Enkephalin in vacuum. Integrated autocorrelation times are found to be reduced by factors close to two and a similar improvement due to generalized ensemble methods enters multiplicatively.
Differences in the emergent coding properties of cortical and striatal ensembles

PubMed Central

Ma, L.; Hyman, J.M.; Lindsay, A.J.; Phillips, A.G.; Seamans, J.K.

2016-01-01

The function of a given brain region is often defined by the coding properties of its individual neurons, yet how this information is combined at the ensemble level is an equally important consideration. In the present study, multiple neurons from the anterior cingulate cortex (ACC) and the dorsal striatum (DS) were recorded simultaneously as rats performed different sequences of the same three actions. Sequence and lever decoding was remarkably similar on a per-neuron basis in the two regions. At the ensemble level, sequence-specific representations in the DS appeared synchronously but transiently along with the representation of lever location, while these two streams of information appeared independently and asynchronously in the ACC. As a result the ACC achieved superior ensemble decoding accuracy overall. Thus, the manner in which information was combined across neurons in an ensemble determined the functional separation of the ACC and DS on this task. PMID:24974796
Dual-Beam Atom Laser Driven by Spinor Dynamics

NASA Technical Reports Server (NTRS)

Thompson, Robert; Lundblad, Nathan; Maleki, Lute; Aveline, David

2007-01-01

An atom laser now undergoing development simultaneously generates two pulsed beams of correlated Rb-87 atoms. (An atom laser is a source of atoms in beams characterized by coherent matter waves, analogous to a conventional laser, which is a source of coherent light waves.) The pumping mechanism of this atom laser is based on spinor dynamics in a Bose-Einstein condensate. By virtue of the angular-momentum conserving collisions that generate the two beams, the number of atoms in one beam is correlated with the number of atoms in the other beam. Such correlations are intimately linked to entanglement and squeezing in atomic ensembles, and atom lasers like this one could be used in exploring related aspects of Bose-Einstein condensates, and as components of future sensors relying on atom interferometry. In this atom-laser apparatus, a Bose-Einstein condensate of about 2 x 10(exp 6) Rb-87 atoms at a temperature of about 120 micro-K is first formed through all-optical means in a relatively weak singlebeam running-wave dipole trap that has been formed by focusing of a CO2-laser beam. By a technique that is established in the art, the trap is loaded from an ultrahigh-vacuum magnetooptical trap that is, itself, loaded via a cold atomic beam from an upstream two-dimensional magneto-optical trap that resides in a rubidium-vapor cell that is differentially pumped from an adjoining vacuum chamber, wherein are performed scientific observations of the beams ultimately generated by the atom laser.
Building alternate protein structures using the elastic network model.

PubMed

Yang, Qingyi; Sharp, Kim A

2009-02-15

We describe a method for efficiently generating ensembles of alternate, all-atom protein structures that (a) differ significantly from the starting structure, (b) have good stereochemistry (bonded geometry), and (c) have good steric properties (absence of atomic overlap). The method uses reconstruction from a series of backbone framework structures that are obtained from a modified elastic network model (ENM) by perturbation along low-frequency normal modes. To ensure good quality backbone frameworks, the single force parameter ENM is modified by introducing two more force parameters to characterize the interaction between the consecutive carbon alphas and those within the same secondary structure domain. The relative stiffness of the three parameters is parameterized to reproduce B-factors, while maintaining good bonded geometry. After parameterization, violations of experimental Calpha-Calpha distances and Calpha-Calpha-Calpha pseudo angles along the backbone are reduced to less than 1%. Simultaneously, the average B-factor correlation coefficient improves to R = 0.77. Two applications illustrate the potential of the approach. (1) 102,051 protein backbones spanning a conformational space of 15 A root mean square deviation were generated from 148 nonredundant proteins in the PDB database, and all-atom models with minimal bonded and nonbonded violations were produced from this ensemble of backbone structures using the SCWRL side chain building program. (2) Improved backbone templates for homology modeling. Fifteen query sequences were each modeled on two targets. For each of the 30 target frameworks, dozens of improved templates could be produced In all cases, improved full atom homology models resulted, of which 50% could be identified blind using the D-Fire statistical potential. (c) 2008 Wiley-Liss, Inc.
Single-Atom Catalyst of Platinum Supported on Titanium Nitride for Selective Electrochemical Reactions.

PubMed

Yang, Sungeun; Kim, Jiwhan; Tak, Young Joo; Soon, Aloysius; Lee, Hyunjoo

2016-02-05

As a catalyst, single-atom platinum may provide an ideal structure for platinum minimization. Herein, a single-atom catalyst of platinum supported on titanium nitride nanoparticles were successfully prepared with the aid of chlorine ligands. Unlike platinum nanoparticles, the single-atom active sites predominantly produced hydrogen peroxide in the electrochemical oxygen reduction with the highest mass activity reported so far. The electrocatalytic oxidation of small organic molecules, such as formic acid and methanol, also exhibited unique selectivity on the single-atom platinum catalyst. A lack of platinum ensemble sites changed the reaction pathway for the oxygen-reduction reaction toward a two-electron pathway and formic acid oxidation toward direct dehydrogenation, and also induced no activity for the methanol oxidation. This work demonstrates that single-atom platinum can be an efficient electrocatalyst with high mass activity and unique selectivity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Improvement of an Atomic Clock using Squeezed Vacuum

NASA Astrophysics Data System (ADS)

Kruse, I.; Lange, K.; Peise, J.; Lücke, B.; Pezzè, L.; Arlt, J.; Ertmer, W.; Lisdat, C.; Santos, L.; Smerzi, A.; Klempt, C.

2016-09-01

Since the pioneering work of Ramsey, atom interferometers are employed for precision metrology, in particular to measure time and to realize the second. In a classical interferometer, an ensemble of atoms is prepared in one of the two input states, whereas the second one is left empty. In this case, the vacuum noise restricts the precision of the interferometer to the standard quantum limit (SQL). Here, we propose and experimentally demonstrate a novel clock configuration that surpasses the SQL by squeezing the vacuum in the empty input state. We create a squeezed vacuum state containing an average of 0.75 atoms to improve the clock sensitivity of 10000 atoms by 2.05-0.37 +0 .34 dB . The SQL poses a significant limitation for today's microwave fountain clocks, which serve as the main time reference. We evaluate the major technical limitations and challenges for devising a next generation of fountain clocks based on atomic squeezed vacuum.
Structural investigation of the (010) surface of the Al13 Fe4 catalyst.

PubMed

Ledieu, J; Gaudry, É; Loli, L N Serkovic; Villaseca, S Alarcón; de Weerd, M-C; Hahne, M; Gille, P; Grin, Y; Dubois, J-M; Fournée, V

2013-02-15

We have investigated the structure of the Al(13)Fe(4)(010) surface using both experimental and ab initio computational methods. The results indicate that the topmost surface layers correspond to incomplete puckered (P) planes present in the bulk crystal structure. The main building block of the corrugated termination consists of two adjacent pentagons of Al atoms, each centered by a protruding Fe atom. These motifs are interconnected via additional Al atoms referred to as "glue" atoms which partially desorb above 873 K. The surface structure of lower atomic density compared to the bulk P plane is explained by a strong Fe-Al-Fe covalent polar interaction that preserves intact clusters at the surface. The proposed surface model with identified Fe-containing atomic ensembles could explain the Al(13)Fe(4) catalytic properties recently reported in line with the site-isolation concept [M. Armbrüster et al., Nat. Mater. 11, 690 (2012)].
Coherent all-optical control of ultracold atoms arrays in permanent magnetic traps.

PubMed

Abdelrahman, Ahmed; Mukai, Tetsuya; Häffner, Hartmut; Byrnes, Tim

2014-02-10

We propose a hybrid architecture for quantum information processing based on magnetically trapped ultracold atoms coupled via optical fields. The ultracold atoms, which can be either Bose-Einstein condensates or ensembles, are trapped in permanent magnetic traps and are placed in microcavities, connected by silica based waveguides on an atom chip structure. At each trapping center, the ultracold atoms form spin coherent states, serving as a quantum memory. An all-optical scheme is used to initialize, measure and perform a universal set of quantum gates on the single and two spin-coherent states where entanglement can be generated addressably between spatially separated trapped ultracold atoms. This allows for universal quantum operations on the spin coherent state quantum memories. We give detailed derivations of the composite cavity system mediated by a silica waveguide as well as the control scheme. Estimates for the necessary experimental conditions for a working hybrid device are given.
Controllable vacuum-induced diffraction of matter-wave superradiance using an all-optical dispersive cavity

NASA Astrophysics Data System (ADS)

Su, Shih-Wei; Lu, Zhen-Kai; Gou, Shih-Chuan; Liao, Wen-Te

2016-10-01

Cavity quantum electrodynamics (CQED) has played a central role in demonstrating the fundamental principles of the quantum world, and in particular those of atom-light interactions. Developing fast, dynamical and non-mechanical control over a CQED system is particularly desirable for controlling atomic dynamics and building future quantum networks at high speed. However conventional mirrors do not allow for such flexible and fast controls over their coupling to intracavity atoms mediated by photons. Here we theoretically investigate a novel all-optical CQED system composed of a binary Bose-Einstein condensate (BEC) sandwiched by two atomic ensembles. The highly tunable atomic dispersion of the CQED system enables the medium to act as a versatile, all-optically controlled atomic mirror that can be employed to manipulate the vacuum-induced diffraction of matter-wave superradiance. Our study illustrates a innovative all-optical element of atomtroics and sheds new light on controlling light-matter interactions.
Demonstration of a memory for tightly guided light in an optical nanofiber.

PubMed

Gouraud, B; Maxein, D; Nicolas, A; Morin, O; Laurat, J

2015-05-08

We report the experimental observation of slow-light and coherent storage in a setting where light is tightly confined in the transverse directions. By interfacing a tapered optical nanofiber with a cold atomic ensemble, electromagnetically induced transparency is observed and light pulses at the single-photon level are stored in and retrieved from the atomic medium. The decay of efficiency with storage time is also measured and related to concurrent decoherence mechanisms. Collapses and revivals can be additionally controlled by an applied magnetic field. Our results based on subdiffraction-limited optical mode interacting with atoms via the strong evanescent field demonstrate an alternative to free-space focusing and a novel capability for information storage in an all-fibered quantum network.
Quantifying Nucleic Acid Ensembles with X-ray Scattering Interferometry.

PubMed

Shi, Xuesong; Bonilla, Steve; Herschlag, Daniel; Harbury, Pehr

2015-01-01

The conformational ensemble of a macromolecule is the complete description of the macromolecule's solution structures and can reveal important aspects of macromolecular folding, recognition, and function. However, most experimental approaches determine an average or predominant structure, or follow transitions between states that each can only be described by an average structure. Ensembles have been extremely difficult to experimentally characterize. We present the unique advantages and capabilities of a new biophysical technique, X-ray scattering interferometry (XSI), for probing and quantifying structural ensembles. XSI measures the interference of scattered waves from two heavy metal probes attached site specifically to a macromolecule. A Fourier transform of the interference pattern gives the fractional abundance of different probe separations directly representing the multiple conformation states populated by the macromolecule. These probe-probe distance distributions can then be used to define the structural ensemble of the macromolecule. XSI provides accurate, calibrated distance in a model-independent fashion with angstrom scale sensitivity in distances. XSI data can be compared in a straightforward manner to atomic coordinates determined experimentally or predicted by molecular dynamics simulations. We describe the conceptual framework for XSI and provide a detailed protocol for carrying out an XSI experiment. © 2015 Elsevier Inc. All rights reserved.
From a structural average to the conformational ensemble of a DNA bulge

PubMed Central

Shi, Xuesong; Beauchamp, Kyle A.; Harbury, Pehr B.; Herschlag, Daniel

2014-01-01

Direct experimental measurements of conformational ensembles are critical for understanding macromolecular function, but traditional biophysical methods do not directly report the solution ensemble of a macromolecule. Small-angle X-ray scattering interferometry has the potential to overcome this limitation by providing the instantaneous distance distribution between pairs of gold-nanocrystal probes conjugated to a macromolecule in solution. Our X-ray interferometry experiments reveal an increasing bend angle of DNA duplexes with bulges of one, three, and five adenosine residues, consistent with previous FRET measurements, and further reveal an increasingly broad conformational ensemble with increasing bulge length. The distance distributions for the AAA bulge duplex (3A-DNA) with six different Au-Au pairs provide strong evidence against a simple elastic model in which fluctuations occur about a single conformational state. Instead, the measured distance distributions suggest a 3A-DNA ensemble with multiple conformational states predominantly across a region of conformational space with bend angles between 24 and 85 degrees and characteristic bend directions and helical twists and displacements. Additional X-ray interferometry experiments revealed perturbations to the ensemble from changes in ionic conditions and the bulge sequence, effects that can be understood in terms of electrostatic and stacking contributions to the ensemble and that demonstrate the sensitivity of X-ray interferometry. Combining X-ray interferometry ensemble data with molecular dynamics simulations gave atomic-level models of representative conformational states and of the molecular interactions that may shape the ensemble, and fluorescence measurements with 2-aminopurine-substituted 3A-DNA provided initial tests of these atomistic models. More generally, X-ray interferometry will provide powerful benchmarks for testing and developing computational methods. PMID:24706812
Ensemble Response in Mushroom Body Output Neurons of the Honey Bee Outpaces Spatiotemporal Odor Processing Two Synapses Earlier in the Antennal Lobe

PubMed Central

Strube-Bloss, Martin F.; Herrera-Valdez, Marco A.; Smith, Brian H.

2012-01-01

Neural representations of odors are subject to computations that involve sequentially convergent and divergent anatomical connections across different areas of the brains in both mammals and insects. Furthermore, in both mammals and insects higher order brain areas are connected via feedback connections. In order to understand the transformations and interactions that this connectivity make possible, an ideal experiment would compare neural responses across different, sequential processing levels. Here we present results of recordings from a first order olfactory neuropile – the antennal lobe (AL) – and a higher order multimodal integration and learning center – the mushroom body (MB) – in the honey bee brain. We recorded projection neurons (PN) of the AL and extrinsic neurons (EN) of the MB, which provide the outputs from the two neuropils. Recordings at each level were made in different animals in some experiments and simultaneously in the same animal in others. We presented two odors and their mixture to compare odor response dynamics as well as classification speed and accuracy at each neural processing level. Surprisingly, the EN ensemble significantly starts separating odor stimuli rapidly and before the PN ensemble has reached significant separation. Furthermore the EN ensemble at the MB output reaches a maximum separation of odors between 84–120 ms after odor onset, which is 26 to 133 ms faster than the maximum separation at the AL output ensemble two synapses earlier in processing. It is likely that a subset of very fast PNs, which respond before the ENs, may initiate the rapid EN ensemble response. We suggest therefore that the timing of the EN ensemble activity would allow retroactive integration of its signal into the ongoing computation of the AL via centrifugal feedback. PMID:23209711
Watching proteins function with picosecond X-ray crystallography and molecular dynamics simulations.

NASA Astrophysics Data System (ADS)

Anfinrud, Philip

2006-03-01

Time-resolved electron density maps of myoglobin, a ligand-binding heme protein, have been stitched together into movies that unveil with < 2-å spatial resolution and 150-ps time-resolution the correlated protein motions that accompany and/or mediate ligand migration within the hydrophobic interior of a protein. A joint analysis of all-atom molecular dynamics (MD) calculations and picosecond time-resolved X-ray structures provides single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin following ligand dissociation reproduce the direction, amplitude, and timescales of crystallographically-determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories, which identify and structurally characterize a conformational switch that directs dissociated ligands to one of two nearby protein cavities. This unique combination of simulation and experiment unveils functional protein motions and illustrates at an atomic level relationships among protein structure, dynamics, and function. In collaboration with Friedrich Schotte and Gerhard Hummer, NIH.
Measuring qutrit-qutrit entanglement of orbital angular momentum states of an atomic ensemble and a photon.

PubMed

Inoue, R; Yonehara, T; Miyamoto, Y; Koashi, M; Kozuma, M

2009-09-11

Three-dimensional entanglement of orbital angular momentum states of an atomic qutrit and a single photon qutrit has been observed. Their full state was reconstructed using quantum state tomography. The fidelity to the maximally entangled state of Schmidt rank 3 exceeds the threshold 2/3. This result confirms that the density matrix cannot be decomposed into an ensemble of pure states of Schmidt rank 1 or 2. That is, the Schmidt number of the density matrix must be equal to or greater than 3.
Stereo-selective partitioning of translation-to-internal energy conversion in gas ensembles

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

McCaffery, Anthony J., E-mail: A.J.McCaffery@sussex.ac.uk

2014-11-07

A recent computational study of translation-to-internal energy transfer to H{sub 2} (v = 0,j = 0), hereinafter denoted H{sub 2} (0;0), in a bath of H atoms [A. J. McCaffery and R. J. Marsh, J. Chem. Phys. 139, 234310 (2013)] revealed an unexpected energy partitioning in which the H{sub 2} vibrational temperature greatly exceeds that of rotation. This occurs despite rotation and vibration distributions being close to Boltzmann from early in ensemble evolution. In this work, the study is extended to include H{sub 2} (0;0), O{sub 2} (0;0), and HF (0;0) in a wide range of atomic bath gases comprisingmore » some 22 ensembles in all. Translation-to-internal energy conversion in the systems studied was found to be relatively inefficient, falling approximately with (√μ′){sup −1} as bath gas mass increases, where μ′ is the reduced mass of the diatomic–bath gas pair. In all 22 systems studied, T{sub v} exceeds T{sub r} – by a factor > 4 for some pairs. Analysis of the constraints that influence (0;0) → (1;j) excitation for each diatomic–atom pair in momentum–angular momentum space demonstrates that a vibrational preference results from energy constraints that limit permitted collision trajectories to those of low effective impact parameter, i.e., to those that are axial or near axial on impact with the Newton surface. This implies that a steric constraint is an inherent feature of vibration-rotation excitation and arises because momentum and energy barriers must be overcome before rotational states may be populated in the higher vibrational level.« less

Quantum teleportation between light and matter.

PubMed

Sherson, Jacob F; Krauter, Hanna; Olsson, Rasmus K; Julsgaard, Brian; Hammerer, Klemens; Cirac, Ignacio; Polzik, Eugene S

2006-10-05

Quantum teleportation is an important ingredient in distributed quantum networks, and can also serve as an elementary operation in quantum computers. Teleportation was first demonstrated as a transfer of a quantum state of light onto another light beam; later developments used optical relays and demonstrated entanglement swapping for continuous variables. The teleportation of a quantum state between two single material particles (trapped ions) has now also been achieved. Here we demonstrate teleportation between objects of a different nature--light and matter, which respectively represent 'flying' and 'stationary' media. A quantum state encoded in a light pulse is teleported onto a macroscopic object (an atomic ensemble containing 10 caesium atoms). Deterministic teleportation is achieved for sets of coherent states with mean photon number (n) up to a few hundred. The fidelities are 0.58 +/- 0.02 for n = 20 and 0.60 +/- 0.02 for n = 5--higher than any classical state transfer can possibly achieve. Besides being of fundamental interest, teleportation using a macroscopic atomic ensemble is relevant for the practical implementation of a quantum repeater. An important factor for the implementation of quantum networks is the teleportation distance between transmitter and receiver; this is 0.5 metres in the present experiment. As our experiment uses propagating light to achieve the entanglement of light and atoms required for teleportation, the present approach should be scalable to longer distances.
Direct imaging of slow, stored and stationary EIT polaritons

NASA Astrophysics Data System (ADS)

Campbell, Geoff T.; Cho, Young-Wook; Su, Jian; Everett, Jesse; Robins, Nicholas; Lam, Ping Koy; Buchler, Ben

2017-09-01

Stationary and slow light effects are of great interest for quantum information applications. Using laser-cooled Rb87 atoms, we performed side imaging of our atomic ensemble under slow and stationary light conditions, which allows direct comparison with numerical models. The polaritons were generated using electromagnetically induced transparency (EIT), with stationary light generated using counter-propagating control fields. By controlling the power ratio of the two control fields, we show fine control of the group velocity of the stationary light. We also compare the dynamics of stationary light using monochromatic and bichromatic control fields. Our results show negligible difference between the two situations, in contrast to previous work in EIT-based systems.
Sensitivity to perturbations and quantum phase transitions.

PubMed

Wisniacki, D A; Roncaglia, A J

2013-05-01

The local density of states or its Fourier transform, usually called fidelity amplitude, are important measures of quantum irreversibility due to imperfect evolution. In this Rapid Communication we study both quantities in a paradigmatic many body system, the Dicke Hamiltonian, where a single-mode bosonic field interacts with an ensemble of N two-level atoms. This model exhibits a quantum phase transition in the thermodynamic limit, while for finite instances the system undergoes a transition from quasi-integrability to quantum chaotic. We show that the width of the local density of states clearly points out the imprints of the transition from integrability to chaos but no trace remains of the quantum phase transition. The connection with the decay of the fidelity amplitude is also established.
Effects of quantum coherence and interference in atoms near nanoparticles

NASA Astrophysics Data System (ADS)

Dhayal, Suman; Rostovtsev, Yuri V.

2016-04-01

Optical properties of ensembles of realistic quantum emitters coupled to plasmonic systems are studied by using adequate models that can take into account full atomic geometry. In particular, the coherent effects such as forming "dark states," optical pumping, coherent Raman scattering, and the stimulated Raman adiabatic passage (STIRAP) are revisited in the presence of metallic nanoparticles. It is shown that the dark states are still formed but they have more complicated structure, and the optical pumping and the STIRAP cannot be employed in the vicinity of plasmonic nanostructures. Also, there is a huge difference in the behavior of the local atomic polarization and the atomic polarization averaged over an ensemble of atoms homogeneously spread near nanoparticles. The average polarization is strictly related to the polarization induced by the external field, while the local polarization can be very different from the one induced by the external field. This is important for the excitation of single molecules, e.g., different components of scattering from single molecules can be used for their efficient detection.
Steady-state entanglement in levitated optomechanical systems coupled to a higher order excited atomic ensemble

NASA Astrophysics Data System (ADS)

Chen, Aixi; Nie, Wenjie; Li, Ling; Zeng, Wei; Liao, Qinghong; Xiao, Xianbo

2017-11-01

We investigate the steady-state entanglement in an optomechanical system with a levitated dielectric nanosphere and a higher order excited atomic ensemble. The single nanosphere is trapped by an external harmonic dipole trap and coupled to the single-mode cavity field by the effective optomechanical coupling, which depends on the steady-state position of the nanosphere. We show that the steady-state optomechanical entanglement can be generated via the effective optomechanical interaction between the mechanical motion and the cavity mode. Further, these exist an optimal effective cavity detuning that maximizes the optomechanical entanglement. We also analyze in detail the influences of the excitation number of atoms, the radius of the nanosphere and the thermal noise strength on the steady-state optomechanical entanglement. It is found that the steady-state entanglement can be enhanced by increasing the excitation number of atoms and the radius of the nanosphere.
Ensemble averaged structure–function relationship for nanocrystals: effective superparamagnetic Fe clusters with catalytically active Pt skin

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

Petkov, Valeri; Prasai, Binay; Shastri, Sarvjit

2017-09-12

Practical applications require the production and usage of metallic nanocrystals (NCs) in large ensembles. Besides, due to their cluster-bulk solid duality, metallic NCs exhibit a large degree of structural diversity. This poses the question as to what atomic-scale basis is to be used when the structure–function relationship for metallic NCs is to be quantified precisely. In this paper, we address the question by studying bi-functional Fe core-Pt skin type NCs optimized for practical applications. In particular, the cluster-like Fe core and skin-like Pt surface of the NCs exhibit superparamagnetic properties and a superb catalytic activity for the oxygen reduction reaction,more » respectively. We determine the atomic-scale structure of the NCs by non-traditional resonant high-energy X-ray diffraction coupled to atomic pair distribution function analysis. Using the experimental structure data we explain the observed magnetic and catalytic behavior of the NCs in a quantitative manner. Lastly, we demonstrate that NC ensemble-averaged 3D positions of atoms obtained by advanced X-ray scattering techniques are a very proper basis for not only establishing but also quantifying the structure–function relationship for the increasingly complex metallic NCs explored for practical applications.« less
Insights into the deterministic skill of air quality ensembles ...

EPA Pesticide Factsheets

Simulations from chemical weather models are subject to uncertainties in the input data (e.g. emission inventory, initial and boundary conditions) as well as those intrinsic to the model (e.g. physical parameterization, chemical mechanism). Multi-model ensembles can improve the forecast skill, provided that certain mathematical conditions are fulfilled. In this work, four ensemble methods were applied to two different datasets, and their performance was compared for ozone (O3), nitrogen dioxide (NO2) and particulate matter (PM10). Apart from the unconditional ensemble average, the approach behind the other three methods relies on adding optimum weights to members or constraining the ensemble to those members that meet certain conditions in time or frequency domain. The two different datasets were created for the first and second phase of the Air Quality Model Evaluation International Initiative (AQMEII). The methods are evaluated against ground level observations collected from the EMEP (European Monitoring and Evaluation Programme) and AirBase databases. The goal of the study is to quantify to what extent we can extract predictable signals from an ensemble with superior skill over the single models and the ensemble mean. Verification statistics show that the deterministic models simulate better O3 than NO2 and PM10, linked to different levels of complexity in the represented processes. The unconditional ensemble mean achieves higher skill compared to each stati
Dicke superradiance as nondestructive probe for the state of atoms in optical lattices

NASA Astrophysics Data System (ADS)

ten Brinke, Nicolai; Schützhold, Ralf

2016-04-01

We present a proposal for a probing scheme utilizing Dicke superradiance to obtain information about ultracold atoms in optical lattices. A probe photon is absorbed collectively by an ensemble of lattice atoms generating a Dicke state. The lattice dynamics (e.g., tunneling) affects the coherence properties of that Dicke state and thus alters the superradiant emission characteristics - which in turn provides insight into the lattice (dynamics). Comparing the Bose-Hubbard and the Fermi-Hubbard model, we find similar superradiance in the strongly interacting Mott insulator regime, but crucial differences in the weakly interacting (superfluid or metallic) phase. Furthermore, we study the possibility to detect whether a quantum phase transition between the two regimes can be considered adiabatic or a quantum quench.
Prediction of conformationally dependent atomic multipole moments in carbohydrates

PubMed Central

Cardamone, Salvatore

2015-01-01

The conformational flexibility of carbohydrates is challenging within the field of computational chemistry. This flexibility causes the electron density to change, which leads to fluctuating atomic multipole moments. Quantum Chemical Topology (QCT) allows for the partitioning of an “atom in a molecule,” thus localizing electron density to finite atomic domains, which permits the unambiguous evaluation of atomic multipole moments. By selecting an ensemble of physically realistic conformers of a chemical system, one evaluates the various multipole moments at defined points in configuration space. The subsequent implementation of the machine learning method kriging delivers the evaluation of an analytical function, which smoothly interpolates between these points. This allows for the prediction of atomic multipole moments at new points in conformational space, not trained for but within prediction range. In this work, we demonstrate that the carbohydrates erythrose and threose are amenable to the above methodology. We investigate how kriging models respond when the training ensemble incorporating multiple energy minima and their environment in conformational space. Additionally, we evaluate the gains in predictive capacity of our models as the size of the training ensemble increases. We believe this approach to be entirely novel within the field of carbohydrates. For a modest training set size of 600, more than 90% of the external test configurations have an error in the total (predicted) electrostatic energy (relative to ab initio) of maximum 1 kJ mol−1 for open chains and just over 90% an error of maximum 4 kJ mol−1 for rings. © 2015 Wiley Periodicals, Inc. PMID:26547500
Prediction of conformationally dependent atomic multipole moments in carbohydrates.

PubMed

Cardamone, Salvatore; Popelier, Paul L A

2015-12-15

The conformational flexibility of carbohydrates is challenging within the field of computational chemistry. This flexibility causes the electron density to change, which leads to fluctuating atomic multipole moments. Quantum Chemical Topology (QCT) allows for the partitioning of an "atom in a molecule," thus localizing electron density to finite atomic domains, which permits the unambiguous evaluation of atomic multipole moments. By selecting an ensemble of physically realistic conformers of a chemical system, one evaluates the various multipole moments at defined points in configuration space. The subsequent implementation of the machine learning method kriging delivers the evaluation of an analytical function, which smoothly interpolates between these points. This allows for the prediction of atomic multipole moments at new points in conformational space, not trained for but within prediction range. In this work, we demonstrate that the carbohydrates erythrose and threose are amenable to the above methodology. We investigate how kriging models respond when the training ensemble incorporating multiple energy minima and their environment in conformational space. Additionally, we evaluate the gains in predictive capacity of our models as the size of the training ensemble increases. We believe this approach to be entirely novel within the field of carbohydrates. For a modest training set size of 600, more than 90% of the external test configurations have an error in the total (predicted) electrostatic energy (relative to ab initio) of maximum 1 kJ mol(-1) for open chains and just over 90% an error of maximum 4 kJ mol(-1) for rings. © 2015 Wiley Periodicals, Inc.
Stochastic simulation of the spray formation assisted by a high pressure

NASA Astrophysics Data System (ADS)

Gorokhovski, M.; Chtab-Desportes, A.; Voloshina, I.; Askarova, A.

2010-03-01

The stochastic model of spray formation in the vicinity of the injector and in the far-field has been described and assessed by comparison with measurements in Diesel-like conditions. In the proposed mesh-free approach, the 3D configuration of continuous liquid core is simulated stochastically by ensemble of spatial trajectories of the specifically introduced stochastic particles. The parameters of the stochastic process are presumed from the physics of primary atomization. The spray formation model consists in computation of spatial distribution of the probability of finding the non-fragmented liquid jet in the near-to-injector region. This model is combined with KIVA II computation of atomizing Diesel spray in two-ways. First, simultaneously with the gas phase RANS computation, the ensemble of stochastic particles is tracking and the probability field of their positions is calculated, which is used for sampling of initial locations of primary blobs. Second, the velocity increment of the gas due to the liquid injection is computed from the mean volume fraction of the simulated liquid core. Two novelties are proposed in the secondary atomization modeling. The first one is due to unsteadiness of the injection velocity. When the injection velocity increment in time is decreasing, the supplementary breakup may be induced. Therefore the critical Weber number is based on such increment. Second, a new stochastic model of the secondary atomization is proposed, in which the intermittent turbulent stretching is taken into account as the main mechanism. The measurements reported by Arcoumanis et al. (time-history of the mean axial centre-line velocity of droplet, and of the centre-line Sauter Mean Diameter), are compared with computations.
Homogenization of Doppler broadening in spin-noise spectroscopy

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

NASA Astrophysics Data System (ADS)

Niedzielski, Tomasz; Mizinski, Bartlomiej

2016-04-01

The HydroProg system has been elaborated in frame of the research project no. 2011/01/D/ST10/04171 of the National Science Centre of Poland and is steadily producing multimodel ensemble predictions of hydrograph in real time. Although there are six ensemble members available at present, the longest record of predictions and their statistics is available for two data-based models (uni- and multivariate autoregressive models). Thus, we consider 3-hour predictions of water levels, with lead times ranging from 15 to 180 minutes, computed every 15 minutes since August 2013 for the Nysa Klodzka basin (SW Poland) using the two approaches and their two-model ensemble. Since the launch of the HydroProg system there have been 12 high flow episodes, and the objective of this work is to present the performance of the two-model ensemble in the process of forecasting these events. For a sake of brevity, we limit our investigation to a single gauge located at the Nysa Klodzka river in the town of Klodzko, which is centrally located in the studied basin. We identified certain regular scenarios of how the models perform in predicting the high flows in Klodzko. At the initial phase of the high flow, well before the rising limb of hydrograph, the two-model ensemble is found to provide the most skilful prognoses of water levels. However, while forecasting the rising limb of hydrograph, either the two-model solution or the vector autoregressive model offers the best predictive performance. In addition, it is hypothesized that along with the development of the rising limb phase, the vector autoregression becomes the most skilful approach amongst the scrutinized ones. Our simple two-model exercise confirms that multimodel hydrologic ensemble predictions cannot be treated as universal solutions suitable for forecasting the entire high flow event, but their superior performance may hold only for certain phases of a high flow.
Entanglement between a Photonic Time-Bin Qubit and a Collective Atomic Spin Excitation.

PubMed

Farrera, Pau; Heinze, Georg; de Riedmatten, Hugues

2018-03-09

Entanglement between light and matter combines the advantage of long distance transmission of photonic qubits with the storage and processing capabilities of atomic qubits. To distribute photonic states efficiently over long distances several schemes to encode qubits have been investigated-time-bin encoding being particularly promising due to its robustness against decoherence in optical fibers. Here, we demonstrate the generation of entanglement between a photonic time-bin qubit and a single collective atomic spin excitation (spin wave) in a cold atomic ensemble, followed by the mapping of the atomic qubit onto another photonic qubit. A magnetic field that induces a periodic dephasing and rephasing of the atomic excitation ensures the temporal distinguishability of the two time bins and plays a central role in the entanglement generation. To analyze the generated quantum state, we use largely imbalanced Mach-Zehnder interferometers to perform projective measurements in different qubit bases and verify the entanglement by violating a Clauser-Horne-Shimony-Holt Bell inequality.
Structural Investigation of the (010) Surface of the Al13Fe4 Catalyst

NASA Astrophysics Data System (ADS)

Ledieu, J.; Gaudry, É.; Loli, L. N. Serkovic; Villaseca, S. Alarcón; de Weerd, M.-C.; Hahne, M.; Gille, P.; Grin, Y.; Dubois, J.-M.; Fournée, V.

2013-02-01

We have investigated the structure of the Al13Fe4(010) surface using both experimental and ab initio computational methods. The results indicate that the topmost surface layers correspond to incomplete puckered (P) planes present in the bulk crystal structure. The main building block of the corrugated termination consists of two adjacent pentagons of Al atoms, each centered by a protruding Fe atom. These motifs are interconnected via additional Al atoms referred to as “glue” atoms which partially desorb above 873 K. The surface structure of lower atomic density compared to the bulk P plane is explained by a strong Fe-Al-Fe covalent polar interaction that preserves intact clusters at the surface. The proposed surface model with identified Fe-containing atomic ensembles could explain the Al13Fe4 catalytic properties recently reported in line with the site-isolation concept [M. Armbrüster , Nat. Mater. 11, 690 (2012)NMAACR1476-1122].
Entanglement between a Photonic Time-Bin Qubit and a Collective Atomic Spin Excitation

NASA Astrophysics Data System (ADS)

Farrera, Pau; Heinze, Georg; de Riedmatten, Hugues

2018-03-01

Entanglement between light and matter combines the advantage of long distance transmission of photonic qubits with the storage and processing capabilities of atomic qubits. To distribute photonic states efficiently over long distances several schemes to encode qubits have been investigated—time-bin encoding being particularly promising due to its robustness against decoherence in optical fibers. Here, we demonstrate the generation of entanglement between a photonic time-bin qubit and a single collective atomic spin excitation (spin wave) in a cold atomic ensemble, followed by the mapping of the atomic qubit onto another photonic qubit. A magnetic field that induces a periodic dephasing and rephasing of the atomic excitation ensures the temporal distinguishability of the two time bins and plays a central role in the entanglement generation. To analyze the generated quantum state, we use largely imbalanced Mach-Zehnder interferometers to perform projective measurements in different qubit bases and verify the entanglement by violating a Clauser-Horne-Shimony-Holt Bell inequality.
Ensemble-based evaluation for protein structure models.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2016-06-15

Comparing protein tertiary structures is a fundamental procedure in structural biology and protein bioinformatics. Structure comparison is important particularly for evaluating computational protein structure models. Most of the model structure evaluation methods perform rigid body superimposition of a structure model to its crystal structure and measure the difference of the corresponding residue or atom positions between them. However, these methods neglect intrinsic flexibility of proteins by treating the native structure as a rigid molecule. Because different parts of proteins have different levels of flexibility, for example, exposed loop regions are usually more flexible than the core region of a protein structure, disagreement of a model to the native needs to be evaluated differently depending on the flexibility of residues in a protein. We propose a score named FlexScore for comparing protein structures that consider flexibility of each residue in the native state of proteins. Flexibility information may be extracted from experiments such as NMR or molecular dynamics simulation. FlexScore considers an ensemble of conformations of a protein described as a multivariate Gaussian distribution of atomic displacements and compares a query computational model with the ensemble. We compare FlexScore with other commonly used structure similarity scores over various examples. FlexScore agrees with experts' intuitive assessment of computational models and provides information of practical usefulness of models. https://bitbucket.org/mjamroz/flexscore dkihara@purdue.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.
Ensemble-based evaluation for protein structure models

PubMed Central

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2016-01-01

Motivation: Comparing protein tertiary structures is a fundamental procedure in structural biology and protein bioinformatics. Structure comparison is important particularly for evaluating computational protein structure models. Most of the model structure evaluation methods perform rigid body superimposition of a structure model to its crystal structure and measure the difference of the corresponding residue or atom positions between them. However, these methods neglect intrinsic flexibility of proteins by treating the native structure as a rigid molecule. Because different parts of proteins have different levels of flexibility, for example, exposed loop regions are usually more flexible than the core region of a protein structure, disagreement of a model to the native needs to be evaluated differently depending on the flexibility of residues in a protein. Results: We propose a score named FlexScore for comparing protein structures that consider flexibility of each residue in the native state of proteins. Flexibility information may be extracted from experiments such as NMR or molecular dynamics simulation. FlexScore considers an ensemble of conformations of a protein described as a multivariate Gaussian distribution of atomic displacements and compares a query computational model with the ensemble. We compare FlexScore with other commonly used structure similarity scores over various examples. FlexScore agrees with experts’ intuitive assessment of computational models and provides information of practical usefulness of models. Availability and implementation: https://bitbucket.org/mjamroz/flexscore Contact: dkihara@purdue.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307633
Fundamental limitations of cavity-assisted atom interferometry

NASA Astrophysics Data System (ADS)

Dovale-Álvarez, M.; Brown, D. D.; Jones, A. W.; Mow-Lowry, C. M.; Miao, H.; Freise, A.

2017-11-01

Atom interferometers employing optical cavities to enhance the beam splitter pulses promise significant advances in science and technology, notably for future gravitational wave detectors. Long cavities, on the scale of hundreds of meters, have been proposed in experiments aiming to observe gravitational waves with frequencies below 1 Hz, where laser interferometers, such as LIGO, have poor sensitivity. Alternatively, short cavities have also been proposed for enhancing the sensitivity of more portable atom interferometers. We explore the fundamental limitations of two-mirror cavities for atomic beam splitting, and establish upper bounds on the temperature of the atomic ensemble as a function of cavity length and three design parameters: the cavity g factor, the bandwidth, and the optical suppression factor of the first and second order spatial modes. A lower bound to the cavity bandwidth is found which avoids elongation of the interaction time and maximizes power enhancement. An upper limit to cavity length is found for symmetric two-mirror cavities, restricting the practicality of long baseline detectors. For shorter cavities, an upper limit on the beam size was derived from the geometrical stability of the cavity. These findings aim to aid the design of current and future cavity-assisted atom interferometers.
NMR Studies of Dynamic Biomolecular Conformational Ensembles

PubMed Central

Torchia, Dennis A.

2015-01-01

Multidimensional heteronuclear NMR approaches can provide nearly complete sequential signal assignments of isotopically enriched biomolecules. The availability of assignments together with measurements of spin relaxation rates, residual spin interactions, J-couplings and chemical shifts provides information at atomic resolution about internal dynamics on timescales ranging from ps to ms, both in solution and in the solid state. However, due to the complexity of biomolecules, it is not possible to extract a unique atomic-resolution description of biomolecular motions even from extensive NMR data when many conformations are sampled on multiple timescales. For this reason, powerful computational approaches are increasingly applied to large NMR data sets to elucidate conformational ensembles sampled by biomolecules. In the past decade, considerable attention has been directed at an important class of biomolecules that function by binding to a wide variety of target molecules. Questions of current interest are: “Does the free biomolecule sample a conformational ensemble that encompasses the conformations found when it binds to various targets; and if so, on what time scale is the ensemble sampled?” This article reviews recent efforts to answer these questions, with a focus on comparing ensembles obtained for the same biomolecules by different investigators. A detailed comparison of results obtained is provided for three biomolecules: ubiquitin, calmodulin and the HIV-1 trans-activation response RNA. PMID:25669739

Ramsey interferometry of Rydberg ensembles inside microwave cavities

NASA Astrophysics Data System (ADS)

Sommer, Christian; Genes, Claudiu

2018-06-01

We study ensembles of Rydberg atoms in a confined electromagnetic environment such as is provided by a microwave cavity. The competition between standard free space Ising type and cavity-mediated interactions leads to the emergence of different regimes where the particle‑particle couplings range from the typical van der Waals r ‑6 behavior to r ‑3 and to r-independence. We apply a Ramsey spectroscopic technique to map the two-body interactions into a characteristic signal such as intensity and contrast decay curves. As opposed to previous treatments requiring high-densities for considerable contrast and phase decay (Takei et al 2016 Nat. Comms. 7 13449; Sommer et al 2016 Phys. Rev. A 94 053607), the cavity scenario can exhibit similar behavior at much lower densities.
Temporal correlation and correlated momentum distribution in nonsequential double ionization of Mg by circularly polarized laser fields

NASA Astrophysics Data System (ADS)

Xu, Tong-Tong; Ben, Shuai; Guo, Pei-Ying; Song, Kai-Li; Zhang, Jun; Liu, Xue-Shen

2017-07-01

We use the classical ensemble method to investigate the nonsequential double ionization (NSDI) process of Mg atoms in circularly polarized laser fields at a lower laser intensity. We illustrate the temporal correlation of the ‘side-by-side’ and the ‘back-to-back emission’. It indicates that the two electrons are more likely to be emitted at the same time for the ‘side-by-side emission’. We demonstrate the electronic trajectories from recollision-induced ionization (RII) and recollision-induced excitation with subsequent ionization (RESI). The distribution of the angle between the two ionized directions of the two electrons and the ion momentum distribution show that the anticorrelation distribution is dominant in the RESI mechanism and correlation distribution is dominant in the RII mechanism. The momentum distributions of Mg atoms for the slow and the fast electrons present a similar structure to the experimental observation of Ar atoms by Liu et al 2014 (Phys. Rev. Lett. 112 013003).
A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent

NASA Astrophysics Data System (ADS)

Higo, Junichi; Umezawa, Koji; Nakamura, Haruki

2013-05-01

We propose a novel generalized ensemble method, a virtual-system coupled multicanonical molecular dynamics (V-McMD), to enhance conformational sampling of biomolecules expressed by an all-atom model in an explicit solvent. In this method, a virtual system, of which physical quantities can be set arbitrarily, is coupled with the biomolecular system, which is the target to be studied. This method was applied to a system of an Endothelin-1 derivative, KR-CSH-ET1, known to form an antisymmetric homodimer at room temperature. V-McMD was performed starting from a configuration in which two KR-CSH-ET1 molecules were mutually distant in an explicit solvent. The lowest free-energy state (the most thermally stable state) at room temperature coincides with the experimentally determined native complex structure. This state was separated to other non-native minor clusters by a free-energy barrier, although the barrier disappeared with elevated temperature. V-McMD produced a canonical ensemble faster than a conventional McMD method.
Expected distributions of root-mean-square positional deviations in proteins.

PubMed

Pitera, Jed W

2014-06-19

The atom positional root-mean-square deviation (RMSD) is a standard tool for comparing the similarity of two molecular structures. It is used to characterize the quality of biomolecular simulations, to cluster conformations, and as a reaction coordinate for conformational changes. This work presents an approximate analytic form for the expected distribution of RMSD values for a protein or polymer fluctuating about a stable native structure. The mean and maximum of the expected distribution are independent of chain length for long chains and linearly proportional to the average atom positional root-mean-square fluctuations (RMSF). To approximate the RMSD distribution for random-coil or unfolded ensembles, numerical distributions of RMSD were generated for ensembles of self-avoiding and non-self-avoiding random walks. In both cases, for all reference structures tested for chains more than three monomers long, the distributions have a maximum distant from the origin with a power-law dependence on chain length. The purely entropic nature of this result implies that care must be taken when interpreting stable high-RMSD regions of the free-energy landscape as "intermediates" or well-defined stable states.
Quantum memory Quantum memory

NASA Astrophysics Data System (ADS)

Le Gouët, Jean-Louis; Moiseev, Sergey

2012-06-01

Interaction of quantum radiation with multi-particle ensembles has sparked off intense research efforts during the past decade. Emblematic of this field is the quantum memory scheme, where a quantum state of light is mapped onto an ensemble of atoms and then recovered in its original shape. While opening new access to the basics of light-atom interaction, quantum memory also appears as a key element for information processing applications, such as linear optics quantum computation and long-distance quantum communication via quantum repeaters. Not surprisingly, it is far from trivial to practically recover a stored quantum state of light and, although impressive progress has already been accomplished, researchers are still struggling to reach this ambitious objective. This special issue provides an account of the state-of-the-art in a fast-moving research area that makes physicists, engineers and chemists work together at the forefront of their discipline, involving quantum fields and atoms in different media, magnetic resonance techniques and material science. Various strategies have been considered to store and retrieve quantum light. The explored designs belong to three main—while still overlapping—classes. In architectures derived from photon echo, information is mapped over the spectral components of inhomogeneously broadened absorption bands, such as those encountered in rare earth ion doped crystals and atomic gases in external gradient magnetic field. Protocols based on electromagnetic induced transparency also rely on resonant excitation and are ideally suited to the homogeneous absorption lines offered by laser cooled atomic clouds or ion Coulomb crystals. Finally off-resonance approaches are illustrated by Faraday and Raman processes. Coupling with an optical cavity may enhance the storage process, even for negligibly small atom number. Multiple scattering is also proposed as a way to enlarge the quantum interaction distance of light with matter. The quest for higher efficiency, better fidelity, broader bandwidth, multimode capacity and longer storage lifetime is pursued in all those approaches, as shown in this special issue. The improvement of quantum memory operation specifically requires in-depth study and control of numerous physical processes leading to atomic decoherence. The present issue reflects the development of rare earth ion doped matrices offering long lifetime superposition states, either as bulk crystals or as optical waveguides. The need for quantum sources and high efficiency detectors at the single photon level is also illustrated. Several papers address the networking of quantum memories either in long-haul cryptography or in the prospect of quantum processing. In this context, much attention has been paid recently to interfacing quantum light with superconducting qubits and with nitrogen-vacancy centers in diamond. Finally, the quantum interfacing of light with matter raises questions on entanglement. The last two papers are devoted to the generation of entanglement by dissipative processes. It is shown that long lifetime entanglement may be built in this way. We hope this special issue will help readers to become familiar with the exciting field of ensemble-based quantum memories and will stimulate them to bring deeper insights and new ideas to this area.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuraptsev, A. S., E-mail: aleksej-kurapcev@yandex.ru; Sokolov, I. M.

We develop a consistent quantum theory of the collective effects that take place when electromagnetic radiation interacts with a dense ensemble of impurity centers embedded in a transparent dielectric and placed in a Fabry–Perot cavity. We have calculated the spontaneous decay dynamics of an excited impurity atom as a specific example of applying the developed general theory. We analyze the dependence of the decay rate on the density of impurity centers and the sample sizes as well as on the characteristic level shifts of impurity atoms caused by the internal fields of the dielectric. We show that a cavity canmore » affect significantly the pattern of collective processes, in particular, the lifetimes of collective states.« less
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.
Ensemble density variational methods with self- and ghost-interaction-corrected functionals

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

Pastorczak, Ewa; Pernal, Katarzyna, E-mail: pernalk@gmail.com

2014-05-14

Ensemble density functional theory (DFT) offers a way of predicting excited-states energies of atomic and molecular systems without referring to a density response function. Despite a significant theoretical work, practical applications of the proposed approximations have been scarce and they do not allow for a fair judgement of the potential usefulness of ensemble DFT with available functionals. In the paper, we investigate two forms of ensemble density functionals formulated within ensemble DFT framework: the Gross, Oliveira, and Kohn (GOK) functional proposed by Gross et al. [Phys. Rev. A 37, 2809 (1988)] alongside the orbital-dependent eDFT form of the functional introducedmore » by Nagy [J. Phys. B 34, 2363 (2001)] (the acronym eDFT proposed in analogy to eHF – ensemble Hartree-Fock method). Local and semi-local ground-state density functionals are employed in both approaches. Approximate ensemble density functionals contain not only spurious self-interaction but also the so-called ghost-interaction which has no counterpart in the ground-state DFT. We propose how to correct the GOK functional for both kinds of interactions in approximations that go beyond the exact-exchange functional. Numerical applications lead to a conclusion that functionals free of the ghost-interaction by construction, i.e., eDFT, yield much more reliable results than approximate self- and ghost-interaction-corrected GOK functional. Additionally, local density functional corrected for self-interaction employed in the eDFT framework yields excitations energies of the accuracy comparable to that of the uncorrected semi-local eDFT functional.« less
Phase-insensitive storage of coherences by reversible mapping onto long-lived populations

NASA Astrophysics Data System (ADS)

Mieth, Simon; Genov, Genko T.; Yatsenko, Leonid P.; Vitanov, Nikolay V.; Halfmann, Thomas

2016-01-01

We theoretically develop and experimentally demonstrate a coherence population mapping (CPM) protocol to store atomic coherences in long-lived populations, enabling storage times far beyond the typically very short decoherence times of quantum systems. The amplitude and phase of an atomic coherence is written onto the populations of a three-state system by specifically designed sequences of radiation pulses from two coupling fields. As an important feature, the CPM sequences enable a retrieval efficiency, which is insensitive to the phase of the initial coherence. The information is preserved in every individual atom of the medium, enabling applications in purely homogeneously or inhomogeneously broadened ensembles even when stochastic phase jumps are the main source of decoherence. We experimentally confirm the theoretical predictions by applying CPM for storage of atomic coherences in a doped solid, reaching storage times in the regime of 1 min.
Large Fizeau's light-dragging effect in a moving electromagnetically induced transparent medium.

