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].

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.

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.

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.

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.

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.

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.

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.

Highly retrievable spin-wave-photon entanglement source.

PubMed

Yang, Sheng-Jun; Wang, Xu-Jie; Li, Jun; Rui, Jun; Bao, Xiao-Hui; Pan, Jian-Wei

2015-05-29

Entanglement between a single photon and a quantum memory forms the building blocks for a quantum repeater and quantum network. Previous entanglement sources are typically with low retrieval efficiency, which limits future larger-scale applications. Here, we report a source of highly retrievable spin-wave-photon entanglement. Polarization entanglement is created through interaction of a single photon with an ensemble of atoms inside a low-finesse ring cavity. The cavity is engineered to be resonant for dual spin-wave modes, which thus enables efficient retrieval of the spin-wave qubit. An intrinsic retrieval efficiency up to 76(4)% has been observed. Such a highly retrievable atom-photon entanglement source will be very useful in future larger-scale quantum repeater and quantum network applications.

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.

Telecom-Wavelength Atomic Quantum Memory in Optical Fiber for Heralded Polarization Qubits.

PubMed

Jin, Jeongwan; Saglamyurek, Erhan; Puigibert, Marcel lí Grimau; Verma, Varun; Marsili, Francesco; Nam, Sae Woo; Oblak, Daniel; Tittel, Wolfgang

2015-10-02

Polarization-encoded photons at telecommunication wavelengths provide a compelling platform for practical realizations of photonic quantum information technologies due to the ease of performing single qubit manipulations, the availability of polarization-entangled photon-pair sources, and the possibility of leveraging existing fiber-optic links for distributing qubits over long distances. An optical quantum memory compatible with this platform could serve as a building block for these technologies. Here we present the first experimental demonstration of an atomic quantum memory that directly allows for reversible mapping of quantum states encoded in the polarization degree of freedom of a telecom-wavelength photon. We show that heralded polarization qubits at a telecom wavelength are stored and retrieved with near-unity fidelity by implementing the atomic frequency comb protocol in an ensemble of erbium atoms doped into an optical fiber. Despite remaining limitations in our proof-of-principle demonstration such as small storage efficiency and storage time, our broadband light-matter interface reveals the potential for use in future quantum information processing.

Influence of blocking on Northern European and Western Russian heatwaves in large climate model ensembles

NASA Astrophysics Data System (ADS)

Schaller, N.; Sillmann, J.; Anstey, J.; Fischer, E. M.; Grams, C. M.; Russo, S.

2018-05-01

Better preparedness for summer heatwaves could mitigate their adverse effects on society. This can potentially be attained through an increased understanding of the relationship between heatwaves and one of their main dynamical drivers, atmospheric blocking. In the 1979–2015 period, we find that there is a significant correlation between summer heatwave magnitudes and the number of days influenced by atmospheric blocking in Northern Europe and Western Russia. Using three large global climate model ensembles, we find similar correlations, indicating that these three models are able to represent the relationship between extreme temperature and atmospheric blocking, despite having biases in their simulation of individual climate variables such as temperature or geopotential height. Our results emphasize the need to use large ensembles of different global climate models as single realizations do not always capture this relationship. The three large ensembles further suggest that the relationship between summer heatwaves and atmospheric blocking will not change in the future. This could be used to statistically model heatwaves with atmospheric blocking as a covariate and aid decision-makers in planning disaster risk reduction and adaptation to climate change.

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.

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.

Ensemble Weight Enumerators for Protograph LDPC Codes

NASA Technical Reports Server (NTRS)

Divsalar, Dariush

2006-01-01

Recently LDPC codes with projected graph, or protograph structures have been proposed. In this paper, finite length ensemble weight enumerators for LDPC codes with protograph structures are obtained. Asymptotic results are derived as the block size goes to infinity. In particular we are interested in obtaining ensemble average weight enumerators for protograph LDPC codes which have minimum distance that grows linearly with block size. As with irregular ensembles, linear minimum distance property is sensitive to the proportion of degree-2 variable nodes. In this paper the derived results on ensemble weight enumerators show that linear minimum distance condition on degree distribution of unstructured irregular LDPC codes is a sufficient but not a necessary condition for protograph LDPC codes.

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

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.

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.

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.

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.

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.

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.

Spectral partitioning in equitable graphs.

PubMed

Barucca, Paolo

2017-06-01

Graph partitioning problems emerge in a wide variety of complex systems, ranging from biology to finance, but can be rigorously analyzed and solved only for a few graph ensembles. Here, an ensemble of equitable graphs, i.e., random