PubMed

Kuan, Pei-Chen; Huang, Chang; Chan, Wei Sheng; Kosen, Sandoko; Lan, Shau-Yu

2016-10-03

As one of the most influential experiments on the development of modern macroscopic theory from Newtonian mechanics to Einstein's special theory of relativity, the phenomenon of light dragging in a moving medium has been discussed and observed extensively in different types of systems. To have a significant dragging effect, the long duration of light travelling in the medium is preferred. Here we demonstrate a light-dragging experiment in an electromagnetically induced transparent cold atomic ensemble and enhance the dragging effect by at least three orders of magnitude compared with the previous experiments. With a large enhancement of the dragging effect, we realize an atom-based velocimeter that has a sensitivity two orders of magnitude higher than the velocity width of the atomic medium used. Such a demonstration could pave the way for motional sensing using the collective state of atoms in a room temperature vapour cell or solid state material.
A fully-nonlocal energy-based formulation and high-performance realization of the quasicontinuum method

NASA Astrophysics Data System (ADS)

Amelang, Jeff

The quasicontinuum (QC) method was introduced to coarse-grain crystalline atomic ensembles in order to bridge the scales from individual atoms to the micro- and mesoscales. Though many QC formulations have been proposed with varying characteristics and capabilities, a crucial cornerstone of all QC techniques is the concept of summation rules, which attempt to efficiently approximate the total Hamiltonian of a crystalline atomic ensemble by a weighted sum over a small subset of atoms. In this work we propose a novel, fully-nonlocal, energy-based formulation of the QC method with support for legacy and new summation rules through a general energy-sampling scheme. Our formulation does not conceptually differentiate between atomistic and coarse-grained regions and thus allows for seamless bridging without domain-coupling interfaces. Within this structure, we introduce a new class of summation rules which leverage the affine kinematics of this QC formulation to most accurately integrate thermodynamic quantities of interest. By comparing this new class of summation rules to commonly-employed rules through analysis of energy and spurious force errors, we find that the new rules produce no residual or spurious force artifacts in the large-element limit under arbitrary affine deformation, while allowing us to seamlessly bridge to full atomistics. We verify that the new summation rules exhibit significantly smaller force artifacts and energy approximation errors than all comparable previous summation rules through a comprehensive suite of examples with spatially non-uniform QC discretizations in two and three dimensions. Due to the unique structure of these summation rules, we also use the new formulation to study scenarios with large regions of free surface, a class of problems previously out of reach of the QC method. Lastly, we present the key components of a high-performance, distributed-memory realization of the new method, including a novel algorithm for supporting unparalleled levels of deformation. Overall, this new formulation and implementation allows us to efficiently perform simulations containing an unprecedented number of degrees of freedom with low approximation error.
Light storage in a cold atomic ensemble with a high optical depth

NASA Astrophysics Data System (ADS)

Park, Kwang-Kyoon; Chough, Young-Tak; Kim, Yoon-Ho

2017-06-01

A quantum memory with a high storage efficiency and a long coherence time is an essential element in quantum information applications. Here, we report our recent development of an optical quantum memory with a rubidium-87 cold atom ensemble. By increasing the optical depth of the medium, we have achieved a storage efficiency of 65% and a coherence time of 51 μs for a weak laser pulse. The result of a numerical analysis based on the Maxwell-Bloch equations agrees well with the experimental results. Our result paves the way toward an efficient optical quantum memory and may find applications in photonic quantum information processing.
From deep TLS validation to ensembles of atomic models built from elemental motions

DOE PAGES

Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.; ...

2015-07-28

The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy severalmore » conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.« less
Coherent coupling of a superconducting flux qubit to an electron spin ensemble in diamond.

PubMed

Zhu, Xiaobo; Saito, Shiro; Kemp, Alexander; Kakuyanagi, Kosuke; Karimoto, Shin-ichi; Nakano, Hayato; Munro, William J; Tokura, Yasuhiro; Everitt, Mark S; Nemoto, Kae; Kasu, Makoto; Mizuochi, Norikazu; Semba, Kouichi

2011-10-12

During the past decade, research into superconducting quantum bits (qubits) based on Josephson junctions has made rapid progress. Many foundational experiments have been performed, and superconducting qubits are now considered one of the most promising systems for quantum information processing. However, the experimentally reported coherence times are likely to be insufficient for future large-scale quantum computation. A natural solution to this problem is a dedicated engineered quantum memory based on atomic and molecular systems. The question of whether coherent quantum coupling is possible between such natural systems and a single macroscopic artificial atom has attracted considerable attention since the first demonstration of macroscopic quantum coherence in Josephson junction circuits. Here we report evidence of coherent strong coupling between a single macroscopic superconducting artificial atom (a flux qubit) and an ensemble of electron spins in the form of nitrogen-vacancy colour centres in diamond. Furthermore, we have observed coherent exchange of a single quantum of energy between a flux qubit and a macroscopic ensemble consisting of about 3 × 10(7) such colour centres. This provides a foundation for future quantum memories and hybrid devices coupling microwave and optical systems.
Modified dipole-dipole interaction and dissipation in an atomic ensemble near surfaces

NASA Astrophysics Data System (ADS)

Jones, Ryan; Needham, Jemma A.; Lesanovsky, Igor; Intravaia, Francesco; Olmos, Beatriz

2018-05-01

We study how the radiative properties of a dense ensemble of atoms can be modified when they are placed near or between metallic or dielectric surfaces. If the average separation between the atoms is comparable or smaller than the wavelength of the scattered photons, the coupling to the radiation field induces long-range coherent interactions based on the interatomic exchange of virtual photons. Moreover, the incoherent scattering of photons back to the electromagnetic field is known to be a many-body process, characterized by the appearance of superradiant and subradiant emission modes. By changing the radiation field properties, in this case by considering a layered medium where the atoms are near metallic or dielectric surfaces, these scattering properties can be dramatically modified. We perform a detailed study of these effects, with focus on experimentally relevant parameter regimes. We finish with a specific application in the context of quantum information storage, where the presence of a nearby surface is shown to increase the storage time of an atomic excitation that is transported across a one-dimensional chain.
Statistical properties and condensate fluctuation of attractive Bose gas with finite number of particles

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Biedermann, G. W.; McGuinness, H. J.; Rakholia, A. V.

Here, we demonstrate matter-wave interference in a warm vapor of rubidium atoms. Established approaches to light-pulse atom interferometry rely on laser cooling to concentrate a large ensemble of atoms into a velocity class resonant with the atom optical light pulse. In our experiment, we show that clear interference signals may be obtained without laser cooling. This effect relies on the Doppler selectivity of the atom interferometer resonance. Lastly, this interferometer may be configured to measure accelerations, and we demonstrate that multiple interferometers may be operated simultaneously by addressing multiple velocity classes.
Development of an Atom Interferometer Gravity Gradiometer for Earth Sciences

NASA Technical Reports Server (NTRS)

Rakholia, A.; Sugarbaker, A.; Black, A.; Kasecivh, M.; Saif, B.; Luthcke, S.; Callahan, L.; Seery, B.; Feinberg, L.; Mather, J.;

2017-01-01

We report progress towards a prototype atom interferometer gravity gradiometer for Earth science studies from a satellite in low Earth orbit.The terrestrial prototype has a target sensitivity of 8 x 10(exp -2) E/Hz(sup 1/2) and consists of two atom sources running simultaneous interferometers with interrogation time T = 300 ms and 12 hk photon recoils, separated by a baseline of 2 m. By employing Raman side band cooling and magnetic lensing, we will generate atomic ensembles with N = 10(exp 6) atoms at a temperature of 3 nK. The sensitivity extrapolates to 7 x 10(exp -5) E/Hz(sup 1/2) in microgravity on board a satellite. Simulations derived from this sensitivity demonstrate a monthly time-variable gravity accuracy of 1 cm equivalent water height at 200 km resolution, yielding an improvement over GRACE by 1-2 orders of magnitude. A gravity gradiometer with this sensitivity would also benefit future planetary, lunar, and asteroidal missions.

Invariant measures in brain dynamics

NASA Astrophysics Data System (ADS)

Boyarsky, Abraham; Góra, Paweł

2006-10-01

This note concerns brain activity at the level of neural ensembles and uses ideas from ergodic dynamical systems to model and characterize chaotic patterns among these ensembles during conscious mental activity. Central to our model is the definition of a space of neural ensembles and the assumption of discrete time ensemble dynamics. We argue that continuous invariant measures draw the attention of deeper brain processes, engendering emergent properties such as consciousness. Invariant measures supported on a finite set of ensembles reflect periodic behavior, whereas the existence of continuous invariant measures reflect the dynamics of nonrepeating ensemble patterns that elicit the interest of deeper mental processes. We shall consider two different ways to achieve continuous invariant measures on the space of neural ensembles: (1) via quantum jitters, and (2) via sensory input accompanied by inner thought processes which engender a “folding” property on the space of ensembles.

Nanosystem self-assembly pathways discovered via all-atom multiscale analysis.

PubMed

Pankavich, Stephen D; Ortoleva, Peter J

2012-07-26

We consider the self-assembly of composite structures from a group of nanocomponents, each consisting of particles within an N-atom system. Self-assembly pathways and rates for nanocomposites are derived via a multiscale analysis of the classical Liouville equation. From a reduced statistical framework, rigorous stochastic equations for population levels of beginning, intermediate, and final aggregates are also derived. It is shown that the definition of an assembly type is a self-consistency criterion that must strike a balance between precision and the need for population levels to be slowly varying relative to the time scale of atomic motion. The deductive multiscale approach is complemented by a qualitative notion of multicomponent association and the ensemble of exact atomic-level configurations consistent with them. In processes such as viral self-assembly from proteins and RNA or DNA, there are many possible intermediates, so that it is usually difficult to predict the most efficient assembly pathway. However, in the current study, rates of assembly of each possible intermediate can be predicted. This avoids the need, as in a phenomenological approach, for recalibration with each new application. The method accounts for the feedback across scales in space and time that is fundamental to nanosystem self-assembly. The theory has applications to bionanostructures, geomaterials, engineered composites, and nanocapsule therapeutic delivery systems.
A dark-line two-dimensional magneto-optical trap of 85Rb atoms with high optical depth.

PubMed

Zhang, Shanchao; Chen, J F; Liu, Chang; Zhou, Shuyu; Loy, M M T; Wong, G K L; Du, Shengwang

2012-07-01

We describe the apparatus of a dark-line two-dimensional (2D) magneto-optical trap (MOT) of (85)Rb cold atoms with high optical depth (OD). Different from the conventional configuration, two (of three) pairs of trapping laser beams in our 2D MOT setup do not follow the symmetry axes of the quadrupole magnetic field: they are aligned with 45° angles to the longitudinal axis. Two orthogonal repumping laser beams have a dark-line volume in the longitudinal axis at their cross over. With a total trapping laser power of 40 mW and repumping laser power of 18 mW, we obtain an atomic OD up to 160 in an electromagnetically induced transparency (EIT) scheme, which corresponds to an atomic-density-length product NL = 2.05 × 10(15) m(-2). In a closed two-state system, the OD can become as large as more than 600. Our 2D MOT configuration allows full optical access of the atoms in its longitudinal direction without interfering with the trapping and repumping laser beams spatially. Moreover, the zero magnetic field along the longitudinal axis allows the cold atoms maintain a long ground-state coherence time without switching off the MOT magnetic field, which makes it possible to operate the MOT at a high repetition rate and a high duty cycle. Our 2D MOT is ideal for atomic-ensemble-based quantum optics applications, such as EIT, entangled photon pair generation, optical quantum memory, and quantum information processing.
Energy-efficient quantum frequency estimation

NASA Astrophysics Data System (ADS)

Liuzzo-Scorpo, Pietro; Correa, Luis A.; Pollock, Felix A.; Górecka, Agnieszka; Modi, Kavan; Adesso, Gerardo

2018-06-01

The problem of estimating the frequency of a two-level atom in a noisy environment is studied. Our interest is to minimise both the energetic cost of the protocol and the statistical uncertainty of the estimate. In particular, we prepare a probe in a ‘GHZ-diagonal’ state by means of a sequence of qubit gates applied on an ensemble of n atoms in thermal equilibrium. Noise is introduced via a phenomenological time-non-local quantum master equation, which gives rise to a phase-covariant dissipative dynamics. After an interval of free evolution, the n-atom probe is globally measured at an interrogation time chosen to minimise the error bars of the final estimate. We model explicitly a measurement scheme which becomes optimal in a suitable parameter range, and are thus able to calculate the total energetic expenditure of the protocol. Interestingly, we observe that scaling up our multipartite entangled probes offers no precision enhancement when the total available energy {\\boldsymbol{ \\mathcal E }} is limited. This is at stark contrast with standard frequency estimation, where larger probes—more sensitive but also more ‘expensive’ to prepare—are always preferred. Replacing {\\boldsymbol{ \\mathcal E }} by the resource that places the most stringent limitation on each specific experimental setup, would thus help to formulate more realistic metrological prescriptions.
Unbiased, scalable sampling of protein loop conformations from probabilistic priors.

PubMed

Zhang, Yajia; Hauser, Kris

2013-01-01

Protein loops are flexible structures that are intimately tied to function, but understanding loop motion and generating loop conformation ensembles remain significant computational challenges. Discrete search techniques scale poorly to large loops, optimization and molecular dynamics techniques are prone to local minima, and inverse kinematics techniques can only incorporate structural preferences in adhoc fashion. This paper presents Sub-Loop Inverse Kinematics Monte Carlo (SLIKMC), a new Markov chain Monte Carlo algorithm for generating conformations of closed loops according to experimentally available, heterogeneous structural preferences. Our simulation experiments demonstrate that the method computes high-scoring conformations of large loops (>10 residues) orders of magnitude faster than standard Monte Carlo and discrete search techniques. Two new developments contribute to the scalability of the new method. First, structural preferences are specified via a probabilistic graphical model (PGM) that links conformation variables, spatial variables (e.g., atom positions), constraints and prior information in a unified framework. The method uses a sparse PGM that exploits locality of interactions between atoms and residues. Second, a novel method for sampling sub-loops is developed to generate statistically unbiased samples of probability densities restricted by loop-closure constraints. Numerical experiments confirm that SLIKMC generates conformation ensembles that are statistically consistent with specified structural preferences. Protein conformations with 100+ residues are sampled on standard PC hardware in seconds. Application to proteins involved in ion-binding demonstrate its potential as a tool for loop ensemble generation and missing structure completion.
Unbiased, scalable sampling of protein loop conformations from probabilistic priors

PubMed Central

2013-01-01

Background Protein loops are flexible structures that are intimately tied to function, but understanding loop motion and generating loop conformation ensembles remain significant computational challenges. Discrete search techniques scale poorly to large loops, optimization and molecular dynamics techniques are prone to local minima, and inverse kinematics techniques can only incorporate structural preferences in adhoc fashion. This paper presents Sub-Loop Inverse Kinematics Monte Carlo (SLIKMC), a new Markov chain Monte Carlo algorithm for generating conformations of closed loops according to experimentally available, heterogeneous structural preferences. Results Our simulation experiments demonstrate that the method computes high-scoring conformations of large loops (>10 residues) orders of magnitude faster than standard Monte Carlo and discrete search techniques. Two new developments contribute to the scalability of the new method. First, structural preferences are specified via a probabilistic graphical model (PGM) that links conformation variables, spatial variables (e.g., atom positions), constraints and prior information in a unified framework. The method uses a sparse PGM that exploits locality of interactions between atoms and residues. Second, a novel method for sampling sub-loops is developed to generate statistically unbiased samples of probability densities restricted by loop-closure constraints. Conclusion Numerical experiments confirm that SLIKMC generates conformation ensembles that are statistically consistent with specified structural preferences. Protein conformations with 100+ residues are sampled on standard PC hardware in seconds. Application to proteins involved in ion-binding demonstrate its potential as a tool for loop ensemble generation and missing structure completion. PMID:24565175
Atom Interferometry in a Warm Vapor

DOE PAGES

Biedermann, G. W.; McGuinness, H. J.; Rakholia, A. V.; ...

2017-04-17

Here, we demonstrate matter-wave interference in a warm vapor of rubidium atoms. Established approaches to light-pulse atom interferometry rely on laser cooling to concentrate a large ensemble of atoms into a velocity class resonant with the atom optical light pulse. In our experiment, we show that clear interference signals may be obtained without laser cooling. This effect relies on the Doppler selectivity of the atom interferometer resonance. Lastly, this interferometer may be configured to measure accelerations, and we demonstrate that multiple interferometers may be operated simultaneously by addressing multiple velocity classes.
Atom-chip-based interferometry with Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Gebbe, Martina; Abend, Sven; Gersemann, Matthias; Ahlers, Holger; Muentinga, Hauke; Herrmann, Sven; Laemmerzahl, Claus; Ertmer, Wolfgang; Rasel, Ernst M.; Quantus Collaboration

2017-04-01

Due to their small spatial and momentum width ultracold Bose-Einstein condensates (BEC) or even delta-kick collimated (DKC) atomic ensembles are very well suited for high precision atom interferometry and measure, for example, inertial forces with high accuracy. We generate such an ensemble in a miniaturized atom-chip setup, where BEC generation and DKC can be performed in a fast and reliable way. Using the chip as a retroreflector we have realized the first atom-chip-based gravimeter. All atom-optical operations including detection take place inside a volume of a one centimeter cube. In order to investigate new geometries we studied symmetric double Bragg diffraction as well as the coherent acceleration of atoms with Bloch oscillations. By combining both techniques we developed a novel relaunch mechanism, which we use to span a fountain geometry within our gravimeter. The relaunch increases the free fall time and, thus, enhances the device's sensitivity. Additionally, we employ these techniques to implement symmetric scalable large momentum beam splitters. This work is supported by the CRC 1128 geo-Q and the DLR with funds provided by the Federal Ministry of Economic Affairs and Energy (BMWi) due to an enactment of the German Bundestag under Grant No. DLR 50WM1552-1557 (QUANTUS-IV-Fallturm).
Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry

PubMed Central

Walker, Peter

2017-01-01

Abstract The conformational ensembles of structured RNA's are crucial for biological function, but they remain difficult to elucidate experimentally. We demonstrate with HIV-1 TAR RNA that X-ray scattering interferometry (XSI) can be used to determine RNA conformational ensembles. X-ray scattering interferometry (XSI) is based on site-specifically labeling RNA with pairs of heavy atom probes, and precisely measuring the distribution of inter-probe distances that arise from a heterogeneous mixture of RNA solution structures. We show that the XSI-based model of the TAR RNA ensemble closely resembles an independent model derived from NMR-RDC data. Further, we show how the TAR RNA ensemble changes shape at different salt concentrations. Finally, we demonstrate that a single hybrid model of the TAR RNA ensemble simultaneously fits both the XSI and NMR-RDC data set and show that XSI can be combined with NMR-RDC to further improve the quality of the determined ensemble. The results suggest that XSI-RNA will be a powerful approach for characterizing the solution conformational ensembles of RNAs and RNA-protein complexes under diverse solution conditions. PMID:28108663
Quantum memory with optically trapped atoms.

PubMed

Chuu, Chih-Sung; Strassel, Thorsten; Zhao, Bo; Koch, Markus; Chen, Yu-Ao; Chen, Shuai; Yuan, Zhen-Sheng; Schmiedmayer, Jörg; Pan, Jian-Wei

2008-09-19

We report the experimental demonstration of quantum memory for collective atomic states in a far-detuned optical dipole trap. Generation of the collective atomic state is heralded by the detection of a Raman scattered photon and accompanied by storage in the ensemble of atoms. The optical dipole trap provides confinement for the atoms during the quantum storage while retaining the atomic coherence. We probe the quantum storage by cross correlation of the photon pair arising from the Raman scattering and the retrieval of the atomic state stored in the memory. Nonclassical correlations are observed for storage times up to 60 mus.
GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.

PubMed

Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji

2015-07-01

GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310-323. doi: 10.1002/wcms.1220.
Deep neural ensemble for retinal vessel segmentation in fundus images towards achieving label-free angiography.

PubMed

Lahiri, A; Roy, Abhijit Guha; Sheet, Debdoot; Biswas, Prabir Kumar

2016-08-01

Automated segmentation of retinal blood vessels in label-free fundus images entails a pivotal role in computed aided diagnosis of ophthalmic pathologies, viz., diabetic retinopathy, hypertensive disorders and cardiovascular diseases. The challenge remains active in medical image analysis research due to varied distribution of blood vessels, which manifest variations in their dimensions of physical appearance against a noisy background. In this paper we formulate the segmentation challenge as a classification task. Specifically, we employ unsupervised hierarchical feature learning using ensemble of two level of sparsely trained denoised stacked autoencoder. First level training with bootstrap samples ensures decoupling and second level ensemble formed by different network architectures ensures architectural revision. We show that ensemble training of auto-encoders fosters diversity in learning dictionary of visual kernels for vessel segmentation. SoftMax classifier is used for fine tuning each member autoencoder and multiple strategies are explored for 2-level fusion of ensemble members. On DRIVE dataset, we achieve maximum average accuracy of 95.33% with an impressively low standard deviation of 0.003 and Kappa agreement coefficient of 0.708. Comparison with other major algorithms substantiates the high efficacy of our model.
Miniaturized Lab System for Future Cold Atom Experiments in Microgravity

NASA Astrophysics Data System (ADS)

Kulas, Sascha; Vogt, Christian; Resch, Andreas; Hartwig, Jonas; Ganske, Sven; Matthias, Jonas; Schlippert, Dennis; Wendrich, Thijs; Ertmer, Wolfgang; Maria Rasel, Ernst; Damjanic, Marcin; Weßels, Peter; Kohfeldt, Anja; Luvsandamdin, Erdenetsetseg; Schiemangk, Max; Grzeschik, Christoph; Krutzik, Markus; Wicht, Andreas; Peters, Achim; Herrmann, Sven; Lämmerzahl, Claus

2017-02-01

We present the technical realization of a compact system for performing experiments with cold 87Rb and 39K atoms in microgravity in the future. The whole system fits into a capsule to be used in the drop tower Bremen. One of the advantages of a microgravity environment is long time evolution of atomic clouds which yields higher sensitivities in atom interferometer measurements. We give a full description of the system containing an experimental chamber with ultra-high vacuum conditions, miniaturized laser systems, a high-power thulium-doped fiber laser, the electronics and the power management. In a two-stage magneto-optical trap atoms should be cooled to the low μK regime. The thulium-doped fiber laser will create an optical dipole trap which will allow further cooling to sub- μK temperatures. The presented system fulfills the demanding requirements on size and power management for cold atom experiments on a microgravity platform, especially with respect to the use of an optical dipole trap. A first test in microgravity, including the creation of a cold Rb ensemble, shows the functionality of the system.
Quantum synchronization and the no-photon laser

NASA Astrophysics Data System (ADS)

Holland, Murray

2014-03-01

This talk will present a new approach to lasers that is based on the quantum synchronization of many atoms. Such lasers are predicted to produce light of unprecedented spectral purity and coherence, some two orders of magnitude better than any system available today. The idea is based on superradiant emission, where an ensemble of atoms with an extremely narrow atomic transition can phase-lock and form a macroscopic dipole that radiates light collectively. This is quite unlike a typical laser where atoms essentially act independently. The resulting light source is expected to have a spectral linewidth of just a few millihertz and could lead to more accurate and stable atomic clocks. Atomic clocks based on optical transitions have improved tremendously in recent years, giving clocks that tick 1015 times per second, and can have a fractional stability exceeding one part in 1016. This new sharper light source aims to push the frontier even further, so that fundamental tests of physics, such as the time variation of constants and tests of gravity, might even be possible. We acknowledge support from NSF and the DARPA QuASAR program.
Optical vector network analysis of ultranarrow transitions in 166Er3+ : 7LiYF4 crystal.

PubMed

Kukharchyk, N; Sholokhov, D; Morozov, O; Korableva, S L; Cole, J H; Kalachev, A A; Bushev, P A

2018-02-15

We present optical vector network analysis (OVNA) of an isotopically purified Er166 3+ :LiYF 4 7 crystal. The OVNA method is based on generation and detection of a modulated optical sideband by using a radio-frequency vector network analyzer. This technique is widely used in the field of microwave photonics for the characterization of optical responses of optical devices such as filters and high-Q resonators. However, dense solid-state atomic ensembles induce a large phase shift on one of the optical sidebands that results in the appearance of extra features on the measured transmission response. We present a simple theoretical model that accurately describes the observed spectra and helps to reconstruct the absorption profile of a solid-state atomic ensemble as well as corresponding change of the refractive index in the vicinity of atomic resonances.
Long-distance quantum communication with atomic ensembles and linear optics.

PubMed

Duan, L M; Lukin, M D; Cirac, J I; Zoller, P

2001-11-22

Quantum communication holds promise for absolutely secure transmission of secret messages and the faithful transfer of unknown quantum states. Photonic channels appear to be very attractive for the physical implementation of quantum communication. However, owing to losses and decoherence in the channel, the communication fidelity decreases exponentially with the channel length. Here we describe a scheme that allows the implementation of robust quantum communication over long lossy channels. The scheme involves laser manipulation of atomic ensembles, beam splitters, and single-photon detectors with moderate efficiencies, and is therefore compatible with current experimental technology. We show that the communication efficiency scales polynomially with the channel length, and hence the scheme should be operable over very long distances.
Quantitative Phase Analysis of Plasma-Treated High-Silica Materials

NASA Astrophysics Data System (ADS)

Kosmachev, P. V.; Abzaev, Yu. A.; Vlasov, V. A.

2018-06-01

The paper presents the X-ray diffraction (XRD) analysis of the crystal structure of SiO2 in two modifications, namely quartzite and quartz sand before and after plasma treatment. Plasma treatment enables the raw material to melt and evaporate after which the material quenches and condenses to form nanoparticles. The Rietveld refinement method is used to identify the lattice parameters of SiO2 phases. It is found that after plasma treatment SiO2 oxides are in the amorphous state, which are modeled within the microcanonical ensemble. Experiments show that amorphous phases are stable, and model X-ray reflection intensities approximate the experimental XRD patterns with fine precision. Within the modeling, full information is obtained for SiO2 crystalline and amorphous phases, which includes atom arrangement, structural parameters, atomic population of silicon and oxygen atoms in lattice sites.
Ensemble framework based real-time respiratory motion prediction for adaptive radiotherapy applications.

PubMed

Tatinati, Sivanagaraja; Nazarpour, Kianoush; Tech Ang, Wei; Veluvolu, Kalyana C

2016-08-01

Successful treatment of tumors with motion-adaptive radiotherapy requires accurate prediction of respiratory motion, ideally with a prediction horizon larger than the latency in radiotherapy system. Accurate prediction of respiratory motion is however a non-trivial task due to the presence of irregularities and intra-trace variabilities, such as baseline drift and temporal changes in fundamental frequency pattern. In this paper, to enhance the accuracy of the respiratory motion prediction, we propose a stacked regression ensemble framework that integrates heterogeneous respiratory motion prediction algorithms. We further address two crucial issues for developing a successful ensemble framework: (1) selection of appropriate prediction methods to ensemble (level-0 methods) among the best existing prediction methods; and (2) finding a suitable generalization approach that can successfully exploit the relative advantages of the chosen level-0 methods. The efficacy of the developed ensemble framework is assessed with real respiratory motion traces acquired from 31 patients undergoing treatment. Results show that the developed ensemble framework improves the prediction performance significantly compared to the best existing methods. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.
Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation

PubMed Central

Iida, Shinji; Nakamura, Haruki; Higo, Junichi

2016-01-01

We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein–protein or protein–ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks. PMID:27288028
Correlating single-molecule and ensemble-average measurements of peptide adsorption onto different inorganic materials.

PubMed

Kim, Seong-Oh; Jackman, Joshua A; Mochizuki, Masahito; Yoon, Bo Kyeong; Hayashi, Tomohiro; Cho, Nam-Joon

2016-06-07

The coating of solid-binding peptides (SBPs) on inorganic material surfaces holds significant potential for improved surface functionalization at nano-bio interfaces. In most related studies, the goal has been to engineer peptides with selective and high binding affinity for a target material. The role of the material substrate itself in modulating the adsorption behavior of a peptide molecule remains less explored and there are few studies that compare the interaction of one peptide with different inorganic substrates. Herein, using a combination of two experimental techniques, we investigated the adsorption of a 16 amino acid-long random coil peptide to various inorganic substrates - gold, silicon oxide, titanium oxide and aluminum oxide. Quartz crystal microbalance-dissipation (QCM-D) experiments were performed in order to measure the peptide binding affinity for inorganic solid supports at the ensemble average level, and atomic force microscopy (AFM) experiments were conducted in order to determine the adhesion force of a single peptide molecule. A positive trend was observed between the total mass uptake of attached peptide and the single-molecule adhesion force on each substrate. Peptide affinity for gold was appreciably greater than for the oxide substrates. Collectively, the results obtained in this study offer insight into the ways in which inorganic materials can differentially influence and modulate the adhesion of SBPs.
Moisture Damage Modeling in Lime and Chemically Modified Asphalt at Nanolevel Using Ensemble Computational Intelligence

PubMed Central

2018-01-01

This paper measures the adhesion/cohesion force among asphalt molecules at nanoscale level using an Atomic Force Microscopy (AFM) and models the moisture damage by applying state-of-the-art Computational Intelligence (CI) techniques (e.g., artificial neural network (ANN), support vector regression (SVR), and an Adaptive Neuro Fuzzy Inference System (ANFIS)). Various combinations of lime and chemicals as well as dry and wet environments are used to produce different asphalt samples. The parameters that were varied to generate different asphalt samples and measure the corresponding adhesion/cohesion forces are percentage of antistripping agents (e.g., Lime and Unichem), AFM tips K values, and AFM tip types. The CI methods are trained to model the adhesion/cohesion forces given the variation in values of the above parameters. To achieve enhanced performance, the statistical methods such as average, weighted average, and regression of the outputs generated by the CI techniques are used. The experimental results show that, of the three individual CI methods, ANN can model moisture damage to lime- and chemically modified asphalt better than the other two CI techniques for both wet and dry conditions. Moreover, the ensemble of CI along with statistical measurement provides better accuracy than any of the individual CI techniques. PMID:29849551

Gradient Echo Quantum Memory in Warm Atomic Vapor

PubMed Central

Pinel, Olivier; Hosseini, Mahdi; Sparkes, Ben M.; Everett, Jesse L.; Higginbottom, Daniel; Campbell, Geoff T.; Lam, Ping Koy; Buchler, Ben C.

2013-01-01

Gradient echo memory (GEM) is a protocol for storing optical quantum states of light in atomic ensembles. The primary motivation for such a technology is that quantum key distribution (QKD), which uses Heisenberg uncertainty to guarantee security of cryptographic keys, is limited in transmission distance. The development of a quantum repeater is a possible path to extend QKD range, but a repeater will need a quantum memory. In our experiments we use a gas of rubidium 87 vapor that is contained in a warm gas cell. This makes the scheme particularly simple. It is also a highly versatile scheme that enables in-memory refinement of the stored state, such as frequency shifting and bandwidth manipulation. The basis of the GEM protocol is to absorb the light into an ensemble of atoms that has been prepared in a magnetic field gradient. The reversal of this gradient leads to rephasing of the atomic polarization and thus recall of the stored optical state. We will outline how we prepare the atoms and this gradient and also describe some of the pitfalls that need to be avoided, in particular four-wave mixing, which can give rise to optical gain. PMID:24300586
Gradient echo quantum memory in warm atomic vapor.

PubMed

Pinel, Olivier; Hosseini, Mahdi; Sparkes, Ben M; Everett, Jesse L; Higginbottom, Daniel; Campbell, Geoff T; Lam, Ping Koy; Buchler, Ben C

2013-11-11

Gradient echo memory (GEM) is a protocol for storing optical quantum states of light in atomic ensembles. The primary motivation for such a technology is that quantum key distribution (QKD), which uses Heisenberg uncertainty to guarantee security of cryptographic keys, is limited in transmission distance. The development of a quantum repeater is a possible path to extend QKD range, but a repeater will need a quantum memory. In our experiments we use a gas of rubidium 87 vapor that is contained in a warm gas cell. This makes the scheme particularly simple. It is also a highly versatile scheme that enables in-memory refinement of the stored state, such as frequency shifting and bandwidth manipulation. The basis of the GEM protocol is to absorb the light into an ensemble of atoms that has been prepared in a magnetic field gradient. The reversal of this gradient leads to rephasing of the atomic polarization and thus recall of the stored optical state. We will outline how we prepare the atoms and this gradient and also describe some of the pitfalls that need to be avoided, in particular four-wave mixing, which can give rise to optical gain.
Statistical mechanics of few-particle systems: exact results for two useful models

NASA Astrophysics Data System (ADS)

Miranda, Enrique N.

2017-11-01

The statistical mechanics of small clusters (n ˜ 10-50 elements) of harmonic oscillators and two-level systems is studied exactly, following the microcanonical, canonical and grand canonical formalisms. For clusters with several hundred particles, the results from the three formalisms coincide with those found in the thermodynamic limit. However, for clusters formed by a few tens of elements, the three ensembles yield different results. For a cluster with a few tens of harmonic oscillators, when the heat capacity per oscillator is evaluated within the canonical formalism, it reaches a limit value equal to k B , as in the thermodynamic case, while within the microcanonical formalism the limit value is k B (1-1/n). This difference could be measured experimentally. For a cluster with a few tens of two-level systems, the heat capacity evaluated within the canonical and microcanonical ensembles also presents differences that could be detected experimentally. Both the microcanonical and grand canonical formalism show that the entropy is non-additive for systems this small, while the canonical ensemble reaches the opposite conclusion. These results suggest that the microcanonical ensemble is the most appropriate for dealing with systems with tens of particles.
Relationship between ion pair geometries and electrostatic strengths in proteins.

PubMed Central

Kumar, Sandeep; Nussinov, Ruth

2002-01-01

The electrostatic free energy contribution of an ion pair in a protein depends on two factors, geometrical orientation of the side-chain charged groups with respect to each other and the structural context of the ion pair in the protein. Conformers in NMR ensembles enable studies of the relationship between geometry and electrostatic strengths of ion pairs, because the protein structural contexts are highly similar across different conformers. We have studied this relationship using a dataset of 22 unique ion pairs in 14 NMR conformer ensembles for 11 nonhomologous proteins. In different NMR conformers, the ion pairs are classified as salt bridges, nitrogen-oxygen (N-O) bridges and longer-range ion pairs on the basis of geometrical criteria. In salt bridges, centroids of the side-chain charged groups and at least a pair of side-chain nitrogen and oxygen atoms of the ion-pairing residues are within a 4 A distance. In N-O bridges, at least a pair of the side-chain nitrogen and oxygen atoms of the ion-pairing residues are within 4 A distance, but the distance between the side-chain charged group centroids is greater than 4 A. In the longer-range ion pairs, the side-chain charged group centroids as well as the side-chain nitrogen and oxygen atoms are more than 4 A apart. Continuum electrostatic calculations indicate that most of the ion pairs have stabilizing electrostatic contributions when their side-chain charged group centroids are within 5 A distance. Hence, most (approximately 92%) of the salt bridges and a majority (68%) of the N-O bridges are stabilizing. Most (approximately 89%) of the destabilizing ion pairs are the longer-range ion pairs. In the NMR conformer ensembles, the electrostatic interaction between side-chain charged groups of the ion-pairing residues is the strongest for salt bridges, considerably weaker for N-O bridges, and the weakest for longer-range ion pairs. These results suggest empirical rules for stabilizing electrostatic interactions in proteins. PMID:12202384
Desynchronization in an ensemble of globally coupled chaotic bursting neuronal oscillators by dynamic delayed feedback control

NASA Astrophysics Data System (ADS)

Che, Yanqiu; Yang, Tingting; Li, Ruixue; Li, Huiyan; Han, Chunxiao; Wang, Jiang; Wei, Xile

2015-09-01

In this paper, we propose a dynamic delayed feedback control approach or desynchronization of chaotic-bursting synchronous activities in an ensemble of globally coupled neuronal oscillators. We demonstrate that the difference signal between an ensemble's mean field and its time delayed state, filtered and fed back to the ensemble, can suppress the self-synchronization in the ensemble. These individual units are decoupled and stabilized at the desired desynchronized states while the stimulation signal reduces to the noise level. The effectiveness of the method is illustrated by examples of two different populations of globally coupled chaotic-bursting neurons. The proposed method has potential for mild, effective and demand-controlled therapy of neurological diseases characterized by pathological synchronization.
Summation rules for a fully nonlocal energy-based quasicontinuum method

NASA Astrophysics Data System (ADS)

Amelang, J. S.; Venturini, G. N.; Kochmann, D. M.

2015-09-01

The quasicontinuum (QC) method coarse-grains crystalline atomic ensembles in order to bridge the scales from individual atoms to the micro- and mesoscales. A crucial cornerstone of all QC techniques, summation or quadrature rules efficiently approximate the thermodynamic quantities of interest. Here, we investigate summation rules for a fully nonlocal, energy-based QC method to approximate the total Hamiltonian of a crystalline atomic ensemble by a weighted sum over a small subset of all atoms in the crystal lattice. Our formulation does not conceptually differentiate between atomistic and coarse-grained regions and thus allows for seamless bridging without domain-coupling interfaces. We review traditional summation rules and discuss their strengths and weaknesses with a focus on energy approximation errors and spurious force artifacts. Moreover, we introduce summation rules which produce no residual or spurious force artifacts in centrosymmetric crystals in the large-element limit under arbitrary affine deformations in two dimensions (and marginal force artifacts in three dimensions), while allowing us to seamlessly bridge to full atomistics. Through a comprehensive suite of examples with spatially non-uniform QC discretizations in two and three dimensions, we compare the accuracy of the new scheme to various previous ones. Our results confirm that the new summation rules exhibit significantly smaller force artifacts and energy approximation errors. Our numerical benchmark examples include the calculation of elastic constants from completely random QC meshes and the inhomogeneous deformation of aggressively coarse-grained crystals containing nano-voids. In the elastic regime, we directly compare QC results to those of full atomistics to assess global and local errors in complex QC simulations. Going beyond elasticity, we illustrate the performance of the energy-based QC method with the new second-order summation rule by the help of nanoindentation examples with automatic mesh adaptation. Overall, our findings provide guidelines for the selection of summation rules for the fully nonlocal energy-based QC method.
Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry.

PubMed

Shi, Xuesong; Walker, Peter; Harbury, Pehr B; Herschlag, Daniel

2017-05-05

The conformational ensembles of structured RNA's are crucial for biological function, but they remain difficult to elucidate experimentally. We demonstrate with HIV-1 TAR RNA that X-ray scattering interferometry (XSI) can be used to determine RNA conformational ensembles. X-ray scattering interferometry (XSI) is based on site-specifically labeling RNA with pairs of heavy atom probes, and precisely measuring the distribution of inter-probe distances that arise from a heterogeneous mixture of RNA solution structures. We show that the XSI-based model of the TAR RNA ensemble closely resembles an independent model derived from NMR-RDC data. Further, we show how the TAR RNA ensemble changes shape at different salt concentrations. Finally, we demonstrate that a single hybrid model of the TAR RNA ensemble simultaneously fits both the XSI and NMR-RDC data set and show that XSI can be combined with NMR-RDC to further improve the quality of the determined ensemble. The results suggest that XSI-RNA will be a powerful approach for characterizing the solution conformational ensembles of RNAs and RNA-protein complexes under diverse solution conditions. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
Individual differences in ensemble perception reveal multiple, independent levels of ensemble representation.

PubMed

Haberman, Jason; Brady, Timothy F; Alvarez, George A

2015-04-01

Ensemble perception, including the ability to "see the average" from a group of items, operates in numerous feature domains (size, orientation, speed, facial expression, etc.). Although the ubiquity of ensemble representations is well established, the large-scale cognitive architecture of this process remains poorly defined. We address this using an individual differences approach. In a series of experiments, observers saw groups of objects and reported either a single item from the group or the average of the entire group. High-level ensemble representations (e.g., average facial expression) showed complete independence from low-level ensemble representations (e.g., average orientation). In contrast, low-level ensemble representations (e.g., orientation and color) were correlated with each other, but not with high-level ensemble representations (e.g., facial expression and person identity). These results suggest that there is not a single domain-general ensemble mechanism, and that the relationship among various ensemble representations depends on how proximal they are in representational space. (c) 2015 APA, all rights reserved).
Quantum simulation of the Hubbard model with dopant atoms in silicon

PubMed Central

Salfi, J.; Mol, J. A.; Rahman, R.; Klimeck, G.; Simmons, M. Y.; Hollenberg, L. C. L.; Rogge, S.

2016-01-01

In quantum simulation, many-body phenomena are probed in controllable quantum systems. Recently, simulation of Bose–Hubbard Hamiltonians using cold atoms revealed previously hidden local correlations. However, fermionic many-body Hubbard phenomena such as unconventional superconductivity and spin liquids are more difficult to simulate using cold atoms. To date the required single-site measurements and cooling remain problematic, while only ensemble measurements have been achieved. Here we simulate a two-site Hubbard Hamiltonian at low effective temperatures with single-site resolution using subsurface dopants in silicon. We measure quasi-particle tunnelling maps of spin-resolved states with atomic resolution, finding interference processes from which the entanglement entropy and Hubbard interactions are quantified. Entanglement, determined by spin and orbital degrees of freedom, increases with increasing valence bond length. We find separation-tunable Hubbard interaction strengths that are suitable for simulating strongly correlated phenomena in larger arrays of dopants, establishing dopants as a platform for quantum simulation of the Hubbard model. PMID:27094205
Non-stationary and relaxation phenomena in cavity-assisted quantum memories

NASA Astrophysics Data System (ADS)

Veselkova, N. G.; Sokolov, I. V.

2017-12-01

We investigate the non-stationary and relaxation phenomena in cavity-assisted quantum memories for light. As a storage medium we consider an ensemble of cold atoms with standard Lambda-scheme of working levels. Some theoretical aspects of the problem were treated previously by many authors, and recent experiments stimulate more deep insight into the ultimate ability and limitations of the device. Since quantum memories can be used not only for the storage of quantum information, but also for a substantial manipulation of ensembles of quantum states, the speed of such manipulation and hence the ability to write and retrieve the signals of relatively short duration becomes important. In our research we do not apply the so-called bad cavity limit, and consider the memory operation of the signals whose duration is not much larger than the cavity field lifetime, accounting also for the finite lifetime of atomic coherence. In our paper we present an effective approach that makes it possible to find the non-stationary amplitude and phase behavior of strong classical control field, that matches the desirable time profile of both the envelope and the phase of the retrieved quantized signal. The phase properties of the retrieved quantized signals are of importance for the detection and manipulation of squeezing, entanglement, etc by means of optical mixing and homodyning.
Synthesis and crystal structure of catena-bis(nicotinamide)aqua({mu}-phthalato)copper(II) hemihydrate

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

Sadikov, G. G., E-mail: sadgg@igic.ras.ru; Koksharova, T. V.; Antsyshkina, A. S.

2008-07-15

The copper(II) phthalate complex with nicotinamide [CuL{sub 2}({mu}-Pht)(H{sub 2}O)] . 0.5H{sub 2}O(I) (where L is nicotinamide and Pht{sup 2-} is an anion of phthalic acid) is synthesized and investigated using IR spectroscopy and X-ray diffraction. The crystals of compound I are monoclinic, a = 13.368(2) A, b = 7.891(3) A, c = 20.480(2) A, {beta} = 108.69(2){sup o}, Z = 4, and space group P2{sub 1}/c. The structural units of crystal I are linear chains formed by bridging phthalate anions and crystallization water molecules. The copper atom is coordinated by two pyridine nitrogen atoms of two nicotinamide ligands (Cu-N, 2.001more » and 2.045 A), two oxygen atoms of different phthalate anions (Cu-O, 1.964 and 2.235 A), and the oxygen atom of the H{sub 2} O molecule (Cu-O, 2.014 A). The coordination polyhedron of the copper atom is completed to an elongated (4 + 1 + 1) tetragonal bipyramid by the second (chelating) oxygen atom of the carboxyl group (Cu-O, 2.587 A), which is one of the anions of phthalic acid. The linear polymer molecules are joined into complex macromolecular dimers with the closest internal contacts of the specific type. The macromolecular dimers are the main supramolecular ensembles of the crystal structure.« less
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.
Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps

PubMed Central

2011-01-01

Background Molecular dynamics (MD) simulations are powerful tools to investigate the conformational dynamics of proteins that is often a critical element of their function. Identification of functionally relevant conformations is generally done clustering the large ensemble of structures that are generated. Recently, Self-Organising Maps (SOMs) were reported performing more accurately and providing more consistent results than traditional clustering algorithms in various data mining problems. We present a novel strategy to analyse and compare conformational ensembles of protein domains using a two-level approach that combines SOMs and hierarchical clustering. Results The conformational dynamics of the α-spectrin SH3 protein domain and six single mutants were analysed by MD simulations. The Cα's Cartesian coordinates of conformations sampled in the essential space were used as input data vectors for SOM training, then complete linkage clustering was performed on the SOM prototype vectors. A specific protocol to optimize a SOM for structural ensembles was proposed: the optimal SOM was selected by means of a Taguchi experimental design plan applied to different data sets, and the optimal sampling rate of the MD trajectory was selected. The proposed two-level approach was applied to single trajectories of the SH3 domain independently as well as to groups of them at the same time. The results demonstrated the potential of this approach in the analysis of large ensembles of molecular structures: the possibility of producing a topological mapping of the conformational space in a simple 2D visualisation, as well as of effectively highlighting differences in the conformational dynamics directly related to biological functions. Conclusions The use of a two-level approach combining SOMs and hierarchical clustering for conformational analysis of structural ensembles of proteins was proposed. It can easily be extended to other study cases and to conformational ensembles from other sources. PMID:21569575
Comparative study of atomic fluorescence spectroscopy and inductively coupled plasma mass spectrometry for mercury and arsenic multispeciation.

PubMed

Gómez-Ariza, José Luis; Lorenzo, Fernando; García-Barrera, Tamara

2005-05-01

Mercury and arsenic are two elements of undoubted importance owing to their toxic character. Although speciation of these elements has been developed separately, in this work for the first time the speciation of As and Hg using two atomic fluorescence detectors in a sequential ensemble is presented. A coupling based on the combination of high-performance liquid chromatography (where mercury and arsenic species are separated) and two atomic fluorescence detectors in series, with several online treatments, including photooxidation (UV) and hydride generation, has allowed the determination of mercury and arsenic compounds simultaneously. The detection limits for this device were 16, 3, 17, 12 and 8 ng mL(-1) for As(III), monomethylarsinic acid, As(V), Hg2+ and methylmercury, respectively. This coupling was compared with an analogous one based on inductively coupled plasma-mass spectrometry (ICP-MS) detection, with detection limits of 0.7, 0.5, 0.8, 0.9 and 1.1 ng mL(-1), respectively. Multispeciation based on ICP-MS exhibits better sensitivity than the coupling based on tandem atomic fluorescence, but this second device is a very robust system and exhibits obvious advantages related to the low cost of acquisition and maintenance, as well as easy handling, which makes it a suitable system for routine laboratories.
Coherent single-atom superradiance

NASA Astrophysics Data System (ADS)

Kim, Junki; Yang, Daeho; Oh, Seung-hoon; An, Kyungwon

2018-02-01

Superradiance is a quantum phenomenon emerging in macroscopic systems whereby correlated single atoms cooperatively emit photons. Demonstration of controlled collective atom-field interactions has resulted from the ability to directly imprint correlations with an atomic ensemble. Here we report cavity-mediated coherent single-atom superradiance: Single atoms with predefined correlation traverse a high–quality factor cavity one by one, emitting photons cooperatively with the N atoms that have already gone through the cavity (N represents the number of atoms). Enhanced collective photoemission of N-squared dependence was observed even when the intracavity atom number was less than unity. The correlation among single atoms was achieved by nanometer-precision position control and phase-aligned state manipulation of atoms by using a nanohole-array aperture. Our results demonstrate a platform for phase-controlled atom-field interactions.
Atomic-Scale Nuclear Spin Imaging Using Quantum-Assisted Sensors in Diamond

NASA Astrophysics Data System (ADS)

Ajoy, A.; Bissbort, U.; Lukin, M. D.; Walsworth, R. L.; Cappellaro, P.

2015-01-01

Nuclear spin imaging at the atomic level is essential for the understanding of fundamental biological phenomena and for applications such as drug discovery. The advent of novel nanoscale sensors promises to achieve the long-standing goal of single-protein, high spatial-resolution structure determination under ambient conditions. In particular, quantum sensors based on the spin-dependent photoluminescence of nitrogen-vacancy (NV) centers in diamond have recently been used to detect nanoscale ensembles of external nuclear spins. While NV sensitivity is approaching single-spin levels, extracting relevant information from a very complex structure is a further challenge since it requires not only the ability to sense the magnetic field of an isolated nuclear spin but also to achieve atomic-scale spatial resolution. Here, we propose a method that, by exploiting the coupling of the NV center to an intrinsic quantum memory associated with the nitrogen nuclear spin, can reach a tenfold improvement in spatial resolution, down to atomic scales. The spatial resolution enhancement is achieved through coherent control of the sensor spin, which creates a dynamic frequency filter selecting only a few nuclear spins at a time. We propose and analyze a protocol that would allow not only sensing individual spins in a complex biomolecule, but also unraveling couplings among them, thus elucidating local characteristics of the molecule structure.
GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

PubMed Central

Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji

2015-01-01

GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310–323. doi: 10.1002/wcms.1220 PMID:26753008
Invariant-Based Inverse Engineering of Crane Control Parameters

NASA Astrophysics Data System (ADS)

González-Resines, S.; Guéry-Odelin, D.; Tobalina, A.; Lizuain, I.; Torrontegui, E.; Muga, J. G.

2017-11-01

By applying invariant-based inverse engineering in the small-oscillation regime, we design the time dependence of the control parameters of an overhead crane (trolley displacement and rope length) to transport a load between two positions at different heights with minimal final-energy excitation for a microcanonical ensemble of initial conditions. The analogy between ion transport in multisegmented traps or neutral-atom transport in moving optical lattices and load manipulation by cranes opens a route for a useful transfer of techniques among very different fields.
Using simulation to interpret experimental data in terms of protein conformational ensembles.

PubMed

Allison, Jane R

2017-04-01

In their biological environment, proteins are dynamic molecules, necessitating an ensemble structural description. Molecular dynamics simulations and solution-state experiments provide complimentary information in the form of atomically detailed coordinates and averaged or distributions of structural properties or related quantities. Recently, increases in the temporal and spatial scale of conformational sampling and comparison of the more diverse conformational ensembles thus generated have revealed the importance of sampling rare events. Excitingly, new methods based on maximum entropy and Bayesian inference are promising to provide a statistically sound mechanism for combining experimental data with molecular dynamics simulations. Copyright © 2016 Elsevier Ltd. All rights reserved.
Entanglement and asymmetric steering over two octaves of frequency difference

NASA Astrophysics Data System (ADS)

Olsen, M. K.

2017-12-01

The development of quantum technologies which use quantum states of the light field interacting with other systems creates a demand for entangled states spanning wide frequency ranges. In this work we analyze a parametric scheme of cascaded harmonic generation which promises to deliver bipartite entangled states in which the two modes are separated by two octaves in frequency. This scheme is potentially very useful for applications in quantum communication and computation networks as well as providing for quantum interfaces between a wider range of light and atomic ensembles than is presently practicable. It doubles the frequency range over which entanglement is presently available.

Excitation of Nuclei and Atoms Trapping in Optical Fields of High Intensity

DTIC Science & Technology

2006-11-01

the new relativistic wave equation for half- spin particle interacting with the electromagnetic field. The proposed equation is Lorentz and gauge ...CONTENTS Task 1. Gamma-ray laser with hidden inversion of nuclear state populations 3 Introduction 3 Recoil-accompanied nuclear...31 Task 2. Extended ensemble of monoenergetic atoms 33 Introduction 33 Results 37 Conclusion 66
Observation of ground-state quantum beats in atomic spontaneous emission.

PubMed

Norris, D G; Orozco, L A; Barberis-Blostein, P; Carmichael, H J

2010-09-17

We report ground-state quantum beats in spontaneous emission from a continuously driven atomic ensemble. Beats are visible only in an intensity autocorrelation and evidence spontaneously generated coherence in radiative decay. Our measurement realizes a quantum eraser where a first photon detection prepares a superposition and a second erases the "which path" information in the intermediate state.
Diffraction-Based Density Restraints for Membrane and Membrane-Peptide Molecular Dynamics Simulations

PubMed Central

Benz, Ryan W.; Nanda, Hirsh; Castro-Román, Francisco; White, Stephen H.; Tobias, Douglas J.

2006-01-01

We have recently shown that current molecular dynamics (MD) atomic force fields are not yet able to produce lipid bilayer structures that agree with experimentally-determined structures within experimental errors. Because of the many advantages offered by experimentally validated simulations, we have developed a novel restraint method for membrane MD simulations that uses experimental diffraction data. The restraints, introduced into the MD force field, act upon specified groups of atoms to restrain their mean positions and widths to values determined experimentally. The method was first tested using a simple liquid argon system, and then applied to a neat dioleoylphosphatidylcholine (DOPC) bilayer at 66% relative humidity and to the same bilayer containing the peptide melittin. Application of experiment-based restraints to the transbilayer double-bond and water distributions of neat DOPC bilayers led to distributions that agreed with the experimental values. Based upon the experimental structure, the restraints improved the simulated structure in some regions while introducing larger differences in others, as might be expected from imperfect force fields. For the DOPC-melittin system, the experimental transbilayer distribution of melittin was used as a restraint. The addition of the peptide caused perturbations of the simulated bilayer structure, but which were larger than observed experimentally. The melittin distribution of the simulation could be fit accurately to a Gaussian with parameters close to the observed ones, indicating that the restraints can be used to produce an ensemble of membrane-bound peptide conformations that are consistent with experiments. Such ensembles pave the way for understanding peptide-bilayer interactions at the atomic level. PMID:16950837
Inertial quantum sensors using light and matter

NASA Astrophysics Data System (ADS)

Barrett, B.; Bertoldi, A.; Bouyer, P.

2016-05-01

The past few decades have seen dramatic progress in our ability to manipulate and coherently control matter-waves. Although the duality between particles and waves has been well tested since de Broglie introduced the matter-wave analog of the optical wavelength in 1924, manipulating atoms with a level of coherence that enables one to use these properties for precision measurements has only become possible with our ability to produce atomic samples exhibiting temperatures of only a few millionths of a degree above absolute zero. Since the initial experiments a few decades ago, the field of atom optics has developed in many ways, with both fundamental and applied significance. The exquisite control of matter waves offers the prospect of a new generation of force sensors exhibiting unprecedented sensitivity and accuracy, for applications from navigation and geophysics to tests of general relativity. Thanks to the latest developments in this field, the first commercial products using this quantum technology are now available. In the future, our ability to create large coherent ensembles of atoms will allow us an even more precise control of the matter-wave and the ability to create highly entangled states for non-classical atom interferometry.
Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension

PubMed Central

Sonne, Jacob; Jensen, Morten Ø.; Hansen, Flemming Y.; Hemmingsen, Lars; Peters, Günther H.

2007-01-01

Molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (NPT) ensemble give highly ordered, gel-like bilayers with an area per lipid of ∼48 Å2. To obtain fluid (Lα) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 ± 0.1 Å2. Compared to the 48 Å2, the new value of 60.4 Å2 is in fair agreement with the experimental value of 64 Å2. In addition, the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field. PMID:17400696
Photon number dependent group velocity in vacuum induced transparency

NASA Astrophysics Data System (ADS)

Lauk, Nikolai; Fleischhauer, Michael

2015-05-01

Vacuum induced transparency (VIT) is an effect which occurs in an ensemble of three level atoms in a Λ configuration that interact with two quantized fields. Coupling of one transition to a cavity mode induces transparency for the second field on the otherwise opaque transition similar to the well known EIT effect. In the strong coupling regime even an empty cavity leads to transparency, in contrast to EIT where the presence of a strong control field is required. This transparency is accompanied by a reduction of the group velocity for the propagating field. However, unlike in EIT the group velocity in VIT depends on the number of incoming photons, i.e. different photon number components propagate with different velocities. Here we investigate the possibility of using this effect to spatially separate different photon number components of an initially coherent pulse. We present the results of our calculations and discuss a possible experimental realization.
Input Decimated Ensembles

NASA Technical Reports Server (NTRS)

Tumer, Kagan; Oza, Nikunj C.; Clancy, Daniel (Technical Monitor)

2001-01-01

Using an ensemble of classifiers instead of a single classifier has been shown to improve generalization performance in many pattern recognition problems. However, the extent of such improvement depends greatly on the amount of correlation among the errors of the base classifiers. Therefore, reducing those correlations while keeping the classifiers' performance levels high is an important area of research. In this article, we explore input decimation (ID), a method which selects feature subsets for their ability to discriminate among the classes and uses them to decouple the base classifiers. We provide a summary of the theoretical benefits of correlation reduction, along with results of our method on two underwater sonar data sets, three benchmarks from the Probenl/UCI repositories, and two synthetic data sets. The results indicate that input decimated ensembles (IDEs) outperform ensembles whose base classifiers use all the input features; randomly selected subsets of features; and features created using principal components analysis, on a wide range of domains.
Attribution of the 1995 and 2006 storm surge events in the southern Baltic Sea

NASA Astrophysics Data System (ADS)

Klehmet, K.; Rockel, B.; von Storch, H.

2016-12-01

In November 1995 and 2006, the German Baltic Sea coast experienced severe storm surge conditions. Exceptional water level heights of about 1.8m above mean sea level were measured at German tide gauges. Extreme event attribution poses unique challenges trying to distinguish the role of anthropogenic influence, as e.g. greenhouse gas emissions or land-use changes, from natural variability. This study, which is part of the EUCLEIA project (EUropean CLimate and weather Events: Interpretation and Attribution, www. eucleia.eu), aims to estimate how the contribution of anthropogenic drivers has altered the probability of single extreme events such as the 1995 and 2006 storm surge events. We explore these aspects using two 7-member ensembles of Hadley Centre Global Environmental Model version 3-A (HadGEM3-A), the atmosphere only component of the HadGEM3, provided by the Met Office Hadley Centre. The ensemble of HadGEM3-A consists of two multi-decadal experiments from 1960-2013 - one with anthropogenic forcing factors and natural forcings representing the actual climate. The second experiment represents the natural climate including only natural forcing factors. These two 7-member ensembles of about 60km spatial resolution are used as atmospheric forcing data to drive the regional ocean model TRIM-NP in order to calculate water level in the Baltic Sea in 12.8km spatial resolution. Findings indicate some limitations of the regional model ensemble to reproduce the magnitude of extreme water levels well. It is tested whether increased spatial resolution of atmospheric forcing fields can improve the representation of Baltic Sea extreme water levels along the coast and thus add value in the attribution analysis.
Self-bound droplets of a dilute magnetic quantum liquid

NASA Astrophysics Data System (ADS)

Schmitt, Matthias; Wenzel, Matthias; Böttcher, Fabian; Ferrier-Barbut, Igor; Pfau, Tilman

2016-11-01

Self-bound many-body systems are formed through a balance of attractive and repulsive forces and occur in many physical scenarios. Liquid droplets are an example of a self-bound system, formed by a balance of the mutual attractive and repulsive forces that derive from different components of the inter-particle potential. It has been suggested that self-bound ensembles of ultracold atoms should exist for atom number densities that are 108 times lower than in a helium droplet, which is formed from a dense quantum liquid. However, such ensembles have been elusive up to now because they require forces other than the usual zero-range contact interaction, which is either attractive or repulsive but never both. On the basis of the recent finding that an unstable bosonic dipolar gas can be stabilized by a repulsive many-body term, it was predicted that three-dimensional self-bound quantum droplets of magnetic atoms should exist. Here we report the observation of such droplets in a trap-free levitation field. We find that this dilute magnetic quantum liquid requires a minimum, critical number of atoms, below which the liquid evaporates into an expanding gas as a result of the quantum pressure of the individual constituents. Consequently, around this critical atom number we observe an interaction-driven phase transition between a gas and a self-bound liquid in the quantum degenerate regime with ultracold atoms. These droplets are the dilute counterpart of strongly correlated self-bound systems such as atomic nuclei and helium droplets.
Self-bound droplets of a dilute magnetic quantum liquid.

PubMed

Schmitt, Matthias; Wenzel, Matthias; Böttcher, Fabian; Ferrier-Barbut, Igor; Pfau, Tilman

2016-11-10

Self-bound many-body systems are formed through a balance of attractive and repulsive forces and occur in many physical scenarios. Liquid droplets are an example of a self-bound system, formed by a balance of the mutual attractive and repulsive forces that derive from different components of the inter-particle potential. It has been suggested that self-bound ensembles of ultracold atoms should exist for atom number densities that are 10 8 times lower than in a helium droplet, which is formed from a dense quantum liquid. However, such ensembles have been elusive up to now because they require forces other than the usual zero-range contact interaction, which is either attractive or repulsive but never both. On the basis of the recent finding that an unstable bosonic dipolar gas can be stabilized by a repulsive many-body term, it was predicted that three-dimensional self-bound quantum droplets of magnetic atoms should exist. Here we report the observation of such droplets in a trap-free levitation field. We find that this dilute magnetic quantum liquid requires a minimum, critical number of atoms, below which the liquid evaporates into an expanding gas as a result of the quantum pressure of the individual constituents. Consequently, around this critical atom number we observe an interaction-driven phase transition between a gas and a self-bound liquid in the quantum degenerate regime with ultracold atoms. These droplets are the dilute counterpart of strongly correlated self-bound systems such as atomic nuclei and helium droplets.
Photodeposited Pd Nanoparticles with Disordered Structure for Phenylacetylene Semihydrogenation

PubMed Central

Fan, Qining; He, Sha; Hao, Lin; Liu, Xin; Zhu, Yue; Xu, Sailong; Zhang, Fazhi

2017-01-01

Developing effective heterogeneous metal catalysts with high selectivity and satisfactory activity for chemoselective hydrogenation of alkyne to alkene is of great importance in the chemical industry. Herein, we report our efforts to fabricate TiO2-supported Pd catalysts by a photodeposition method at room temperature for phenylacetylene semihydrogenation to styrene. The resulting Pd/TiO2 catalyst, possessing smaller Pd ensembles with ambiguous lattice fringes and more low coordination Pd sites, exhibits higher styrene selectivity compared to two contrastive Pd/TiO2 samples with larger ensembles and well-organized crystal structure fabricated by deposition-precipitation or photodeposition with subsequent thermal treatment at 300 °C. The sample derived from photodeposition exhibits greatly slow styrene hydrogenation in kinetic evaluation because the disordered structure of Pd particles in photodeposited Pd/TiO2 may prevent the formation of β-hydride phases and probably produce more surface H atoms, which may favor high styrene selectivity. PMID:28176843
Photodeposited Pd Nanoparticles with Disordered Structure for Phenylacetylene Semihydrogenation

NASA Astrophysics Data System (ADS)

Fan, Qining; He, Sha; Hao, Lin; Liu, Xin; Zhu, Yue; Xu, Sailong; Zhang, Fazhi

2017-02-01

Developing effective heterogeneous metal catalysts with high selectivity and satisfactory activity for chemoselective hydrogenation of alkyne to alkene is of great importance in the chemical industry. Herein, we report our efforts to fabricate TiO2-supported Pd catalysts by a photodeposition method at room temperature for phenylacetylene semihydrogenation to styrene. The resulting Pd/TiO2 catalyst, possessing smaller Pd ensembles with ambiguous lattice fringes and more low coordination Pd sites, exhibits higher styrene selectivity compared to two contrastive Pd/TiO2 samples with larger ensembles and well-organized crystal structure fabricated by deposition-precipitation or photodeposition with subsequent thermal treatment at 300 °C. The sample derived from photodeposition exhibits greatly slow styrene hydrogenation in kinetic evaluation because the disordered structure of Pd particles in photodeposited Pd/TiO2 may prevent the formation of β-hydride phases and probably produce more surface H atoms, which may favor high styrene selectivity.
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
Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation.

PubMed

Iida, Shinji; Nakamura, Haruki; Higo, Junichi

2016-06-15

We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein-protein or protein-ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks. © 2016 The Author(s).
CABS-flex: server for fast simulation of protein structure fluctuations

PubMed Central

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2013-01-01

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

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2013-07-01

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

PubMed

Chen, Wenlan; Beck, Kristin M; Bücker, Robert; Gullans, Michael; Lukin, Mikhail D; Tanji-Suzuki, Haruka; Vuletić, Vladan

2013-08-16

The realization of an all-optical transistor, in which one "gate" photon controls a "source" light beam, is a long-standing goal in optics. By stopping a light pulse in an atomic ensemble contained inside an optical resonator, we realized a device in which one stored gate photon controls the resonator transmission of subsequently applied source photons. A weak gate pulse induces bimodal transmission distribution, corresponding to zero and one gate photons. One stored gate photon produces fivefold source attenuation and can be retrieved from the atomic ensemble after switching more than one source photon. Without retrieval, one stored gate photon can switch several hundred source photons. With improved storage and retrieval efficiency, our work may enable various new applications, including photonic quantum gates and deterministic multiphoton entanglement.
Atom-chip-based quantum gravimetry for the precise determination of absolute gravity

NASA Astrophysics Data System (ADS)

Abend, Sven; Schubert, Christian; Ertmer, Wolfgang; Rasel, Ernst

2017-04-01

We present a novel technique for the precise measurement of absolute local gravity with a quantum gravimeter based on an atom chip. Atom interferometry utilizes the interference of matter waves interrogated by laser light to read out inertial forces. Today's generation of these devices typically operate with test mass samples, that consists of ensembles of laser cooled atoms. Their performance is limited by the velocity spread and finite-size of the test masses that impose systematic uncertainties at the level of a few μGal [1]. Rather than laser cooled atoms we employ quantum degenerate ensembles, so called Bose-Einstein condensates [2], as ultra-sensitive probes for gravity. These sources offer unique properties that will allow to overcome the current limitations in the next generation of sensors. Furthermore, atom-chip technology offers the possibility to generate Bose-Einstein condensates in a fast and reliable way. We present a lab-based prototype that uses the atom chip itself to retro-reflect the interrogation laser and thus serves as inertial reference inside the vacuum [3]. With this setup, it is possible to demonstrate all necessary steps to measure gravity, including the preparation of the source, spanning an interferometer as well as the detection of the output signal. All steps are pursued on a baseline of 1 cm right below the atom chip and to analyze relevant systematic effects. In the framework of the center of excellence geoQ a next generation device is under construction at the Institut für Quantenoptik, that will target for in-field measurements. This device will feature a state-of-the-art atom-chip source with a high-flux of ultra-cold atoms at a repetition rate of 1-2 Hz [4]. The device will be characterized in cooperation with the Müller group at the Institut für Erdmessung the sensor and finally employed in a campaign to measure the Fennoscandian uplift at the level of 1 μGal. The presented work is supported by the CRC 1227 DQ-mat, the CRC 1128 geo-Q, the RTG 1729, the QUEST-LFS, by the German Space Agency (DLR) with funds provided by the Federal Ministry of Economic Affairs and Energy (BMWi) due to an enactment of the German Bundestag under Grant No. DLR 50WM1552-1557. [1] A. Peters et al., Nature 400, 849, 1999; A. Louchet-Chauvet et al., New J. Phys. 13, 065026, 2011; C. Freier et al., J. of Phys.: Conf. Series 723, 012050, 2016; V. Schkolnik et al., Appl. Phys. B 120, 311-316 (2015). [2] K. B. Davis et al., Phys. Rev. Lett. 74, 5202, 1995; M. H. Anderson et al., Science 269, 198, 1995; C. C. Bradley et al., Phys. Rev. Lett. 75, 1687, 1995. [3] S. Abend et al., Phys. Rev. Lett. 117, 203003, 2016. [4] J. Rudolph et al., New J. Phys. 17, 065001, 2015.
The role of protein homochirality in shaping the energy landscape of folding

PubMed Central

Nanda, Vikas; Andrianarijaona, Aina; Narayanan, Chitra

2007-01-01

The homochirality, or isotacticity, of the natural amino acids facilitates the formation of regular secondary structures such as α-helices and β-sheets. However, many examples exist in nature where novel polypeptide topologies use both l- and d-amino acids. In this study, we explore how stereochemistry of the polypeptide backbone influences basic properties such as compactness and the size of fold space by simulating both lattice and all-atom polypeptide chains. We formulate a rectangular lattice chain model in both two and three dimensions, where monomers are chiral, having the effect of restricting local conformation. Syndiotactic chains with alternating chirality of adjacent monomers have a very large ensemble of accessible conformations characterized predominantly by extended structures. Isotactic chains on the other hand, have far fewer possible conformations and a significant fraction of these are compact. Syndiotactic chains are often unable to access maximally compact states available to their isotactic counterparts of the same length. Similar features are observed in all-atom models of isotactic versus syndiotactic polyalanine. Our results suggest that protein isotacticity has evolved to increase the enthalpy of chain collapse by facilitating compact helical states and to reduce the entropic cost of folding by restricting the size of the unfolded ensemble of competing states. PMID:17600146
Systematic methods for defining coarse-grained maps in large biomolecules.

PubMed

Zhang, Zhiyong

2015-01-01

Large biomolecules are involved in many important biological processes. It would be difficult to use large-scale atomistic molecular dynamics (MD) simulations to study the functional motions of these systems because of the computational expense. Therefore various coarse-grained (CG) approaches have attracted rapidly growing interest, which enable simulations of large biomolecules over longer effective timescales than all-atom MD simulations. The first issue in CG modeling is to construct CG maps from atomic structures. In this chapter, we review the recent development of a novel and systematic method for constructing CG representations of arbitrarily complex biomolecules, in order to preserve large-scale and functionally relevant essential dynamics (ED) at the CG level. In this ED-CG scheme, the essential dynamics can be characterized by principal component analysis (PCA) on a structural ensemble, or elastic network model (ENM) of a single atomic structure. Validation and applications of the method cover various biological systems, such as multi-domain proteins, protein complexes, and even biomolecular machines. The results demonstrate that the ED-CG method may serve as a very useful tool for identifying functional dynamics of large biomolecules at the CG level.

Interfacing broadband photonic qubits to on-chip cavity-protected rare-earth ensembles

PubMed Central

Zhong, Tian; Kindem, Jonathan M.; Rochman, Jake; Faraon, Andrei

2017-01-01

Ensembles of solid-state optical emitters enable broadband quantum storage and transduction of photonic qubits, with applications in high-rate quantum networks for secure communications and interconnecting future quantum computers. To transfer quantum states using ensembles, rephasing techniques are used to mitigate fast decoherence resulting from inhomogeneous broadening, but these techniques generally limit the bandwidth, efficiency and active times of the quantum interface. Here, we use a dense ensemble of neodymium rare-earth ions strongly coupled to a nanophotonic resonator to demonstrate a significant cavity protection effect at the single-photon level—a technique to suppress ensemble decoherence due to inhomogeneous broadening. The protected Rabi oscillations between the cavity field and the atomic super-radiant state enable ultra-fast transfer of photonic frequency qubits to the ions (∼50 GHz bandwidth) followed by retrieval with 98.7% fidelity. With the prospect of coupling to other long-lived rare-earth spin states, this technique opens the possibilities for broadband, always-ready quantum memories and fast optical-to-microwave transducers. PMID:28090078
Self-stabilized narrow-bandwidth and high-fidelity entangled photons generated from cold atoms

NASA Astrophysics Data System (ADS)

Yu, Y. C.; Ding, D. S.; Dong, M. X.; Shi, S.; Zhang, W.; Shi, B. S.

2018-04-01

Entangled photon pairs are critically important in fundamental quantum mechanics research as well as in many areas within the field of quantum information, such as quantum communication, quantum computation, and quantum cryptography. Previous demonstrations of entangled photons based on atomic ensembles were achieved by using a reference laser to stabilize the phase of two spontaneous four-wave mixing paths. Here, we demonstrate a convenient and efficient scheme to generate polarization-entangled photons with a narrow bandwidth of 57.2 ±1.6 MHz and a high-fidelity of 96.3 ±0.8 % by using a phase self-stabilized multiplexing system formed by two beam displacers and two half-wave plates where the relative phase between the different signal paths can be eliminated completely. It is possible to stabilize an entangled photon pair for a long time with this system and produce all four Bell states, making this a vital step forward in the field of quantum information.
How to Deal with Low-Resolution Target Structures: Using SAR, Ensemble Docking, Hydropathic Analysis, and 3D-QSAR to Definitively Map the αβ-Tubulin Colchicine Site

PubMed Central

Da, Chenxiao; Mooberry, Susan L.; Gupton, John T.; Kellogg, Glen E.

2013-01-01

αβ-tubulin colchicine site inhibitors (CSIs) from four scaffolds that we previously tested for antiproliferative activity were modeled to better understand their effect on microtubules. Docking models, constructed by exploiting the SAR of a pyrrole subset and HINT scoring, guided ensemble docking of all 59 compounds. This conformation set and two variants having progressively less structure knowledge were subjected to CoMFA, CoMFA+HINT, and CoMSIA 3D-QSAR analyses. The CoMFA+HINT model (docked alignment) showed the best statistics: leave-one-out q2 of 0.616, r2 of 0.949 and r2pred (internal test set) of 0.755. An external (tested in other laboratories) collection of 24 CSIs from eight scaffolds were evaluated with the 3D-QSAR models, which correctly ranked their activity trends in 7/8 scaffolds for CoMFA+HINT (8/8 for CoMFA). The combination of SAR, ensemble docking, hydropathic analysis and 3D-QSAR provides an atomic-scale colchicine site model more consistent with a target structure resolution much higher than the ~3.6 Å available for αβ-tubulin. PMID:23961916
An algorithm for the Italian atomic time scale

NASA Technical Reports Server (NTRS)

Cordara, F.; Vizio, G.; Tavella, P.; Pettiti, V.

1994-01-01

During the past twenty years, the time scale at the IEN has been realized by a commercial cesium clock, selected from an ensemble of five, whose rate has been continuously steered towards UTC to maintain a long term agreement within 3 x 10(exp -13). A time scale algorithm, suitable for a small clock ensemble and capable of improving the medium and long term stability of the IEN time scale, has been recently designed taking care of reducing the effects of the seasonal variations and the sudden frequency anomalies of the single cesium clocks. The new time scale, TA(IEN), is obtained as a weighted average of the clock ensemble computed once a day from the time comparisons between the local reference UTC(IEN) and the single clocks. It is foreseen to include in the computation also ten cesium clocks maintained in other Italian laboratories to further improve its reliability and its long term stability. To implement this algorithm, a personal computer program in Quick Basic has been prepared and it has been tested at the IEN time and frequency laboratory. Results obtained using this algorithm on the real clocks data relative to a period of about two years are presented.
Hyperfine state entanglement of spinor BEC and scattering atom

NASA Astrophysics Data System (ADS)

Li, Zhibing; Bao, Chengguang; Zheng, Wei

2018-05-01

Condensate of spin-1 atoms frozen in a unique spatial mode may possess large internal degrees of freedom. The scattering amplitudes of polarized cold atoms scattered by the condensate are obtained with the method of fractional parentage coefficients that treats the spin degrees of freedom rigorously. Channels with scattering cross sections enhanced by the square of the atom number of the condensate are found. Entanglement between the condensate and the propagating atom can be established by scattering. Entanglement entropy is analytically obtained for arbitrary initial states. Our results also give a hint for the establishment of quantum thermal ensembles in the hyperfine space of spin states.
NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers.

PubMed

Sekhar, Ashok; Kay, Lewis E

2013-08-06

The importance of dynamics to biomolecular function is becoming increasingly clear. A description of the structure-function relationship must, therefore, include the role of motion, requiring a shift in paradigm from focus on a single static 3D picture to one where a given biomolecule is considered in terms of an ensemble of interconverting conformers, each with potentially diverse activities. In this Perspective, we describe how recent developments in solution NMR spectroscopy facilitate atomic resolution studies of sparsely populated, transiently formed biomolecular conformations that exchange with the native state. Examples of how this methodology is applied to protein folding and misfolding, ligand binding, and molecular recognition are provided as a means of illustrating both the power of the new techniques and the significant roles that conformationally excited protein states play in biology.
g_contacts: Fast contact search in bio-molecular ensemble data

NASA Astrophysics Data System (ADS)

Blau, Christian; Grubmuller, Helmut

2013-12-01

Short-range interatomic interactions govern many bio-molecular processes. Therefore, identifying close interaction partners in ensemble data is an essential task in structural biology and computational biophysics. A contact search can be cast as a typical range search problem for which efficient algorithms have been developed. However, none of those has yet been adapted to the context of macromolecular ensembles, particularly in a molecular dynamics (MD) framework. Here a set-decomposition algorithm is implemented which detects all contacting atoms or residues in maximum O(Nlog(N)) run-time, in contrast to the O(N2) complexity of a brute-force approach. Catalogue identifier: AEQA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEQA_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 8945 No. of bytes in distributed program, including test data, etc.: 981604 Distribution format: tar.gz Programming language: C99. Computer: PC. Operating system: Linux. RAM: ≈Size of input frame Classification: 3, 4.14. External routines: Gromacs 4.6[1] Nature of problem: Finding atoms or residues that are closer to one another than a given cut-off. Solution method: Excluding distant atoms from distance calculations by decomposing the given set of atoms into disjoint subsets. Running time:≤O(Nlog(N)) References: [1] S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J.C. Smith, P. M. Kasson, D. van der Spoel, B. Hess and Erik Lindahl, Gromacs 4.5: a high-throughput and highly parallel open source molecular simulation toolkit, Bioinformatics 29 (7) (2013).
Linking Vegetation Structure and Spider Diversity in Riparian and Adjacent Habitats in Two Rivers of Central Argentina: An Analysis at Two Conceptual Levels.

PubMed

Griotti, Mariana; Muñoz-Escobar, Christian; Ferretti, Nelson E

2017-08-01

The link between vegetation structure and spider diversity has been well explored in the literature. However, few studies have compared spider diversity and its response to vegetation at two conceptual levels: assemblage (species diversity) and ensemble (guild diversity). Because of this, we studied spider diversity in riparian and adjacent habitats of a river system from the Chacoan subregion in central Argentina and evaluated their linkage with vegetation structure at these two levels. To assess vegetation structure, we measured plant species richness and vegetation cover in the herb and shrub - tree layers. We collected spiders for over 6 months by using vacuum netting, sweep netting and pitfall traps. We collected 3,808 spiders belonging to 119 morphospecies, 24 families and 9 guilds. At spider assemblage level, SIMPROF analysis showed significant differences among studied habitats. At spider ensemble level, nevertheless, we found no significant differences among habitats. Concerning the linkage with vegetation structure, BIOENV test showed that spider diversity at either assemblage or ensemble level was not significantly correlated with the vegetation variables assessed. Our results indicated that spider diversity was not affected by vegetation structure. Hence, even though we found a pattern in spider assemblages among habitats, this could not be attributed to vegetation structure. In this study, we show that analyzing a community at two conceptual levels will be useful for recognizing different responses of spider communities to vegetation structure in diverse habitat types. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
Coherently coupling distinct spin ensembles through a high critical temperature superconducting resonator

NASA Astrophysics Data System (ADS)

Ghirri, Alberto; Bonizzoni, Claudio; Troiani, Filippo; Affronte, Marco

The problem of coupling remote ensembles of two-level systems through cavity photons is revisited by using molecular spin centers and a high critical temperature superconducting coplanar resonator. By using PyBTM organic radicals, we achieved the strong coupling regime with values of the cooperativity reaching 4300 at 2 K. We show that up to three distinct spin ensembles are simultaneously coupled through the resonator mode. The ensembles are made physically distinguishable by chemically varying the g-factor and by exploiting the inhomogeneities of the applied magnetic field. The coherent mixing of the spin and field modes is demonstrated by the observed multiple anticrossing, along with the simulations performed within the input-output formalism, and quantified by suitable entropic measures.
Symmetry Transition Preserving Chirality in QCD: A Versatile Random Matrix Model

NASA Astrophysics Data System (ADS)

Kanazawa, Takuya; Kieburg, Mario

2018-06-01

We consider a random matrix model which interpolates between the chiral Gaussian unitary ensemble and the Gaussian unitary ensemble while preserving chiral symmetry. This ensemble describes flavor symmetry breaking for staggered fermions in 3D QCD as well as in 4D QCD at high temperature or in 3D QCD at a finite isospin chemical potential. Our model is an Osborn-type two-matrix model which is equivalent to the elliptic ensemble but we consider the singular value statistics rather than the complex eigenvalue statistics. We report on exact results for the partition function and the microscopic level density of the Dirac operator in the ɛ regime of QCD. We compare these analytical results with Monte Carlo simulations of the matrix model.
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
Future Flows Hydrology: an ensemble of daily river flow and monthly groundwater levels for use for climate change impact assessment across Great Britain

NASA Astrophysics Data System (ADS)

Prudhomme, C.; Haxton, T.; Crooks, S.; Jackson, C.; Barkwith, A.; Williamson, J.; Kelvin, J.; Mackay, J.; Wang, L.; Young, A.; Watts, G.

2012-12-01

The dataset Future Flows Hydrology was developed as part of the project "Future Flows and Groundwater Levels" to provide a consistent set of transient daily river flow and monthly groundwater levels projections across England, Wales and Scotland to enable the investigation of the role of climate variability on river flow and groundwater levels nationally and how this may change in the future. Future Flows Hydrology is derived from Future Flows Climate, a national ensemble projection derived from the Hadley Centre's ensemble projection HadRM3-PPE to provide a consistent set of climate change projections for the whole of Great Britain at both space and time resolutions appropriate for hydrological applications. Three hydrological models and one groundwater level model were used to derive Future Flows Hydrology, with 30 river sites simulated by two hydrological models to enable assessment of hydrological modelling uncertainty in studying the impact of climate change on the hydrology. Future Flows Hydrology contains an 11-member ensemble of transient projections from January 1951 to December 2098, each associated with a single realisation from a different variant of HadRM3 and a single hydrological model. Daily river flows are provided for 281 river catchments and monthly groundwater levels at 24 boreholes as .csv files containing all 11 ensemble members. When separate simulations are done with two hydrological models, two separate .csv files are provided. Because of potential biases in the climate-hydrology modelling chain, catchment fact sheets are associated with each ensemble. These contain information on the uncertainty associated with the hydrological modelling when driven using observed climate and Future Flows Climate for a period representative of the reference time slice 1961-1990 as described by key hydrological statistics. Graphs of projected changes for selected hydrological indicators are also provided for the 2050s time slice. Limitations associated with the dataset are provided, along with practical recommendation of use. Future Flows Hydrology is freely available for non-commercial use under certain licensing conditions. For each study site, catchment averages of daily precipitation and monthly potential evapotranspiration, used to drive the hydrological models, are made available, so that hydrological modelling uncertainty under climate change conditions can be explored further. doi:10.5285/f3723162-4fed-4d9d-92c6-dd17412fa37b.
Future Flows Hydrology: an ensemble of daily river flow and monthly groundwater levels for use for climate change impact assessment across Great Britain

NASA Astrophysics Data System (ADS)

Prudhomme, C.; Haxton, T.; Crooks, S.; Jackson, C.; Barkwith, A.; Williamson, J.; Kelvin, J.; Mackay, J.; Wang, L.; Young, A.; Watts, G.

2013-03-01

The dataset Future Flows Hydrology was developed as part of the project "Future Flows and Groundwater Levels'' to provide a consistent set of transient daily river flow and monthly groundwater level projections across England, Wales and Scotland to enable the investigation of the role of climate variability on river flow and groundwater levels nationally and how this may change in the future. Future Flows Hydrology is derived from Future Flows Climate, a national ensemble projection derived from the Hadley Centre's ensemble projection HadRM3-PPE to provide a consistent set of climate change projections for the whole of Great Britain at both space and time resolutions appropriate for hydrological applications. Three hydrological models and one groundwater level model were used to derive Future Flows Hydrology, with 30 river sites simulated by two hydrological models to enable assessment of hydrological modelling uncertainty in studying the impact of climate change on the hydrology. Future Flows Hydrology contains an 11-member ensemble of transient projections from January 1951 to December 2098, each associated with a single realisation from a different variant of HadRM3 and a single hydrological model. Daily river flows are provided for 281 river catchments and monthly groundwater levels at 24 boreholes as .csv files containing all 11 ensemble members. When separate simulations are done with two hydrological models, two separate .csv files are provided. Because of potential biases in the climate-hydrology modelling chain, catchment fact sheets are associated with each ensemble. These contain information on the uncertainty associated with the hydrological modelling when driven using observed climate and Future Flows Climate for a period representative of the reference time slice 1961-1990 as described by key hydrological statistics. Graphs of projected changes for selected hydrological indicators are also provided for the 2050s time slice. Limitations associated with the dataset are provided, along with practical recommendation of use. Future Flows Hydrology is freely available for non-commercial use under certain licensing conditions. For each study site, catchment averages of daily precipitation and monthly potential evapotranspiration, used to drive the hydrological models, are made available, so that hydrological modelling uncertainty under climate change conditions can be explored further. doi:10.5285/f3723162-4fed-4d9d-92c6-dd17412fa37b
Water Dynamics in Nafion Fuel Cell Membranes: the Effects of Confinement and Structural Changes on the Hydrogen Bond Network

PubMed Central

Moilanen, David E.; Piletic, Ivan R.; Fayer, Michael D.

2008-01-01

The complex environments experienced by water molecules in the hydrophilic channels of Nafion membranes are studied by ultrafast infrared pump-probe spectroscopy. A wavelength dependent study of the vibrational lifetime of the O-D stretch of dilute HOD in H2O confined in Nafion membranes provides evidence of two distinct ensembles of water molecules. While only two ensembles are present at each level of membrane hydration studied, the characteristics of the two ensembles change as the water content of the membrane changes. Time dependent anisotropy measurements show that the orientational motions of water molecules in Nafion membranes are significantly slower than in bulk water and that lower hydration levels result in slower orientational relaxation. Initial wavelength dependent results for the anisotropy show no clear variation in the time scale for orientational motion across a broad range of frequencies. The anisotropy decay is analyzed using a model based on restricted orientational diffusion within a hydrogen bond configuration followed by total reorientation through jump diffusion. PMID:18728757
Spatial shaping for generating arbitrary optical dipole traps for ultracold degenerate gases

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

Lee, Jeffrey G., E-mail: jglee@umd.edu; Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742; Hill, W. T., E-mail: wth@umd.edu

2014-10-15

We present two spatial-shaping approaches – phase and amplitude – for creating two-dimensional optical dipole potentials for ultracold neutral atoms. When combined with an attractive or repulsive Gaussian sheet formed by an astigmatically focused beam, atoms are trapped in three dimensions resulting in planar confinement with an arbitrary network of potentials – a free-space atom chip. The first approach utilizes an adaptation of the generalized phase-contrast technique to convert a phase structure embedded in a beam after traversing a phase mask, to an identical intensity profile in the image plane. Phase masks, and a requisite phase-contrast filter, can be chemicallymore » etched into optical material (e.g., fused silica) or implemented with spatial light modulators; etching provides the highest quality while spatial light modulators enable prototyping and realtime structure modification. This approach was demonstrated on an ensemble of thermal atoms. Amplitude shaping is possible when the potential structure is made as an opaque mask in the path of a dipole trap beam, followed by imaging the shadow onto the plane of the atoms. While much more lossy, this very simple and inexpensive approach can produce dipole potentials suitable for containing degenerate gases. High-quality amplitude masks can be produced with standard photolithography techniques. Amplitude shaping was demonstrated on a Bose-Einstein condensate.« less
Use of ultraviolet-fluorescence-based simulation in evaluation of personal protective equipment worn for first assessment and care of a patient with suspected high-consequence infectious disease.

PubMed

Hall, S; Poller, B; Bailey, C; Gregory, S; Clark, R; Roberts, P; Tunbridge, A; Poran, V; Evans, C; Crook, B

2018-06-01

Variations currently exist across the UK in the choice of personal protective equipment (PPE) used by healthcare workers when caring for patients with suspected high-consequence infectious diseases (HCIDs). To test the protection afforded to healthcare workers by current PPE ensembles during assessment of a suspected HCID case, and to provide an evidence base to justify proposal of a unified PPE ensemble for healthcare workers across the UK. One 'basic level' (enhanced precautions) PPE ensemble and five 'suspected case' PPE ensembles were evaluated in volunteer trials using 'Violet'; an ultraviolet-fluorescence-based simulation exercise to visualize exposure/contamination events. Contamination was photographed and mapped. There were 147 post-simulation and 31 post-doffing contamination events, from a maximum of 980, when evaluating the basic level of PPE. Therefore, this PPE ensemble did not afford adequate protection, primarily due to direct contamination of exposed areas of the skin. For the five suspected case ensembles, 1584 post-simulation contamination events were recorded, from a maximum of 5110. Twelve post-doffing contamination events were also observed (face, two events; neck, one event; forearm, one event; lower legs, eight events). All suspected case PPE ensembles either had post-doffing contamination events or other significant disadvantages to their use. This identified the need to design a unified PPE ensemble and doffing procedure, incorporating the most protective PPE considered for each body area. This work has been presented to, and reviewed by, key stakeholders to decide on a proposed unified ensemble, subject to further evaluation. Crown Copyright © 2018. Published by Elsevier Ltd. All rights reserved.
Cooperative Effects in Closely Packed Quantum Emitters with Collective Dephasing

NASA Astrophysics Data System (ADS)

Prasanna Venkatesh, B.; Juan, M. L.; Romero-Isart, O.

2018-01-01

In a closely packed ensemble of quantum emitters, cooperative effects are typically suppressed due to the dephasing induced by the dipole-dipole interactions. Here, we show that by adding sufficiently strong collective dephasing, cooperative effects can be restored. Specifically, we show that the dipole force on a closely packed ensemble of strongly driven two-level quantum emitters, which collectively dephase, is enhanced in comparison to the dipole force on an independent noninteracting ensemble. Our results are relevant to solid-state systems with embedded quantum emitters such as color centers in diamond and superconducting qubits in microwave cavities and waveguides.
The density matrix method in photonic bandgap and antiferromagnetic materials

NASA Astrophysics Data System (ADS)

Barrie, Scott B.

In this thesis, a theory for dispersive polaritonic bandgap (DPBG) and photonic bandgap (PBG) materials is developed. An ensemble of multi-level nanoparticles, such as non-interacting two-, three- and four-level atoms doped in DPBG and PBG materials is considered. The optical properties of these materials such as spontaneous emission, line broadening, fluorescence and narrowing of the natural linewidth have been studied using the density matrix method. Numerical simulations for these properties have been performed for the DPBG materials SiC and InAs, and for a PBG material with a 20 percent gap-to-midgap ratio. When a three-level nanoparticle is doped into a DPBG material, it is predicted that one or two bound states exist when one or both resonance energies, respectively, lie in the bandgap. It is shown when a resonance energy lies below the bandgap, its spectral density peak weakens and broadens as the resonance energy increases to the lower band edge. For the first time it is predicted that when a nanoparticle's resonance energy lies above the bandgap, its spectral density peak weakens and broadens as the resonance energy increases. A relation is also found between spectral structure and gap-to-midgap ratios. The dressed states of a two-level atom doped into a DPBG material under the influence of an intense monochromatic laser field are examined. The splitting of the dressed state energies is calculated, and it is predicted that the splitting depends on the polariton density of states and the Rabi frequency of laser field. The fluoresence is also examined, and for the first time two distinct control processes are found for the transition from one peak to three peaks. It was previously known that the Rabi frequency controlled the Stark effect, but this thesis predicts that the local of the peak with respect to the optical bandgap can cause a transition from one to three peaks even with a weak Rabi frequency. The transient linewidth narrowing of PBG crystal emission peaks doped with four-level atoms is studied. It is found that linewidth narrowing is only dependent upon time delay when the resonance energy is not near a band edge. This is a new discovery. The density matrix method is employed to find the critical magnetic field at which spin flopping occurs in antiferromagnetic high temperature superconductors. It is found that this magnetic field depends upon the temperature, the anisotropy parameter and the doping concentration. Results are calculated for 1-2-3 HTSCs. Keywords. Quantum Optics, Density Matrix, Photonic Bandgap Materials, Dispersive Polaritonic Bandgap Materials, Antiferromagnets.
Study of alloy disorder in quantum dots through multi-million atom simulations

NASA Technical Reports Server (NTRS)

Kilmeck, Gerhard; Oyafuso, Fabiano; Boykin, T. B.; Bowen, R. C.; von Allmen, Paul A.

2003-01-01

A tight binding model which includes s, p, d, s orbitals is used to examine the electronic structures of an ensemble of dome-shaped In0.6 Ga0.4 As quantum dots. Given ensembles of identically sized quantum dots, variations in composition and configuration yield a linewidth broadening of less than 0.35 meV, much smaller than the total broadening determined from photoluminescence experiments. It is also found that the computed disorder-induced broadening is very sensitive to the applied boundary conditions, so that care must be taken to ensure proper convergence of the numerical results. Examination of local eigenenergies as functions of position shows similar convergence problems and indicates that an inaccurate resolution of the equilibrium atomic positions due to truncation of the simulation domain may be the source of the slow ground state convergence.

Continuous variable quantum optical simulation for time evolution of quantum harmonic oscillators

PubMed Central

Deng, Xiaowei; Hao, Shuhong; Guo, Hong; Xie, Changde; Su, Xiaolong

2016-01-01

Quantum simulation enables one to mimic the evolution of other quantum systems using a controllable quantum system. Quantum harmonic oscillator (QHO) is one of the most important model systems in quantum physics. To observe the transient dynamics of a QHO with high oscillation frequency directly is difficult. We experimentally simulate the transient behaviors of QHO in an open system during time evolution with an optical mode and a logical operation system of continuous variable quantum computation. The time evolution of an atomic ensemble in the collective spontaneous emission is analytically simulated by mapping the atomic ensemble onto a QHO. The measured fidelity, which is used for quantifying the quality of the simulation, is higher than its classical limit. The presented simulation scheme provides a new tool for studying the dynamic behaviors of QHO. PMID:26961962
Stresses and elastic constants of crystalline sodium, from molecular dynamics

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

Schiferl, S.K.

1985-02-01

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

PubMed

Kim, Jiyeon; Dick, Jeffrey E; Bard, Allen J

2016-11-15

Metal clusters are very important as building blocks for nanoparticles (NPs) for electrocatalysis and electroanalysis in both fundamental and applied electrochemistry. Attention has been given to understanding of traditional nucleation and growth of metal clusters and to their catalytic activities for various electrochemical applications in energy harvesting as well as analytical sensing. Importantly, understanding the properties of these clusters, primarily the relationship between catalysis and morphology, is required to optimize catalytic function. This has been difficult due to the heterogeneities in the size, shape, and surface properties. Thus, methods that address these issues are necessary to begin understanding the reactivity of individual catalytic centers as opposed to ensemble measurements, where the effect of size and morphology on the catalysis is averaged out in the measurement. This Account introduces our advanced electrochemical approaches to focus on each isolated metal cluster, where we electrochemically fabricated clusters or NPs atom by atom to nanometer by nanometer and explored their electrochemistry for their kinetic and catalytic behavior. Such approaches expand the dimensions of analysis, to include the electrochemistry of (1) a discrete atomic cluster, (2) solely a single NP, or (3) individual NPs in the ensemble sample. Specifically, we studied the electrocatalysis of atomic metal clusters as a nascent electrocatalyst via direct electrodeposition on carbon ultramicroelectrode (C UME) in a femtomolar metal ion precursor. In addition, we developed tunneling ultramicroelectrodes (TUMEs) to study electron transfer (ET) kinetics of a redox probe at a single metal NP electrodeposited on this TUME. Owing to the small dimension of a NP as an active area of a TUME, extremely high mass transfer conditions yielded a remarkably high standard ET rate constant, k 0 , of 36 cm/s for outer-sphere ET reaction. Most recently, we advanced nanoscale scanning electrochemical microscopy (SECM) imaging to resolve the electrocatalytic activity of individual electrodeposited NPs within an ensemble sample yielding consistent high k 0 values of ≥2 cm/s for the hydrogen oxidation reaction (HOR) at different NPs. We envision that our advanced electrochemical approaches will enable us to systematically address structure effects on the catalytic activity, thus providing a quantitative guideline for electrocatalysts in energy-related applications.
Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics

PubMed Central

Shevchuk, Roman; Hub, Jochen S.

2017-01-01

Small-angle X-ray scattering is an increasingly popular technique used to detect protein structures and ensembles in solution. However, the refinement of structures and ensembles against SAXS data is often ambiguous due to the low information content of SAXS data, unknown systematic errors, and unknown scattering contributions from the solvent. We offer a solution to such problems by combining Bayesian inference with all-atom molecular dynamics simulations and explicit-solvent SAXS calculations. The Bayesian formulation correctly weights the SAXS data versus prior physical knowledge, it quantifies the precision or ambiguity of fitted structures and ensembles, and it accounts for unknown systematic errors due to poor buffer matching. The method further provides a probabilistic criterion for identifying the number of states required to explain the SAXS data. The method is validated by refining ensembles of a periplasmic binding protein against calculated SAXS curves. Subsequently, we derive the solution ensembles of the eukaryotic chaperone heat shock protein 90 (Hsp90) against experimental SAXS data. We find that the SAXS data of the apo state of Hsp90 is compatible with a single wide-open conformation, whereas the SAXS data of Hsp90 bound to ATP or to an ATP-analogue strongly suggest heterogenous ensembles of a closed and a wide-open state. PMID:29045407
Computer simulation of formation and decomposition of Au13 nanoparticles

NASA Astrophysics Data System (ADS)

Stishenko, P.; Svalova, A.

2017-08-01

To study the Ostwald ripening process of Au13 nanoparticles a two-scale model is constructed: analytical approximation of average nanoparticle energy as function of nanoparticle size and structural motive, and the Monte Carlo model of 1000 particles ensemble. Simulation results show different behavior of particles of different structural motives. The change of the distributions of atom coordination numbers during the Ostwald ripening process was observed. The nanoparticles of the equal size and shape with the face-centered cubic structure of the largest sizes appeared to be the most stable.
Improved spin squeezing of an atomic ensemble through internal state control

NASA Astrophysics Data System (ADS)

Hemmer, Daniel; Montano, Enrique; Deutsch, Ivan; Jessen, Poul

2016-05-01

Squeezing of collective atomic spins is typically generated by quantum backaction from a QND measurement of the relevant spin component. In this scenario the degree of squeezing is determined by the measurement resolution relative to the quantum projection noise (QPN) of a spin coherent state (SCS). Greater squeezing can be achieved through optimization of the 3D geometry of probe and atom cloud, or by placing the atoms in an optical cavity. We explore here a complementary strategy that relies on quantum control of the large internal spin available in alkali atoms such as Cs. Using a combination of rf and uw magnetic fields, we coherently map the internal spins in our ensemble from the SCS (| f = 4, m = 4>) to a ``cat'' state which is an equal superposition of | f = 4, m = 4>and | f = 4, m = -4>. This increases QPN by a factor of 2 f = 8 relative to the SCS, and therefore the amount of backaction and spin-spin entanglement produced by our QND measurement. In a final step, squeezing generated in the cat state basis can be mapped back to the SCS basis, where it corresponds to increased squeezing of the physical spin. Our experiments suggest that up to 8dB of metrologically useful squeezing can be generated in this way, compared to ~ 3 dB in an otherwise identical experiment starting from a SCS.
Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles.

PubMed

Davey, James A; Chica, Roberto A

2014-05-01

Multistate computational protein design (MSD) with backbone ensembles approximating conformational flexibility can predict higher quality sequences than single-state design with a single fixed backbone. However, it is currently unclear what characteristics of backbone ensembles are required for the accurate prediction of protein sequence stability. In this study, we aimed to improve the accuracy of protein stability predictions made with MSD by using a variety of backbone ensembles to recapitulate the experimentally measured stability of 85 Streptococcal protein G domain β1 sequences. Ensembles tested here include an NMR ensemble as well as those generated by molecular dynamics (MD) simulations, by Backrub motions, and by PertMin, a new method that we developed involving the perturbation of atomic coordinates followed by energy minimization. MSD with the PertMin ensembles resulted in the most accurate predictions by providing the highest number of stable sequences in the top 25, and by correctly binning sequences as stable or unstable with the highest success rate (≈90%) and the lowest number of false positives. The performance of PertMin ensembles is due to the fact that their members closely resemble the input crystal structure and have low potential energy. Conversely, the NMR ensemble as well as those generated by MD simulations at 500 or 1000 K reduced prediction accuracy due to their low structural similarity to the crystal structure. The ensembles tested herein thus represent on- or off-target models of the native protein fold and could be used in future studies to design for desired properties other than stability. Copyright © 2013 Wiley Periodicals, Inc.
Formation and evolution of multimodal size distributions of InAs/GaAs quantum dots

NASA Astrophysics Data System (ADS)

Pohl, U. W.; Pötschke, K.; Schliwa, A.; Lifshits, M. B.; Shchukin, V. A.; Jesson, D. E.; Bimberg, D.

2006-05-01

Self-organized formation and evolution of quantum dot (QD) ensembles with a multimodal size distribution is reported. Such ensembles form after fast deposition near the critical thickness during a growth interruption (GRI) prior to cap layer growth and consist of pure InAs truncated pyramids with heights varying in steps of complete InAs monolayers, thereby creating well-distinguishable sub-ensembles. Ripening during GRI manifests itself by an increase of sub-ensembles of larger QDs at the expense of sub-ensembles of smaller ones, leaving the wetting layer unchanged. The dynamics of the multimodal QD size distribution is theoretically described using a kinetic approach. Starting from a broad distribution of flat QDs, a predominantly vertical growth is found due to strain-induced barriers for nucleation of a next atomic layer on different facets. QDs having initially a shorter base length attain a smaller height, accounting for the experimentally observed sub-ensemble structure. The evolution of the distribution is described by a master equation, which accounts for growth or dissolution of the QDs by mass exchange between the QDs and the adatom sea. The numerical solution is in good agreement with the measured dynamics.
Entanglement via Faraday effect - an old tool at a new job for Quantum Networks

NASA Astrophysics Data System (ADS)

Polzik, Eugene

2002-05-01

A new approach to the problem of the quantum interface between light and atoms has been developed [1,2]. The method utilizes free space dispersive interaction of pulses of light with spin polarized atomic ensembles. Entanglement between the polarization state of light and the collective spin state of atoms is established by measurement, more precisely by detection of light in certain polarization basis. In the first demonstration of this approach [3] we have generated a long-lived entangled state of two separate macroscopic atomic samples by a polarization measurement on light transmitted through the samples. We then have shown that this approach also works for mapping of a quantum state of light onto long-lived atomic spin state [4] paving the road towards realization of the quantum memory for light. Progress with other communication protocols such as atomic state teleportation and multiparty networks will be presented. 1. A. Kuzmich and E. S. Polzik, Phys. Rev. Lett. (2000) 85, 5639. 2. Lu-Ming Duan, J.I. Cirac, P. Zoller and E. S. Polzik, Phys. Rev. Lett. (2000) 85, (25), 5643. 3. B. Julsgaard, A. Kozhekin, and E. S. Polzik, Nature, 413, 400 (2001). 4. J. L. Sorensen, B. Julsgaard, C. Schori and E. S. Polzik, submitted for publication.
A 3D-analysis of cluster formation and dynamics of the X(-)-benzene (X = F, Cl, Br, I) ionic dimer solvated by Ar atoms.

PubMed

Albertí, Margarita; Huarte-Larrañaga, Fermín; Aguilar, Antonio; Lucas, José M; Pirani, Fernando

2011-05-14

The specific influence of X(-) ions (X = F,Cl, Br, I) in the solvation process of halide-benzene (X(-)-Bz) ionic heterodimers by Ar atoms is investigated by means of molecular dynamic (MD) simulations. The gradual evolution from cluster rearrangement to solvation dynamics is discussed by considering ensembles of n (n = 1-15 and n = 30) Ar atoms around the X(-)-Bz stable ionic dimers. The potential energy surfaces employed are based on an atom/ion-atom and atom/ion-bond decomposition, which has been developed previously by some of the authors. The outcome of the dynamics is analyzed by employing radial distribution functions (RDF) and tridimensional (3D) probability densities.
Optical storage with electromagnetically induced transparency in cold atoms at a high optical depth

NASA Astrophysics Data System (ADS)

Zhang, Shanchao; Zhou, Shuyu; Liu, Chang; Chen, J. F.; Wen, Jianming; Loy, M. M. T.; Wong, G. K. L.; Du, Shengwang

2012-06-01

We report experimental demonstration of efficient optical storage with electromagnetically induced transparency (EIT) in a dense cold ^85Rb atomic ensemble trapped in a two-dimensional magneto-optical trap. By varying the optical depth (OD) from 0 to 140, we observe that the optimal storage efficiency for coherent optical pulses has a saturation value of 50% as OD > 50. Our result is consistent with that obtained from hot vapor cell experiments which suggest that a four-wave mixing nonlinear process degrades the EIT storage coherence and efficiency. We apply this EIT quantum memory for narrow-band single photons with controllable waveforms, and obtain an optimal storage efficiency of 49±3% for single-photon wave packets. This is the highest single-photon storage efficiency reported up to today and brings the EIT atomic quantum memory close to practical application because an efficiency of above 50% is necessary to operate the memory within non-cloning regime and beat the classical limit.
Light Stops at Exceptional Points

NASA Astrophysics Data System (ADS)

Goldzak, Tamar; Mailybaev, Alexei A.; Moiseyev, Nimrod

2018-01-01

Almost twenty years ago, light was slowed down to less than 10-7 of its vacuum speed in a cloud of ultracold atoms of sodium. Upon a sudden turn-off of the coupling laser, a slow light pulse can be imprinted on cold atoms such that it can be read out and converted into a photon again. In this process, the light is stopped by absorbing it and storing its shape within the atomic ensemble. Alternatively, the light can be stopped at the band edge in photonic-crystal waveguides, where the group speed vanishes. Here, we extend the phenomenon of stopped light to the new field of parity-time (P T ) symmetric systems. We show that zero group speed in P T symmetric optical waveguides can be achieved if the system is prepared at an exceptional point, where two optical modes coalesce. This effect can be tuned for optical pulses in a wide range of frequencies and bandwidths, as we demonstrate in a system of coupled waveguides with gain and loss.
Propellant Handler's Ensemble (PHE) Aka Self-Contained Atmospheric Protective Ensemble (SCAPE), Ventilator Improvement Study Project

NASA Technical Reports Server (NTRS)

Oliva-Buisson, Yvette J. (Compiler)

2014-01-01

The overall objective for this project is to evaluate two candidate alternatives for the existing Propellant Handler's Ensemble (PHE) escape ventilator. The new candidate ventilators use newer technology with similar quantities of air at approximately half the weight of the current ventilator. Ventilators are typically used to ingress/egress a hazardous work area when hard line air is provided at the work area but the hose is not long enough to get the operator to and from the staging area to the work area. The intent of this test is to verify that the new ventilators perform as well as or better than the current ventilators in maintaining proper oxygen (O2) and carbon dioxide (CO2) levels in the PHE during a typical use for the rated time period (10 minutes). We will evaluate two new units comparing them to the existing unit. Subjects will wear the Category I version of the Propellant Handler's Ensemble with the rear suit pouch snapped.
Atom-Pair Kinetics with Strong Electric-Dipole Interactions.

PubMed

Thaicharoen, N; Gonçalves, L F; Raithel, G

2016-05-27

Rydberg-atom ensembles are switched from a weakly to a strongly interacting regime via adiabatic transformation of the atoms from an approximately nonpolar into a highly dipolar quantum state. The resultant electric dipole-dipole forces are probed using a device akin to a field ion microscope. Ion imaging and pair-correlation analysis reveal the kinetics of the interacting atoms. Dumbbell-shaped pair-correlation images demonstrate the anisotropy of the binary dipolar force. The dipolar C_{3} coefficient, derived from the time dependence of the images, agrees with the value calculated from the permanent electric-dipole moment of the atoms. The results indicate many-body dynamics akin to disorder-induced heating in strongly coupled particle systems.
Enhanced squeezing of a collective spin via control of its qudit subsystems.

PubMed

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

2012-10-26

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

PubMed

Chen, Shuai; Chen, Yu-Ao; Strassel, Thorsten; Yuan, Zhen-Sheng; Zhao, Bo; Schmiedmayer, Jörg; Pan, Jian-Wei

2006-10-27

A single-photon source is realized with a cold atomic ensemble (87Rb atoms). A single excitation, written in an atomic quantum memory by Raman scattering of a laser pulse, is retrieved deterministically as a single photon at a predetermined time. It is shown that the production rate of single photons can be enhanced considerably by a feedback circuit while the single-photon quality is conserved. Such a single-photon source is well suited for future large-scale realization of quantum communication and linear optical quantum computation.
Evaluation of atomic pressure in the multiple time-step integration algorithm.

PubMed

Andoh, Yoshimichi; Yoshii, Noriyuki; Yamada, Atsushi; Okazaki, Susumu

2017-04-15

In molecular dynamics (MD) calculations, reduction in calculation time per MD loop is essential. A multiple time-step (MTS) integration algorithm, the RESPA (Tuckerman and Berne, J. Chem. Phys. 1992, 97, 1990-2001), enables reductions in calculation time by decreasing the frequency of time-consuming long-range interaction calculations. However, the RESPA MTS algorithm involves uncertainties in evaluating the atomic interaction-based pressure (i.e., atomic pressure) of systems with and without holonomic constraints. It is not clear which intermediate forces and constraint forces in the MTS integration procedure should be used to calculate the atomic pressure. In this article, we propose a series of equations to evaluate the atomic pressure in the RESPA MTS integration procedure on the basis of its equivalence to the Velocity-Verlet integration procedure with a single time step (STS). The equations guarantee time-reversibility even for the system with holonomic constrants. Furthermore, we generalize the equations to both (i) arbitrary number of inner time steps and (ii) arbitrary number of force components (RESPA levels). The atomic pressure calculated by our equations with the MTS integration shows excellent agreement with the reference value with the STS, whereas pressures calculated using the conventional ad hoc equations deviated from it. Our equations can be extended straightforwardly to the MTS integration algorithm for the isothermal NVT and isothermal-isobaric NPT ensembles. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble

NASA Astrophysics Data System (ADS)

Müller, Christian L.; Sbalzarini, Ivo F.; van Gunsteren, Wilfred F.; Žagrović, Bojan; Hünenberger, Philippe H.

2009-06-01

The concept of high-resolution shapes (also referred to as folds or states, depending on the context) of a polymer chain plays a central role in polymer science, structural biology, bioinformatics, and biopolymer dynamics. However, although the idea of shape is intuitively very useful, there is no unambiguous mathematical definition for this concept. In the present work, the distributions of high-resolution shapes within the ideal random-walk ensembles with N =3,…,6 beads (or up to N =10 for some properties) are investigated using a systematic (grid-based) approach based on a simple working definition of shapes relying on the root-mean-square atomic positional deviation as a metric (i.e., to define the distance between pairs of structures) and a single cutoff criterion for the shape assignment. Although the random-walk ensemble appears to represent the paramount of homogeneity and randomness, this analysis reveals that the distribution of shapes within this ensemble, i.e., in the total absence of interatomic interactions characteristic of a specific polymer (beyond the generic connectivity constraint), is significantly inhomogeneous. In particular, a specific (densest) shape occurs with a local probability that is 1.28, 1.79, 2.94, and 10.05 times (N =3,…,6) higher than the corresponding average over all possible shapes (these results can tentatively be extrapolated to a factor as large as about 1028 for N =100). The qualitative results of this analysis lead to a few rather counterintuitive suggestions, namely, that, e.g., (i) a fold classification analysis applied to the random-walk ensemble would lead to the identification of random-walk "folds;" (ii) a clustering analysis applied to the random-walk ensemble would also lead to the identification random-walk "states" and associated relative free energies; and (iii) a random-walk ensemble of polymer chains could lead to well-defined diffraction patterns in hypothetical fiber or crystal diffraction experiments. The inhomogeneous nature of the shape probability distribution identified here for random walks may represent a significant underlying baseline effect in the analysis of real polymer chain ensembles (i.e., in the presence of specific interatomic interactions). As a consequence, a part of what is called a polymer shape may actually reside just "in the eye of the beholder" rather than in the nature of the interactions between the constituting atoms, and the corresponding observation-related bias should be taken into account when drawing conclusions from shape analyses as applied to real structural ensembles.
In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble.

PubMed

Müller, Christian L; Sbalzarini, Ivo F; van Gunsteren, Wilfred F; Zagrović, Bojan; Hünenberger, Philippe H

2009-06-07

The concept of high-resolution shapes (also referred to as folds or states, depending on the context) of a polymer chain plays a central role in polymer science, structural biology, bioinformatics, and biopolymer dynamics. However, although the idea of shape is intuitively very useful, there is no unambiguous mathematical definition for this concept. In the present work, the distributions of high-resolution shapes within the ideal random-walk ensembles with N=3,...,6 beads (or up to N=10 for some properties) are investigated using a systematic (grid-based) approach based on a simple working definition of shapes relying on the root-mean-square atomic positional deviation as a metric (i.e., to define the distance between pairs of structures) and a single cutoff criterion for the shape assignment. Although the random-walk ensemble appears to represent the paramount of homogeneity and randomness, this analysis reveals that the distribution of shapes within this ensemble, i.e., in the total absence of interatomic interactions characteristic of a specific polymer (beyond the generic connectivity constraint), is significantly inhomogeneous. In particular, a specific (densest) shape occurs with a local probability that is 1.28, 1.79, 2.94, and 10.05 times (N=3,...,6) higher than the corresponding average over all possible shapes (these results can tentatively be extrapolated to a factor as large as about 10(28) for N=100). The qualitative results of this analysis lead to a few rather counterintuitive suggestions, namely, that, e.g., (i) a fold classification analysis applied to the random-walk ensemble would lead to the identification of random-walk "folds;" (ii) a clustering analysis applied to the random-walk ensemble would also lead to the identification random-walk "states" and associated relative free energies; and (iii) a random-walk ensemble of polymer chains could lead to well-defined diffraction patterns in hypothetical fiber or crystal diffraction experiments. The inhomogeneous nature of the shape probability distribution identified here for random walks may represent a significant underlying baseline effect in the analysis of real polymer chain ensembles (i.e., in the presence of specific interatomic interactions). As a consequence, a part of what is called a polymer shape may actually reside just "in the eye of the beholder" rather than in the nature of the interactions between the constituting atoms, and the corresponding observation-related bias should be taken into account when drawing conclusions from shape analyses as applied to real structural ensembles.
Large ensemble modeling of the last deglacial retreat of the West Antarctic Ice Sheet: comparison of simple and advanced statistical techniques

NASA Astrophysics Data System (ADS)

Pollard, David; Chang, Won; Haran, Murali; Applegate, Patrick; DeConto, Robert

2016-05-01

A 3-D hybrid ice-sheet model is applied to the last deglacial retreat of the West Antarctic Ice Sheet over the last ˜ 20 000 yr. A large ensemble of 625 model runs is used to calibrate the model to modern and geologic data, including reconstructed grounding lines, relative sea-level records, elevation-age data and uplift rates, with an aggregate score computed for each run that measures overall model-data misfit. Two types of statistical methods are used to analyze the large-ensemble results: simple averaging weighted by the aggregate score, and more advanced Bayesian techniques involving Gaussian process-based emulation and calibration, and Markov chain Monte Carlo. The analyses provide sea-level-rise envelopes with well-defined parametric uncertainty bounds, but the simple averaging method only provides robust results with full-factorial parameter sampling in the large ensemble. Results for best-fit parameter ranges and envelopes of equivalent sea-level rise with the simple averaging method agree well with the more advanced techniques. Best-fit parameter ranges confirm earlier values expected from prior model tuning, including large basal sliding coefficients on modern ocean beds.

Ensemble coding remains accurate under object and spatial visual working memory load.

PubMed

Epstein, Michael L; Emmanouil, Tatiana A

2017-10-01

A number of studies have provided evidence that the visual system statistically summarizes large amounts of information that would exceed the limitations of attention and working memory (ensemble coding). However the necessity of working memory resources for ensemble coding has not yet been tested directly. In the current study, we used a dual task design to test the effect of object and spatial visual working memory load on size averaging accuracy. In Experiment 1, we tested participants' accuracy in comparing the mean size of two sets under various levels of object visual working memory load. Although the accuracy of average size judgments depended on the difference in mean size between the two sets, we found no effect of working memory load. In Experiment 2, we tested the same average size judgment while participants were under spatial visual working memory load, again finding no effect of load on averaging accuracy. Overall our results reveal that ensemble coding can proceed unimpeded and highly accurately under both object and spatial visual working memory load, providing further evidence that ensemble coding reflects a basic perceptual process distinct from that of individual object processing.
A Zeeman slower for diatomic molecules

NASA Astrophysics Data System (ADS)

Petzold, M.; Kaebert, P.; Gersema, P.; Siercke, M.; Ospelkaus, S.

2018-04-01

We present a novel slowing scheme for beams of laser-coolable diatomic molecules reminiscent of Zeeman slowing of atomic beams. The scheme results in efficient compression of the one-dimensional velocity distribution to velocities trappable by magnetic or magneto-optical traps. We experimentally demonstrate our method in an atomic testbed and show an enhancement of flux below v = 35 m s‑1 by a factor of ≈20 compared to white light slowing. 3D Monte Carlo simulations performed to model the experiment show excellent agreement. We apply the same simulations to the prototype molecule 88Sr19F and expect 15% of the initial flux to be continuously compressed in a narrow velocity window at around 10 m s‑1. This is the first experimentally shown continuous and dissipative slowing technique in molecule-like level structures, promising to provide the missing link for the preparation of large ultracold molecular ensembles.
Thermodynamics of phase-separating nanoalloys: Single particles and particle assemblies

NASA Astrophysics Data System (ADS)

Fèvre, Mathieu; Le Bouar, Yann; Finel, Alphonse

2018-05-01

The aim of this paper is to investigate the consequences of finite-size effects on the thermodynamics of nanoparticle assemblies and isolated particles. We consider a binary phase-separating alloy with a negligible atomic size mismatch, and equilibrium states are computed using off-lattice Monte Carlo simulations in several thermodynamic ensembles. First, a semi-grand-canonical ensemble is used to describe infinite assemblies of particles with the same size. When decreasing the particle size, we obtain a significant decrease of the solid/liquid transition temperatures as well as a growing asymmetry of the solid-state miscibility gap related to surface segregation effects. Second, a canonical ensemble is used to analyze the thermodynamic equilibrium of finite monodisperse particle assemblies. Using a general thermodynamic formulation, we show that a particle assembly may split into two subassemblies of identical particles. Moreover, if the overall average canonical concentration belongs to a discrete spectrum, the subassembly concentrations are equal to the semi-grand-canonical equilibrium ones. We also show that the equilibrium of a particle assembly with a prescribed size distribution combines a size effect and the fact that a given particle size assembly can adopt two configurations. Finally, we have considered the thermodynamics of an isolated particle to analyze whether a phase separation can be defined within a particle. When studying rather large nanoparticles, we found that the region in which a two-phase domain can be identified inside a particle is well below the bulk phase diagram, but the concentration of the homogeneous core remains very close to the bulk solubility limit.
Quantum storage of orbital angular momentum entanglement in an atomic ensemble.

PubMed

Ding, Dong-Sheng; Zhang, Wei; Zhou, Zhi-Yuan; Shi, Shuai; Xiang, Guo-Yong; Wang, Xi-Shi; Jiang, Yun-Kun; Shi, Bao-Sen; Guo, Guang-Can

2015-02-06

Constructing a quantum memory for a photonic entanglement is vital for realizing quantum communication and network. Because of the inherent infinite dimension of orbital angular momentum (OAM), the photon's OAM has the potential for encoding a photon in a high-dimensional space, enabling the realization of high channel capacity communication. Photons entangled in orthogonal polarizations or optical paths had been stored in a different system, but there have been no reports on the storage of a photon pair entangled in OAM space. Here, we report the first experimental realization of storing an entangled OAM state through the Raman protocol in a cold atomic ensemble. We reconstruct the density matrix of an OAM entangled state with a fidelity of 90.3%±0.8% and obtain the Clauser-Horne-Shimony-Holt inequality parameter S of 2.41±0.06 after a programed storage time. All results clearly show the preservation of entanglement during the storage.
The Population Inversion and the Entropy of a Moving Two-Level Atom in Interaction with a Quantized Field

NASA Astrophysics Data System (ADS)

Abo-Kahla, D. A. M.; Abdel-Aty, M.; Farouk, A.

2018-05-01

An atom with only two energy eigenvalues is described by a two-dimensional state space spanned by the two energy eigenstates is called a two-level atom. We consider the interaction between a two-level atom system with a constant velocity. An analytic solution of the systems which interacts with a quantized field is provided. Furthermore, the significant effect of the temperature on the atomic inversion, the purity and the information entropy are discussed in case of the initial state either an exited state or a maximally mixed state. Additionally, the effect of the half wavelengths number of the field-mode is investigated.
Atomic Structure. Independent Learning Project for Advanced Chemistry (ILPAC). Unit S2.

ERIC Educational Resources Information Center

Inner London Education Authority (England).

This unit on atomic structure is one of 10 first year units produced by the Independent Learning Project for Advanced Chemistry (ILPAC). The unit consists of two levels. Level one focuses on the atomic nucleus. Level two focuses on the arrangement of extranuclear electrons, approaching atomic orbitals through both electron bombardment and spectra.…
Defining Tropospheric Chemistry As A Heterogeneous Ensemble Of Reactive Air Parcels

NASA Astrophysics Data System (ADS)

Prather, M. J.; Zhu, X.; Flynn, C.; Mao, J.; Strode, S. A.; Steenrod, S. D.; Strahan, S. E.; Lamarque, J. F.; Fiore, A. M.; Horowitz, L. W.; Shindell, D. T.; Murray, L. T.

2016-12-01

Two major challenges in model-measurement comparisons have been: Which measurements are the most important to match? At what level do models need to simulate the variegated fine structures observed in trace gases and aerosols? This talk presents a novel approach for evaluating high-resolution global chemistry models (1/2 to 1 deg) that is integral to NASA's Atmospheric Tomography (ATom) mission. The approach seeks to develop a chemical climatology for tropospheric regions rather than just event-based testing of specific observations. It enables chemistry-climate models to be readily compared and more severely tested with observations. It uses the reactivity of air parcels (e.g., loss of methane, production and loss of ozone) to weight each parcel in terms of its importance in controlling the two most important chemically reactive greenhouse gases. It looks at the entire statistical distribution of air parcels in terms of a chemical phase space for those species that control the reactivity (e.g., O3, H2O, CH4, CO, NOx, HNO3, HNO4, PAN, CH3NO3, HCHO, HOOH, CH3OOH, C2H6, C3H6O, and other VOCs when present in sufficiently large abundances). It builds statistics of chemically extreme air parcels such as pollution layers to determine if a model failure to match such cases affects the overall reactivity of the region. This approach was designed for the ATom in situ measurements using the DC-8 to slice through the middle of the Pacific and Atlantic Ocean basins each season. The ATom payload will measure the above key trace gases and many other gases and aerosols in every designated air parcel (i.e., 10-sec averages). The first ATom measurements will not be available until mid-2017 and this presentation shows how this climatology looks when sampled with different models. Six global chemistry models have simulated one day in August (no particular year), and we sample all six showing how the 2D probability density plots highlight different regions when weighted by chemical reactivity. These models pre-simulation of ATom provide a target for the ATom measurements. The models also enable us to estimate the representativeness of ATom's single tomographic slice down the ocean basins, and therefore just how well we can observationally determine this chemical climatology of the reactivity of the troposphere.
Construction, MD simulation, and hydrodynamic validation of an all-atom model of a monoclonal IgG antibody.

PubMed

Brandt, J Paul; Patapoff, Thomas W; Aragon, Sergio R

2010-08-04

At 150 kDa, antibodies of the IgG class are too large for their structure to be determined with current NMR methodologies. Because of hinge-region flexibility, it is difficult to obtain atomic-level structural information from the crystal, and questions regarding antibody structure and dynamics in solution remain unaddressed. Here we describe the construction of a model of a human IgG1 monoclonal antibody (trastuzumab) from the crystal structures of fragments. We use a combination of molecular-dynamics (MD) simulation, continuum hydrodynamics modeling, and experimental diffusion measurements to explore antibody behavior in aqueous solution. Hydrodynamic modeling provides a link between the atomic-level details of MD simulation and the size- and shape-dependent data provided by hydrodynamic measurements. Eight independent 40 ns MD trajectories were obtained with the AMBER program suite. The ensemble average of the computed transport properties over all of the MD trajectories agrees remarkably well with the value of the translational diffusion coefficient obtained with dynamic light scattering at 20 degrees C and 27 degrees C, and the intrinsic viscosity measured at 20 degrees C. Therefore, our MD results likely represent a realistic sampling of the conformational space that an antibody explores in aqueous solution. 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Temperature for a dynamic spin ensemble

NASA Astrophysics Data System (ADS)

Ma, Pui-Wai; Dudarev, S. L.; Semenov, A. A.; Woo, C. H.

2010-09-01

In molecular dynamics simulations, temperature is evaluated, via the equipartition principle, by computing the mean kinetic energy of atoms. There is no similar recipe yet for evaluating temperature of a dynamic system of interacting spins. By solving semiclassical Langevin spin-dynamics equations, and applying the fluctuation-dissipation theorem, we derive an equation for the temperature of a spin ensemble, expressed in terms of dynamic spin variables. The fact that definitions for the kinetic and spin temperatures are fully consistent is illustrated using large-scale spin dynamics and spin-lattice dynamics simulations.
Hardware-efficient Bell state preparation using Quantum Zeno Dynamics in superconducting circuits

NASA Astrophysics Data System (ADS)

Flurin, Emmanuel; Blok, Machiel; Hacohen-Gourgy, Shay; Martin, Leigh S.; Livingston, William P.; Dove, Allison; Siddiqi, Irfan

By preforming a continuous joint measurement on a two qubit system, we restrict the qubit evolution to a chosen subspace of the total Hilbert space. This extension of the quantum Zeno effect, called Quantum Zeno Dynamics, has already been explored in various physical systems such as superconducting cavities, single rydberg atoms, atomic ensembles and Bose Einstein condensates. In this experiment, two superconducting qubits are strongly dispersively coupled to a high-Q cavity (χ >> κ) allowing for the doubly excited state | 11 〉 to be selectively monitored. The Quantum Zeno Dynamics in the complementary subspace enables us to coherently prepare a Bell state. As opposed to dissipation engineering schemes, we emphasize that our protocol is deterministic, does not rely direct coupling between qubits and functions only using single qubit controls and cavity readout. Such Quantum Zeno Dynamics can be generalized to larger Hilbert space enabling deterministic generation of many-body entangled states, and thus realizes a decoherence-free subspace allowing alternative noise-protection schemes.
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.
Detuning dependence of Rabi oscillations in an InAs self-assembled quantum dot ensemble

NASA Astrophysics Data System (ADS)

Suzuki, Takeshi; Singh, Rohan; Bayer, Manfred; Ludzwig, Arne; Wieck, Andreas D.; Cundiff, Steven T.

2018-04-01

We study the coherent evolution of an InAs self-assembled quantum dot (QD) ensemble in the ultrafast regime. The evolution of the entire frequency distribution is revealed by performing prepulse two-dimensional (2D) coherent spectroscopy. Charged and neutral QDs display distinct nonlinear responses arising from two-level trion and four-level exciton-biexciton systems, respectively, and each signal is clearly separated in 2D spectra. Whereas the signals for charged QDs are symmetric with respect to the detuning, those for neutral QDs are asymmetric due to the asymmetric four-level energy structure. Experimental results for charged and neutral QDs are well reproduced by solving the optical Bloch equations, including detuning and excitation-induced dephasing (EID) effects. The temperature dependence suggests that wetting-layer carriers play an important role in EID.
Nonsequential double ionization channels control of Ar with few-cycle elliptically polarized laser pulse by carrier-envelope-phase.

PubMed

Ben, Shuai; Wang, Tian; Xu, Tongtong; Guo, Jing; Liu, Xueshen

2016-04-04

The carrier-envelop-phase (CEP) dependence of nonsequential double ionization (NSDI) of atomic Ar with few-cycle elliptically polarized laser pulse is investigated using 2D classical ensemble method. We distinguish two particular recollision channels in NSDI, which are recollision-impact ionization (RII) and recollision-induced excitation with subsequent ionization (RESI). We separate the RII and RESI channels according to the delay time between recollision and final double ionization. By tracing the history of the trajectories, we find the electron correlation spectra as well as the competition between the two channels are sensitively dependent on the laser field CEP. Finally, control can be achieved between the two channels by varying the CEP.
Efficient multiparticle entanglement via asymmetric Rydberg blockade.

PubMed

Saffman, M; Mølmer, K

2009-06-19

We present an efficient method for producing N particle entangled states using Rydberg blockade interactions. Optical excitation of Rydberg states that interact weakly, yet have a strong coupling to a second control state is used to achieve state dependent qubit rotations in small ensembles. On the basis of quantitative calculations, we predict that an entangled quantum superposition state of eight atoms can be produced with a fidelity of 84% in cold Rb atoms.
Quantum control and measurement of atomic spins in polarization spectroscopy

NASA Astrophysics Data System (ADS)

Deutsch, Ivan H.; Jessen, Poul S.

2010-03-01

Quantum control and measurement are two sides of the same coin. To affect a dynamical map, well-designed time-dependent control fields must be applied to the system of interest. To read out the quantum state, information about the system must be transferred to a probe field. We study a particular example of this dual action in the context of quantum control and measurement of atomic spins through the light-shift interaction with an off-resonant optical probe. By introducing an irreducible tensor decomposition, we identify the coupling of the Stokes vector of the light field with moments of the atomic spin state. This shows how polarization spectroscopy can be used for continuous weak measurement of atomic observables that evolve as a function of time. Simultaneously, the state-dependent light shift induced by the probe field can drive nonlinear dynamics of the spin, and can be used to generate arbitrary unitary transformations on the atoms. We revisit the derivation of the master equation in order to give a unified description of spin dynamics in the presence of both nonlinear dynamics and photon scattering. Based on this formalism, we review applications to quantum control, including the design of state-to-state mappings, and quantum-state reconstruction via continuous weak measurement on a dynamically controlled ensemble.
Self-consistent Maxwell-Bloch model of quantum-dot photonic-crystal-cavity lasers

NASA Astrophysics Data System (ADS)

Cartar, William; Mørk, Jesper; Hughes, Stephen

2017-08-01

We present a powerful computational approach to simulate the threshold behavior of photonic-crystal quantum-dot (QD) lasers. Using a finite-difference time-domain (FDTD) technique, Maxwell-Bloch equations representing a system of thousands of statistically independent and randomly positioned two-level emitters are solved numerically. Phenomenological pure dephasing and incoherent pumping is added to the optical Bloch equations to allow for a dynamical lasing regime, but the cavity-mediated radiative dynamics and gain coupling of each QD dipole (artificial atom) is contained self-consistently within the model. These Maxwell-Bloch equations are implemented by using Lumerical's flexible material plug-in tool, which allows a user to define additional equations of motion for the nonlinear polarization. We implement the gain ensemble within triangular-lattice photonic-crystal cavities of various length N (where N refers to the number of missing holes), and investigate the cavity mode characteristics and the threshold regime as a function of cavity length. We develop effective two-dimensional model simulations which are derived after studying the full three-dimensional passive material structures by matching the cavity quality factors and resonance properties. We also demonstrate how to obtain the correct point-dipole radiative decay rate from Fermi's golden rule, which is captured naturally by the FDTD method. Our numerical simulations predict that the pump threshold plateaus around cavity lengths greater than N =9 , which we identify as a consequence of the complex spatial dynamics and gain coupling from the inhomogeneous QD ensemble. This behavior is not expected from simple rate-equation analysis commonly adopted in the literature, but is in qualitative agreement with recent experiments. Single-mode to multimode lasing is also observed, depending on the spectral peak frequency of the QD ensemble. Using a statistical modal analysis of the average decay rates, we also show how the average radiative decay rate decreases as a function of cavity size. In addition, we investigate the role of structural disorder on both the passive cavity and active lasers, where the latter show a general increase in the pump threshold for cavity lengths greater than N =7 , and a reduction in the nominal cavity mode volume for increasing amounts of disorder.
Mirror-assisted coherent backscattering from the Mollow sidebands

NASA Astrophysics Data System (ADS)

Piovella, N.; Teixeira, R. Celistrino; Kaiser, R.; Courteille, Ph. W.; Bachelard, R.

2017-11-01

In front of a mirror, the radiation of weakly driven large disordered clouds presents an interference fringe in the backward direction, on top of an incoherent background. Although strongly driven atoms usually present little coherent scattering, we show here that the mirror-assisted version can produce high contrast fringes, for arbitrarily high saturation parameters. The contrast of the fringes oscillates with the Rabi frequency of the atomic transition and the distance between the mirror and the atoms, due to the coherent interference between the carrier and the Mollow sidebands of the saturated resonant fluorescence spectrum emitted by the atoms. The setup thus represents a powerful platform to study the spectral properties of ensembles of correlated scatterers.
ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution

PubMed Central

Kurkcuoglu, Zeynep; Bahar, Ivet; Doruker, Pemra

2016-01-01

Accurate sampling of conformational space and, in particular, the transitions between functional substates has been a challenge in molecular dynamic (MD) simulations of large biomolecular systems. We developed an Elastic Network Model (ENM)-based computational method, ClustENM, for sampling large conformational changes of biomolecules with various sizes and oligomerization states. ClustENM is an iterative method that combines ENM with energy minimization and clustering steps. It is an unbiased technique, which requires only an initial structure as input, and no information about the target conformation. To test the performance of ClustENM, we applied it to six biomolecular systems: adenylate kinase (AK), calmodulin, p38 MAP kinase, HIV-1 reverse transcriptase (RT), triosephosphate isomerase (TIM), and the 70S ribosomal complex. The generated ensembles of conformers determined at atomic resolution show good agreement with experimental data (979 structures resolved by X-ray and/or NMR) and encompass the subspaces covered in independent MD simulations for TIM, p38, and RT. ClustENM emerges as a computationally efficient tool for characterizing the conformational space of large systems at atomic detail, in addition to generating a representative ensemble of conformers that can be advantageously used in simulating substrate/ligand-binding events. PMID:27494296
Crossover between the Gaussian orthogonal ensemble, the Gaussian unitary ensemble, and Poissonian statistics.

PubMed

Schweiner, Frank; Laturner, Jeanine; Main, Jörg; Wunner, Günter

2017-11-01

Until now only for specific crossovers between Poissonian statistics (P), the statistics of a Gaussian orthogonal ensemble (GOE), or the statistics of a Gaussian unitary ensemble (GUE) have analytical formulas for the level spacing distribution function been derived within random matrix theory. We investigate arbitrary crossovers in the triangle between all three statistics. To this aim we propose an according formula for the level spacing distribution function depending on two parameters. Comparing the behavior of our formula for the special cases of P→GUE, P→GOE, and GOE→GUE with the results from random matrix theory, we prove that these crossovers are described reasonably. Recent investigations by F. Schweiner et al. [Phys. Rev. E 95, 062205 (2017)2470-004510.1103/PhysRevE.95.062205] have shown that the Hamiltonian of magnetoexcitons in cubic semiconductors can exhibit all three statistics in dependence on the system parameters. Evaluating the numerical results for magnetoexcitons in dependence on the excitation energy and on a parameter connected with the cubic valence band structure and comparing the results with the formula proposed allows us to distinguish between regular and chaotic behavior as well as between existent or broken antiunitary symmetries. Increasing one of the two parameters, transitions between different crossovers, e.g., from the P→GOE to the P→GUE crossover, are observed and discussed.
Simultaneously exciting two atoms with photon-mediated Raman interactions

NASA Astrophysics Data System (ADS)

Zhao, Peng; Tan, Xinsheng; Yu, Haifeng; Zhu, Shi-Liang; Yu, Yang

2017-06-01

We propose an approach to simultaneously excite two atoms by using a cavity-assisted Raman process in combination with a cavity-photon-mediated interaction. The system consists of a two-level atom and a Λ -type or V -type three-level atom, which are coupled together with a cavity mode. Having derived the effective Hamiltonian, we find that under certain circumstances a single photon can simultaneously excite two atoms. In addition, multiple photons and even a classical field can also simultaneously excite two atoms. As an example, we show a scheme to realize our proposal in a circuit QED setup, which is artificial atoms coupled with a cavity. The dynamics and the quantum-statistical properties of the process are investigated with experimentally feasible parameters.

Fidelity decay of the two-level bosonic embedded ensembles of random matrices

NASA Astrophysics Data System (ADS)

Benet, Luis; Hernández-Quiroz, Saúl; Seligman, Thomas H.

2010-12-01

We study the fidelity decay of the k-body embedded ensembles of random matrices for bosons distributed over two single-particle states. Fidelity is defined in terms of a reference Hamiltonian, which is a purely diagonal matrix consisting of a fixed one-body term and includes the diagonal of the perturbing k-body embedded ensemble matrix, and the perturbed Hamiltonian which includes the residual off-diagonal elements of the k-body interaction. This choice mimics the typical mean-field basis used in many calculations. We study separately the cases k = 2 and 3. We compute the ensemble-averaged fidelity decay as well as the fidelity of typical members with respect to an initial random state. Average fidelity displays a revival at the Heisenberg time, t = tH = 1, and a freeze in the fidelity decay, during which periodic revivals of period tH are observed. We obtain the relevant scaling properties with respect to the number of bosons and the strength of the perturbation. For certain members of the ensemble, we find that the period of the revivals during the freeze of fidelity occurs at fractional times of tH. These fractional periodic revivals are related to the dominance of specific k-body terms in the perturbation.
Crossover ensembles of random matrices and skew-orthogonal polynomials

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

Kumar, Santosh, E-mail: skumar.physics@gmail.com; Pandey, Akhilesh, E-mail: ap0700@mail.jnu.ac.in

2011-08-15

Highlights: > We study crossover ensembles of Jacobi family of random matrices. > We consider correlations for orthogonal-unitary and symplectic-unitary crossovers. > We use the method of skew-orthogonal polynomials and quaternion determinants. > We prove universality of spectral correlations in crossover ensembles. > We discuss applications to quantum conductance and communication theory problems. - Abstract: In a recent paper (S. Kumar, A. Pandey, Phys. Rev. E, 79, 2009, p. 026211) we considered Jacobi family (including Laguerre and Gaussian cases) of random matrix ensembles and reported exact solutions of crossover problems involving time-reversal symmetry breaking. In the present paper we givemore » details of the work. We start with Dyson's Brownian motion description of random matrix ensembles and obtain universal hierarchic relations among the unfolded correlation functions. For arbitrary dimensions we derive the joint probability density (jpd) of eigenvalues for all transitions leading to unitary ensembles as equilibrium ensembles. We focus on the orthogonal-unitary and symplectic-unitary crossovers and give generic expressions for jpd of eigenvalues, two-point kernels and n-level correlation functions. This involves generalization of the theory of skew-orthogonal polynomials to crossover ensembles. We also consider crossovers in the circular ensembles to show the generality of our method. In the large dimensionality limit, correlations in spectra with arbitrary initial density are shown to be universal when expressed in terms of a rescaled symmetry breaking parameter. Applications of our crossover results to communication theory and quantum conductance problems are also briefly discussed.« less
Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition.

PubMed

Sullivan, David C; Lim, Carmay

2006-08-24

Quantifying the density of conformations over phase space (the conformational distribution) is needed to model important macromolecular processes such as protein folding. In this work, we quantify the conformational distribution for a simple polypeptide (N-mer polyalanine) using the cumulative distribution function (CDF), which gives the probability that two randomly selected conformations are separated by less than a "conformational" distance and whose inverse gives conformation counts as a function of conformational radius. An important finding is that the conformation counts obtained by the CDF inverse depend critically on the assignment of a conformation's distance span and the ensemble (e.g., unfolded state model): varying ensemble and conformation definition (1 --> 2 A) varies the CDF-based conformation counts for Ala(50) from 10(11) to 10(69). In particular, relatively short molecular dynamics (MD) relaxation of Ala(50)'s random-walk ensemble reduces the number of conformers from 10(55) to 10(14) (using a 1 A root-mean-square-deviation radius conformation definition) pointing to potential disconnections in comparing the results from simplified models of unfolded proteins with those from all-atom MD simulations. Explicit waters are found to roughen the landscape considerably. Under some common conformation definitions, the results herein provide (i) an upper limit to the number of accessible conformations that compose unfolded states of proteins, (ii) the optimal clustering radius/conformation radius for counting conformations for a given energy and solvent model, (iii) a means of comparing various studies, and (iv) an assessment of the applicability of random search in protein folding.
Relaxation and thermalization in the one-dimensional Bose-Hubbard model: A case study for the interaction quantum quench from the atomic limit

NASA Astrophysics Data System (ADS)

Heidrich-Meisner, Fabian; Pollet, Lode; Sorg, Stefan; Vidmar, Lev

2015-03-01

We study the relaxation dynamics and thermalization in the one-dimensional Bose-Hubbard model induced by a global interaction quench. Specifically, we start from an initial state that has exactly one boson per site and is the ground state of a system with infinitely strong repulsive interactions at unit filling. The same interaction quench was realized in a recent experiment. Using exact diagonalization and the density-matrix renormalization-group method, we compute the time dependence of such observables as the multiple occupancy and the momentum distribution function. We discuss our numerical results in the framework of the eigenstate thermalization hypothesis and we observe that the microcanonical ensemble describes the time averages of many observables reasonably well for small and intermediate interaction strength. Moreover, the diagonal and the canonical ensembles are practically identical for our initial conditions already on the level of their respective energy distributions for small interaction strengths. Supported by the DFG through FOR 801 and the Alexander von Humboldt foundation.
On the Local Equivalence Between the Canonical and the Microcanonical Ensembles for Quantum Spin Systems

NASA Astrophysics Data System (ADS)

Tasaki, Hal

2018-06-01

We study a quantum spin system on the d-dimensional hypercubic lattice Λ with N=L^d sites with periodic boundary conditions. We take an arbitrary translation invariant short-ranged Hamiltonian. For this system, we consider both the canonical ensemble with inverse temperature β _0 and the microcanonical ensemble with the corresponding energy U_N(β _0) . For an arbitrary self-adjoint operator \\hat{A} whose support is contained in a hypercubic block B inside Λ , we prove that the expectation values of \\hat{A} with respect to these two ensembles are close to each other for large N provided that β _0 is sufficiently small and the number of sites in B is o(N^{1/2}) . This establishes the equivalence of ensembles on the level of local states in a large but finite system. The result is essentially that of Brandao and Cramer (here restricted to the case of the canonical and the microcanonical ensembles), but we prove improved estimates in an elementary manner. We also review and prove standard results on the thermodynamic limits of thermodynamic functions and the equivalence of ensembles in terms of thermodynamic functions. The present paper assumes only elementary knowledge on quantum statistical mechanics and quantum spin systems.
Temporal Variation in Single-Cell Power-Law Rheology Spans the Ensemble Variation of Cell Population.

PubMed

Cai, PingGen; Takahashi, Ryosuke; Kuribayashi-Shigetomi, Kaori; Subagyo, Agus; Sueoka, Kazuhisa; Maloney, John M; Van Vliet, Krystyn J; Okajima, Takaharu

2017-08-08

Changes in the cytoskeletal organization within cells can be characterized by large spatial and temporal variations in rheological properties of the cell (e.g., the complex shear modulus G ∗ ). Although the ensemble variation in G ∗ of single cells has been elucidated, the detailed temporal variation of G ∗ remains unknown. In this study, we investigated how the rheological properties of individual fibroblast cells change under a spatially confined environment in which the cell translational motion is highly restricted and the whole cell shape remains unchanged. The temporal evolution of single-cell rheology was probed at the same measurement location within the cell, using atomic force microscopy-based oscillatory deformation. The measurements reveal that the temporal variation in the power-law rheology of cells is quantitatively consistent with the ensemble variation, indicating that the cell system satisfies an ergodic hypothesis in which the temporal statistics are identical to the ensemble statistics. The autocorrelation of G ∗ implies that the cell mechanical state evolves in the ensemble of possible states with a characteristic timescale. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Composite pulses for interferometry in a thermal cold atom cloud

NASA Astrophysics Data System (ADS)

Dunning, Alexander; Gregory, Rachel; Bateman, James; Cooper, Nathan; Himsworth, Matthew; Jones, Jonathan A.; Freegarde, Tim

2014-09-01

Atom interferometric sensors and quantum information processors must maintain coherence while the evolving quantum wave function is split, transformed, and recombined, but suffer from experimental inhomogeneities and uncertainties in the speeds and paths of these operations. Several error-correction techniques have been proposed to isolate the variable of interest. Here we apply composite pulse methods to velocity-sensitive Raman state manipulation in a freely expanding thermal atom cloud. We compare several established pulse sequences, and follow the state evolution within them. The agreement between measurements and simple predictions shows the underlying coherence of the atom ensemble, and the inversion infidelity in a ˜80μK atom cloud is halved. Composite pulse techniques, especially if tailored for atom interferometric applications, should allow greater interferometer areas, larger atomic samples, and longer interaction times, and hence improve the sensitivity of quantum technologies from inertial sensing and clocks to quantum information processors and tests of fundamental physics.
Superradiators created atom by atom

NASA Astrophysics Data System (ADS)

Meschede, Dieter

2018-02-01

High radiation rates are usually associated with macroscopic lasers. Laser radiation is “coherent”—its amplitude and phase are well-defined—but its generation requires energy inputs to overcome loss. Excited atoms spontaneously emit in a random and incoherent fashion, and for N such atoms, the emission rate simply increases as N. However, if these atoms are in close proximity and coherently coupled by a radiation field, this microscopic ensemble acts as a single emitter whose emission rate increases as N2 and becomes “superradiant,” to use Dicke's terminology (1). On page 662 of this issue, Kim et al. (2) show the buildup of coherent light fields through collective emission from atomic radiators injected one by one into a resonator field. There is only one atom ever in the cavity, but the emission is still collective and superradiant. These results suggest another route toward thresholdless lasing.
Characteristics of level-spacing statistics in chaotic graphene billiards.

PubMed

Huang, Liang; Lai, Ying-Cheng; Grebogi, Celso

2011-03-01

A fundamental result in nonrelativistic quantum nonlinear dynamics is that the spectral statistics of quantum systems that possess no geometric symmetry, but whose classical dynamics are chaotic, are described by those of the Gaussian orthogonal ensemble (GOE) or the Gaussian unitary ensemble (GUE), in the presence or absence of time-reversal symmetry, respectively. For massless spin-half particles such as neutrinos in relativistic quantum mechanics in a chaotic billiard, the seminal work of Berry and Mondragon established the GUE nature of the level-spacing statistics, due to the combination of the chirality of Dirac particles and the confinement, which breaks the time-reversal symmetry. A question is whether the GOE or the GUE statistics can be observed in experimentally accessible, relativistic quantum systems. We demonstrate, using graphene confinements in which the quasiparticle motions are governed by the Dirac equation in the low-energy regime, that the level-spacing statistics are persistently those of GOE random matrices. We present extensive numerical evidence obtained from the tight-binding approach and a physical explanation for the GOE statistics. We also find that the presence of a weak magnetic field switches the statistics to those of GUE. For a strong magnetic field, Landau levels become influential, causing the level-spacing distribution to deviate markedly from the random-matrix predictions. Issues addressed also include the effects of a number of realistic factors on level-spacing statistics such as next nearest-neighbor interactions, different lattice orientations, enhanced hopping energy for atoms on the boundary, and staggered potential due to graphene-substrate interactions.
MSEBAG: a dynamic classifier ensemble generation based on `minimum-sufficient ensemble' and bagging

NASA Astrophysics Data System (ADS)

Chen, Lei; Kamel, Mohamed S.

2016-01-01

In this paper, we propose a dynamic classifier system, MSEBAG, which is characterised by searching for the 'minimum-sufficient ensemble' and bagging at the ensemble level. It adopts an 'over-generation and selection' strategy and aims to achieve a good bias-variance trade-off. In the training phase, MSEBAG first searches for the 'minimum-sufficient ensemble', which maximises the in-sample fitness with the minimal number of base classifiers. Then, starting from the 'minimum-sufficient ensemble', a backward stepwise algorithm is employed to generate a collection of ensembles. The objective is to create a collection of ensembles with a descending fitness on the data, as well as a descending complexity in the structure. MSEBAG dynamically selects the ensembles from the collection for the decision aggregation. The extended adaptive aggregation (EAA) approach, a bagging-style algorithm performed at the ensemble level, is employed for this task. EAA searches for the competent ensembles using a score function, which takes into consideration both the in-sample fitness and the confidence of the statistical inference, and averages the decisions of the selected ensembles to label the test pattern. The experimental results show that the proposed MSEBAG outperforms the benchmarks on average.
Quantum memory with a controlled homogeneous splitting

NASA Astrophysics Data System (ADS)

Hétet, G.; Wilkowski, D.; Chanelière, T.

2013-04-01

We propose a quantum memory protocol where an input light field can be stored onto and released from a single ground state atomic ensemble by controlling dynamically the strength of an external static and homogeneous field. The technique relies on the adiabatic following of a polaritonic excitation onto a state for which the forward collective radiative emission is forbidden. The resemblance with the archetypal electromagnetically induced transparency is only formal because no ground state coherence-based slow-light propagation is considered here. As compared to the other grand category of protocols derived from the photon-echo technique, our approach only involves a homogeneous static field. We discuss two physical situations where the effect can be observed, and show that in the limit where the excited state lifetime is longer than the storage time; the protocols are perfectly efficient and noise free. We compare the technique with other quantum memories, and propose atomic systems where the experiment can be realized.
Quantum principle of sensing gravitational waves: From the zero-point fluctuations to the cosmological stochastic background of spacetime

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

PubMed Central

2015-01-01

Computation of the solvation free energy for chemical and biological processes has long been of significant interest. The key challenges to effective solvation modeling center on the choice of potential function and configurational sampling. Herein, an energy sampling approach termed the “Movable Type” (MT) method, and a statistical energy function for solvation modeling, “Knowledge-based and Empirical Combined Scoring Algorithm” (KECSA) are developed and utilized to create an implicit solvation model: KECSA-Movable Type Implicit Solvation Model (KMTISM) suitable for the study of chemical and biological systems. KMTISM is an implicit solvation model, but the MT method performs energy sampling at the atom pairwise level. For a specific molecular system, the MT method collects energies from prebuilt databases for the requisite atom pairs at all relevant distance ranges, which by its very construction encodes all possible molecular configurations simultaneously. Unlike traditional statistical energy functions, KECSA converts structural statistical information into categorized atom pairwise interaction energies as a function of the radial distance instead of a mean force energy function. Within the implicit solvent model approximation, aqueous solvation free energies are then obtained from the NVT ensemble partition function generated by the MT method. Validation is performed against several subsets selected from the Minnesota Solvation Database v2012. Results are compared with several solvation free energy calculation methods, including a one-to-one comparison against two commonly used classical implicit solvation models: MM-GBSA and MM-PBSA. Comparison against a quantum mechanics based polarizable continuum model is also discussed (Cramer and Truhlar’s Solvation Model 12). PMID:25691832
Single-photon superradiance and cooperative Lamb shift in an optoelectronic device (Conference Presentation)

NASA Astrophysics Data System (ADS)

Sirtori, Carlo

2017-02-01

Superradiance is one of the many fascinating phenomena predicted by quantum electrodynamics that have first been experimentally demonstrated in atomic systems and more recently in condensed matter systems like quantum dots, superconducting q-bits, cyclotron transitions and plasma oscillations in quantum wells (QWs). It occurs when a dense collection of N identical two-level emitters are phased via the exchange of photons, giving rise to enhanced light-matter interaction, hence to a faster emission rate. Of great interest is the regime where the ensemble interacts with one photon only and therefore all of the atoms, but one, are in the ground state. In this case the quantum superposition of all possible configurations produces a symmetric state that decays radiatively with a rate N times larger than that of the individual oscillators. This phenomenon, called single photon superradiance, results from the exchange of real photons among the N emitters. Yet, to single photon superradiance is also associated another collective effect that renormalizes the emission frequency, known as cooperative Lamb shift. In this work, we show that single photon superradiance and cooperative Lamb shift can be engineered in a semiconductor device by coupling spatially separated plasma resonances arising from the collective motion of confined electrons in QWs. These resonances hold a giant dipole along the growth direction z and have no mutual Coulomb coupling. They thus behave as a collection of macro-atoms on different positions along the z axis. Our device is therefore a test bench to simulate the low excitation regime of quantum electrodynamics.
Upper Limit of Weights in TAI Computation

NASA Technical Reports Server (NTRS)

Thomas, Claudine; Azoubib, Jacques

1996-01-01

The international reference time scale International Atomic Time (TAI) computed by the Bureau International des Poids et Mesures (BIPM) relies on a weighted average of data from a large number of atomic clocks. In it, the weight attributed to a given clock depends on its long-term stability. In this paper the TAI algorithm is used as the basis for a discussion of how to implement an upper limit of weight for clocks contributing to the ensemble time. This problem is approached through the comparison of two different techniques. In one case, a maximum relative weight is fixed: no individual clock can contribute more than a given fraction to the resulting time scale. The weight of each clock is then adjusted according to the qualities of the whole set of contributing elements. In the other case, a parameter characteristic of frequency stability is chosen: no individual clock can appear more stable than the stated limit. This is equivalent to choosing an absolute limit of weight and attributing this to to the most stable clocks independently of the other elements of the ensemble. The first technique is more robust than the second and automatically optimizes the stability of the resulting time scale, but leads to a more complicated computatio. The second technique has been used in the TAI algorithm since the very beginning. Careful analysis of tests on real clock data shows that improvement of the stability of the time scale requires revision from time to time of the fixed value chosen for the upper limit of absolute weight. In particular, we present results which confirm the decision of the CCDS Working Group on TAI to increase the absolute upper limit by a factor of 2.5. We also show that the use of an upper relative contribution further helps to improve the stability and may be a useful step towards better use of the massive ensemble of HP 507IA clocks now contributing to TAI.
Measuring ensemble interdependence in a string quartet through analysis of multidimensional performance data

PubMed Central

Papiotis, Panos; Marchini, Marco; Perez-Carrillo, Alfonso; Maestre, Esteban

2014-01-01

In a musical ensemble such as a string quartet, the musicians interact and influence each other's actions in several aspects of the performance simultaneously in order to achieve a common aesthetic goal. In this article, we present and evaluate a computational approach for measuring the degree to which these interactions exist in a given performance. We recorded a number of string quartet exercises under two experimental conditions (solo and ensemble), acquiring both audio and bowing motion data. Numerical features in the form of time series were extracted from the data as performance descriptors representative of four distinct dimensions of the performance: Intonation, Dynamics, Timbre, and Tempo. Four different interdependence estimation methods (two linear and two nonlinear) were applied to the extracted features in order to assess the overall level of interdependence between the four musicians. The obtained results suggest that it is possible to correctly discriminate between the two experimental conditions by quantifying interdependence between the musicians in each of the studied performance dimensions; the nonlinear methods appear to perform best for most of the numerical features tested. Moreover, by using the solo recordings as a reference to which the ensemble recordings are contrasted, it is feasible to compare the amount of interdependence that is established between the musicians in a given performance dimension across all exercises, and relate the results to the underlying goal of the exercise. We discuss our findings in the context of ensemble performance research, the current limitations of our approach, and the ways in which it can be expanded and consolidated. PMID:25228894
Triatomic molecules laser-cooled

NASA Astrophysics Data System (ADS)

2017-06-01

Molecules containing three atoms have been laser-cooled to ultracold temperatures for the first time. John Doyle and colleagues at Harvard University in the US used a technique called Sisyphus cooling to chill an ensemble of about a million strontium-monohydroxide molecules to 750 μK.
Dynamic of cold-atom tips in anharmonic potentials

PubMed Central

Menold, Tobias; Federsel, Peter; Rogulj, Carola; Hölscher, Hendrik; Fortágh, József

2016-01-01

Background: Understanding the dynamics of ultracold quantum gases in an anharmonic potential is essential for applications in the new field of cold-atom scanning probe microscopy. Therein, cold atomic ensembles are used as sensitive probe tips to investigate nanostructured surfaces and surface-near potentials, which typically cause anharmonic tip motion. Results: Besides a theoretical description of this anharmonic tip motion, we introduce a novel method for detecting the cold-atom tip dynamics in situ and real time. In agreement with theory, the first measurements show that particle interactions and anharmonic motion have a significant impact on the tip dynamics. Conclusion: Our findings will be crucial for the realization of high-sensitivity force spectroscopy with cold-atom tips and could possibly allow for the development of advanced spectroscopic techniques such as Q-control. PMID:28144505
Conjoint representation of texture ensemble and location in the parahippocampal place area.

PubMed

Park, Jeongho; Park, Soojin

2017-04-01

Texture provides crucial information about the category or identity of a scene. Nonetheless, not much is known about how the texture information in a scene is represented in the brain. Previous studies have shown that the parahippocampal place area (PPA), a scene-selective part of visual cortex, responds to simple patches of texture ensemble. However, in natural scenes textures exist in spatial context within a scene. Here we tested two hypotheses that make different predictions on how textures within a scene context are represented in the PPA. The Texture-Only hypothesis suggests that the PPA represents texture ensemble (i.e., the kind of texture) as is, irrespective of its location in the scene. On the other hand, the Texture and Location hypothesis suggests that the PPA represents texture and its location within a scene (e.g., ceiling or wall) conjointly. We tested these two hypotheses across two experiments, using different but complementary methods. In experiment 1 , by using multivoxel pattern analysis (MVPA) and representational similarity analysis, we found that the representational similarity of the PPA activation patterns was significantly explained by the Texture-Only hypothesis but not by the Texture and Location hypothesis. In experiment 2 , using a repetition suppression paradigm, we found no repetition suppression for scenes that had the same texture ensemble but differed in location (supporting the Texture and Location hypothesis). On the basis of these results, we propose a framework that reconciles contrasting results from MVPA and repetition suppression and draw conclusions about how texture is represented in the PPA. NEW & NOTEWORTHY This study investigates how the parahippocampal place area (PPA) represents texture information within a scene context. We claim that texture is represented in the PPA at multiple levels: the texture ensemble information at the across-voxel level and the conjoint information of texture and its location at the within-voxel level. The study proposes a working hypothesis that reconciles contrasting results from multivoxel pattern analysis and repetition suppression, suggesting that the methods are complementary to each other but not necessarily interchangeable. Copyright © 2017 the American Physiological Society.
Multimillion atom simulations of dynamics of oxidation of an aluminum nanoparticle and nanoindentation on ceramics.

PubMed

Vashishta, Priya; Kalia, Rajiv K; Nakano, Aiichiro

2006-03-02

We have developed a first-principles-based hierarchical simulation framework, which seamlessly integrates (1) a quantum mechanical description based on the density functional theory (DFT), (2) multilevel molecular dynamics (MD) simulations based on a reactive force field (ReaxFF) that describes chemical reactions and polarization, a nonreactive force field that employs dynamic atomic charges, and an effective force field (EFF), and (3) an atomistically informed continuum model to reach macroscopic length scales. For scalable hierarchical simulations, we have developed parallel linear-scaling algorithms for (1) DFT calculation based on a divide-and-conquer algorithm on adaptive multigrids, (2) chemically reactive MD based on a fast ReaxFF (F-ReaxFF) algorithm, and (3) EFF-MD based on a space-time multiresolution MD (MRMD) algorithm. On 1920 Intel Itanium2 processors, we have demonstrated 1.4 million atom (0.12 trillion grid points) DFT, 0.56 billion atom F-ReaxFF, and 18.9 billion atom MRMD calculations, with parallel efficiency as high as 0.953. Through the use of these algorithms, multimillion atom MD simulations have been performed to study the oxidation of an aluminum nanoparticle. Structural and dynamic correlations in the oxide region are calculated as well as the evolution of charges, surface oxide thickness, diffusivities of atoms, and local stresses. In the microcanonical ensemble, the oxidizing reaction becomes explosive in both molecular and atomic oxygen environments, due to the enormous energy release associated with Al-O bonding. In the canonical ensemble, an amorphous oxide layer of a thickness of approximately 40 angstroms is formed after 466 ps, in good agreement with experiments. Simulations have been performed to study nanoindentation on crystalline, amorphous, and nanocrystalline silicon nitride and silicon carbide. Simulation on nanocrystalline silicon carbide reveals unusual deformation mechanisms in brittle nanophase materials, due to coexistence of brittle grains and soft amorphous-like grain boundary phases. Simulations predict a crossover from intergranular continuous deformation to intragrain discrete deformation at a critical indentation depth.

Empirical relationships between gas abundances and UV selective extinction

NASA Technical Reports Server (NTRS)

Joseph, Charles L.

1990-01-01

Several studies of gas-phase abundances in lines of sight through the outer edges of dense clouds are summarized. These lines of sight have 0.4 less than E(B-V) less than 1.1 and have inferred spatial densities of a few hundred cm(-3). The primary thrust of these studies has been to compare gaseous abundances in interstellar clouds that have various types of peculiar selective extinction. To date, the most notable result has been an empirical relationship between the CN/Fe I abundance ratio and the depth of the 2200 A extinction bump. It is not clear at the present time, however, whether these two parameters are linearly correlated or the data are organized into two discrete ensembles. Based on 19 samples and assuming the clouds form discrete ensembles, lines of sight that have a CN/Fe I abundance ratio greater than 0.3 (dex) appear to have a shallow 2.57 plus or minus 0.55 bump compared to 3.60 plus or minus 0.36 for other dense clouds and compared to the 3.6 Seaton (1979) average. The difference in the strength of the extinction bump between these two ensembles is 1.03 plus or minus 0.23. Although a high-resolution IUE survey of dense clouds is far from complete, the few lines of sight with shallow extinction bumps all show preferential depletion of certain elements, while those lines of sight with normal 2200 A bumps do not. Ca II, Cr II, and Mn II appear to exhibit the strongest preferential depletion compared to S II, P II, and Mg II. Fe II and Si II depletions also appear to be enhanced somewhat in the shallow-bump lines of sight. It should be noted that Copernicus data suggest all elements, including the so-called nondepletors, deplete in diffuse clouds (Snow and Jenkins 1980, Joseph 1988). Those lines of sight through dense clouds that have normal 2200 A extinction bumps appear to be extensions of the depletions found in the diffuse interstellar medium. That is, the overall level of depletion is enhanced, but the element-to-element abundances are similar to those in diffuse clouds. In a separate study, the abundances of neutral atoms were studied in a dense cloud having a shallow 2200 A bump and in one with a normal strength bump.
Nonlinear and quantum optics near nanoparticles

NASA Astrophysics Data System (ADS)

Dhayal, Suman

We study the behavior of electric fields in and around dielectric and metal nanoparticles, and prepare the ground for their applications to a variety of systems viz. photovoltaics, imaging and detection techniques, and molecular spectroscopy. We exploit the property of nanoparticles being able to focus the radiation field into small regions and study some of the interesting nonlinear, and quantum coherence and interference phenomena near them. The traditional approach to study the nonlinear light-matter interactions involves the use of the slowly varying amplitude approximation (SVAA) as it simplifies the theoretical analysis. However, SVVA cannot be used for systems which are of the order of the wavelength of the light. We use the exact solutions of the Maxwell's equations to obtain the fields created due to metal and dielectric nanoparticles, and study nonlinear and quantum optical phenomena near these nanoparticles. We begin with the theoretical description of the electromagnetic fields created due to the nonlinear wavemixing process, namely, second-order nonlinearity in an nonlinear sphere. The phase-matching condition has been revisited in such particles and we found that it is not satisfied in the sphere. We have suggested a way to obtain optimal conditions for any type and size of material medium. We have also studied the modifications of the electromagnetic fields in a collection of nanoparticles due to strong near field nonlinear interactions using the generalized Mie theory for the case of many particles applicable in photovoltaics (PV). We also consider quantum coherence phenomena such as modification of dark states, stimulated Raman adiabatic passage (STIRAP), optical pumping in 4-level atoms near nanoparticles by using rotating wave approximation to describe the Hamiltonian of the atomic system. We also considered the behavior of atomic and the averaged atomic polarization in 7-level atoms near nanoparticles. This could be used as a prototype to study any n-level atomic system experimentally in the presence of ensembles of quantum emitters. In the last chapter, we suggested a variant of a pulse-shaping technique applicable in stimulated Raman spectroscopy (SRS) for detection of atoms and molecules in multiscattering media. We used discrete-dipole approximation to obtain the fields created by the nanoparticles.
New type of chimera and mutual synchronization of spatiotemporal structures in two coupled ensembles of nonlocally interacting chaotic maps

NASA Astrophysics Data System (ADS)

Bukh, Andrei; Rybalova, Elena; Semenova, Nadezhda; Strelkova, Galina; Anishchenko, Vadim

2017-11-01

We study numerically the dynamics of a network made of two coupled one-dimensional ensembles of discrete-time systems. The first ensemble is represented by a ring of nonlocally coupled Henon maps and the second one by a ring of nonlocally coupled Lozi maps. We find that the network of coupled ensembles can realize all the spatio-temporal structures which are observed both in the Henon map ensemble and in the Lozi map ensemble while uncoupled. Moreover, we reveal a new type of spatiotemporal structure, a solitary state chimera, in the considered network. We also establish and describe the effect of mutual synchronization of various complex spatiotemporal patterns in the system of two coupled ensembles of Henon and Lozi maps.
Preparation of a pure molecular quantum gas.

PubMed

Herbig, Jens; Kraemer, Tobias; Mark, Michael; Weber, Tino; Chin, Cheng; Nägerl, Hanns-Christoph; Grimm, Rudolf

2003-09-12

An ultracold molecular quantum gas is created by application of a magnetic field sweep across a Feshbach resonance to a Bose-Einstein condensate of cesium atoms. The ability to separate the molecules from the atoms permits direct imaging of the pure molecular sample. Magnetic levitation enables study of the dynamics of the ensemble on extended time scales. We measured ultralow expansion energies in the range of a few nanokelvin for a sample of 3000 molecules. Our observations are consistent with the presence of a macroscopic molecular matter wave.
Generation of single photons with highly tunable wave shape from a cold atomic ensemble

PubMed Central

Farrera, Pau; Heinze, Georg; Albrecht, Boris; Ho, Melvyn; Chávez, Matías; Teo, Colin; Sangouard, Nicolas; de Riedmatten, Hugues

2016-01-01

The generation of ultra-narrowband, pure and storable single photons with widely tunable wave shape is an enabling step toward hybrid quantum networks requiring interconnection of remote disparate quantum systems. It allows interaction of quantum light with several material systems, including photonic quantum memories, single trapped ions and opto-mechanical systems. Previous approaches have offered a limited tuning range of the photon duration of at most one order of magnitude. Here we report on a heralded single photon source with controllable emission time based on a cold atomic ensemble, which can generate photons with temporal durations varying over three orders of magnitude up to 10 μs without a significant change of the readout efficiency. We prove the nonclassicality of the emitted photons, show that they are emitted in a pure state, and demonstrate that ultra-long photons with nonstandard wave shape can be generated, which are ideally suited for several quantum information tasks. PMID:27886166
Ensemble-based evaluation of extreme water levels for the eastern Baltic Sea

NASA Astrophysics Data System (ADS)

Eelsalu, Maris; Soomere, Tarmo

2016-04-01

The risks and damages associated with coastal flooding that are naturally associated with an increase in the magnitude of extreme storm surges are one of the largest concerns of countries with extensive low-lying nearshore areas. The relevant risks are even more contrast for semi-enclosed water bodies such as the Baltic Sea where subtidal (weekly-scale) variations in the water volume of the sea substantially contribute to the water level and lead to large spreading of projections of future extreme water levels. We explore the options for using large ensembles of projections to more reliably evaluate return periods of extreme water levels. Single projections of the ensemble are constructed by means of fitting several sets of block maxima with various extreme value distributions. The ensemble is based on two simulated data sets produced in the Swedish Meteorological and Hydrological Institute. A hindcast by the Rossby Centre Ocean model is sampled with a resolution of 6 h and a similar hindcast by the circulation model NEMO with a resolution of 1 h. As the annual maxima of water levels in the Baltic Sea are not always uncorrelated, we employ maxima for calendar years and for stormy seasons. As the shape parameter of the Generalised Extreme Value distribution changes its sign and substantially varies in magnitude along the eastern coast of the Baltic Sea, the use of a single distribution for the entire coast is inappropriate. The ensemble involves projections based on the Generalised Extreme Value, Gumbel and Weibull distributions. The parameters of these distributions are evaluated using three different ways: maximum likelihood method and method of moments based on both biased and unbiased estimates. The total number of projections in the ensemble is 40. As some of the resulting estimates contain limited additional information, the members of pairs of projections that are highly correlated are assigned weights 0.6. A comparison of the ensemble-based projection of extreme water levels and their return periods with similar estimates derived from local observations reveals an interesting pattern of match and mismatch. The match is almost perfect in measurement sites where local effects (e.g., wave-induced set-up or local surge in very shallow areas that are not resolved by circulation models) do not contribute to the observed values of water level. There is, however, substantial mismatch between projected and observed extreme values for most of the Estonian coast. The mismatch is largest for sections that are open to high waves and for several bays that are deeply cut into mainland but open for predominant strong wind directions. Detailed quantification of this mismatch eventually makes it possible to develop substantially improved estimates of extreme water levels in sections where local effects considerably contribute into the total water level.
Constructing better classifier ensemble based on weighted accuracy and diversity measure.

PubMed

Zeng, Xiaodong; Wong, Derek F; Chao, Lidia S

2014-01-01

A weighted accuracy and diversity (WAD) method is presented, a novel measure used to evaluate the quality of the classifier ensemble, assisting in the ensemble selection task. The proposed measure is motivated by a commonly accepted hypothesis; that is, a robust classifier ensemble should not only be accurate but also different from every other member. In fact, accuracy and diversity are mutual restraint factors; that is, an ensemble with high accuracy may have low diversity, and an overly diverse ensemble may negatively affect accuracy. This study proposes a method to find the balance between accuracy and diversity that enhances the predictive ability of an ensemble for unknown data. The quality assessment for an ensemble is performed such that the final score is achieved by computing the harmonic mean of accuracy and diversity, where two weight parameters are used to balance them. The measure is compared to two representative measures, Kappa-Error and GenDiv, and two threshold measures that consider only accuracy or diversity, with two heuristic search algorithms, genetic algorithm, and forward hill-climbing algorithm, in ensemble selection tasks performed on 15 UCI benchmark datasets. The empirical results demonstrate that the WAD measure is superior to others in most cases.
Constructing Better Classifier Ensemble Based on Weighted Accuracy and Diversity Measure

PubMed Central

Chao, Lidia S.

2014-01-01

A weighted accuracy and diversity (WAD) method is presented, a novel measure used to evaluate the quality of the classifier ensemble, assisting in the ensemble selection task. The proposed measure is motivated by a commonly accepted hypothesis; that is, a robust classifier ensemble should not only be accurate but also different from every other member. In fact, accuracy and diversity are mutual restraint factors; that is, an ensemble with high accuracy may have low diversity, and an overly diverse ensemble may negatively affect accuracy. This study proposes a method to find the balance between accuracy and diversity that enhances the predictive ability of an ensemble for unknown data. The quality assessment for an ensemble is performed such that the final score is achieved by computing the harmonic mean of accuracy and diversity, where two weight parameters are used to balance them. The measure is compared to two representative measures, Kappa-Error and GenDiv, and two threshold measures that consider only accuracy or diversity, with two heuristic search algorithms, genetic algorithm, and forward hill-climbing algorithm, in ensemble selection tasks performed on 15 UCI benchmark datasets. The empirical results demonstrate that the WAD measure is superior to others in most cases. PMID:24672402
THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures

PubMed Central

Theobald, Douglas L.; Wuttke, Deborah S.

2008-01-01

Summary THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. PMID:16777907
Memory-assisted quantum key distribution resilient against multiple-excitation effects

NASA Astrophysics Data System (ADS)

Lo Piparo, Nicolò; Sinclair, Neil; Razavi, Mohsen

2018-01-01

Memory-assisted measurement-device-independent quantum key distribution (MA-MDI-QKD) has recently been proposed as a technique to improve the rate-versus-distance behavior of QKD systems by using existing, or nearly-achievable, quantum technologies. The promise is that MA-MDI-QKD would require less demanding quantum memories than the ones needed for probabilistic quantum repeaters. Nevertheless, early investigations suggest that, in order to beat the conventional memory-less QKD schemes, the quantum memories used in the MA-MDI-QKD protocols must have high bandwidth-storage products and short interaction times. Among different types of quantum memories, ensemble-based memories offer some of the required specifications, but they typically suffer from multiple excitation effects. To avoid the latter issue, in this paper, we propose two new variants of MA-MDI-QKD both relying on single-photon sources for entangling purposes. One is based on known techniques for entanglement distribution in quantum repeaters. This scheme turns out to offer no advantage even if one uses ideal single-photon sources. By finding the root cause of the problem, we then propose another setup, which can outperform single memory-less setups even if we allow for some imperfections in our single-photon sources. For such a scheme, we compare the key rate for different types of ensemble-based memories and show that certain classes of atomic ensembles can improve the rate-versus-distance behavior.
Imprinting and recalling cortical ensembles.

PubMed

Carrillo-Reid, Luis; Yang, Weijian; Bando, Yuki; Peterka, Darcy S; Yuste, Rafael

2016-08-12

Neuronal ensembles are coactive groups of neurons that may represent building blocks of cortical circuits. These ensembles could be formed by Hebbian plasticity, whereby synapses between coactive neurons are strengthened. Here we report that repetitive activation with two-photon optogenetics of neuronal populations from ensembles in the visual cortex of awake mice builds neuronal ensembles that recur spontaneously after being imprinted and do not disrupt preexisting ones. Moreover, imprinted ensembles can be recalled by single- cell stimulation and remain coactive on consecutive days. Our results demonstrate the persistent reconfiguration of cortical circuits by two-photon optogenetics into neuronal ensembles that can perform pattern completion. Copyright © 2016, American Association for the Advancement of Science.
Faradaurate-940: Synthesis, Mass Spectrometry, STEM, PDF, and SAXS Study of Au~940(SR)~160 Nanocrystals

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

Kumara, Chanaka; Zuo, Xiaobing; Cullen, David A

2014-01-01

Obtaining monodisperse nanocrystals, and determining its composition to the atomic level and its atomic structure is highly desirable, but is generally lacking. Here, we report the discovery and comprehensive characterization of a 3-nm plasmonic nanocrystal with a composition of Au940 20(SCH2CH2Ph)160 4, which is, the largest mass spectrometrically characterized gold thiolate nanoparticle produced to date. The compositional assignment has been made using electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS). The MS results show an unprecedented size monodispersity, where the number of Au atoms vary by only 40 atoms (940 20). The mass spectrometrically-determined sizemore » and composition are supported by aberration-corrected scanning transmission electron microscopy (STEM) and synchrotron-based methods such as atomic pair distribution function (PDF) and small angle X-ray scattering (SAXS). Lower resolution STEM images show an ensemble of particles 1000 s per frame visually demonstrating monodispersity. Modelling of SAXS on statistically significant nanoparticle population approximately 1012 individual nanoparticles - shows that the diameter is 3.0 0.2nm, supporting mass spectrometry and electron microscopy results on monodispersity. Atomic PDF based on high energy X-ray diffraction experiments show decent match with either a Marks decahedral or truncated octrahedral structure. Atomic resolution STEM images of single particles and its FFT suggest face-centered cubic (fcc) arrangement. UV-visible spectroscopy data shows that the 940-atom size supports a surface plasmon resonance peak at 505 nm. These monodisperse plasmonic nanoparticles minimize averaging effects and has potential application in solar cells, nano-optical devices, catalysis and drug delivery.« less
Mitosis detection using generic features and an ensemble of cascade adaboosts.

PubMed

Tek, F Boray

2013-01-01

Mitosis count is one of the factors that pathologists use to assess the risk of metastasis and survival of the patients, which are affected by the breast cancer. We investigate an application of a set of generic features and an ensemble of cascade adaboosts to the automated mitosis detection. Calculation of the features rely minimally on object-level descriptions and thus require minimal segmentation. The proposed work was developed and tested on International Conference on Pattern Recognition (ICPR) 2012 mitosis detection contest data. We plotted receiver operating characteristics curves of true positive versus false positive rates; calculated recall, precision, F-measure, and region overlap ratio measures. WE TESTED OUR FEATURES WITH TWO DIFFERENT CLASSIFIER CONFIGURATIONS: 1) An ensemble of single adaboosts, 2) an ensemble of cascade adaboosts. On the ICPR 2012 mitosis detection contest evaluation, the cascade ensemble scored 54, 62.7, and 58, whereas the non-cascade version scored 68, 28.1, and 39.7 for the recall, precision, and F-measure measures, respectively. Mostly used features in the adaboost classifier rules were a shape-based feature, which counted granularity and a color-based feature, which relied on Red, Green, and Blue channel statistics. The features, which express the granular structure and color variations, are found useful for mitosis detection. The ensemble of adaboosts performs better than the individual adaboost classifiers. Moreover, the ensemble of cascaded adaboosts was better than the ensemble of single adaboosts for mitosis detection.
Spatial EPR entanglement in atomic vapor quantum memory

NASA Astrophysics Data System (ADS)

Parniak, Michal; Dabrowski, Michal; Wasilewski, Wojciech

Spatially-structured quantum states of light are staring to play a key role in modern quantum science with the rapid development of single-photon sensitive cameras. In particular, spatial degree of freedom holds a promise to enhance continous-variable quantum memories. Here we present the first demonstration of spatial entanglement between an atomic spin-wave and a photon measured with an I-sCMOS camera. The system is realized in a warm atomic vapor quantum memory based on rubidium atoms immersed in inert buffer gas. In the experiment we create and characterize a 12-dimensional entangled state exhibiting quantum correlations between a photon and an atomic ensemble in position and momentum bases. This state allows us to demonstrate the Einstein-Podolsky-Rosen paradox in its original version, with an unprecedented delay time of 6 μs between generation of entanglement and detection of the atomic state.
Task switching in a hierarchical task structure: evidence for the fragility of the task repetition benefit.

PubMed

Lien, Mei-Ching; Ruthruff, Eric

2004-05-01

This study examined how task switching is affected by hierarchical task organization. Traditional task-switching studies, which use a constant temporal and spatial distance between each task element (defined as a stimulus requiring a response), promote a flat task structure. Using this approach, Experiment 1 revealed a large switch cost of 238 ms. In Experiments 2-5, adjacent task elements were grouped temporally and/or spatially (forming an ensemble) to create a hierarchical task organization. Results indicate that the effect of switching at the ensemble level dominated the effect of switching at the element level. Experiments 6 and 7, using an ensemble of 3 task elements, revealed that the element-level switch cost was virtually absent between ensembles but was large within an ensemble. The authors conclude that the element-level task repetition benefit is fragile and can be eliminated in a hierarchical task organization.
Task switching in a hierarchical task structure: evidence for the fragility of the task repetition benefit

NASA Technical Reports Server (NTRS)

Lien, Mei-Ching; Ruthruff, Eric

2004-01-01

This study examined how task switching is affected by hierarchical task organization. Traditional task-switching studies, which use a constant temporal and spatial distance between each task element (defined as a stimulus requiring a response), promote a flat task structure. Using this approach, Experiment 1 revealed a large switch cost of 238 ms. In Experiments 2-5, adjacent task elements were grouped temporally and/or spatially (forming an ensemble) to create a hierarchical task organization. Results indicate that the effect of switching at the ensemble level dominated the effect of switching at the element level. Experiments 6 and 7, using an ensemble of 3 task elements, revealed that the element-level switch cost was virtually absent between ensembles but was large within an ensemble. The authors conclude that the element-level task repetition benefit is fragile and can be eliminated in a hierarchical task organization.
Estimation of Uncertainties in the Global Distance Test (GDT_TS) for CASP Models.

PubMed

Li, Wenlin; Schaeffer, R Dustin; Otwinowski, Zbyszek; Grishin, Nick V

2016-01-01

The Critical Assessment of techniques for protein Structure Prediction (or CASP) is a community-wide blind test experiment to reveal the best accomplishments of structure modeling. Assessors have been using the Global Distance Test (GDT_TS) measure to quantify prediction performance since CASP3 in 1998. However, identifying significant score differences between close models is difficult because of the lack of uncertainty estimations for this measure. Here, we utilized the atomic fluctuations caused by structure flexibility to estimate the uncertainty of GDT_TS scores. Structures determined by nuclear magnetic resonance are deposited as ensembles of alternative conformers that reflect the structural flexibility, whereas standard X-ray refinement produces the static structure averaged over time and space for the dynamic ensembles. To recapitulate the structural heterogeneous ensemble in the crystal lattice, we performed time-averaged refinement for X-ray datasets to generate structural ensembles for our GDT_TS uncertainty analysis. Using those generated ensembles, our study demonstrates that the time-averaged refinements produced structure ensembles with better agreement with the experimental datasets than the averaged X-ray structures with B-factors. The uncertainty of the GDT_TS scores, quantified by their standard deviations (SDs), increases for scores lower than 50 and 70, with maximum SDs of 0.3 and 1.23 for X-ray and NMR structures, respectively. We also applied our procedure to the high accuracy version of GDT-based score and produced similar results with slightly higher SDs. To facilitate score comparisons by the community, we developed a user-friendly web server that produces structure ensembles for NMR and X-ray structures and is accessible at http://prodata.swmed.edu/SEnCS. Our work helps to identify the significance of GDT_TS score differences, as well as to provide structure ensembles for estimating SDs of any scores.
Ab initio molecular dynamics study of thermite reaction at Al and CuO nano-interfaces at different temperatures

NASA Astrophysics Data System (ADS)

Tang, Cui-Ming; Chen, Xiao-Xu; Cheng, Xin-Lu; Zhang, Chao-Yang; Lu, Zhi-Peng

2018-05-01

The thermite reaction at Al/CuO nano-interfaces is investigated with ab initio molecular dynamics calculations in canonical ensemble at 500 K, 800 K, 1200 K and 1500 K, respectively. The reaction process and reaction products are analyzed in terms of chemical bonds, average charge, time constants and total potential energy. The activity of the reactants enhances with increasing temperature, which induces a faster thermite reaction. The alloy reaction obviously expands outward at Cu-rich interface of Al/CuO system, and the reaction between Al and O atoms obviously expands outward at O-rich interface as temperature increases. Different reaction products are found at the outermost layer of different interfaces in the Al/CuO system. In generally, the average charge of the outer layer aluminum atoms (i.e., Al1, Al2, Al5 and Al6) increases with temperature. The potential energy of Al/CuO system decreases significantly, which indicates that drastic exothermic reaction occurs at the Al/CuO system. This research enhances fundamental understanding in temperature effect on the thermite reaction at atomic level, which can potentially open new possibilities for its industrial application.
Quantum Yield Heterogeneity among Single Nonblinking Quantum Dots Revealed by Atomic Structure-Quantum Optics Correlation

DOE PAGES

Orfield, Noah J.; McBride, James R.; Wang, Feng; ...

2016-02-05

Physical variations in colloidal nanostructures give rise to heterogeneity in expressed optical behavior. This correlation between nanoscale structure and function demands interrogation of both atomic structure and photophysics at the level of single nanostructures to be fully understood. In this paper, by conducting detailed analyses of fine atomic structure, chemical composition, and time-resolved single-photon photoluminescence data for the same individual nanocrystals, we reveal inhomogeneity in the quantum yields of single nonblinking “giant” CdSe/CdS core/shell quantum dots (g-QDs). We find that each g-QD possesses distinctive single exciton and biexciton quantum yields that result mainly from variations in the degree of charging,more » rather than from volume or structure inhomogeneity. We further establish that there is a very limited nonemissive “dark” fraction (<2%) among the studied g-QDs and present direct evidence that the g-QD core must lack inorganic passivation for the g-QD to be “dark”. Finally and therefore, in contrast to conventional QDs, ensemble photoluminescence quantum yield is principally defined by charging processes rather than the existence of dark g-QDs.« less
CABS-flex predictions of protein flexibility compared with NMR ensembles

PubMed Central

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2014-01-01

Motivation: Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an efficient alternative to conventional all-atom molecular dynamics (MD). In this work, we evaluate CABS-flex and MD predictions by comparison with protein structural variations within NMR ensembles. Results: Based on a benchmark set of 140 proteins, we show that the relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles. On average, this correlation is stronger than that between MD and NMR ensembles. In conclusion, CABS-flex is useful and complementary to MD in predicting protein regions that undergo conformational changes as well as the extent of such changes. Availability and implementation: The CABS-flex is freely available to all users at http://biocomp.chem.uw.edu.pl/CABSflex. Contact: sekmi@chem.uw.edu.pl Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24735558

Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach

NASA Astrophysics Data System (ADS)

Lam, Polo C.-H.; Abagyan, Ruben; Totrov, Maxim

2018-01-01

Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace.
CABS-flex predictions of protein flexibility compared with NMR ensembles.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2014-08-01

Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an efficient alternative to conventional all-atom molecular dynamics (MD). In this work, we evaluate CABS-flex and MD predictions by comparison with protein structural variations within NMR ensembles. Based on a benchmark set of 140 proteins, we show that the relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles. On average, this correlation is stronger than that between MD and NMR ensembles. In conclusion, CABS-flex is useful and complementary to MD in predicting protein regions that undergo conformational changes as well as the extent of such changes. The CABS-flex is freely available to all users at http://biocomp.chem.uw.edu.pl/CABSflex. sekmi@chem.uw.edu.pl Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.
Coherent population trapping with a controlled dissipation: applications in optical metrology

NASA Astrophysics Data System (ADS)

Nicolas, L.; Delord, T.; Jamonneau, P.; Coto, R.; Maze, J.; Jacques, V.; Hétet, G.

2018-03-01

We analyze the properties of a pulsed coherent population trapping protocol that uses a controlled decay from the excited state in a Λ-level scheme. We study this problem analytically and numerically and find regimes where narrow transmission, absorption, or fluorescence spectral lines occur. We then look for optimal frequency measurements using these spectral features by computing the Allan deviation in the presence of ground state decoherence and show that the protocol is on a par with Ramsey-CPT. We discuss possible implementations with ensembles of alkali atoms and single ions and demonstrate that typical pulsed-CPT experiments that are realized on femto-second timescales can be implemented on micro-seconds timescales using this scheme.
High efficiency Raman memory by suppressing radiation trapping

NASA Astrophysics Data System (ADS)

Thomas, S. E.; Munns, J. H. D.; Kaczmarek, K. T.; Qiu, C.; Brecht, B.; Feizpour, A.; Ledingham, P. M.; Walmsley, I. A.; Nunn, J.; Saunders, D. J.

2017-06-01

Raman interactions in alkali vapours are used in applications such as atomic clocks, optical signal processing, generation of squeezed light and Raman quantum memories for temporal multiplexing. To achieve a strong interaction the alkali ensemble needs both a large optical depth and a high level of spin-polarisation. We implement a technique known as quenching using a molecular buffer gas which allows near-perfect spin-polarisation of over 99.5 % in caesium vapour at high optical depths of up to ˜ 2× {10}5; a factor of 4 higher than can be achieved without quenching. We use this system to explore efficient light storage with high gain in a GHz bandwidth Raman memory.
Reducing false-positive incidental findings with ensemble genotyping and logistic regression based variant filtering methods.

PubMed

Hwang, Kyu-Baek; Lee, In-Hee; Park, Jin-Ho; Hambuch, Tina; Choe, Yongjoon; Kim, MinHyeok; Lee, Kyungjoon; Song, Taemin; Neu, Matthew B; Gupta, Neha; Kohane, Isaac S; Green, Robert C; Kong, Sek Won

2014-08-01

As whole genome sequencing (WGS) uncovers variants associated with rare and common diseases, an immediate challenge is to minimize false-positive findings due to sequencing and variant calling errors. False positives can be reduced by combining results from orthogonal sequencing methods, but costly. Here, we present variant filtering approaches using logistic regression (LR) and ensemble genotyping to minimize false positives without sacrificing sensitivity. We evaluated the methods using paired WGS datasets of an extended family prepared using two sequencing platforms and a validated set of variants in NA12878. Using LR or ensemble genotyping based filtering, false-negative rates were significantly reduced by 1.1- to 17.8-fold at the same levels of false discovery rates (5.4% for heterozygous and 4.5% for homozygous single nucleotide variants (SNVs); 30.0% for heterozygous and 18.7% for homozygous insertions; 25.2% for heterozygous and 16.6% for homozygous deletions) compared to the filtering based on genotype quality scores. Moreover, ensemble genotyping excluded > 98% (105,080 of 107,167) of false positives while retaining > 95% (897 of 937) of true positives in de novo mutation (DNM) discovery in NA12878, and performed better than a consensus method using two sequencing platforms. Our proposed methods were effective in prioritizing phenotype-associated variants, and an ensemble genotyping would be essential to minimize false-positive DNM candidates. © 2014 WILEY PERIODICALS, INC.
Reducing false positive incidental findings with ensemble genotyping and logistic regression-based variant filtering methods

PubMed Central

Hwang, Kyu-Baek; Lee, In-Hee; Park, Jin-Ho; Hambuch, Tina; Choi, Yongjoon; Kim, MinHyeok; Lee, Kyungjoon; Song, Taemin; Neu, Matthew B.; Gupta, Neha; Kohane, Isaac S.; Green, Robert C.; Kong, Sek Won

2014-01-01

As whole genome sequencing (WGS) uncovers variants associated with rare and common diseases, an immediate challenge is to minimize false positive findings due to sequencing and variant calling errors. False positives can be reduced by combining results from orthogonal sequencing methods, but costly. Here we present variant filtering approaches using logistic regression (LR) and ensemble genotyping to minimize false positives without sacrificing sensitivity. We evaluated the methods using paired WGS datasets of an extended family prepared using two sequencing platforms and a validated set of variants in NA12878. Using LR or ensemble genotyping based filtering, false negative rates were significantly reduced by 1.1- to 17.8-fold at the same levels of false discovery rates (5.4% for heterozygous and 4.5% for homozygous SNVs; 30.0% for heterozygous and 18.7% for homozygous insertions; 25.2% for heterozygous and 16.6% for homozygous deletions) compared to the filtering based on genotype quality scores. Moreover, ensemble genotyping excluded > 98% (105,080 of 107,167) of false positives while retaining > 95% (897 of 937) of true positives in de novo mutation (DNM) discovery, and performed better than a consensus method using two sequencing platforms. Our proposed methods were effective in prioritizing phenotype-associated variants, and ensemble genotyping would be essential to minimize false positive DNM candidates. PMID:24829188
Evaluation of NMME temperature and precipitation bias and forecast skill for South Asia

NASA Astrophysics Data System (ADS)

Cash, Benjamin A.; Manganello, Julia V.; Kinter, James L.

2017-08-01

Systematic error and forecast skill for temperature and precipitation in two regions of Southern Asia are investigated using hindcasts initialized May 1 from the North American Multi-Model Ensemble. We focus on two contiguous but geographically and dynamically diverse regions: the Extended Indian Monsoon Rainfall (70-100E, 10-30 N) and the nearby mountainous area of Pakistan and Afghanistan (60-75E, 23-39 N). Forecast skill is assessed using the Sign test framework, a rigorous statistical method that can be applied to non-Gaussian variables such as precipitation and to different ensemble sizes without introducing bias. We find that models show significant systematic error in both precipitation and temperature for both regions. The multi-model ensemble mean (MMEM) consistently yields the lowest systematic error and the highest forecast skill for both regions and variables. However, we also find that the MMEM consistently provides a statistically significant increase in skill over climatology only in the first month of the forecast. While the MMEM tends to provide higher overall skill than climatology later in the forecast, the differences are not significant at the 95% level. We also find that MMEMs constructed with a relatively small number of ensemble members per model can equal or outperform MMEMs constructed with more members in skill. This suggests some ensemble members either provide no contribution to overall skill or even detract from it.
Two-photon-excited fluorescence spectroscopy of atomic fluorine at 170 nm

NASA Technical Reports Server (NTRS)

Herring, G. C.; Dyer, Mark J.; Jusinski, Leonard E.; Bischel, William K.

1988-01-01

Two-photon-excited fluorescence spectroscopy of atomic fluorine is reported. A doubled dye laser at 286-nm is Raman shifted in H2 to 170 nm (sixth anti-Stokes order) to excite ground-state 2P(0)J fluorine atoms to the 2D(0)J level. The fluorine atoms are detected by one of two methods: observing the fluorescence decay to the 2PJ level or observing F(+) production through the absorption of an additional photon by the excited atoms. Relative two-photon absorption cross sections to and the radiative lifetimes of the 2D(0)J states are measured.
Large ensemble modeling of last deglacial retreat of the West Antarctic Ice Sheet: comparison of simple and advanced statistical techniques

NASA Astrophysics Data System (ADS)

Pollard, D.; Chang, W.; Haran, M.; Applegate, P.; DeConto, R.

2015-11-01

A 3-D hybrid ice-sheet model is applied to the last deglacial retreat of the West Antarctic Ice Sheet over the last ~ 20 000 years. A large ensemble of 625 model runs is used to calibrate the model to modern and geologic data, including reconstructed grounding lines, relative sea-level records, elevation-age data and uplift rates, with an aggregate score computed for each run that measures overall model-data misfit. Two types of statistical methods are used to analyze the large-ensemble results: simple averaging weighted by the aggregate score, and more advanced Bayesian techniques involving Gaussian process-based emulation and calibration, and Markov chain Monte Carlo. Results for best-fit parameter ranges and envelopes of equivalent sea-level rise with the simple averaging method agree quite well with the more advanced techniques, but only for a large ensemble with full factorial parameter sampling. Best-fit parameter ranges confirm earlier values expected from prior model tuning, including large basal sliding coefficients on modern ocean beds. Each run is extended 5000 years into the "future" with idealized ramped climate warming. In the majority of runs with reasonable scores, this produces grounding-line retreat deep into the West Antarctic interior, and the analysis provides sea-level-rise envelopes with well defined parametric uncertainty bounds.
A two-stage method of quantitative flood risk analysis for reservoir real-time operation using ensemble-based hydrologic forecasts

NASA Astrophysics Data System (ADS)

Liu, P.

2013-12-01

Quantitative analysis of the risk for reservoir real-time operation is a hard task owing to the difficulty of accurate description of inflow uncertainties. The ensemble-based hydrologic forecasts directly depict the inflows not only the marginal distributions but also their persistence via scenarios. This motivates us to analyze the reservoir real-time operating risk with ensemble-based hydrologic forecasts as inputs. A method is developed by using the forecast horizon point to divide the future time into two stages, the forecast lead-time and the unpredicted time. The risk within the forecast lead-time is computed based on counting the failure number of forecast scenarios, and the risk in the unpredicted time is estimated using reservoir routing with the design floods and the reservoir water levels of forecast horizon point. As a result, a two-stage risk analysis method is set up to quantify the entire flood risks by defining the ratio of the number of scenarios that excessive the critical value to the total number of scenarios. The China's Three Gorges Reservoir (TGR) is selected as a case study, where the parameter and precipitation uncertainties are implemented to produce ensemble-based hydrologic forecasts. The Bayesian inference, Markov Chain Monte Carlo, is used to account for the parameter uncertainty. Two reservoir operation schemes, the real operated and scenario optimization, are evaluated for the flood risks and hydropower profits analysis. With the 2010 flood, it is found that the improvement of the hydrologic forecast accuracy is unnecessary to decrease the reservoir real-time operation risk, and most risks are from the forecast lead-time. It is therefore valuable to decrease the avarice of ensemble-based hydrologic forecasts with less bias for a reservoir operational purpose.
Teleporting entanglements of cavity-field states

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

Pires, Geisa; Baseia, B.; Almeida, N.G. de

2004-08-01

We present a scheme to teleport an entanglement of zero- and one-photon states from one cavity to another. The scheme, which has 100% success probability, relies on two perfect and identical bimodal cavities, a collection of two kinds of two-level atoms, a three-level atom in a ladder configuration driven by a classical field, Ramsey zones, and selective atomic-state detectors.
Resonance fluorescence based two- and three-dimensional atom localization

NASA Astrophysics Data System (ADS)

Wahab, Abdul; Rahmatullah; Qamar, Sajid

2016-06-01

Two- and three-dimensional atom localization in a two-level atom-field system via resonance fluorescence is suggested. For the two-dimensional localization, the atom interacts with two orthogonal standing-wave fields, whereas for the three-dimensional atom localization, the atom interacts with three orthogonal standing-wave fields. The effect of the detuning and phase shifts associated with the corresponding standing-wave fields is investigated. A precision enhancement in position measurement of the single atom can be noticed via the control of the detuning and phase shifts.
Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles

PubMed Central

2013-01-01

The ability to interact with different partners is one of the most important features in proteins. Proteins that bind a large number of partners (hubs) have been often associated with intrinsic disorder. However, many examples exist of hubs with an ordered structure, and evidence of a general mechanism promoting promiscuity in ordered proteins is still elusive. An intriguing hypothesis is that promiscuous binding sites have specific dynamical properties, distinct from the rest of the interface and pre-existing in the protein isolated state. Here, we present the first comprehensive study of the intrinsic dynamics of promiscuous residues in a large protein data set. Different computational methods, from coarse-grained elastic models to geometry-based sampling methods and to full-atom Molecular Dynamics simulations, were used to generate conformational ensembles for the isolated proteins. The flexibility and dynamic correlations of interface residues with a different degree of binding promiscuity were calculated and compared considering side chain and backbone motions, the latter both on a local and on a global scale. The study revealed that (a) promiscuous residues tend to be more flexible than nonpromiscuous ones, (b) this additional flexibility has a higher degree of organization, and (c) evolutionary conservation and binding promiscuity have opposite effects on intrinsic dynamics. Findings on simulated ensembles were also validated on ensembles of experimental structures extracted from the Protein Data Bank (PDB). Additionally, the low occurrence of single nucleotide polymorphisms observed for promiscuous residues indicated a tendency to preserve binding diversity at these positions. A case study on two ubiquitin-like proteins exemplifies how binding promiscuity in evolutionary related proteins can be modulated by the fine-tuning of the interface dynamics. The interplay between promiscuity and flexibility highlighted here can inspire new directions in protein–protein interaction prediction and design methods. PMID:24250278
Level statistics of a noncompact cosmological billiard

NASA Astrophysics Data System (ADS)

Csordas, Andras; Graham, Robert; Szepfalusy, Peter

1991-08-01

A noncompact chaotic billiard on a two-dimensional space of constant negative curvature, the infinite equilateral triangle describing anisotropy oscillations in the very early universe, is studied quantum-mechanically. A Weyl formula with a logarithmic correction term is derived for the smoothed number of states function. For one symmetry class of the eigenfunctions, the level spacing distribution, the spectral rigidity Delta3, and the Sigma2 statistics are determined numerically using the finite matrix approximation. Systematic deviations are found both from the Gaussian orthogonal ensemble (GOE) and the Poissonian ensemble. However, good agreement with the GOE is found if the fundamental triangle is deformed in such a way that it no longer tiles the space.
Arbitrary Dicke-State Control of Symmetric Rydberg Ensembles

NASA Astrophysics Data System (ADS)

Deutsch, Ivan

2017-04-01

We study the production of arbitrary superpositions of Dicke states via optimal control. We show that N atomic hyperfine qubits, interacting symmetrically via the Rydberg blockade, are well described by the Jaynes-Cummings Model (JCM), familiar in cavity QED. In this isomorphism, the presence or absence of a collective Rydberg excitation plays the role of the two-level system and the number of symmetric excitations of the hyperfine qubits plays the role of the bosonic excitations of the JCM. This system is fully controllable through the addition of phase-modulated microwaves that drive transitions between the Rydberg-dressed states. In the weak dressing regime, this results in a single-axis twisting Hamiltonian, plus time-dependent rotations of the collective spin. For strong dressing we control the entire Jaynes-Cummings ladder. Using optimal control, we design microwave waveforms that can generate arbitrary states in the symmetric subspace. This includes cat states, Dicke states, and spin squeezed states. With currently feasible parameters, it is possible to generate arbitrary symmetric states of _10 hyperfine qubits in 1 microsec, assuming a fast microwave phase switching time. The same control can be achieved with a ``dressed-ground control'' scheme, which reduces the demands for fast phase switching at the expense of increased total control time. More generally, we can achieve control on larger ensembles of qubits by designing waveforms that are bandwidth limited within the coherence time of the system. We use this to study general questions of the ``quantum speed limit'' and information content in a waveform that is needed to generate arbitrary quantum states.
De Haas-van Alphen effect of a two-dimensional ultracold atomic gas

NASA Astrophysics Data System (ADS)

Farias, B.; Furtado, C.

2016-01-01

In this paper, we show how the ultracold atom analogue of the two-dimensional de Haas-van Alphen effect in electronic condensed matter systems can be induced by optical fields in a neutral atomic system. The interaction between the suitable spatially varying laser fields and tripod-type trapped atoms generates a synthetic magnetic field which leads the particles to organize themselves in Landau levels. Initially, with the atomic gas in a regime of lowest Landau level, we display the oscillatory behaviour of the atomic energy and its derivative with respect to the effective magnetic field (B) as a function of 1/B. Furthermore, we estimate the area of the Fermi circle of the two-dimensional atomic gas.
Finite-temperature stress calculations in atomic models using moments of position.

PubMed

Parthasarathy, Ranganathan; Misra, Anil; Ouyang, Lizhi

2018-07-04

Continuum modeling of finite temperature mechanical behavior of atomic systems requires refined description of atomic motions. In this paper, we identify additional kinematical quantities that are relevant for a more accurate continuum description as the system is subjected to step-wise loading. The presented formalism avoids the necessity for atomic trajectory mapping with deformation, provides the definitions of the kinematic variables and their conjugates in real space, and simplifies local work conjugacy. The total work done on an atom under deformation is decomposed into the work corresponding to changing its equilibrium position and work corresponding to changing its second moment about equilibrium position. Correspondingly, we define two kinematic variables: a deformation gradient tensor and a vibration tensor, and derive their stress conjugates, termed here as static and vibration stresses, respectively. The proposed approach is validated using MD simulation in NVT ensembles for fcc aluminum subjected to uniaxial extension. The observed evolution of second moments in the MD simulation with macroscopic deformation is not directly related to the transformation of atomic trajectories through the deformation gradient using generator functions. However, it is noteworthy that deformation leads to a change in the second moment of the trajectories. Correspondingly, the vibration part of the Piola stress becomes particularly significant at high temperature and high tensile strain as the crystal approaches the softening limit. In contrast to the eigenvectors of the deformation gradient, the eigenvectors of the vibration tensor show strong spatial heterogeneity in the vicinity of softening. More importantly, the elliptic distribution of local atomic density transitions to a dumbbell shape, before significant non-affinity in equilibrium positions has occurred.
Finite-temperature stress calculations in atomic models using moments of position

NASA Astrophysics Data System (ADS)

Parthasarathy, Ranganathan; Misra, Anil; Ouyang, Lizhi

2018-07-01

Continuum modeling of finite temperature mechanical behavior of atomic systems requires refined description of atomic motions. In this paper, we identify additional kinematical quantities that are relevant for a more accurate continuum description as the system is subjected to step-wise loading. The presented formalism avoids the necessity for atomic trajectory mapping with deformation, provides the definitions of the kinematic variables and their conjugates in real space, and simplifies local work conjugacy. The total work done on an atom under deformation is decomposed into the work corresponding to changing its equilibrium position and work corresponding to changing its second moment about equilibrium position. Correspondingly, we define two kinematic variables: a deformation gradient tensor and a vibration tensor, and derive their stress conjugates, termed here as static and vibration stresses, respectively. The proposed approach is validated using MD simulation in NVT ensembles for fcc aluminum subjected to uniaxial extension. The observed evolution of second moments in the MD simulation with macroscopic deformation is not directly related to the transformation of atomic trajectories through the deformation gradient using generator functions. However, it is noteworthy that deformation leads to a change in the second moment of the trajectories. Correspondingly, the vibration part of the Piola stress becomes particularly significant at high temperature and high tensile strain as the crystal approaches the softening limit. In contrast to the eigenvectors of the deformation gradient, the eigenvectors of the vibration tensor show strong spatial heterogeneity in the vicinity of softening. More importantly, the elliptic distribution of local atomic density transitions to a dumbbell shape, before significant non-affinity in equilibrium positions has occurred.
Influence of atomic densities on propagation property for ultrashort pulses in a two-level medium

NASA Astrophysics Data System (ADS)

Liu, Bingxin; Gong, Shangqing; Song, Xiaohong; Jin, Shiqi

2005-05-01

The influence of atomic densities on the propagation property for ultrashort pulses in a two-level atom (TLA) medium is investigated. With higher atomic densities, the self-induced transparency (SIT) cannot be recovered even for 2? ultrashort pulses. New features such as pulse splitting, red-shift and blue-shift of the corresponding spectra arise, and the component of central frequency gradually disappears.
Post-processing of multi-model ensemble river discharge forecasts using censored EMOS

NASA Astrophysics Data System (ADS)

Hemri, Stephan; Lisniak, Dmytro; Klein, Bastian

2014-05-01

When forecasting water levels and river discharge, ensemble weather forecasts are used as meteorological input to hydrologic process models. As hydrologic models are imperfect and the input ensembles tend to be biased and underdispersed, the output ensemble forecasts for river runoff typically are biased and underdispersed, too. Thus, statistical post-processing is required in order to achieve calibrated and sharp predictions. Standard post-processing methods such as Ensemble Model Output Statistics (EMOS) that have their origins in meteorological forecasting are now increasingly being used in hydrologic applications. Here we consider two sub-catchments of River Rhine, for which the forecasting system of the Federal Institute of Hydrology (BfG) uses runoff data that are censored below predefined thresholds. To address this methodological challenge, we develop a censored EMOS method that is tailored to such data. The censored EMOS forecast distribution can be understood as a mixture of a point mass at the censoring threshold and a continuous part based on a truncated normal distribution. Parameter estimates of the censored EMOS model are obtained by minimizing the Continuous Ranked Probability Score (CRPS) over the training dataset. Model fitting on Box-Cox transformed data allows us to take account of the positive skewness of river discharge distributions. In order to achieve realistic forecast scenarios over an entire range of lead-times, there is a need for multivariate extensions. To this end, we smooth the marginal parameter estimates over lead-times. In order to obtain realistic scenarios of discharge evolution over time, the marginal distributions have to be linked with each other. To this end, the multivariate dependence structure can either be adopted from the raw ensemble like in Ensemble Copula Coupling (ECC), or be estimated from observations in a training period. The censored EMOS model has been applied to multi-model ensemble forecasts issued on a daily basis over a period of three years. For the two catchments considered, this resulted in well calibrated and sharp forecast distributions over all lead-times from 1 to 114 h. Training observations tended to be better indicators for the dependence structure than the raw ensemble.

From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation

DOE PAGES

Afonine, Pavel V.; Adams, Paul D.; Urzhumtsev, Alexandre

2018-06-08

TLS modelling was developed by Schomaker and Trueblood to describe atomic displacement parameters through concerted (rigid-body) harmonic motions of an atomic group [Schomaker & Trueblood (1968), Acta Cryst. B 24 , 63–76]. The results of a TLS refinement are T , L and S matrices that provide individual anisotropic atomic displacement parameters (ADPs) for all atoms belonging to the group. These ADPs can be calculated analytically using a formula that relates the elements of the TLS matrices to atomic parameters. Alternatively, ADPs can be obtained numerically from the parameters of concerted atomic motions corresponding to the TLS matrices. Both proceduresmore » are expected to produce the same ADP values and therefore can be used to assess the results of TLS refinement. Here, the implementation of this approach in PHENIX is described and several illustrations, including the use of all models from the PDB that have been subjected to TLS refinement, are provided.« less
From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation

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

Afonine, Pavel V.; Adams, Paul D.; Urzhumtsev, Alexandre

TLS modelling was developed by Schomaker and Trueblood to describe atomic displacement parameters through concerted (rigid-body) harmonic motions of an atomic group [Schomaker & Trueblood (1968), Acta Cryst. B 24 , 63–76]. The results of a TLS refinement are T , L and S matrices that provide individual anisotropic atomic displacement parameters (ADPs) for all atoms belonging to the group. These ADPs can be calculated analytically using a formula that relates the elements of the TLS matrices to atomic parameters. Alternatively, ADPs can be obtained numerically from the parameters of concerted atomic motions corresponding to the TLS matrices. Both proceduresmore » are expected to produce the same ADP values and therefore can be used to assess the results of TLS refinement. Here, the implementation of this approach in PHENIX is described and several illustrations, including the use of all models from the PDB that have been subjected to TLS refinement, are provided.« less
Optical Rabi Oscillations in a Quantum Dot Ensemble

NASA Astrophysics Data System (ADS)

Kujiraoka, Mamiko; Ishi-Hayase, Junko; Akahane, Kouichi; Yamamoto, Naokatsu; Ema, Kazuhiro; Sasaki, Masahide

2010-09-01

We have investigated Rabi oscillations of exciton polarization in a self-assembled InAs quantum dot ensemble. The four-wave mixing signals measured as a function of the average of the pulse area showed the large in-plane anisotropy and nonharmonic oscillations. The experimental results can be well reproduced by a two-level model calculation including three types of inhomogeneities without any fitting parameter. The large anisotropy can be well explained by the anisotropic dipole moments. We also find that the nonharmonic behaviors partly originate from the polarization interference.
Relative Energy Shift of a Two-Level Atom in a Cylindrical Spacetime

NASA Astrophysics Data System (ADS)

Zhang, Jia-Lin

2012-11-01

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

NASA Astrophysics Data System (ADS)

Warner, Thomas T.; Sheu, Rong-Shyang; Bowers, James F.; Sykes, R. Ian; Dodd, Gregory C.; Henn, Douglas S.

2002-05-01

Ensemble simulations made using a coupled atmospheric dynamic model and a probabilistic Lagrangian puff dispersion model were employed in a forensic analysis of the transport and dispersion of a toxic gas that may have been released near Al Muthanna, Iraq, during the Gulf War. The ensemble study had two objectives, the first of which was to determine the sensitivity of the calculated dosage fields to the choices that must be made about the configuration of the atmospheric dynamic model. In this test, various choices were used for model physics representations and for the large-scale analyses that were used to construct the model initial and boundary conditions. The second study objective was to examine the dispersion model's ability to use ensemble inputs to predict dosage probability distributions. Here, the dispersion model was used with the ensemble mean fields from the individual atmospheric dynamic model runs, including the variability in the individual wind fields, to generate dosage probabilities. These are compared with the explicit dosage probabilities derived from the individual runs of the coupled modeling system. The results demonstrate that the specific choices made about the dynamic-model configuration and the large-scale analyses can have a large impact on the simulated dosages. For example, the area near the source that is exposed to a selected dosage threshold varies by up to a factor of 4 among members of the ensemble. The agreement between the explicit and ensemble dosage probabilities is relatively good for both low and high dosage levels. Although only one ensemble was considered in this study, the encouraging results suggest that a probabilistic dispersion model may be of value in quantifying the effects of uncertainties in a dynamic-model ensemble on dispersion model predictions of atmospheric transport and dispersion.
Coastal aquifer management under parameter uncertainty: Ensemble surrogate modeling based simulation-optimization

NASA Astrophysics Data System (ADS)

Janardhanan, S.; Datta, B.

2011-12-01

Surrogate models are widely used to develop computationally efficient simulation-optimization models to solve complex groundwater management problems. Artificial intelligence based models are most often used for this purpose where they are trained using predictor-predictand data obtained from a numerical simulation model. Most often this is implemented with the assumption that the parameters and boundary conditions used in the numerical simulation model are perfectly known. However, in most practical situations these values are uncertain. Under these circumstances the application of such approximation surrogates becomes limited. In our study we develop a surrogate model based coupled simulation optimization methodology for determining optimal pumping strategies for coastal aquifers considering parameter uncertainty. An ensemble surrogate modeling approach is used along with multiple realization optimization. The methodology is used to solve a multi-objective coastal aquifer management problem considering two conflicting objectives. Hydraulic conductivity and the aquifer recharge are considered as uncertain values. Three dimensional coupled flow and transport simulation model FEMWATER is used to simulate the aquifer responses for a number of scenarios corresponding to Latin hypercube samples of pumping and uncertain parameters to generate input-output patterns for training the surrogate models. Non-parametric bootstrap sampling of this original data set is used to generate multiple data sets which belong to different regions in the multi-dimensional decision and parameter space. These data sets are used to train and test multiple surrogate models based on genetic programming. The ensemble of surrogate models is then linked to a multi-objective genetic algorithm to solve the pumping optimization problem. Two conflicting objectives, viz, maximizing total pumping from beneficial wells and minimizing the total pumping from barrier wells for hydraulic control of saltwater intrusion are considered. The salinity levels resulting at strategic locations due to these pumping are predicted using the ensemble surrogates and are constrained to be within pre-specified levels. Different realizations of the concentration values are obtained from the ensemble predictions corresponding to each candidate solution of pumping. Reliability concept is incorporated as the percent of the total number of surrogate models which satisfy the imposed constraints. The methodology was applied to a realistic coastal aquifer system in Burdekin delta area in Australia. It was found that all optimal solutions corresponding to a reliability level of 0.99 satisfy all the constraints and as reducing reliability level decreases the constraint violation increases. Thus ensemble surrogate model based simulation-optimization was found to be useful in deriving multi-objective optimal pumping strategies for coastal aquifers under parameter uncertainty.
Probing interactions of thermal Sr Rydberg atoms using simultaneous optical and ion detection

NASA Astrophysics Data System (ADS)

Hanley, Ryan K.; Bounds, Alistair D.; Huillery, Paul; Keegan, Niamh C.; Faoro, Riccardo; Bridge, Elizabeth M.; Weatherill, Kevin J.; Jones, Matthew P. A.

2017-06-01

We demonstrate a method for probing interaction effects in a thermal beam of strontium atoms using simultaneous measurements of Rydberg EIT and spontaneously created ions or electrons. We present a Doppler-averaged optical Bloch equation model that reproduces the optical signals and allows us to connect the optical coherences and the populations. We use this to determine that the spontaneous ionization process in our system occurs due to collisions between Rydberg and ground state atoms in the EIT regime. We measure the cross section of this process to be 0.6+/- 0.2 {σ }{geo}, where {σ }{geo} is the geometrical cross section of the Rydberg atom. This result adds complementary insight to a range of recent studies of interacting thermal Rydberg ensembles.
Forced synchronization of large-scale circulation to increase predictability of surface states

NASA Astrophysics Data System (ADS)

Shen, Mao-Lin; Keenlyside, Noel; Selten, Frank; Wiegerinck, Wim; Duane, Gregory

2016-04-01

Numerical models are key tools in the projection of the future climate change. The lack of perfect initial condition and perfect knowledge of the laws of physics, as well as inherent chaotic behavior limit predictions. Conceptually, the atmospheric variables can be decomposed into a predictable component (signal) and an unpredictable component (noise). In ensemble prediction the anomaly of ensemble mean is regarded as the signal and the ensemble spread the noise. Naturally the prediction skill will be higher if the signal-to-noise ratio (SNR) is larger in the initial conditions. We run two ensemble experiments in order to explore a way to reduce the SNR of surface winds and temperature. One ensemble experiment is AGCM with prescribing sea surface temperature (SST); the other is AGCM with both prescribing SST and nudging the high-level temperature and winds to ERA-Interim. Each ensemble has 30 members. Larger SNR is expected and found over the tropical ocean in the first experiment because the tropical circulation is associated with the convection and the associated surface wind convergence as these are to a large extent driven by the SST. However, small SNR is found over high latitude ocean and land surface due to the chaotic and non-synchronized atmosphere states. In the second experiment the higher level temperature and winds are forced to be synchronized (nudged to reanalysis) and hence a larger SNR of surface winds and temperature is expected. Furthermore, different nudging coefficients are also tested in order to understand the limitation of both synchronization of large-scale circulation and the surface states. These experiments will be useful for the developing strategies to synchronize the 3-D states of atmospheric models that can be later used to build a super model.
Fidelity decay in interacting two-level boson systems: Freezing and revivals

NASA Astrophysics Data System (ADS)

Benet, Luis; Hernández-Quiroz, Saúl; Seligman, Thomas H.

2011-05-01

We study the fidelity decay in the k-body embedded ensembles of random matrices for bosons distributed in two single-particle states, considering the reference or unperturbed Hamiltonian as the one-body terms and the diagonal part of the k-body embedded ensemble of random matrices and the perturbation as the residual off-diagonal part of the interaction. We calculate the ensemble-averaged fidelity with respect to an initial random state within linear response theory to second order on the perturbation strength and demonstrate that it displays the freeze of the fidelity. During the freeze, the average fidelity exhibits periodic revivals at integer values of the Heisenberg time tH. By selecting specific k-body terms of the residual interaction, we find that the periodicity of the revivals during the freeze of fidelity is an integer fraction of tH, thus relating the period of the revivals with the range of the interaction k of the perturbing terms. Numerical calculations confirm the analytical results.
A simple molecular mechanics integrator in mixed rigid body and dihedral angle space

PubMed Central

Vitalis, Andreas; Pappu, Rohit V.

2014-01-01

We propose a numerical scheme to integrate equations of motion in a mixed space of rigid-body and dihedral angle coordinates. The focus of the presentation is biomolecular systems and the framework is applicable to polymers with tree-like topology. By approximating the effective mass matrix as diagonal and lumping all bias torques into the time dependencies of the diagonal elements, we take advantage of the formal decoupling of individual equations of motion. We impose energy conservation independently for every degree of freedom and this is used to derive a numerical integration scheme. The cost of all auxiliary operations is linear in the number of atoms. By coupling the scheme to one of two popular thermostats, we extend the method to sample constant temperature ensembles. We demonstrate that the integrator of choice yields satisfactory stability and is free of mass-metric tensor artifacts, which is expected by construction of the algorithm. Two fundamentally different systems, viz., liquid water and an α-helical peptide in a continuum solvent are used to establish the applicability of our method to a wide range of problems. The resultant constant temperature ensembles are shown to be thermodynamically accurate. The latter relies on detailed, quantitative comparisons to data from reference sampling schemes operating on exactly the same sets of degrees of freedom. PMID:25053299
Random matrix ensembles for many-body quantum systems

NASA Astrophysics Data System (ADS)

Vyas, Manan; Seligman, Thomas H.

2018-04-01

Classical random matrix ensembles were originally introduced in physics to approximate quantum many-particle nuclear interactions. However, there exists a plethora of quantum systems whose dynamics is explained in terms of few-particle (predom-inantly two-particle) interactions. The random matrix models incorporating the few-particle nature of interactions are known as embedded random matrix ensembles. In the present paper, we provide a brief overview of these two ensembles and illustrate how the embedded ensembles can be successfully used to study decoherence of a qubit interacting with an environment, both for fermionic and bosonic embedded ensembles. Numerical calculations show the dependence of decoherence on the nature of the environment.
Quantum quench in an atomic one-dimensional Ising chain.

PubMed

Meinert, F; Mark, M J; Kirilov, E; Lauber, K; Weinmann, P; Daley, A J; Nägerl, H-C

2013-08-02

We study nonequilibrium dynamics for an ensemble of tilted one-dimensional atomic Bose-Hubbard chains after a sudden quench to the vicinity of the transition point of the Ising paramagnetic to antiferromagnetic quantum phase transition. The quench results in coherent oscillations for the orientation of effective Ising spins, detected via oscillations in the number of doubly occupied lattice sites. We characterize the quench by varying the system parameters. We report significant modification of the tunneling rate induced by interactions and show clear evidence for collective effects in the oscillatory response.
Sensitivity of sea-level forecasting to the horizontal resolution and sea surface forcing for different configurations of an oceanographic model of the Adriatic Sea

NASA Astrophysics Data System (ADS)

Bressan, Lidia; Valentini, Andrea; Paccagnella, Tiziana; Montani, Andrea; Marsigli, Chiara; Stefania Tesini, Maria

2017-04-01

At the Hydro-meteo-climate service of the Regional environmental agency of Emilia-Romagna, Italy (Arpae-SIMC), the oceanographic numerical model AdriaROMS is used in the operational forecasting suite to compute sea level, temperature, salinity and 3-D current fields of the Adriatic Sea (northern Mediterranean Sea). In order to evaluate the performance of the sea-level forecast and to study different configurations of the ROMS model, two marine storms occurred on the Emilia Romagna coast during the winter 2015-2016 are investigated. The main focus of this study is to analyse the sensitivity of the model to the horizontal resolution and to the meteorological forcing. To this end, the model is run with two different configurations and with two horizontal grids at 1 and 2 km resolution. To study the influence of the meteorological forcing, the two storms have been reproduced by running ROMS in ensemble mode, forced by the 16-members of the meteorological ensemble COSMO-LEPS system. Possible optimizations of the model set-up are deduced by the comparison of the different run outputs.
Method for generating maximally entangled states of multiple three-level atoms in cavity QED

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

Jin Guangsheng; Li Shushen; Feng Songlin

2004-03-01

We propose a scheme to generate maximally entangled states (MESs) of multiple three-level atoms in microwave cavity QED based on the resonant atom-cavity interaction. In the scheme, multiple three-level atoms initially in their ground states are sequently sent through two suitably prepared cavities. After a process of appropriate atom-cavity interaction, a subsequent measurement on the second cavity field projects the atoms onto the MESs. The practical feasibility of this method is also discussed.
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.
A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations

PubMed Central

Frappier, Vincent; Najmanovich, Rafael J.

2014-01-01

Normal mode analysis (NMA) methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM) methods with Cα−only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations. PMID:24762569
Arbitrary-quantum-state preparation of a harmonic oscillator via optimal control

NASA Astrophysics Data System (ADS)

Rojan, Katharina; Reich, Daniel M.; Dotsenko, Igor; Raimond, Jean-Michel; Koch, Christiane P.; Morigi, Giovanna

2014-08-01

The efficient initialization of a quantum system is a prerequisite for quantum technological applications. Here we show that several classes of quantum states of a harmonic oscillator can be efficiently prepared by means of a Jaynes-Cummings interaction with a single two-level system. This is achieved by suitably tailoring external fields which drive the dipole and/or the oscillator. The time-dependent dynamics that leads to the target state is identified by means of optimal control theory (OCT) based on Krotov's method. Infidelities below 10-4 can be reached for the parameters of the experiment of Raimond, Haroche, Brune and co-workers, where the oscillator is a mode of a high-Q microwave cavity and the dipole is a Rydberg transition of an atom. For this specific situation we analyze the limitations on the fidelity due to parameter fluctuations and identify robust dynamics based on pulses found using ensemble OCT. Our analysis can be extended to quantum-state preparation of continuous-variable systems in other platforms, such as trapped ions and circuit QED.
Quantum storage of orbital angular momentum entanglement in cold atomic ensembles

NASA Astrophysics Data System (ADS)

Shi, Bao-Sen; Ding, Dong-Sheng; Zhang, Wei

2018-02-01

Electromagnetic waves have both spin momentum and orbital angular momentum (OAM). Light carrying OAM has broad applications in micro-particle manipulation, high-precision optical metrology, and potential high-capacity optical communications. In the concept of quantum information, a photon encoded with information in its OAM degree of freedom enables quantum networks to carry much more information and increase their channel capacity greatly compared with those of current technology because of the inherent infinite dimensions for OAM. Quantum memories are indispensable to construct quantum networks. Storing OAM states has attracted considerable attention recently, and many important advances in this direction have been achieved during the past few years. Here we review recent experimental realizations of quantum memories using OAM states, including OAM qubits and qutrits at true single photon level, OAM states entangled in a two-dimensional or a high-dimensional space, hyperentanglement and hybrid entanglement consisting of OAM and other degree of freedom in a physical system. We believe that all achievements described here are very helpful to study quantum information encoded in a high-dimensional space.
Experimental realization of entanglement in multiple degrees of freedom between two quantum memories.

PubMed

Zhang, Wei; Ding, Dong-Sheng; Dong, Ming-Xin; Shi, Shuai; Wang, Kai; Liu, Shi-Long; Li, Yan; Zhou, Zhi-Yuan; Shi, Bao-Sen; Guo, Guang-Can

2016-11-14

Entanglement in multiple degrees of freedom has many benefits over entanglement in a single one. The former enables quantum communication with higher channel capacity and more efficient quantum information processing and is compatible with diverse quantum networks. Establishing multi-degree-of-freedom entangled memories is not only vital for high-capacity quantum communication and computing, but also promising for enhanced violations of nonlocality in quantum systems. However, there have been yet no reports of the experimental realization of multi-degree-of-freedom entangled memories. Here we experimentally established hyper- and hybrid entanglement in multiple degrees of freedom, including path (K-vector) and orbital angular momentum, between two separated atomic ensembles by using quantum storage. The results are promising for achieving quantum communication and computing with many degrees of freedom.
The effect of Pd ensemble structure on the O2 dissociation and CO oxidation mechanisms on Au—Pd(100) surface alloys

NASA Astrophysics Data System (ADS)

Oǧuz, Ismail-Can; Mineva, Tzonka; Guesmi, Hazar

2018-01-01

The reactivity of various Pd ensembles on the Au—Pd(100) alloy catalyst toward CO oxidation was investigated by using density functional theory (DFT). This study was prompted by the search for efficient catalysts operating at low temperature for the CO oxidation reaction that is of primary environmental importance. To this aim, we considered Pd modified Au(100) surfaces including Pd monomers, Pd dimers, second neighboring Pd atoms, and Pd chains in a comparative study of the minimum energy reaction pathways. The effect of dispersion interactions was included in the calculations of the O2 dissociation reaction pathway by using the DFT-D3 scheme. The addition of the dispersion interaction strongly improves the adsorption ability of O2 on the Au—Pd surface but does not affect the activation energy barriers of the Transitions States (TSs). As for O2 to dissociate, it is imperative that the TS has lower activation energy than the O2 desorption energy. DFT-D3 is found to favor, in some cases, O2 dissociation on configurations being identified from uncorrected DFT calculations as inactive. This is the case of the second neighboring Pd configuration for which uncorrected DFT predicts positive Gibbs free energy (ΔG) of the O2 adsorption, therefore an endergonic reaction. With the addition of D3 correction, ΔG becomes negative that reveals a spontaneous O2 adsorption. Among the investigated Au—Pd (100) ensembles, the Pd chain dissociates most easily O2 and highly stabilizes the dissociated O atoms; however, it has an inferior reactivity toward CO oxidation and CO2 formation. Indeed, CO strongly adsorbs on the palladium bridge sites and therefore poisoning the surface Pd chain. By contrast, the second neighboring Pd configuration that shows somewhat lower ability to dissociate O2 turns out to be more reactive in the CO2 formation step. These results evidence the complex effect of Pd ensembles on the CO oxidation reaction. Associative CO oxidation proceeds with high energy barriers on all the considered Pd ensembles and should be excluded, in agreement with experimental observations.

Appendix A: The Impact of the HP 5071A on International Atomic Time

NASA Technical Reports Server (NTRS)

Allan, David W.; Lepek, Alex; Cutler, Len; Giffard, Robin; Kusters, Jack

1996-01-01

The international clock ensemble, which contributes to the generation of International Atomic Time (TAI and UTC) has improved dramatically over the last few years. The main change has been the introduction of a significant number of HP 5071A clocks. Of the 313 clocks contributing to TAI/UTC during 1994, 94 of these were HP 5071As. The environmental insensitivity of the HP 5071A clocks is more than an order of magnitude better than that of previously contributing clocks. This environmental insensitivity translates to outstanding long-term stability - with a typical flicker floor of a few x10(sup -15). in addition, there are now several hydrogen masers with cavity tuning contributing to TAI/UTC. These not only have outstanding short-term stability, but comparatively low frequency drifts and excellent intermediate-type frequency stability. By analyzing data available from the international ensemble, we have obtained two important results. First the frequency stability obtainable with an optimum algorithm is about 10(sup -15) for both the intermediate and long-term regions. It could be as good in the short-term (if time transfer measurement instabilities were reduced sufficiently. Second, with cooperation, this performance can be made available on an international basis in near real time. The recent enhancements in the contributing clocks are already providing a significant improvement in the accuracy with which UTC is made available to the world from several of the national timing centers, such as the National Institute for Standards and Technology (NIST) and the US Naval Observatory (USNO).
Quantum Computation by Optically Coupled Steady Atoms/Quantum-Dots Inside a Quantum Cavity

NASA Technical Reports Server (NTRS)

Pradhan, P.; Wang, K. L.; Roychowdhury, V. P.; Anantram, M. P.; Mor, T.; Saini, Subhash (Technical Monitor)

1999-01-01

We present a model for quantum computation using $n$ steady 3-level atoms kept inside a quantum cavity, or using $n$ quantum-dots (QDs) kept inside a quantum cavity. In this model one external laser is pointed towards all the atoms/QDs, and $n$ pairs of electrodes are addressing the atoms/QDs, so that each atom is addressed by one pair. The energy levels of each atom/QD are controlled by an external Stark field given to the atom/QD by its external pair of electrodes. Transition between two energy levels of an individual atom/ QD are controlled by the voltage on its electrodes, and by the external laser. Interactions between two atoms/ QDs are performed with the additional help of the cavity mode (using on-resonance condition). Laser frequency, cavity frequency, and energy levels are far off-resonance most of the time, and they are brought to the resonance (using the Stark effect) only at the time of operations. Steps for a controlled-NOT gate between any two atoms/QDs have been described for this model. Our model demands some challenging technological efforts, such as manufacturing single-electron QDs inside a cavity. However, it promises big advantages over other existing models which are currently implemented, and might enable a much easier scale-up, to compute with many more qubits.
Pauci ex tanto numero: reducing redundancy in multi-model ensembles

NASA Astrophysics Data System (ADS)

Solazzo, E.; Riccio, A.; Kioutsioukis, I.; Galmarini, S.

2013-02-01

We explicitly address the fundamental issue of member diversity in multi-model ensembles. To date no attempts in this direction are documented within the air quality (AQ) community, although the extensive use of ensembles in this field. Common biases and redundancy are the two issues directly deriving from lack of independence, undermining the significance of a multi-model ensemble, and are the subject of this study. Shared biases among models will determine a biased ensemble, making therefore essential the errors of the ensemble members to be independent so that bias can cancel out. Redundancy derives from having too large a portion of common variance among the members of the ensemble, producing overconfidence in the predictions and underestimation of the uncertainty. The two issues of common biases and redundancy are analysed in detail using the AQMEII ensemble of AQ model results for four air pollutants in two European regions. We show that models share large portions of bias and variance, extending well beyond those induced by common inputs. We make use of several techniques to further show that subsets of models can explain the same amount of variance as the full ensemble with the advantage of being poorly correlated. Selecting the members for generating skilful, non-redundant ensembles from such subsets proved, however, non-trivial. We propose and discuss various methods of member selection and rate the ensemble performance they produce. In most cases, the full ensemble is outscored by the reduced ones. We conclude that, although independence of outputs may not always guarantee enhancement of scores (but this depends upon the skill being investigated) we discourage selecting the members of the ensemble simply on the basis of scores, that is, independence and skills need to be considered disjointly.
Tunable atom-light beam splitter using electromagnetically induced transparency

NASA Astrophysics Data System (ADS)

Zhu, Xinyu; Wen, Rong; Chen, J. F.

2018-06-01

With electromagnetically induced transmission (EIT), an optical field can be converted into collective atomic excitation and stored in the atomic medium through switching off the strong-coupling field adiabatically. By varying the power of the coupling pulse, we can control the ratio between the transmitted optical field and the stored atomic mode. We use a cloud of cold 85Rb atoms prepared in magneto-optical trap as the experimental platform. Based on a model of EIT dark-state polariton, we consider the real case where the atomic medium has a finite length. The theoretical calculation gives numerical results that agree well with the experimental data. The results show that the ratio can be changed approximately from 0 to 100%, when the maximum power of the coupling pulse (the pulse length is 100 ns) varies from 0 to 20 mW, in the cold atomic ensemble with an optical depth of 40. This process can be used to achieve an atom-light hybrid beam splitter with tunable splitting ratio and thus find potential application in interferometric measurement and quantum information processing.
Sympathetic cooling of a membrane oscillator in a hybrid mechanical-atomic system

NASA Astrophysics Data System (ADS)

Jöckel, Andreas; Faber, Aline; Kampschulte, Tobias; Korppi, Maria; Rakher, Matthew T.; Treutlein, Philipp

2015-01-01

Sympathetic cooling with ultracold atoms and atomic ions enables ultralow temperatures in systems where direct laser or evaporative cooling is not possible. It has so far been limited to the cooling of other microscopic particles, with masses up to 90 times larger than that of the coolant atom. Here, we use ultracold atoms to sympathetically cool the vibrations of a Si3N4 nanomembrane, the mass of which exceeds that of the atomic ensemble by a factor of 1010. The coupling of atomic and membrane vibrations is mediated by laser light over a macroscopic distance and is enhanced by placing the membrane in an optical cavity. We observe cooling of the membrane vibrations from room temperature to 650 ± 230 mK, exploiting the large atom-membrane cooperativity of our hybrid optomechanical system. With technical improvements, our scheme could provide ground-state cooling and quantum control of low-frequency oscillators such as nanomembranes or levitated nanoparticles, in a regime where purely optomechanical techniques cannot reach the ground state.
Verifying and Postprocesing the Ensemble Spread-Error Relationship

NASA Astrophysics Data System (ADS)

Hopson, Tom; Knievel, Jason; Liu, Yubao; Roux, Gregory; Wu, Wanli

2013-04-01

With the increased utilization of ensemble forecasts in weather and hydrologic applications, there is a need to verify their benefit over less expensive deterministic forecasts. One such potential benefit of ensemble systems is their capacity to forecast their own forecast error through the ensemble spread-error relationship. The paper begins by revisiting the limitations of the Pearson correlation alone in assessing this relationship. Next, we introduce two new metrics to consider in assessing the utility an ensemble's varying dispersion. We argue there are two aspects of an ensemble's dispersion that should be assessed. First, and perhaps more fundamentally: is there enough variability in the ensembles dispersion to justify the maintenance of an expensive ensemble prediction system (EPS), irrespective of whether the EPS is well-calibrated or not? To diagnose this, the factor that controls the theoretical upper limit of the spread-error correlation can be useful. Secondly, does the variable dispersion of an ensemble relate to variable expectation of forecast error? Representing the spread-error correlation in relation to its theoretical limit can provide a simple diagnostic of this attribute. A context for these concepts is provided by assessing two operational ensembles: 30-member Western US temperature forecasts for the U.S. Army Test and Evaluation Command and 51-member Brahmaputra River flow forecasts of the Climate Forecast and Applications Project for Bangladesh. Both of these systems utilize a postprocessing technique based on quantile regression (QR) under a step-wise forward selection framework leading to ensemble forecasts with both good reliability and sharpness. In addition, the methodology utilizes the ensemble's ability to self-diagnose forecast instability to produce calibrated forecasts with informative skill-spread relationships. We will describe both ensemble systems briefly, review the steps used to calibrate the ensemble forecast, and present verification statistics using error-spread metrics, along with figures from operational ensemble forecasts before and after calibration.
Reconstructing Ion Spectra from Low-Altitude ENAs: Moderate to Large Storms.

NASA Astrophysics Data System (ADS)

LLera, K.; Goldstein, J.; McComas, D. J.; Valek, P. W.

2015-12-01

Two Wide-angle Imaging Neutral-atom Spectrometers (TWINS) Energetic neutral atom (ENA) imagers regularly observe Low-altitude Emission (LAE) intensifications during geomagnetic storm intervals. Since LAEs are produced by the interaction between ions and the near-Earth exosphere (altitudes ~200-800 km), they are a global signature of how the ring current decays in response to solar wind conditions. In this "optically thick" region, an ENA readily becomes reionized, and an ion is readily neutralized. Therefore, emerging ENAs that contribute to the LAE signal (detectable several RE away) have undergone multiple charge exchange and electron stripping interactions. Accounting for the ~36 eV energy loss per interaction, we developed a model to quantify the total energy lost by emergent LAEs. The analytical tool is applied to an ensemble of moderate to large storms (including the recent 17 March and 23 June storms in 2015) to reconstruct the parent ion spectra from TWINS ENA images. We examine the ion spectra energy characteristics among the various storm events.
Skill and predictability in multimodel ensemble forecasts for Northern Hemisphere regions with dominant winter precipitation

NASA Astrophysics Data System (ADS)

Ehsan, Muhammad Azhar; Tippett, Michael K.; Almazroui, Mansour; Ismail, Muhammad; Yousef, Ahmed; Kucharski, Fred; Omar, Mohamed; Hussein, Mahmoud; Alkhalaf, Abdulrahman A.

2017-05-01

Northern Hemisphere winter precipitation reforecasts from the European Centre for Medium Range Weather Forecast System-4 and six of the models in the North American Multi-Model Ensemble are evaluated, focusing on two regions (Region-A: 20°N-45°N, 10°E-65°E and Region-B: 20°N-55°N, 205°E-255°E) where winter precipitation is a dominant fraction of the annual total and where precipitation from mid-latitude storms is important. Predictability and skill (deterministic and probabilistic) are assessed for 1983-2013 by the multimodel composite (MME) of seven prediction models. The MME climatological mean and variability over the two regions is comparable to observation with some regional differences. The statistically significant decreasing trend observed in Region-B precipitation is captured well by the MME and most of the individual models. El Niño Southern Oscillation is a source of forecast skill, and the correlation coefficient between the Niño3.4 index and precipitation over region A and B is 0.46 and 0.35, statistically significant at the 95 % level. The MME reforecasts weakly reproduce the observed teleconnection. Signal, noise and signal to noise ratio analysis show that the signal variance over two regions is very small as compared to noise variance which tends to reduce the prediction skill. The MME ranked probability skill score is higher than that of individual models, showing the advantage of a multimodel ensemble. Observed Region-A rainfall anomalies are strongly associated with the North Atlantic Oscillation, but none of the models reproduce this relation, which may explain the low skill over Region-A. The superior quality of multimodel ensemble compared with individual models is mainly due to larger ensemble size.
Generating highly accurate prediction hypotheses through collaborative ensemble learning

NASA Astrophysics Data System (ADS)

Arsov, Nino; Pavlovski, Martin; Basnarkov, Lasko; Kocarev, Ljupco

2017-03-01

Ensemble generation is a natural and convenient way of achieving better generalization performance of learning algorithms by gathering their predictive capabilities. Here, we nurture the idea of ensemble-based learning by combining bagging and boosting for the purpose of binary classification. Since the former improves stability through variance reduction, while the latter ameliorates overfitting, the outcome of a multi-model that combines both strives toward a comprehensive net-balancing of the bias-variance trade-off. To further improve this, we alter the bagged-boosting scheme by introducing collaboration between the multi-model’s constituent learners at various levels. This novel stability-guided classification scheme is delivered in two flavours: during or after the boosting process. Applied among a crowd of Gentle Boost ensembles, the ability of the two suggested algorithms to generalize is inspected by comparing them against Subbagging and Gentle Boost on various real-world datasets. In both cases, our models obtained a 40% generalization error decrease. But their true ability to capture details in data was revealed through their application for protein detection in texture analysis of gel electrophoresis images. They achieve improved performance of approximately 0.9773 AUROC when compared to the AUROC of 0.9574 obtained by an SVM based on recursive feature elimination.
Boiling point determination using adiabatic Gibbs ensemble Monte Carlo simulations: Application to metals described by embedded-atom potentials

NASA Astrophysics Data System (ADS)

Gelb, Lev D.; Chakraborty, Somendra Nath

2011-12-01

The normal boiling points are obtained for a series of metals as described by the "quantum-corrected Sutton Chen" (qSC) potentials [S.-N. Luo, T. J. Ahrens, T. Çağın, A. Strachan, W. A. Goddard III, and D. C. Swift, Phys. Rev. B 68, 134206 (2003)]. Instead of conventional Monte Carlo simulations in an isothermal or expanded ensemble, simulations were done in the constant-NPH adabatic variant of the Gibbs ensemble technique as proposed by Kristóf and Liszi [Chem. Phys. Lett. 261, 620 (1996)]. This simulation technique is shown to be a precise tool for direct calculation of boiling temperatures in high-boiling fluids, with results that are almost completely insensitive to system size or other arbitrary parameters as long as the potential truncation is handled correctly. Results obtained were validated using conventional NVT-Gibbs ensemble Monte Carlo simulations. The qSC predictions for boiling temperatures are found to be reasonably accurate, but substantially underestimate the enthalpies of vaporization in all cases. This appears to be largely due to the systematic overestimation of dimer binding energies by this family of potentials, which leads to an unsatisfactory description of the vapor phase.
Selective hydrogenation of 1,3-butadiene on platinum–copper alloys at the single-atom limit

DOE PAGES

Lucci, Felicia R.; Liu, Jilei; Marcinkowski, Matthew D.; ...

2015-10-09

Platinum is ubiquitous in the production sectors of chemicals and fuels; however, its scarcity in nature and high price will limit future proliferation of platinum-catalysed reactions. One definite approach to conserve platinum involves understanding the smallest number of platinum atoms needed to catalyse a reaction, then designing catalysts with the minimal platinum ensembles. Here we design and test a new generation of platinum–copper nanoparticle catalysts for the selective hydrogenation of 1,3-butadiene,, an industrially important reaction. Isolated platinum atom geometries enable hydrogen activation and spillover but are incapable of C–C bond scission that leads to loss of selectivity and catalyst deactivation.more » γ-Alumina-supported single-atom alloy nanoparticle catalysts with <1 platinum atom per 100 copper atoms are found to exhibit high activity and selectivity for butadiene hydrogenation to butenes under mild conditions, demonstrating transferability from the model study to the catalytic reaction under practical conditions.« less
A universal quantum information processor for scalable quantum communication and networks

PubMed Central

Yang, Xihua; Xue, Bolin; Zhang, Junxiang; Zhu, Shiyao

2014-01-01

Entanglement provides an essential resource for quantum computation, quantum communication, and quantum networks. How to conveniently and efficiently realize the generation, distribution, storage, retrieval, and control of multipartite entanglement is the basic requirement for realistic quantum information processing. Here, we present a theoretical proposal to efficiently and conveniently achieve a universal quantum information processor (QIP) via atomic coherence in an atomic ensemble. The atomic coherence, produced through electromagnetically induced transparency (EIT) in the Λ-type configuration, acts as the QIP and has full functions of quantum beam splitter, quantum frequency converter, quantum entangler, and quantum repeater. By employing EIT-based nondegenerate four-wave mixing processes, the generation, exchange, distribution, and manipulation of light-light, atom-light, and atom-atom multipartite entanglement can be efficiently and flexibly achieved in a deterministic way with only coherent light fields. This method greatly facilitates the operations in quantum information processing, and holds promising applications in realistic scalable quantum communication and quantum networks. PMID:25316514
Condensate fluctuations of interacting Bose gases within a microcanonical ensemble.

PubMed

Wang, Jianhui; He, Jizhou; Ma, Yongli

2011-05-01

Based on counting statistics and Bogoliubov theory, we present a recurrence relation for the microcanonical partition function for a weakly interacting Bose gas with a finite number of particles in a cubic box. According to this microcanonical partition function, we calculate numerically the distribution function, condensate fraction, and condensate fluctuations for a finite and isolated Bose-Einstein condensate. For ideal and weakly interacting Bose gases, we compare the condensate fluctuations with those in the canonical ensemble. The present approach yields an accurate account of the condensate fluctuations for temperatures close to the critical region. We emphasize that the interactions between excited atoms turn out to be important for moderate temperatures.
State-to-state, multi-collision, energy transfer in H-H2 gas ensembles.

PubMed

McCaffery, Anthony J; Marsh, Richard J

2013-12-21

We use our recently developed computational model of energy flow in gas ensembles to study translation-to-internal energy conversion in an ensemble consisting of H2(0; 0) in a bath of H atoms. This mixture is found in plasmas of industrial importance and also in interstellar clouds. The storage of energy of relative motion as rovibrational energy of H2 represents a potential mechanism for cooling translation. This may have relevance in astrophysical contexts such as the post-recombination epoch of the early universe when hydrogenic species dominated and cooling was a precondition for the formation of structured objects. We find that conversion of translational motion to H2 vibration and rotation is fast and, in our closed system, is complete within around 100 cycles of ensemble collisions. Large amounts of energy become stored as H2 vibration and a tentative mechanism for this unequal energy distribution is suggested. The "structured dis-equilibrium" we observe is found to persist through many collision cycles. In contrast to the rapidity of excitation, the relaxation of H2(6; 10) in H is very slow and not complete after 10(5) collision cycles. The quasi-equilibrium modal temperatures of translation, rotation, and vibration are found to scale linearly with collision energy but at different rates. This may be useful in estimating the partitioning of energy within a given H + H2 ensemble.
Chemical Structure, Ensemble and Single-Particle Spectroscopy of Thick-Shell InP-ZnSe Quantum Dots.

PubMed

Reid, Kemar R; McBride, James R; Freymeyer, Nathaniel J; Thal, Lucas B; Rosenthal, Sandra J

2018-02-14

Thick-shell (>5 nm) InP-ZnSe colloidal quantum dots (QDs) grown by a continuous-injection shell growth process are reported. The growth of a thick crystalline shell is attributed to the high temperature of the growth process and the relatively low lattice mismatch between the InP core and ZnSe shell. In addition to a narrow ensemble photoluminescence (PL) line-width (∼40 nm), ensemble and single-particle emission dynamics measurements indicate that blinking and Auger recombination are reduced in these heterostructures. More specifically, high single-dot ON-times (>95%) were obtained for the core-shell QDs, and measured ensemble biexciton lifetimes, τ 2x ∼ 540 ps, represent a 7-fold increase compared to InP-ZnS QDs. Further, high-resolution energy dispersive X-ray (EDX) chemical maps directly show for the first time significant incorporation of indium into the shell of the InP-ZnSe QDs. Examination of the atomic structure of the thick-shell QDs by high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) reveals structural defects in subpopulations of particles that may mitigate PL efficiencies (∼40% in ensemble), providing insight toward further synthetic refinement. These InP-ZnSe heterostructures represent progress toward fully cadmium-free QDs with superior photophysical properties important in biological labeling and other emission-based technologies.
The Impact of Density and Ratio on Object-Ensemble Representation in Human Anterior-Medial Ventral Visual Cortex

PubMed Central

Cant, Jonathan S.; Xu, Yaoda

2015-01-01

Behavioral research has demonstrated that observers can extract summary statistics from ensembles of multiple objects. We recently showed that a region of anterior-medial ventral visual cortex, overlapping largely with the scene-sensitive parahippocampal place area (PPA), participates in object-ensemble representation. Here we investigated the encoding of ensemble density in this brain region using fMRI-adaptation. In Experiment 1, we varied density by changing the spacing between objects and found no sensitivity in PPA to such density changes. Thus, density may not be encoded in PPA, possibly because object spacing is not perceived as an intrinsic ensemble property. In Experiment 2, we varied relative density by changing the ratio of 2 types of objects comprising an ensemble, and observed significant sensitivity in PPA to such ratio change. Although colorful ensembles were shown in Experiment 2, Experiment 3 demonstrated that sensitivity to object ratio change was not driven mainly by a change in the ratio of colors. Thus, while anterior-medial ventral visual cortex is insensitive to density (object spacing) changes, it does code relative density (object ratio) within an ensemble. Object-ensemble processing in this region may thus depend on high-level visual information, such as object ratio, rather than low-level information, such as spacing/spatial frequency. PMID:24964917
Protecting a quantum memory for a photonic polarization qubit in a cold atomic ensemble by dynamical decoupling.

PubMed

Wu, Yuelong; Chen, Lirong; Xu, Zhongxiao; Wang, Hai

2014-09-22

We report an experimental demonstration of storage of photonic polarization qubit (PPQ) protected by dynamical decoupling (DD). PPQ's states are stored as a superposition of two spin waves by electromagnetically-induced-transparency (EIT). Carr-Purcell-Meiboom-Gill (CPMG) DD sequences are applied to the spin-wave superposition to suppress its decoherence. Thus, the quantum process fidelity remains better than 0.8 for up to 800 μs storage time, which is 3.4-times longer than the corresponding storage time of ~180 μs without the CPMG sequences. This work is a key step towards the storage of single-photon polarization qubit protected by the CPMG sequences.
Imprinting and Recalling Cortical Ensembles

PubMed Central

Carrillo-Reid, Luis; Yang, Weijian; Bando, Yuki; Peterka, Darcy S.; Yuste, Rafael

2017-01-01

Neuronal ensembles are coactive groups of neurons that may represent emergent building blocks of neural circuits. They could be formed by Hebbian plasticity, whereby synapses between coactive neurons are strengthened. Here we report that repetitive activation with two-photon optogenetics of neuronal populations in visual cortex of awake mice generates artificially induced ensembles which recur spontaneously after being imprinted and do not disrupt preexistent ones. Moreover, imprinted ensembles can be recalled by single cell stimulation and remain coactive on consecutive days. Our results demonstrate the persistent reconfiguration of cortical circuits by two-photon optogenetics into neuronal ensembles that can perform pattern completion. PMID:27516599
Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open ↔ Closed Transitions

PubMed Central

Beckstein, Oliver; Denning, Elizabeth J.; Perilla, Juan R.; Woolf, Thomas B.

2009-01-01

Adenylate kinase (AdK), a phosphotransferase enzyme, plays an important role in cellular energy homeostasis. It undergoes a large conformational change between an open and a closed state, even in the absence of substrate. We investigate the apo-AdK transition at the atomic level both with free energy calculations and our new dynamic importance sampling (DIMS) molecular dynamics (MD) method. DIMS is shown to sample biologically relevant conformations as verified by comparing an ensemble of hundreds of DIMS transitions to AdK crystal structure intermediates. The simulations reveal in atomic detail how hinge regions partially and intermittently unfold during the transition. Conserved salt bridges are seen to have important structural and dynamic roles; in particular four ionic bonds are identified that open in a sequential, zipper-like fashion and thus dominate the free energy landscape of the transition. Transitions between the closed and open conformations only have to overcome moderate free energy barriers. Unexpectedly, the closed and open state encompass broad free energy basins that contain conformations differing in domain hinge motions by up to 40°. The significance of these extended states is discussed in relation to recent experimental FRET measurements. Taken together, these results demonstrate how a small number of cooperative key interactions can shape the overall dynamics of an enzyme and suggest an “all-or-nothing” mechanism for the opening and closing of AdK. Our efficient DIMS-MD computer simulation approach can provide a detailed picture of a functionally important macromolecular transition and thus help to interpret and suggest experiments to probe the conformational landscape of dynamic proteins such as AdK. PMID:19751742
A New Multivariate Approach in Generating Ensemble Meteorological Forcings for Hydrological Forecasting

NASA Astrophysics Data System (ADS)

Khajehei, Sepideh; Moradkhani, Hamid

2015-04-01

Producing reliable and accurate hydrologic ensemble forecasts are subject to various sources of uncertainty, including meteorological forcing, initial conditions, model structure, and model parameters. Producing reliable and skillful precipitation ensemble forecasts is one approach to reduce the total uncertainty in hydrological applications. Currently, National Weather Prediction (NWP) models are developing ensemble forecasts for various temporal ranges. It is proven that raw products from NWP models are biased in mean and spread. Given the above state, there is a need for methods that are able to generate reliable ensemble forecasts for hydrological applications. One of the common techniques is to apply statistical procedures in order to generate ensemble forecast from NWP-generated single-value forecasts. The procedure is based on the bivariate probability distribution between the observation and single-value precipitation forecast. However, one of the assumptions of the current method is fitting Gaussian distribution to the marginal distributions of observed and modeled climate variable. Here, we have described and evaluated a Bayesian approach based on Copula functions to develop an ensemble precipitation forecast from the conditional distribution of single-value precipitation forecasts. Copula functions are known as the multivariate joint distribution of univariate marginal distributions, which are presented as an alternative procedure in capturing the uncertainties related to meteorological forcing. Copulas are capable of modeling the joint distribution of two variables with any level of correlation and dependency. This study is conducted over a sub-basin in the Columbia River Basin in USA using the monthly precipitation forecasts from Climate Forecast System (CFS) with 0.5x0.5 Deg. spatial resolution to reproduce the observations. The verification is conducted on a different period and the superiority of the procedure is compared with Ensemble Pre-Processor approach currently used by National Weather Service River Forecast Centers in USA.

Ensembl genomes 2016: more genomes, more complexity

USDA-ARS?s Scientific Manuscript database

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent...
Coherent control of strong-field two-pulse ionization of Rydberg atoms.

PubMed

Fedorov, M; Poluektov, N

2000-02-28

Strong-field ionization of Rydberg atoms is investigated in its dependence on phase features of the initial coherent population of Rydberg levels. In the case of a resonance between Rydberg levels and some lower-energy atomic level (V-type transitions), this dependence is shown to be very strong: by a proper choice of the initial population an atom can be made either completely or very little ionized by a strong laser pulse. It is shown that phase features of the initial coherent population of Rydberg levels and the ionization yield can be efficiently controlled in a scheme of ionization by two strong laser pulses with a varying delay time between them.
Towards quantitative classification of folded proteins in terms of elementary functions.

PubMed

Hu, Shuangwei; Krokhotin, Andrei; Niemi, Antti J; Peng, Xubiao

2011-04-01

A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a classification scheme that describes a protein starting from its well-organized secondary structures and often involves direct human involvement, with an atomary-level physics-based approach where a protein is fundamentally nothing more than an ensemble of mutually interacting carbon, hydrogen, oxygen, and nitrogen atoms. In order to bridge these two complementary approaches to proteins, conceptually novel tools need to be introduced. Here we explain how an approach toward geometric characterization of entire folded proteins can be based on a single explicit elementary function that is familiar from nonlinear physical systems where it is known as the kink soliton. Our approach enables the conversion of hierarchical structural information into a quantitative form that allows for a folded protein to be characterized in terms of a small number of global parameters that are in principle computable from atomary-level considerations. As an example we describe in detail how the native fold of the myoglobin 1M6C emerges from a combination of kink solitons with a very high atomary-level accuracy. We also verify that our approach describes longer loops and loops connecting α helices with β strands, with the same overall accuracy. ©2011 American Physical Society
Nanoscale current uniformity and injection efficiency of nanowire light emitting diodes

NASA Astrophysics Data System (ADS)

May, Brelon J.; Selcu, Camelia M.; Sarwar, A. T. M. G.; Myers, Roberto C.

2018-02-01

As an alternative to light emitting diodes (LEDs) based on thin films, nanowire based LEDs are the focus of recent development efforts in solid state lighting as they offer distinct photonic advantages and enable direct integration on a variety of different substrates. However, for practical nanowire LEDs to be realized, uniform electrical injection must be achieved through large numbers of nanowire LEDs. Here, we investigate the effect of the integration of a III-Nitride polarization engineered tunnel junction (TJ) in nanowire LEDs on Si on both the overall injection efficiency and nanoscale current uniformity. By using conductive atomic force microscopy (cAFM) and current-voltage (IV) analysis, we explore the link between the nanoscale nonuniformities and the ensemble devices which consist of many diodes wired in parallel. Nanometer resolved current maps reveal that the integration of a TJ on n-Si increases the amount of current a single nanowire can pass at a given applied bias by up to an order of magnitude, with the top 10% of wires passing more than ×3.5 the current of nanowires without a TJ. This manifests at the macroscopic level as a reduction in threshold voltage by more than 3 V and an increase in differential conductance as a direct consequence of the integration of the TJ. These results show the utility of cAFM to quantitatively probe the electrical inhomogeneities in as-grown nanowire ensembles without introducing uncertainty due to additional device processing steps, opening the door to more rapid development of nanowire ensemble based photonics.
A comparison between EDA-EnVar and ETKF-EnVar data assimilation techniques using radar observations at convective scales through a case study of Hurricane Ike (2008)

NASA Astrophysics Data System (ADS)

Shen, Feifei; Xu, Dongmei; Xue, Ming; Min, Jinzhong

2017-07-01

This study examines the impacts of assimilating radar radial velocity (Vr) data for the simulation of hurricane Ike (2008) with two different ensemble generation techniques in the framework of the hybrid ensemble-variational (EnVar) data assimilation system of Weather Research and Forecasting model. For the generation of ensemble perturbations we apply two techniques, the ensemble transform Kalman filter (ETKF) and the ensemble of data assimilation (EDA). For the ETKF-EnVar, the forecast ensemble perturbations are updated by the ETKF, while for the EDA-EnVar, the hybrid is employed to update each ensemble member with perturbed observations. The ensemble mean is analyzed by the hybrid method with flow-dependent ensemble covariance for both EnVar. The sensitivity of analyses and forecasts to the two applied ensemble generation techniques is investigated in our current study. It is found that the EnVar system is rather stable with different ensemble update techniques in terms of its skill on improving the analyses and forecasts. The EDA-EnVar-based ensemble perturbations are likely to include slightly less organized spatial structures than those in ETKF-EnVar, and the perturbations of the latter are constructed more dynamically. Detailed diagnostics reveal that both of the EnVar schemes not only produce positive temperature increments around the hurricane center but also systematically adjust the hurricane location with the hurricane-specific error covariance. On average, the analysis and forecast from the ETKF-EnVar have slightly smaller errors than that from the EDA-EnVar in terms of track, intensity, and precipitation forecast. Moreover, ETKF-EnVar yields better forecasts when verified against conventional observations.
Pauci ex tanto numero: reduce redundancy in multi-model ensembles

NASA Astrophysics Data System (ADS)

Solazzo, E.; Riccio, A.; Kioutsioukis, I.; Galmarini, S.

2013-08-01

We explicitly address the fundamental issue of member diversity in multi-model ensembles. To date, no attempts in this direction have been documented within the air quality (AQ) community despite the extensive use of ensembles in this field. Common biases and redundancy are the two issues directly deriving from lack of independence, undermining the significance of a multi-model ensemble, and are the subject of this study. Shared, dependant biases among models do not cancel out but will instead determine a biased ensemble. Redundancy derives from having too large a portion of common variance among the members of the ensemble, producing overconfidence in the predictions and underestimation of the uncertainty. The two issues of common biases and redundancy are analysed in detail using the AQMEII ensemble of AQ model results for four air pollutants in two European regions. We show that models share large portions of bias and variance, extending well beyond those induced by common inputs. We make use of several techniques to further show that subsets of models can explain the same amount of variance as the full ensemble with the advantage of being poorly correlated. Selecting the members for generating skilful, non-redundant ensembles from such subsets proved, however, non-trivial. We propose and discuss various methods of member selection and rate the ensemble performance they produce. In most cases, the full ensemble is outscored by the reduced ones. We conclude that, although independence of outputs may not always guarantee enhancement of scores (but this depends upon the skill being investigated), we discourage selecting the members of the ensemble simply on the basis of scores; that is, independence and skills need to be considered disjointly.
Joys of Community Ensemble Playing: The Case of the Happy Roll Elastic Ensemble in Taiwan

ERIC Educational Resources Information Center

Hsieh, Yuan-Mei; Kao, Kai-Chi

2012-01-01

The Happy Roll Elastic Ensemble (HREE) is a community music ensemble supported by Tainan Culture Centre in Taiwan. With enjoyment and friendship as its primary goals, it aims to facilitate the joys of ensemble playing and the spirit of social networking. This article highlights the key aspects of HREE's development in its first two years…
Ensemble of Transition State Structures for the Cis-Trans Isomerization of N-Methylacetamide

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

Mantz, Yves A.; Branduardi, Davide; Bussi, Giovanni

2009-09-17

The cis-trans isomerization of N-methylacetamide (NMA), a model peptidic fragment, is studied theoretically in vacuo and in explicit water solvent at 300 K using the metadynamics technique. The computed cis-trans free energy difference is very similar for NMA(g) and NMA(aq), in agreement with experimental measurements of population ratios and theoretical studies at 0 K. By exploiting the flexibility in the definition of a pair of recently introduced collective variables (Branduardi, D.; Gervasio, F. L.; Parrinello, M. J. Chem. Phys. 2007, 126, 054103), an ensemble of transition state structures is generated at finite temperature for both NMA(g) and NMA(aq), as verifiedmore » by computing committor distribution functions. Ensemble members of NMA(g) are shown to have correlated values of the backbone dihedral angle and a second dihedral angle involving the amide hydrogen atom. The dynamical character of these structures is preserved in the presence of solvent, whose influence on the committor functions can be modeled using effective friction/noise terms.« less
Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange.

PubMed

Kubitzki, Marcus B; de Groot, Bert L

2007-06-15

Today's standard molecular dynamics simulations of moderately sized biomolecular systems at full atomic resolution are typically limited to the nanosecond timescale and therefore suffer from limited conformational sampling. Efficient ensemble-preserving algorithms like replica exchange (REX) may alleviate this problem somewhat but are still computationally prohibitive due to the large number of degrees of freedom involved. Aiming at increased sampling efficiency, we present a novel simulation method combining the ideas of essential dynamics and REX. Unlike standard REX, in each replica only a selection of essential collective modes of a subsystem of interest (essential subspace) is coupled to a higher temperature, with the remainder of the system staying at a reference temperature, T(0). This selective excitation along with the replica framework permits efficient approximate ensemble-preserving conformational sampling and allows much larger temperature differences between replicas, thereby considerably enhancing sampling efficiency. Ensemble properties and sampling performance of the method are discussed using dialanine and guanylin test systems, with multi-microsecond molecular dynamics simulations of these test systems serving as references.
Communication and the emergence of collective behavior in living organisms: a quantum approach.

PubMed

Bischof, Marco; Del Giudice, Emilio

2013-01-01

Intermolecular interactions within living organisms have been found to occur not as individual independent events but as a part of a collective array of interconnected events. The problem of the emergence of this collective dynamics and of the correlated biocommunication therefore arises. In the present paper we review the proposals given within the paradigm of modern molecular biology and those given by some holistic approaches to biology. In recent times, the collective behavior of ensembles of microscopic units (atoms/molecules) has been addressed in the conceptual framework of Quantum Field Theory. The possibility of producing physical states where all the components of the ensemble move in unison has been recognized. In such cases, electromagnetic fields trapped within the ensemble appear. In the present paper we present a scheme based on Quantum Field Theory where molecules are able to move in phase-correlated unison among them and with a self-produced electromagnetic field. Experimental corroboration of this scheme is presented. Some consequences for future biological developments are discussed.
Communication and the Emergence of Collective Behavior in Living Organisms: A Quantum Approach

PubMed Central

Bischof, Marco; Del Giudice, Emilio

2013-01-01

Intermolecular interactions within living organisms have been found to occur not as individual independent events but as a part of a collective array of interconnected events. The problem of the emergence of this collective dynamics and of the correlated biocommunication therefore arises. In the present paper we review the proposals given within the paradigm of modern molecular biology and those given by some holistic approaches to biology. In recent times, the collective behavior of ensembles of microscopic units (atoms/molecules) has been addressed in the conceptual framework of Quantum Field Theory. The possibility of producing physical states where all the components of the ensemble move in unison has been recognized. In such cases, electromagnetic fields trapped within the ensemble appear. In the present paper we present a scheme based on Quantum Field Theory where molecules are able to move in phase-correlated unison among them and with a self-produced electromagnetic field. Experimental corroboration of this scheme is presented. Some consequences for future biological developments are discussed. PMID:24288611
Coulomb-repulsion-assisted double ionization from doubly excited states of argon

NASA Astrophysics Data System (ADS)

Liao, Qing; Winney, Alexander H.; Lee, Suk Kyoung; Lin, Yun Fei; Adhikari, Pradip; Li, Wen

2017-08-01

We report a combined experimental and theoretical study to elucidate nonsequential double-ionization dynamics of argon atoms at laser intensities near and below the recollision-induced ionization threshold. Three-dimensional momentum measurements of two electrons arising from strong-field nonsequential double ionization are achieved with a custom-built electron-electron-ion coincidence apparatus, showing laser intensity-dependent Coulomb repulsion effect between the two outgoing electrons. Furthermore, a previously predicted feature of double ionization from doubly excited states is confirmed in the distributions of sum of two-electron momenta. A classical ensemble simulation suggests that Coulomb-repulsion-assisted double ionization from doubly excited states is at play at low laser intensity. This mechanism can explain the dependence of Coulomb repulsion effect on the laser intensity, as well as the transition from side-by-side to back-to-back dominant emission along the laser polarization direction.
Rydberg interaction induced enhanced excitation in thermal atomic vapor.

PubMed

Kara, Dushmanta; Bhowmick, Arup; Mohapatra, Ashok K

2018-03-27

We present the experimental demonstration of interaction induced enhancement in Rydberg excitation or Rydberg anti-blockade in thermal atomic vapor. We have used optical heterodyne detection technique to measure Rydberg population due to two-photon excitation to the Rydberg state. The anti-blockade peak which doesn't satisfy the two-photon resonant condition is observed along with the usual two-photon resonant peak which can't be explained using the model with non-interacting three-level atomic system. A model involving two interacting atoms is formulated for thermal atomic vapor using the dressed states of three-level atomic system to explain the experimental observations. A non-linear dependence of vapor density is observed for the anti-blockade peak which also increases with increase in principal quantum number of the Rydberg state. A good agreement is found between the experimental observations and the proposed interacting model. Our result implies possible applications towards quantum logic gates using Rydberg anti-blockade in thermal atomic vapor.
Time-dependent interaction between a two-level atom and a su(1,1) Lie algebra quantum system

NASA Astrophysics Data System (ADS)

Abdalla, M. Sebaweh; Khalil, E. M.; Obada, A.-S. F.

2017-06-01

The problem of the interaction between a two-level atom and a two-mode field in the parametric amplifier-type is considered. A similar problem appears in an ion trapped in a two-dimensional trap. The problem is transformed into an interaction governed by su(1,1) Lie algebraic operators with phase and coupling parameter depending on time. Under an integrability condition, that relates phase and coupling, a solution to the wavefunction is obtained using the Schrödinger equation. The effects of the functional dependence of the coupling and the initial state of the two-level atom on atomic inversion, the degree of entanglement, the fidelity and the Glauber second-order correlation function are investigated. It is shown that the acceleration term plays an important role in controlling the function behavior of the considered quantities.
Dynamics of entanglement of a three-level atom in motion interacting with two coupled modes including parametric down conversion

NASA Astrophysics Data System (ADS)

Faghihi, M. J.; Tavassoly, M. K.; Hatami, M.

In this paper, a model by which we study the interaction between a motional three-level atom and two-mode field injected simultaneously in a bichromatic cavity is considered; the three-level atom is assumed to be in a Λ-type configuration. As a result, the atom-field and the field-field interaction (parametric down conversion) will be appeared. It is shown that, by applying a canonical transformation, the introduced model can be reduced to a well-known form of the generalized Jaynes-Cummings model. Under particular initial conditions, which may be prepared for the atom and the field, the time evolution of state vector of the entire system is analytically evaluated. Then, the dynamics of atom by considering ‘atomic population inversion’ and two different measures of entanglement, i.e., ‘von Neumann entropy’ and ‘idempotency defect’ is discussed, in detail. It is deduced from the numerical results that, the duration and the maximum amount of the considered physical quantities can be suitably tuned by selecting the proper field-mode structure parameter p and the detuning parameters.
Relaxation in a two-body Fermi-Pasta-Ulam system in the canonical ensemble

NASA Astrophysics Data System (ADS)

Sen, Surajit; Barrett, Tyler

The study of the dynamics of the Fermi-Pasta-Ulam (FPU) chain remains a challenging problem. Inspired by the recent work of Onorato et al. on thermalization in the FPU system, we report a study of relaxation processes in a two-body FPU system in the canonical ensemble. The studies have been carried out using the Recurrence Relations Method introduced by Zwanzig, Mori, Lee and others. We have obtained exact analytical expressions for the first thirteen levels of the continued fraction representation of the Laplace transformed velocity autocorrelation function of the system. Using simple and reasonable extrapolation schemes and known limits we are able to estimate the relaxation behavior of the oscillators in the two-body FPU system and recover the expected behavior in the harmonic limit. Generalizations of the calculations to larger systems will be discussed.
Calibration and validation of coarse-grained models of atomic systems: application to semiconductor manufacturing

NASA Astrophysics Data System (ADS)

Farrell, Kathryn; Oden, J. Tinsley

2014-07-01

Coarse-grained models of atomic systems, created by aggregating groups of atoms into molecules to reduce the number of degrees of freedom, have been used for decades in important scientific and technological applications. In recent years, interest in developing a more rigorous theory for coarse graining and in assessing the predictivity of coarse-grained models has arisen. In this work, Bayesian methods for the calibration and validation of coarse-grained models of atomistic systems in thermodynamic equilibrium are developed. For specificity, only configurational models of systems in canonical ensembles are considered. Among major challenges in validating coarse-grained models are (1) the development of validation processes that lead to information essential in establishing confidence in the model's ability predict key quantities of interest and (2), above all, the determination of the coarse-grained model itself; that is, the characterization of the molecular architecture, the choice of interaction potentials and thus parameters, which best fit available data. The all-atom model is treated as the "ground truth," and it provides the basis with respect to which properties of the coarse-grained model are compared. This base all-atom model is characterized by an appropriate statistical mechanics framework in this work by canonical ensembles involving only configurational energies. The all-atom model thus supplies data for Bayesian calibration and validation methods for the molecular model. To address the first challenge, we develop priors based on the maximum entropy principle and likelihood functions based on Gaussian approximations of the uncertainties in the parameter-to-observation error. To address challenge (2), we introduce the notion of model plausibilities as a means for model selection. This methodology provides a powerful approach toward constructing coarse-grained models which are most plausible for given all-atom data. We demonstrate the theory and methods through applications to representative atomic structures and we discuss extensions to the validation process for molecular models of polymer structures encountered in certain semiconductor nanomanufacturing processes. The powerful method of model plausibility as a means for selecting interaction potentials for coarse-grained models is discussed in connection with a coarse-grained hexane molecule. Discussions of how all-atom information is used to construct priors are contained in an appendix.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Orfield, Noah J.; McBride, James R.; Wang, Feng

Physical variations in colloidal nanostructures give rise to heterogeneity in expressed optical behavior. This correlation between nanoscale structure and function demands interrogation of both atomic structure and photophysics at the level of single nanostructures to be fully understood. In this paper, by conducting detailed analyses of fine atomic structure, chemical composition, and time-resolved single-photon photoluminescence data for the same individual nanocrystals, we reveal inhomogeneity in the quantum yields of single nonblinking “giant” CdSe/CdS core/shell quantum dots (g-QDs). We find that each g-QD possesses distinctive single exciton and biexciton quantum yields that result mainly from variations in the degree of charging,more » rather than from volume or structure inhomogeneity. We further establish that there is a very limited nonemissive “dark” fraction (<2%) among the studied g-QDs and present direct evidence that the g-QD core must lack inorganic passivation for the g-QD to be “dark”. Finally and therefore, in contrast to conventional QDs, ensemble photoluminescence quantum yield is principally defined by charging processes rather than the existence of dark g-QDs.« less
The Effect of Ensemble Performance Quality on the Evaluation of Conducting Expressivity

ERIC Educational Resources Information Center

Silvey, Brian A.

2011-01-01

This study was designed to examine whether the presence of excellent or poor ensemble performances would influence the ratings assigned by ensemble members to conductors who demonstrated highly expressive conducting. Two conductors were videotaped conducting one of two excerpts from an arrangement of Frank Ticheli's "Loch Lomond." These videos…
Nanosecond to submillisecond dynamics in dye-labeled single-stranded DNA, as revealed by ensemble measurements and photon statistics at single-molecule level.

PubMed

Kaji, Takahiro; Ito, Syoji; Iwai, Shigenori; Miyasaka, Hiroshi

2009-10-22

Single-molecule and ensemble time-resolved fluorescence measurements were applied for the investigation of the conformational dynamics of single-stranded DNA, ssDNA, connected with a fluorescein dye by a C6 linker, where the motions both of DNA and the C6 linker affect the geometry of the system. From the ensemble measurement of the fluorescence quenching via photoinduced electron transfer with a guanine base in the DNA sequence, three main conformations were found in aqueous solution: a conformation unaffected by the guanine base in the excited state lifetime of fluorescein, a conformation in which the fluorescence is dynamically quenched in the excited-state lifetime, and a conformation leading to rapid quenching via nonfluorescent complex. The analysis by using the parameters acquired from the ensemble measurements for interphoton time distribution histograms and FCS autocorrelations by the single-molecule measurement revealed that interconversion in these three conformations took place with two characteristic time constants of several hundreds of nanoseconds and tens of microseconds. The advantage of the combination use of the ensemble measurements with the single-molecule detections for rather complex dynamic motions is discussed by integrating the experimental results with those obtained by molecular dynamics simulation.

Nonlocal continuous models for forced vibration analysis of two- and three-dimensional ensembles of single-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Kiani, Keivan

2014-06-01

Novel nonlocal discrete and continuous models are proposed for dynamic analysis of two- and three-dimensional ensembles of single-walled carbon nanotubes (SWCNTs). The generated extra van der Waals forces between adjacent SWCNTs due to their lateral motions are evaluated via Lennard-Jones potential function. Using a nonlocal Rayleigh beam model, the discrete and continuous models are developed for both two- and three-dimensional ensembles of SWCNTs acted upon by transverse dynamic loads. The capabilities of the proposed continuous models in capturing the vibration behavior of SWCNTs ensembles are then examined through various numerical simulations. A reasonably good agreement between the results of the continuous models and those of the discrete ones is also reported. The effects of the applied load frequency, intertube spaces, and small-scale parameter on the transverse dynamic responses of both two- and three-dimensional ensembles of SWCNTs are explained. The proposed continuous models would be very useful for dynamic analyses of large populated ensembles of SWCNTs whose discrete models suffer from both computational efforts and labor costs.
The dynamics of a polariton dimer in a disordered coupled array of cavities

NASA Astrophysics Data System (ADS)

Aiyejina, Abuenameh; Andrews, Roger

2018-03-01

We investigate the effect of disorder in the laser intensity on the dynamics of dark-state polaritons in an array of 20 cavities, each containing an ensemble of four-level atoms that is described by a Bose-Hubbard Hamiltonian. We examine the evolution of the polariton number in the cavities starting from a state with either one or two polaritons in one of the cavities. For the case of a single polariton without disorder in the laser intensity, we calculate the wavefunction of the polariton and find that it disperses away from the initial cavity with time. The addition of disorder results in minimal suppression of the dispersal of the wavefunction. In the case of two polaritons with an on-site repulsion to hopping strength ratio of 20, we find that the polaritons form a repulsively bound state or dimer. Without disorder the dimer wavefunction disperses similarly to the single polariton wavefunction but over a longer time period. The addition of sufficiently strong disorder results in localization of the polariton dimer. The localization length is found to be described by a power law with exponent - 1.31. We also find that we can localise the dimer at any given time by switching on the disorder.
Evolution of Precipitation Extremes in Three Large Ensembles of Climate Simulations - Impact of Spatial and Temporal Resolutions

NASA Astrophysics Data System (ADS)

Martel, J. L.; Brissette, F.; Mailhot, A.; Wood, R. R.; Ludwig, R.; Frigon, A.; Leduc, M.; Turcotte, R.

2017-12-01

Recent studies indicate that the frequency and intensity of extreme precipitation will increase in future climate due to global warming. In this study, we compare annual maxima precipitation series from three large ensembles of climate simulations at various spatial and temporal resolutions. The first two are at the global scale: the Canadian Earth System Model (CanESM2) 50-member large ensemble (CanESM2-LE) at a 2.8° resolution and the Community Earth System Model (CESM1) 40-member large ensemble (CESM1-LE) at a 1° resolution. The third ensemble is at the regional scale over both Eastern North America and Europe: the Canadian Regional Climate Model (CRCM5) 50-member large ensemble (CRCM5-LE) at a 0.11° resolution, driven at its boundaries by the CanESM-LE. The CRCM5-LE is a new ensemble issued from the ClimEx project (http://www.climex-project.org), a Québec-Bavaria collaboration. Using these three large ensembles, change in extreme precipitations over the historical (1980-2010) and future (2070-2100) periods are investigated. This results in 1 500 (30 years x 50 members for CanESM2-LE and CRCM5-LE) and 1200 (30 years x 40 members for CESM1-LE) simulated years over both the historical and future periods. Using these large datasets, the empirical daily (and sub-daily for CRCM5-LE) extreme precipitation quantiles for large return periods ranging from 2 to 100 years are computed. Results indicate that daily extreme precipitations generally will increase over most land grid points of both domains according to the three large ensembles. Regarding the CRCM5-LE, the increase in sub-daily extreme precipitations will be even more important than the one observed for daily extreme precipitations. Considering that many public infrastructures have lifespans exceeding 75 years, the increase in extremes has important implications on service levels of water infrastructures and public safety.
CREATE-IP and CREATE-V: Data and Services Update

NASA Astrophysics Data System (ADS)

Carriere, L.; Potter, G. L.; Hertz, J.; Peters, J.; Maxwell, T. P.; Strong, S.; Shute, J.; Shen, Y.; Duffy, D.

2017-12-01

The NASA Center for Climate Simulation (NCCS) at the Goddard Space Flight Center and the Earth System Grid Federation (ESGF) are working together to build a uniform environment for the comparative study and use of a group of reanalysis datasets of particular importance to the research community. This effort is called the Collaborative REAnalysis Technical Environment (CREATE) and it contains two components: the CREATE-Intercomparison Project (CREATE-IP) and CREATE-V. This year's efforts included generating and publishing an atmospheric reanalysis ensemble mean and spread and improving the analytics available through CREATE-V. Related activities included adding access to subsets of the reanalysis data through ArcGIS and expanding the visualization tool to GMAO forecast data. This poster will present the access mechanisms to this data and use cases including example Jupyter Notebook code. The reanalysis ensemble was generated using two methods, first using standard Python tools for regridding, extracting levels and creating the ensemble mean and spread on a virtual server in the NCCS environment. The second was using a new analytics software suite, the Earth Data Analytics Services (EDAS), coupled with a high-performance Data Analytics and Storage System (DASS) developed at the NCCS. Results were compared to validate the EDAS methodologies, and the results, including time to process, will be presented. The ensemble includes selected 6 hourly and monthly variables, regridded to 1.25 degrees, with 24 common levels used for the 3D variables. Use cases for the new data and services will be presented, including the use of EDAS for the backend analytics on CREATE-V, the use of the GMAO forecast aerosol and cloud data in CREATE-V, and the ability to connect CREATE-V data to NCCS ArcGIS services.
Experimental realization of entanglement in multiple degrees of freedom between two quantum memories

PubMed Central

Zhang, Wei; Ding, Dong-Sheng; Dong, Ming-Xin; Shi, Shuai; Wang, Kai; Liu, Shi-Long; Li, Yan; Zhou, Zhi-Yuan; Shi, Bao-Sen; Guo, Guang-Can

2016-01-01

Entanglement in multiple degrees of freedom has many benefits over entanglement in a single one. The former enables quantum communication with higher channel capacity and more efficient quantum information processing and is compatible with diverse quantum networks. Establishing multi-degree-of-freedom entangled memories is not only vital for high-capacity quantum communication and computing, but also promising for enhanced violations of nonlocality in quantum systems. However, there have been yet no reports of the experimental realization of multi-degree-of-freedom entangled memories. Here we experimentally established hyper- and hybrid entanglement in multiple degrees of freedom, including path (K-vector) and orbital angular momentum, between two separated atomic ensembles by using quantum storage. The results are promising for achieving quantum communication and computing with many degrees of freedom. PMID:27841274
Delineating Hydrofacies Spatial Distribution by Integrating Ensemble Data Assimilation and Indicator Geostatistics

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

Song, Xuehang; Chen, Xingyuan; Ye, Ming

2015-07-01

This study develops a new framework of facies-based data assimilation for characterizing spatial distribution of hydrofacies and estimating their associated hydraulic properties. This framework couples ensemble data assimilation with transition probability-based geostatistical model via a parameterization based on a level set function. The nature of ensemble data assimilation makes the framework efficient and flexible to be integrated with various types of observation data. The transition probability-based geostatistical model keeps the updated hydrofacies distributions under geological constrains. The framework is illustrated by using a two-dimensional synthetic study that estimates hydrofacies spatial distribution and permeability in each hydrofacies from transient head data.more » Our results show that the proposed framework can characterize hydrofacies distribution and associated permeability with adequate accuracy even with limited direct measurements of hydrofacies. Our study provides a promising starting point for hydrofacies delineation in complex real problems.« less
Generation of Light with Multimode Time-Delayed Entanglement Using Storage in a Solid-State Spin-Wave Quantum Memory.

PubMed

Ferguson, Kate R; Beavan, Sarah E; Longdell, Jevon J; Sellars, Matthew J

2016-07-08

Here, we demonstrate generating and storing entanglement in a solid-state spin-wave quantum memory with on-demand readout using the process of rephased amplified spontaneous emission (RASE). Amplified spontaneous emission (ASE), resulting from an inverted ensemble of Pr^{3+} ions doped into a Y_{2}SiO_{5} crystal, generates entanglement between collective states of the praseodymium ensemble and the output light. The ensemble is then rephased using a four-level photon echo technique. Entanglement between the ASE and its echo is confirmed and the inseparability violation preserved when the RASE is stored as a spin wave for up to 5 μs. RASE is shown to be temporally multimode with almost perfect distinguishability between two temporal modes demonstrated. These results pave the way for the use of multimode solid-state quantum memories in scalable quantum networks.
The effect of nonadiabaticity on the efficiency of quantum memory based on an optical cavity

NASA Astrophysics Data System (ADS)

Veselkova, N. G.; Sokolov, I. V.

2017-07-01

Quantum efficiency is an important characteristic of quantum memory devices that are aimed at recording the quantum state of light signals and its storing and reading. In the case of memory based on an ensemble of cold atoms placed in an optical cavity, the efficiency is restricted, in particular, by relaxation processes in the system of active atomic levels. We show how the effect of the relaxation on the quantum efficiency can be determined in a regime of the memory usage in which the evolution of signals in time is not arbitrarily slow on the scale of the field lifetime in the cavity and when the frequently used approximation of the adiabatic elimination of the quantized cavity mode field cannot be applied. Taking into account the effect of the nonadiabaticity on the memory quality is of interest in view of the fact that, in order to increase the field-medium coupling parameter, a higher cavity quality factor is required, whereas storing and processing of sequences of many signals in the memory implies that their duration is reduced. We consider the applicability of the well-known efficiency estimates via the system cooperativity parameter and estimate a more general form. In connection with the theoretical description of the memory of the given type, we also discuss qualitative differences in the behavior of a random source introduced into the Heisenberg-Langevin equations for atomic variables in the cases of a large and a small number of atoms.
Metal Oxide Gas Sensor Drift Compensation Using a Two-Dimensional Classifier Ensemble

PubMed Central

Liu, Hang; Chu, Renzhi; Tang, Zhenan

2015-01-01

Sensor drift is the most challenging problem in gas sensing at present. We propose a novel two-dimensional classifier ensemble strategy to solve the gas discrimination problem, regardless of the gas concentration, with high accuracy over extended periods of time. This strategy is appropriate for multi-class classifiers that consist of combinations of pairwise classifiers, such as support vector machines. We compare the performance of the strategy with those of competing methods in an experiment based on a public dataset that was compiled over a period of three years. The experimental results demonstrate that the two-dimensional ensemble outperforms the other methods considered. Furthermore, we propose a pre-aging process inspired by that applied to the sensors to improve the stability of the classifier ensemble. The experimental results demonstrate that the weight of each multi-class classifier model in the ensemble remains fairly static before and after the addition of new classifier models to the ensemble, when a pre-aging procedure is applied. PMID:25942640
A simple molecular mechanics integrator in mixed rigid body and dihedral angle space

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

Vitalis, Andreas, E-mail: a.vitalis@bioc.uzh.ch; Pappu, Rohit V.

2014-07-21

We propose a numerical scheme to integrate equations of motion in a mixed space of rigid-body and dihedral angle coordinates. The focus of the presentation is biomolecular systems and the framework is applicable to polymers with tree-like topology. By approximating the effective mass matrix as diagonal and lumping all bias torques into the time dependencies of the diagonal elements, we take advantage of the formal decoupling of individual equations of motion. We impose energy conservation independently for every degree of freedom and this is used to derive a numerical integration scheme. The cost of all auxiliary operations is linear inmore » the number of atoms. By coupling the scheme to one of two popular thermostats, we extend the method to sample constant temperature ensembles. We demonstrate that the integrator of choice yields satisfactory stability and is free of mass-metric tensor artifacts, which is expected by construction of the algorithm. Two fundamentally different systems, viz., liquid water and an α-helical peptide in a continuum solvent are used to establish the applicability of our method to a wide range of problems. The resultant constant temperature ensembles are shown to be thermodynamically accurate. The latter relies on detailed, quantitative comparisons to data from reference sampling schemes operating on exactly the same sets of degrees of freedom.« less
THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures.

PubMed

Theobald, Douglas L; Wuttke, Deborah S

2006-09-01

THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. ANSI C source code and selected binaries for various computing platforms are available under the GNU open source license from http://monkshood.colorado.edu/theseus/ or http://www.theseus3d.org.
A shared neural ensemble links distinct contextual memories encoded close in time

NASA Astrophysics Data System (ADS)

Cai, Denise J.; Aharoni, Daniel; Shuman, Tristan; Shobe, Justin; Biane, Jeremy; Song, Weilin; Wei, Brandon; Veshkini, Michael; La-Vu, Mimi; Lou, Jerry; Flores, Sergio E.; Kim, Isaac; Sano, Yoshitake; Zhou, Miou; Baumgaertel, Karsten; Lavi, Ayal; Kamata, Masakazu; Tuszynski, Mark; Mayford, Mark; Golshani, Peyman; Silva, Alcino J.

2016-06-01

Recent studies suggest that a shared neural ensemble may link distinct memories encoded close in time. According to the memory allocation hypothesis, learning triggers a temporary increase in neuronal excitability that biases the representation of a subsequent memory to the neuronal ensemble encoding the first memory, such that recall of one memory increases the likelihood of recalling the other memory. Here we show in mice that the overlap between the hippocampal CA1 ensembles activated by two distinct contexts acquired within a day is higher than when they are separated by a week. Several findings indicate that this overlap of neuronal ensembles links two contextual memories. First, fear paired with one context is transferred to a neutral context when the two contexts are acquired within a day but not across a week. Second, the first memory strengthens the second memory within a day but not across a week. Older mice, known to have lower CA1 excitability, do not show the overlap between ensembles, the transfer of fear between contexts, or the strengthening of the second memory. Finally, in aged mice, increasing cellular excitability and activating a common ensemble of CA1 neurons during two distinct context exposures rescued the deficit in linking memories. Taken together, these findings demonstrate that contextual memories encoded close in time are linked by directing storage into overlapping ensembles. Alteration of these processes by ageing could affect the temporal structure of memories, thus impairing efficient recall of related information.
Entanglement Criteria of Two Two-Level Atoms Interacting with Two Coupled Modes

NASA Astrophysics Data System (ADS)

Baghshahi, Hamid Reza; Tavassoly, Mohammad Kazem; Faghihi, Mohammad Javad

2015-08-01

In this paper, we study the interaction between two two-level atoms and two coupled modes of a quantized radiation field in the form of parametric frequency converter injecting within an optical cavity enclosed by a medium with Kerr nonlinearity. It is demonstrated that, by applying the Bogoliubov-Valatin canonical transformation, the introduced model is reduced to a well-known form of the generalized Jaynes-Cummings model. Then, under particular initial conditions for the atoms (in a coherent superposition of its ground and upper states) and the fields (in a standard coherent state) which may be prepared, the time evolution of state vector of the entire system is analytically evaluated. In order to understand the degree of entanglement between subsystems (atom-field and atom-atom), the dynamics of entanglement through different measures, namely, von Neumann reduced entropy, concurrence and negativity is evaluated. In each case, the effects of Kerr nonlinearity and detuning parameter on the above measures are numerically analyzed, in detail. It is illustrated that the amount of entanglement can be tuned by choosing the evolved parameters, appropriately.
Interference of Single Photons Emitted by Entangled Atoms in Free Space

NASA Astrophysics Data System (ADS)

Araneda, G.; Higginbottom, D. B.; Slodička, L.; Colombe, Y.; Blatt, R.

2018-05-01

The generation and manipulation of entanglement between isolated particles has precipitated rapid progress in quantum information processing. Entanglement is also known to play an essential role in the optical properties of atomic ensembles, but fundamental effects in the controlled emission and absorption from small, well-defined numbers of entangled emitters in free space have remained unobserved. Here we present the control of the emission rate of a single photon from a pair of distant, entangled atoms into a free-space optical mode. Changing the length of the optical path connecting the atoms modulates the single-photon emission rate in the selected mode with a visibility V =0.27 ±0.03 determined by the degree of entanglement shared between the atoms, corresponding directly to the concurrence Cρ=0.31 ±0.10 of the prepared state. This scheme, together with population measurements, provides a fully optical determination of the amount of entanglement. Furthermore, large sensitivity of the interference phase evolution points to applications of the presented scheme in high-precision gradient sensing.
Polarized electron beams elastically scattered by atoms as a tool for testing fundamental predictions of quantum mechanics.

PubMed

Dapor, Maurizio

2018-03-29

Quantum information theory deals with quantum noise in order to protect physical quantum bits (qubits) from its effects. A single electron is an emblematic example of a qubit, and today it is possible to experimentally produce polarized ensembles of electrons. In this paper, the theory of the polarization of electron beams elastically scattered by atoms is briefly summarized. Then the POLARe program suite, a set of computer programs aimed at the calculation of the spin-polarization parameters of electron beams elastically interacting with atomic targets, is described. Selected results of the program concerning Ar, Kr, and Xe atoms are presented together with the comparison with experimental data about the Sherman function for low kinetic energy of the incident electrons (1.5eV-350eV). It is demonstrated that the quantum-relativistic theory of the polarization of electron beams elastically scattered by atoms is in good agreement with experimental data down to energies smaller than a few eV.
Analysis of spatial correlations in a model two-dimensional liquid through eigenvalues and eigenvectors of atomic-level stress matrices.

PubMed

Levashov, V A; Stepanov, M G

2016-01-01

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

NASA Astrophysics Data System (ADS)

Zhao, Peng; Tan, Xinsheng; Yu, Haifeng; Zhu, Shi-Liang; Yu, Yang

2017-10-01

We present a model to describe a generic circuit QED system which consists of multiple artificial three-level atoms, namely, qutrits, strongly coupled to a cavity mode. When the state transition of the atoms disobeys the selection rules the process that does not conserve the number of excitations can happen determinatively. Therefore, we can realize coherent exchange interaction among three or more atoms mediated by the exchange of virtual photons. In addition, we generalize the one-cavity-mode mediated interactions to the multicavity situation, providing a method to entangle atoms located in different cavities. Using experimentally feasible parameters, we investigate the dynamics of the model including three cyclic-transition three-level atoms, for which the two lowest energy levels can be treated as qubits. Hence, we have found that two qubits can jointly exchange excitation with one qubit in a coherent and reversible way. In the whole process, the population in the third level of atoms is negligible and the cavity photon number is far smaller than 1. Our model provides a feasible scheme to couple multiple distant atoms together, which may find applications in quantum information processing.
A regional air quality forecasting system over Europe: the MACC-II daily ensemble production

NASA Astrophysics Data System (ADS)

Marécal, V.; Peuch, V.-H.; Andersson, C.; Andersson, S.; Arteta, J.; Beekmann, M.; Benedictow, A.; Bergström, R.; Bessagnet, B.; Cansado, A.; Chéroux, F.; Colette, A.; Coman, A.; Curier, R. L.; Denier van der Gon, H. A. C.; Drouin, A.; Elbern, H.; Emili, E.; Engelen, R. J.; Eskes, H. J.; Foret, G.; Friese, E.; Gauss, M.; Giannaros, C.; Guth, J.; Joly, M.; Jaumouillé, E.; Josse, B.; Kadygrov, N.; Kaiser, J. W.; Krajsek, K.; Kuenen, J.; Kumar, U.; Liora, N.; Lopez, E.; Malherbe, L.; Martinez, I.; Melas, D.; Meleux, F.; Menut, L.; Moinat, P.; Morales, T.; Parmentier, J.; Piacentini, A.; Plu, M.; Poupkou, A.; Queguiner, S.; Robertson, L.; Rouïl, L.; Schaap, M.; Segers, A.; Sofiev, M.; Thomas, M.; Timmermans, R.; Valdebenito, Á.; van Velthoven, P.; van Versendaal, R.; Vira, J.; Ung, A.

2015-03-01

This paper describes the pre-operational analysis and forecasting system developed during MACC (Monitoring Atmospheric Composition and Climate) and continued in MACC-II (Monitoring Atmospheric Composition and Climate: Interim Implementation) European projects to provide air quality services for the European continent. The paper gives an overall picture of its status at the end of MACC-II (summer 2014). This system is based on seven state-of-the art models developed and run in Europe (CHIMERE, EMEP, EURAD-IM, LOTOS-EUROS, MATCH, MOCAGE and SILAM). These models are used to calculate multi-model ensemble products. The MACC-II system provides daily 96 h forecasts with hourly outputs of 10 chemical species/aerosols (O3, NO2, SO2, CO, PM10, PM2.5, NO, NH3, total NMVOCs and PAN + PAN precursors) over 8 vertical levels from the surface to 5 km height. The hourly analysis at the surface is done a posteriori for the past day using a selection of representative air quality data from European monitoring stations. The performances of the system are assessed daily, weekly and 3 monthly (seasonally) through statistical indicators calculated using the available representative air quality data from European monitoring stations. Results for a case study show the ability of the median ensemble to forecast regional ozone pollution events. The time period of this case study is also used to illustrate that the median ensemble generally outperforms each of the individual models and that it is still robust even if two of the seven models are missing. The seasonal performances of the individual models and of the multi-model ensemble have been monitored since September 2009 for ozone, NO2 and PM10 and show an overall improvement over time. The change of the skills of the ensemble over the past two summers for ozone and the past two winters for PM10 are discussed in the paper. While the evolution of the ozone scores is not significant, there are improvements of PM10 over the past two winters that can be at least partly attributed to new developments on aerosols in the seven individual models. Nevertheless, the year to year changes in the models and ensemble skills are also linked to the variability of the meteorological conditions and of the set of observations used to calculate the statistical indicators. In parallel, a scientific analysis of the results of the seven models and of the ensemble is also done over the Mediterranean area because of the specificity of its meteorology and emissions. The system is robust in terms of the production availability. Major efforts have been done in MACC-II towards the operationalisation of all its components. Foreseen developments and research for improving its performances are discussed in the conclusion.
Programming in the Zone: Repertoire Selection for the Large Ensemble

ERIC Educational Resources Information Center

Hopkins, Michael

2013-01-01

One of the great challenges ensemble directors face is selecting high-quality repertoire that matches the musical and technical levels of their ensembles. Thoughtful repertoire selection can lead to increased student motivation as well as greater enthusiasm for the music program from parents, administrators, teachers, and community members. Common…
Dissipative production of a maximally entangled steady state of two quantum bits.

PubMed

Lin, Y; Gaebler, J P; Reiter, F; Tan, T R; Bowler, R; Sørensen, A S; Leibfried, D; Wineland, D J

2013-12-19

Entangled states are a key resource in fundamental quantum physics, quantum cryptography and quantum computation. Introduction of controlled unitary processes--quantum gates--to a quantum system has so far been the most widely used method to create entanglement deterministically. These processes require high-fidelity state preparation and minimization of the decoherence that inevitably arises from coupling between the system and the environment, and imperfect control of the system parameters. Here we combine unitary processes with engineered dissipation to deterministically produce and stabilize an approximate Bell state of two trapped-ion quantum bits (qubits), independent of their initial states. Compared with previous studies that involved dissipative entanglement of atomic ensembles or the application of sequences of multiple time-dependent gates to trapped ions, we implement our combined process using trapped-ion qubits in a continuous time-independent fashion (analogous to optical pumping of atomic states). By continuously driving the system towards the steady state, entanglement is stabilized even in the presence of experimental noise and decoherence. Our demonstration of an entangled steady state of two qubits represents a step towards dissipative state engineering, dissipative quantum computation and dissipative phase transitions. Following this approach, engineered coupling to the environment may be applied to a broad range of experimental systems to achieve desired quantum dynamics or steady states. Indeed, concurrently with this work, an entangled steady state of two superconducting qubits was demonstrated using dissipation.

Vfold: a web server for RNA structure and folding thermodynamics prediction.

PubMed

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

2014-01-01

The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies. The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization. The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".
Representational analysis of extended disorder in atomistic ensembles derived from total scattering data

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

Neilson, James R.; McQueen, Tyrel M.

With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atomsmore » in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. Lastly, this method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.« less
Representational analysis of extended disorder in atomistic ensembles derived from total scattering data

DOE PAGES

Neilson, James R.; McQueen, Tyrel M.

2015-09-20

With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atomsmore » in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. Lastly, this method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.« less
Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

DOE PAGES

Shi, Jade; Nobrega, R. Paul; Schwantes, Christian; ...

2017-03-08

The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. We report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structuremore » of the excited state ensemble. The resulting prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. We then predict incisive single molecule FRET experiments, using these results, as a means of model validation. Our study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.« less
Boiling point determination using adiabatic Gibbs ensemble Monte Carlo simulations: application to metals described by embedded-atom potentials.

PubMed

Gelb, Lev D; Chakraborty, Somendra Nath

2011-12-14

The normal boiling points are obtained for a series of metals as described by the "quantum-corrected Sutton Chen" (qSC) potentials [S.-N. Luo, T. J. Ahrens, T. Çağın, A. Strachan, W. A. Goddard III, and D. C. Swift, Phys. Rev. B 68, 134206 (2003)]. Instead of conventional Monte Carlo simulations in an isothermal or expanded ensemble, simulations were done in the constant-NPH adabatic variant of the Gibbs ensemble technique as proposed by Kristóf and Liszi [Chem. Phys. Lett. 261, 620 (1996)]. This simulation technique is shown to be a precise tool for direct calculation of boiling temperatures in high-boiling fluids, with results that are almost completely insensitive to system size or other arbitrary parameters as long as the potential truncation is handled correctly. Results obtained were validated using conventional NVT-Gibbs ensemble Monte Carlo simulations. The qSC predictions for boiling temperatures are found to be reasonably accurate, but substantially underestimate the enthalpies of vaporization in all cases. This appears to be largely due to the systematic overestimation of dimer binding energies by this family of potentials, which leads to an unsatisfactory description of the vapor phase. © 2011 American Institute of Physics
Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

NASA Astrophysics Data System (ADS)

Shi, Jade; Nobrega, R. Paul; Schwantes, Christian; Kathuria, Sagar V.; Bilsel, Osman; Matthews, C. Robert; Lane, T. J.; Pande, Vijay S.

2017-03-01

The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. Here, we report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. This prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. Using these results, we then predict incisive single molecule FRET experiments as a means of model validation. This study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.
Population interactions between parietal and primary motor cortices during reach

PubMed Central

Rao, Naveen G.; Bondy, Adrian; Truccolo, Wilson; Donoghue, John P.

2014-01-01

Neural interactions between parietal area 2/5 and primary motor cortex (M1) were examined to determine the timing and behavioral correlates of cortico-cortical interactions. Neural activity in areas 2/5 and M1 was simultaneously recorded with 96-channel microelectrode arrays in three rhesus monkeys performing a center-out reach task. We introduce a new method to reveal parietal-motor interactions at a population level using partial spike-field coherence (PSFC) between ensembles of neurons in one area and a local field potential (LFP) in another. PSFC reflects the extent of phase locking between spike times and LFP, after removing the coherence between LFPs in the two areas. Spectral analysis of M1 LFP revealed three bands: low, medium, and high, differing in power between movement preparation and performance. We focus on PSFC in the 1–10 Hz band, in which coherence was strongest. PSFC was also present in the 10–40 Hz band during movement preparation in many channels but generally nonsignificant in the 60–200 Hz band. Ensemble PSFC revealed stronger interactions than single cell-LFP pairings. PSFC of area 2/5 ensembles with M1 LFP typically rose around movement onset and peaked ∼500 ms afterward. PSFC was typically stronger for subsets of area 2/5 neurons and M1 LFPs with similar directional bias than for those with opposite bias, indicating that area 2/5 contributes movement direction information. Together with linear prediction of M1 LFP by area 2/5 spiking, the ensemble-LFP pairing approach reveals interactions missed by single neuron-LFP pairing, demonstrating that cortico-cortical communication can be more readily observed at the ensemble level. PMID:25210154
Protecting quantum coherence of two-level atoms from vacuum fluctuations of electromagnetic field

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

Liu, Xiaobao; Tian, Zehua; Wang, Jieci

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

NASA Astrophysics Data System (ADS)

Mo, Yuxiang; Lei, Jiangtao; Sun, Yunxiang; Zhang, Qingwen; Wei, Guanghong

2016-09-01

Small oligomers formed early along human islet amyloid polypeptide (hIAPP) aggregation is responsible for the cell death in Type II diabetes. The epigallocatechin gallate (EGCG), a green tea extract, was found to inhibit hIAPP fibrillation. However, the inhibition mechanism and the conformational distribution of the smallest hIAPP oligomer - dimer are mostly unknown. Herein, we performed extensive replica exchange molecular dynamic simulations on hIAPP dimer with and without EGCG molecules. Extended hIAPP dimer conformations, with a collision cross section value similar to that observed by ion mobility-mass spectrometry, were observed in our simulations. Notably, these dimers adopt a three-stranded antiparallel β-sheet and contain the previously reported β-hairpin amyloidogenic precursor. We find that EGCG binding strongly blocks both the inter-peptide hydrophobic and aromatic-stacking interactions responsible for inter-peptide β-sheet formation and intra-peptide interaction crucial for β-hairpin formation, thus abolishes the three-stranded β-sheet structures and leads to the formation of coil-rich conformations. Hydrophobic, aromatic-stacking, cation-π and hydrogen-bonding interactions jointly contribute to the EGCG-induced conformational shift. This study provides, on atomic level, the conformational ensemble of hIAPP dimer and the molecular mechanism by which EGCG inhibits hIAPP aggregation.
Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage mini protein

PubMed Central

Day, Ryan; Paschek, Dietmar; Garcia, Angel E.

2012-01-01

We study the unbiased folding/unfolding thermodynamics of the Trp-cage miniprotein using detailed molecular dynamics simulations of an all-atom model of the protein in explicit solvent, using the Amberff99SB force field. Replica-exchange molecular dynamics (REMD) simulations are used to sample the protein ensembles over a broad range of temperatures covering the folded and unfolded states, and at two densities. The obtained ensembles are shown to reach equilibrium in the 1 μs per replica timescale. The total simulation time employed in the calculations exceeds 100 μs. Ensemble averages of the fraction folded, pressure, and energy differences between the folded and unfolded states as a function of temperature are used to model the free energy of the folding transition, ΔG(P,T), over the whole region of temperature and pressures sampled in the simulations. The ΔG(P,T) diagram describes an ellipse over the range of temperatures and pressures sampled, predicting that the system can undergo pressure induced unfolding and cold denaturation at low temperatures and high pressures, and unfolding at low pressures and high temperatures. The calculated free energy function exhibits remarkably good agreement with the experimental folding transition temperature (Tf = 321 K), free energy and specific heat changes. However, changes in enthalpy and entropy are significantly different than the experimental values. We speculate that these differences may be due to the simplicity of the semi-empirical force field used in the simulations and that more elaborate force fields may be required to describe appropriately the thermodynamics of proteins. PMID:20408169
Modification of optical properties by adiabatic shifting of resonances in a four-level atom

NASA Astrophysics Data System (ADS)

Dutta, Bibhas Kumar; Panchadhyayee, Pradipta

2018-04-01

We describe the linear and nonlinear optical properties of a four-level atomic system, after reducing it to an effective two-level atomic model under the condition of adiabatic shifting of resonances driven by two coherent off-resonant fields. The reduced form of the Hamiltonian corresponding to the two-level system is obtained by employing an adiabatic elimination procedure in the rate equations of the probability amplitudes for the proposed four-level model. For a weak probe field operating in the system, the nonlinear dependence of complex susceptibility on the Rabi frequencies and the detuning parameters of the off-resonant driving fields makes it possible to exhibit coherent control of single-photon and two-photon absorption and transparency, the evolution of enhanced Self-Kerr nonlinearity and noticeable dispersive switching. We have shown how the quantum interference results in the generic four-level model at the adiabatic limit. The present scheme describes the appearance of single-photon transparency without invoking any exact two-photon resonance.
Steric sea level variability (1993-2010) in an ensemble of ocean reanalyses and objective analyses

NASA Astrophysics Data System (ADS)

Storto, Andrea; Masina, Simona; Balmaseda, Magdalena; Guinehut, Stéphanie; Xue, Yan; Szekely, Tanguy; Fukumori, Ichiro; Forget, Gael; Chang, You-Soon; Good, Simon A.; Köhl, Armin; Vernieres, Guillaume; Ferry, Nicolas; Peterson, K. Andrew; Behringer, David; Ishii, Masayoshi; Masuda, Shuhei; Fujii, Yosuke; Toyoda, Takahiro; Yin, Yonghong; Valdivieso, Maria; Barnier, Bernard; Boyer, Tim; Lee, Tony; Gourrion, Jérome; Wang, Ou; Heimback, Patrick; Rosati, Anthony; Kovach, Robin; Hernandez, Fabrice; Martin, Matthew J.; Kamachi, Masafumi; Kuragano, Tsurane; Mogensen, Kristian; Alves, Oscar; Haines, Keith; Wang, Xiaochun

2017-08-01

Quantifying the effect of the seawater density changes on sea level variability is of crucial importance for climate change studies, as the sea level cumulative rise can be regarded as both an important climate change indicator and a possible danger for human activities in coastal areas. In this work, as part of the Ocean Reanalysis Intercomparison Project, the global and regional steric sea level changes are estimated and compared from an ensemble of 16 ocean reanalyses and 4 objective analyses. These estimates are initially compared with a satellite-derived (altimetry minus gravimetry) dataset for a short period (2003-2010). The ensemble mean exhibits a significant high correlation at both global and regional scale, and the ensemble of ocean reanalyses outperforms that of objective analyses, in particular in the Southern Ocean. The reanalysis ensemble mean thus represents a valuable tool for further analyses, although large uncertainties remain for the inter-annual trends. Within the extended intercomparison period that spans the altimetry era (1993-2010), we find that the ensemble of reanalyses and objective analyses are in good agreement, and both detect a trend of the global steric sea level of 1.0 and 1.1 ± 0.05 mm/year, respectively. However, the spread among the products of the halosteric component trend exceeds the mean trend itself, questioning the reliability of its estimate. This is related to the scarcity of salinity observations before the Argo era. Furthermore, the impact of deep ocean layers is non-negligible on the steric sea level variability (22 and 12 % for the layers below 700 and 1500 m of depth, respectively), although the small deep ocean trends are not significant with respect to the products spread.
Experimental generation of tripartite polarization entangled states of bright optical beams

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

Wu, Liang; Liu, Yanhong; Deng, Ruijie

The multipartite polarization entangled states of bright optical beams directly associating with the spin states of atomic ensembles are one of the essential resources in the future quantum information networks, which can be conveniently utilized to transfer and convert quantum states across a network composed of many atomic nodes. In this letter, we present the experimental demonstration of tripartite polarization entanglement described by Stokes operators of optical field. The tripartite entangled states of light at the frequency resonant with D1 line of Rubidium atoms are transformed into the continuous variable polarization entanglement among three bright optical beams via an opticalmore » beam splitter network. The obtained entanglement is confirmed by the extended criterion for polarization entanglement of multipartite quantized optical modes.« less
The Impact of Density and Ratio on Object-Ensemble Representation in Human Anterior-Medial Ventral Visual Cortex.

PubMed

Cant, Jonathan S; Xu, Yaoda

2015-11-01

Behavioral research has demonstrated that observers can extract summary statistics from ensembles of multiple objects. We recently showed that a region of anterior-medial ventral visual cortex, overlapping largely with the scene-sensitive parahippocampal place area (PPA), participates in object-ensemble representation. Here we investigated the encoding of ensemble density in this brain region using fMRI-adaptation. In Experiment 1, we varied density by changing the spacing between objects and found no sensitivity in PPA to such density changes. Thus, density may not be encoded in PPA, possibly because object spacing is not perceived as an intrinsic ensemble property. In Experiment 2, we varied relative density by changing the ratio of 2 types of objects comprising an ensemble, and observed significant sensitivity in PPA to such ratio change. Although colorful ensembles were shown in Experiment 2, Experiment 3 demonstrated that sensitivity to object ratio change was not driven mainly by a change in the ratio of colors. Thus, while anterior-medial ventral visual cortex is insensitive to density (object spacing) changes, it does code relative density (object ratio) within an ensemble. Object-ensemble processing in this region may thus depend on high-level visual information, such as object ratio, rather than low-level information, such as spacing/spatial frequency. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Multi-mode of Four and Six Wave Parametric Amplified Process

NASA Astrophysics Data System (ADS)

Zhu, Dayu; Yang, Yiheng; Zhang, Da; Liu, Ruizhou; Ma, Danmeng; Li, Changbiao; Zhang, Yanpeng

2017-03-01

Multiple quantum modes in correlated fields are essential for future quantum information processing and quantum computing. Here we report the generation of multi-mode phenomenon through parametric amplified four- and six-wave mixing processes in a rubidium atomic ensemble. The multi-mode properties in both frequency and spatial domains are studied. On one hand, the multi-mode behavior is dominantly controlled by the intensity of external dressing effect, or nonlinear phase shift through internal dressing effect, in frequency domain; on the other hand, the multi-mode behavior is visually demonstrated from the images of the biphoton fields directly, in spatial domain. Besides, the correlation of the two output fields is also demonstrated in both domains. Our approach supports efficient applications for scalable quantum correlated imaging.
Multi-mode of Four and Six Wave Parametric Amplified Process.

PubMed

Zhu, Dayu; Yang, Yiheng; Zhang, Da; Liu, Ruizhou; Ma, Danmeng; Li, Changbiao; Zhang, Yanpeng

2017-03-03

Multiple quantum modes in correlated fields are essential for future quantum information processing and quantum computing. Here we report the generation of multi-mode phenomenon through parametric amplified four- and six-wave mixing processes in a rubidium atomic ensemble. The multi-mode properties in both frequency and spatial domains are studied. On one hand, the multi-mode behavior is dominantly controlled by the intensity of external dressing effect, or nonlinear phase shift through internal dressing effect, in frequency domain; on the other hand, the multi-mode behavior is visually demonstrated from the images of the biphoton fields directly, in spatial domain. Besides, the correlation of the two output fields is also demonstrated in both domains. Our approach supports efficient applications for scalable quantum correlated imaging.
Photon statistics and polarization correlations at telecommunications wavelengths from a warm atomic ensemble.

PubMed

Willis, R T; Becerra, F E; Orozco, L A; Rolston, S L

2011-07-18

We present measurements of the polarization correlation and photon statistics of photon pairs that emerge from a laser-pumped warm rubidium vapor cell. The photon pairs occur at 780 nm and 1367 nm and are polarization entangled. We measure the autocorrelation of each of the generated fields as well as the cross-correlation function, and observe a strong violation of the two-beam Cauchy-Schwartz inequality. We evaluate the performance of the system as source of heralded single photons at a telecommunication wavelength. We measure the heralded autocorrelation and see that coincidences are suppressed by a factor of ≈ 20 from a Poissonian source at a generation rate of 1500 s(-1), a heralding efficiency of 10%, and a narrow spectral width.
Grain-Boundary Resistance in Copper Interconnects: From an Atomistic Model to a Neural Network

NASA Astrophysics Data System (ADS)

Valencia, Daniel; Wilson, Evan; Jiang, Zhengping; Valencia-Zapata, Gustavo A.; Wang, Kuang-Chung; Klimeck, Gerhard; Povolotskyi, Michael

2018-04-01

Orientation effects on the specific resistance of copper grain boundaries are studied systematically with two different atomistic tight-binding methods. A methodology is developed to model the specific resistance of grain boundaries in the ballistic limit using the embedded atom model, tight- binding methods, and nonequilibrium Green's functions. The methodology is validated against first-principles calculations for thin films with a single coincident grain boundary, with 6.4% deviation in the specific resistance. A statistical ensemble of 600 large, random structures with grains is studied. For structures with three grains, it is found that the distribution of specific resistances is close to normal. Finally, a compact model for grain-boundary-specific resistance is constructed based on a neural network.
Enhancing light-atom interactions via atomic bunching

NASA Astrophysics Data System (ADS)

Schmittberger, Bonnie L.; Gauthier, Daniel J.

2014-07-01

There is a broad interest in enhancing the strength of light-atom interactions to the point where injecting a single photon induces a nonlinear material response. Here we show theoretically that sub-Doppler-cooled two-level atoms that are spatially organized by weak optical fields give rise to a nonlinear material response that is greatly enhanced beyond that attainable in a homogeneous gas. Specifically, in the regime where the intensity of the applied optical fields is much less than the off-resonance saturation intensity, we show that the third-order nonlinear susceptibility scales inversely with atomic temperature and, due to this scaling, can be two orders of magnitude larger than that of a homogeneous gas for typical experimental parameters. As a result, we predict that spatially bunched two-level atoms can exhibit single-photon nonlinearities. Our model is valid for all regimes of atomic bunching and simultaneously accounts for the backaction of the atoms on the optical fields. Our results agree with previous theoretical and experimental results for light-atom interactions that have considered only limited regimes of atomic bunching. For lattice beams tuned to the low-frequency side of the atomic transition, we find that the nonlinearity transitions from a self-focusing type to a self-defocusing type at a critical intensity. We also show that higher than third-order nonlinear optical susceptibilities are significant in the regime where the dipole potential energy is on the order of the atomic thermal energy. We therefore find that it is crucial to retain high-order nonlinearities to accurately predict interactions of laser fields with spatially organized ultracold atoms. The model presented here is a foundation for modeling low-light-level nonlinear optical processes for ultracold atoms in optical lattices.
Microcavities coupled to multilevel atoms

NASA Astrophysics Data System (ADS)

Schmid, Sandra Isabelle; Evers, Jörg

2011-11-01

A three-level atom in the Λ configuration coupled to a microcavity is studied. The two transitions of the atom are assumed to couple to different counterpropagating mode pairs in the cavity. We analyze the dynamics both in the strong-coupling and the bad-cavity limits. We find that, compared to a two-level setup, the third atomic state and the additional control field modes crucially modify the system dynamics and enable more advanced control schemes. All results are explained using appropriate dressed-state and eigenmode representations. As potential applications, we discuss optical switching and turnstile operations and detection of particles close to the resonator surface.

Operational water management of Rijnland water system and pilot of ensemble forecasting system for flood control

NASA Astrophysics Data System (ADS)

van der Zwan, Rene

2013-04-01

The Rijnland water system is situated in the western part of the Netherlands, and is a low-lying area of which 90% is below sea-level. The area covers 1,100 square kilometres, where 1.3 million people live, work, travel and enjoy leisure. The District Water Control Board of Rijnland is responsible for flood defence, water quantity and quality management. This includes design and maintenance of flood defence structures, control of regulating structures for an adequate water level management, and waste water treatment. For water quantity management Rijnland uses, besides an online monitoring network for collecting water level and precipitation data, a real time control decision support system. This decision support system consists of deterministic hydro-meteorological forecasts with a 24-hr forecast horizon, coupled with a control module that provides optimal operation schedules for the storage basin pumping stations. The uncertainty of the rainfall forecast is not forwarded in the hydrological prediction. At this moment 65% of the pumping capacity of the storage basin pumping stations can be automatically controlled by the decision control system. Within 5 years, after renovation of two other pumping stations, the total capacity of 200 m3/s will be automatically controlled. In critical conditions there is a need of both a longer forecast horizon and a probabilistic forecast. Therefore ensemble precipitation forecasts of the ECMWF are already consulted off-line during dry-spells, and Rijnland is running a pilot operational system providing 10-day water level ensemble forecasts. The use of EPS during dry-spells and the findings of the pilot will be presented. Challenges and next steps towards on-line implementation of ensemble forecasts for risk-based operational management of the Rijnland water system will be discussed. An important element in that discussion is the question: will policy and decision makers, operator and citizens adapt this Anticipatory Water management, including temporary lower storage basin levels and a reduction in extra investments for infrastructural measures.
Microcanonical thermodynamics and statistical fragmentation of dissipative systems. The topological structure of the N-body phase space

NASA Astrophysics Data System (ADS)

Gross, D. H. E.

1997-01-01

This review is addressed to colleagues working in different fields of physics who are interested in the concepts of microcanonical thermodynamics, its relation and contrast to ordinary, canonical or grandcanonical thermodynamics, and to get a first taste of the wide area of new applications of thermodynamical concepts like hot nuclei, hot atomic clusters and gravitating systems. Microcanonical thermodynamics describes how the volume of the N-body phase space depends on the globally conserved quantities like energy, angular momentum, mass, charge, etc. Due to these constraints the microcanonical ensemble can behave quite differently from the conventional, canonical or grandcanonical ensemble in many important physical systems. Microcanonical systems become inhomogeneous at first-order phase transitions, or with rising energy, or with external or internal long-range forces like Coulomb, centrifugal or gravitational forces. Thus, fragmentation of the system into a spatially inhomogeneous distribution of various regions of different densities and/or of different phases is a genuine characteristic of the microcanonical ensemble. In these cases which are realized by the majority of realistic systems in nature, the microcanonical approach is the natural statistical description. We investigate this most fundamental form of thermodynamics in four different nontrivial physical cases: (I) Microcanonical phase transitions of first and second order are studied within the Potts model. The total energy per particle is a nonfluctuating order parameter which controls the phase which the system is in. In contrast to the canonical form the microcanonical ensemble allows to tune the system continuously from one phase to the other through the region of coexisting phases by changing the energy smoothly. The configurations of coexisting phases carry important informations about the nature of the phase transition. This is more remarkable as the canonical ensemble is blind against these configurations. It is shown that the three basic quantities which specify a phase transition of first order - Transition temperature, latent heat, and interphase surface entropy - can be well determined for finite systems from the caloric equation of state T( E) in the coexistence region. Their values are already for a lattice of only ~ 30 ∗ 30 spins close to the ones of the corresponding infinite system. The significance of the backbending of the caloric equation of state T( E) is clarified. It is the signal for a phase transition of first order in a finite isolated system. (II) Fragmentation is shown to be a specific and generic phase transition of finite systems. The caloric equation of state T( E) for hot nuclei is calculated. The phase transition towards fragmentation can unambiguously be identified by the anomalies in T( E). As microcanonical thermodynamics is a full N-body theory it determines all many-body correlations as well. Consequently, various statistical multi-fragment correlations are investigated which give insight into the details of the equilibration mechanism. (III) Fragmentation of neutral and multiply charged atomic clusters is the next example of a realistic application of microcanonical thermodynamics. Our simulation method, microcanonical Metropolis Monte Carlo, combines the explicit microscopic treatment of the fragmentational degrees of freedom with the implicit treatment of the internal degrees of freedom of the fragments described by the experimental bulk specific heat. This micro-macro approach allows us to study the fragmentation of also larger fragments. Characteristic details of the fission of multiply charged metal clusters find their explanation by the different bulk properties. (IV) Finally, the fragmentation of strongly rotating nuclei is discussed as an example for a microcanonical ensemble under the action of a two-dimensional repulsive force.
Application of the maximum entropy principle to determine ensembles of intrinsically disordered proteins from residual dipolar couplings.

PubMed

Sanchez-Martinez, M; Crehuet, R

2014-12-21

We present a method based on the maximum entropy principle that can re-weight an ensemble of protein structures based on data from residual dipolar couplings (RDCs). The RDCs of intrinsically disordered proteins (IDPs) provide information on the secondary structure elements present in an ensemble; however even two sets of RDCs are not enough to fully determine the distribution of conformations, and the force field used to generate the structures has a pervasive influence on the refined ensemble. Two physics-based coarse-grained force fields, Profasi and Campari, are able to predict the secondary structure elements present in an IDP, but even after including the RDC data, the re-weighted ensembles differ between both force fields. Thus the spread of IDP ensembles highlights the need for better force fields. We distribute our algorithm in an open-source Python code.
A Theoretical Analysis of Why Hybrid Ensembles Work.

PubMed

Hsu, Kuo-Wei

2017-01-01

Inspired by the group decision making process, ensembles or combinations of classifiers have been found favorable in a wide variety of application domains. Some researchers propose to use the mixture of two different types of classification algorithms to create a hybrid ensemble. Why does such an ensemble work? The question remains. Following the concept of diversity, which is one of the fundamental elements of the success of ensembles, we conduct a theoretical analysis of why hybrid ensembles work, connecting using different algorithms to accuracy gain. We also conduct experiments on classification performance of hybrid ensembles of classifiers created by decision tree and naïve Bayes classification algorithms, each of which is a top data mining algorithm and often used to create non-hybrid ensembles. Therefore, through this paper, we provide a complement to the theoretical foundation of creating and using hybrid ensembles.
Ensemble-based characterization of unbound and bound states on protein energy landscape

PubMed Central

Ruvinsky, Anatoly M; Kirys, Tatsiana; Tuzikov, Alexander V; Vakser, Ilya A

2013-01-01

Physicochemical description of numerous cell processes is fundamentally based on the energy landscapes of protein molecules involved. Although the whole energy landscape is difficult to reconstruct, increased attention to particular targets has provided enough structures for mapping functionally important subspaces associated with the unbound and bound protein structures. The subspace mapping produces a discrete representation of the landscape, further called energy spectrum. We compiled and characterized ensembles of bound and unbound conformations of six small proteins and explored their spectra in implicit solvent. First, the analysis of the unbound-to-bound changes points to conformational selection as the binding mechanism for four proteins. Second, results show that bound and unbound spectra often significantly overlap. Moreover, the larger the overlap the smaller the root mean square deviation (RMSD) between the bound and unbound conformational ensembles. Third, the center of the unbound spectrum has a higher energy than the center of the corresponding bound spectrum of the dimeric and multimeric states for most of the proteins. This suggests that the unbound states often have larger entropy than the bound states. Fourth, the exhaustively long minimization, making small intrarotamer adjustments (all-atom RMSD ≤ 0.7 Å), dramatically reduces the distance between the centers of the bound and unbound spectra as well as the spectra extent. It condenses unbound and bound energy levels into a thin layer at the bottom of the energy landscape with the energy spacing that varies between 0.8–4.6 and 3.5–10.5 kcal/mol for the unbound and bound states correspondingly. Finally, the analysis of protein energy fluctuations showed that protein vibrations itself can excite the interstate transitions, including the unbound-to-bound ones. PMID:23526684
Development of the Science Data System for the International Space Station Cold Atom Lab

NASA Technical Reports Server (NTRS)

van Harmelen, Chris; Soriano, Melissa A.

2015-01-01

Cold Atom Laboratory (CAL) is a facility that will enable scientists to study ultra-cold quantum gases in a microgravity environment on the International Space Station (ISS) beginning in 2016. The primary science data for each experiment consists of two images taken in quick succession. The first image is of the trapped cold atoms and the second image is of the background. The two images are subtracted to obtain optical density. These raw Level 0 atom and background images are processed into the Level 1 optical density data product, and then into the Level 2 data products: atom number, Magneto-Optical Trap (MOT) lifetime, magnetic chip-trap atom lifetime, and condensate fraction. These products can also be used as diagnostics of the instrument health. With experiments being conducted for 8 hours every day, the amount of data being generated poses many technical challenges, such as downlinking and managing the required data volume. A parallel processing design is described, implemented, and benchmarked. In addition to optimizing the data pipeline, accuracy and speed in producing the Level 1 and 2 data products is key. Algorithms for feature recognition are explored, facilitating image cropping and accurate atom number calculations.
Spatial intensity distribution of controlled-NOT gate carrying orbital angular momentum via photonic band gap structure

NASA Astrophysics Data System (ADS)

Zhang, Yan; Wang, Xiaorui; Zhe Zhang, Yun

2018-07-01

By employing the different topological charges of a Laguerre–Gaussian beam as a qubit, we experimentally demonstrate a controlled-NOT (CNOT) gate with light beams carrying orbital angular momentum via a photonic band gap structure in a hot atomic ensemble. Through a degenerate four-wave mixing process, the spatial distribution of the CNOT gate including splitting and spatial shift can be affected by the Kerr nonlinear effect in multilevel atomic systems. Moreover, the intensity variations of the CNOT gate can be controlled by the relative phase modulation. This research can be useful for applications in quantum information processing.
Spin Self-Rephasing and Very Long Coherence Times in a Trapped Atomic Ensemble

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

Deutsch, C.; Reinhard, F.; Schneider, T.

2010-07-09

We perform Ramsey spectroscopy on the ground state of ultracold {sup 87}Rb atoms magnetically trapped on a chip in the Knudsen regime. Field inhomogeneities over the sample should limit the 1/e contrast decay time to about 3 s, while decay times of 58{+-}12 s are actually observed. We explain this surprising result by a spin self-rephasing mechanism induced by the identical spin rotation effect originating from particle indistinguishability. We propose a theory of this synchronization mechanism and obtain good agreement with the experimental observations. The effect is general and may appear in other physical systems.
Addressing model uncertainty through stochastic parameter perturbations within the High Resolution Rapid Refresh (HRRR) ensemble

NASA Astrophysics Data System (ADS)

Wolff, J.; Jankov, I.; Beck, J.; Carson, L.; Frimel, J.; Harrold, M.; Jiang, H.

2016-12-01

It is well known that global and regional numerical weather prediction ensemble systems are under-dispersive, producing unreliable and overconfident ensemble forecasts. Typical approaches to alleviate this problem include the use of multiple dynamic cores, multiple physics suite configurations, or a combination of the two. While these approaches may produce desirable results, they have practical and theoretical deficiencies and are more difficult and costly to maintain. An active area of research that promotes a more unified and sustainable system for addressing the deficiencies in ensemble modeling is the use of stochastic physics to represent model-related uncertainty. Stochastic approaches include Stochastic Parameter Perturbations (SPP), Stochastic Kinetic Energy Backscatter (SKEB), Stochastic Perturbation of Physics Tendencies (SPPT), or some combination of all three. The focus of this study is to assess the model performance within a convection-permitting ensemble at 3-km grid spacing across the Contiguous United States (CONUS) when using stochastic approaches. For this purpose, the test utilized a single physics suite configuration based on the operational High-Resolution Rapid Refresh (HRRR) model, with ensemble members produced by employing stochastic methods. Parameter perturbations were employed in the Rapid Update Cycle (RUC) land surface model and Mellor-Yamada-Nakanishi-Niino (MYNN) planetary boundary layer scheme. Results will be presented in terms of bias, error, spread, skill, accuracy, reliability, and sharpness using the Model Evaluation Tools (MET) verification package. Due to the high level of complexity of running a frequently updating (hourly), high spatial resolution (3 km), large domain (CONUS) ensemble system, extensive high performance computing (HPC) resources were needed to meet this objective. Supercomputing resources were provided through the National Center for Atmospheric Research (NCAR) Strategic Capability (NSC) project support, allowing for a more extensive set of tests over multiple seasons, consequently leading to more robust results. Through the use of these stochastic innovations and powerful supercomputing at NCAR, further insights and advancements in ensemble forecasting at convection-permitting scales will be possible.
A nanowaveguide platform for collective atom-light interaction

NASA Astrophysics Data System (ADS)

Meng, Y.; Lee, J.; Dagenais, M.; Rolston, S. L.

2015-08-01

We propose a nanowaveguide platform for collective atom-light interaction through evanescent field coupling. We have developed a 1 cm-long silicon nitride nanowaveguide can use evanescent fields to trap and probe an ensemble of 87Rb atoms. The waveguide has a sub-micrometer square mode area and was designed with tapers for high fiber-to-waveguide coupling efficiencies at near-infrared wavelengths (750 nm to 1100 nm). Inverse tapers in the platform adiabatically transfer a weakly guided mode of fiber-coupled light into a strongly guided mode with an evanescent field to trap atoms and then back to a weakly guided mode at the other end of the waveguide. The coupling loss is -1 dB per facet (˜80% coupling efficiency) at 760 nm and 1064 nm, which is estimated by a propagation loss measurement with waveguides of different lengths. The proposed platform has good thermal conductance and can guide high optical powers for trapping atoms in ultra-high vacuum. As an intermediate step, we have observed thermal atom absorption of the evanescent component of a nanowaveguide and have demonstrated the U-wire mirror magneto-optical trap that can transfer atoms to the proximity of the surface.
Approximate conditional teleportation of a Λ-type three-level atomic state based on cavity QED method beyond Bell-state measurement

NASA Astrophysics Data System (ADS)

Sehati, N.; Tavassoly, M. K.

2017-08-01

Inspiring from the scheme proposed in (Zheng in Phys Rev A 69:064,302 2004), our aim is to teleport an unknown qubit atomic state using the cavity QED method without using the explicit Bell-state measurement, and so the additional atom is not required. Two identical Λ-type three-level atoms are interacted separately and subsequently with a two-mode quantized cavity field where each mode is expressed with a single-photon field state. The interaction between atoms and field is well described via the Jaynes-Cummings model. It is then shown that how if the atomic detection results a particular state of atom 1, an unknown state can be appropriately teleported from atom 1 to atom 2. This teleportation procedure successfully leads to the high fidelity F (success probability P_g) in between 69%≲ F≲ 100% (0.14≲ P_g≲ 0.56). At last, we illustrated that our scheme considerably improves similar previous proposals.
Stability of various entanglements in the interaction between two two-level atoms with a quantized field under the influences of several decay sources

NASA Astrophysics Data System (ADS)

Valizadeh, Sh.; Tavassoly, M. K.; Yazdanpanah, N.

2018-02-01

In this paper the interaction between two two-level atoms with a single-mode quantized field is studied. To achieve exact information about the physical properties of the system, one should take into account various sources of dissipation such as photon leakage of cavity, spontaneous emission rate of atoms, internal thermal radiation of cavity and dipole-dipole interaction between the two atoms. In order to achieve the desired goals, we obtain the time evolution of the associated density operator by solving the time-dependent Lindblad equation corresponding to the system. Then, we evaluate the temporal behavior of total population inversion and quantum entanglement between the evolved subsystems, numerically. We clearly show that how the damping parameters affect on the dynamics of considered properties. By analyzing the numerical results, we observe that increasing each of the damping sources leads to faster decay of total population inversion. Also, it is observed that, after starting the interaction, the entanglement between one atom with other parts of the system as well as the entanglement between "atom-atom" subsystem and the "field", tend to some constant values very soon. Moreover, the stable values of entanglement are reduced via increasing the damping factor Γ A (ΓA^{(1)} = ΓA^{(2)} = ΓA ) where ΓA is the spontaneous emission rate of each atom. In addition, we find that by increasing the thermal photons, the entropies (entanglements) tend sooner to some increased stable values. Accordingly, we study the atom-atom entanglement by evaluating the concurrence under the influence of dissipation sources, too. At last, the effects of dissipation sources on the genuine tripartite entanglement between the three subsystems include of two two-level atoms and a quantized field are numerically studied. Due to the important role of stationary entanglement in quantum information processing, our results may provide useful hints for practical protocols which require some appropriate mechanisms to prevent or at least minimize the influence of decoherence phenomenon.
A Comparative Case Study of Non-Music Major Participation in Two Contrasting Collegiate Choral Ensembles

ERIC Educational Resources Information Center

Jones, Sara K.

2018-01-01

The purpose of this comparative case study was to examine the motivation for participation in traditional and non-traditional vocal ensembles by students who are not pursuing a career in music and the perceived benefits of this participation. Participants were selected from a traditional mixed choral ensemble and a student-run a cappella ensemble.…
Ensemble Models

EPA Science Inventory

Ensemble forecasting has been used for operational numerical weather prediction in the United States and Europe since the early 1990s. An ensemble of weather or climate forecasts is used to characterize the two main sources of uncertainty in computer models of physical systems: ...
Formation of Exotic Networks of Water Clusters in Helium Droplets Facilitated by the Presence of Neon Atoms

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

Douberly, Gary E.; Miller, Roger E.; Xantheas, Sotiris S.

Water clusters are formed in helium droplets via the sequential capture of monomers. One or two neon atoms are added to each droplet prior to the addition of water. The infrared spectrum of the droplet ensemble reveals several signatures of polar, water tetramer clusters having dipole moments between 2D and 3D. Comparison with ab initio computations supports the assignment of the cluster networks to noncyclic “3+1” clusters, which are ~5.3 kcal/mol less stable than the global minimum nonpolar cyclic tetramer. The (H2O)3Ne + H2O ring insertion barrier is sufficiently large, such that evaporative helium cooling is capable of kinetically quenchingmore » the nonequilibrium tetramer system prior to its rearrangement to the lower energy cyclic species. To this end, the reported process results in the formation of exotic water cluster networks that are either higher in energy than the most stable gas-phase analogs or not even stable in the gas phase.« less
Control Mechanisms of Photoisomerization in Protonated Schiff Bases.

PubMed

Vuković, Lela; Burmeister, Carl F; Král, Petr; Groenhof, Gerrit

2013-03-21

We performed ab initio excited-state molecular dynamics simulations of a gas-phase photoexcited protonated Schiff base (C1-N2═C3-C4═C5-C6) to search for control mechanisms of its photoisomerization. The excited molecule twists by ∼90° around either the N2C3 bond or the C4C5 bond and relaxes to the ground electronic state through a conical intersection with either a trans or cis outcome. We show that a large initial distortion of several dihedral angles and a specific normal vibrational mode combining pyramidalization and double-bond twisting can lead to a preferential rotation of atoms around the C4C5 bond. We also show that selective pretwisting of several dihedral angles in the initial ground state thermal ensemble (by analogy to a protein pocket) can significantly increase the fraction of photoreactive (cis → trans) trajectories. We demonstrate that new ensembles with higher degrees of control over the photoisomerization reaction can be obtained by a computational directed evolution approach on the ensembles of molecules with the pretwisted geometries.
Multiensemble Markov models of molecular thermodynamics and kinetics.

PubMed

Wu, Hao; Paul, Fabian; Wehmeyer, Christoph; Noé, Frank

2016-06-07

We introduce the general transition-based reweighting analysis method (TRAM), a statistically optimal approach to integrate both unbiased and biased molecular dynamics simulations, such as umbrella sampling or replica exchange. TRAM estimates a multiensemble Markov model (MEMM) with full thermodynamic and kinetic information at all ensembles. The approach combines the benefits of Markov state models-clustering of high-dimensional spaces and modeling of complex many-state systems-with those of the multistate Bennett acceptance ratio of exploiting biased or high-temperature ensembles to accelerate rare-event sampling. TRAM does not depend on any rate model in addition to the widely used Markov state model approximation, but uses only fundamental relations such as detailed balance and binless reweighting of configurations between ensembles. Previous methods, including the multistate Bennett acceptance ratio, discrete TRAM, and Markov state models are special cases and can be derived from the TRAM equations. TRAM is demonstrated by efficiently computing MEMMs in cases where other estimators break down, including the full thermodynamics and rare-event kinetics from high-dimensional simulation data of an all-atom protein-ligand binding model.
Multiensemble Markov models of molecular thermodynamics and kinetics

PubMed Central

Wu, Hao; Paul, Fabian; Noé, Frank

2016-01-01

We introduce the general transition-based reweighting analysis method (TRAM), a statistically optimal approach to integrate both unbiased and biased molecular dynamics simulations, such as umbrella sampling or replica exchange. TRAM estimates a multiensemble Markov model (MEMM) with full thermodynamic and kinetic information at all ensembles. The approach combines the benefits of Markov state models—clustering of high-dimensional spaces and modeling of complex many-state systems—with those of the multistate Bennett acceptance ratio of exploiting biased or high-temperature ensembles to accelerate rare-event sampling. TRAM does not depend on any rate model in addition to the widely used Markov state model approximation, but uses only fundamental relations such as detailed balance and binless reweighting of configurations between ensembles. Previous methods, including the multistate Bennett acceptance ratio, discrete TRAM, and Markov state models are special cases and can be derived from the TRAM equations. TRAM is demonstrated by efficiently computing MEMMs in cases where other estimators break down, including the full thermodynamics and rare-event kinetics from high-dimensional simulation data of an all-atom protein–ligand binding model. PMID:27226302
Free energy reconstruction from steered dynamics without post-processing

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

Athenes, Manuel, E-mail: Manuel.Athenes@cea.f; Condensed Matter and Materials Division, Physics and Life Sciences Directorate, LLNL, Livermore, CA 94551; Marinica, Mihai-Cosmin

2010-09-20

Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable one to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes theorem, we propose a more direct method in which a posterior likelihood function is used both to construct the steered dynamics and to infer the contribution to equilibrium of all the sampled states. The method is implemented with two steering schedules. First, using non-autonomous steering, we calculate the migration barrier of the vacancy in Fe-{alpha}. Second, using an autonomous scheduling related to metadynamics and equivalent to temperature-accelerated molecular dynamics, wemore » accurately reconstruct the two-dimensional free energy landscape of the 38-atom Lennard-Jones cluster as a function of an orientational bond-order parameter and energy, down to the solid-solid structural transition temperature of the cluster and without maximum-likelihood post-processing.« less
Subsurface characterization with localized ensemble Kalman filter employing adaptive thresholding

NASA Astrophysics Data System (ADS)

Delijani, Ebrahim Biniaz; Pishvaie, Mahmoud Reza; Boozarjomehry, Ramin Bozorgmehry

2014-07-01

Ensemble Kalman filter, EnKF, as a Monte Carlo sequential data assimilation method has emerged promisingly for subsurface media characterization during past decade. Due to high computational cost of large ensemble size, EnKF is limited to small ensemble set in practice. This results in appearance of spurious correlation in covariance structure leading to incorrect or probable divergence of updated realizations. In this paper, a universal/adaptive thresholding method is presented to remove and/or mitigate spurious correlation problem in the forecast covariance matrix. This method is, then, extended to regularize Kalman gain directly. Four different thresholding functions have been considered to threshold forecast covariance and gain matrices. These include hard, soft, lasso and Smoothly Clipped Absolute Deviation (SCAD) functions. Three benchmarks are used to evaluate the performances of these methods. These benchmarks include a small 1D linear model and two 2D water flooding (in petroleum reservoirs) cases whose levels of heterogeneity/nonlinearity are different. It should be noted that beside the adaptive thresholding, the standard distance dependant localization and bootstrap Kalman gain are also implemented for comparison purposes. We assessed each setup with different ensemble sets to investigate the sensitivity of each method on ensemble size. The results indicate that thresholding of forecast covariance yields more reliable performance than Kalman gain. Among thresholding function, SCAD is more robust for both covariance and gain estimation. Our analyses emphasize that not all assimilation cycles do require thresholding and it should be performed wisely during the early assimilation cycles. The proposed scheme of adaptive thresholding outperforms other methods for subsurface characterization of underlying benchmarks.

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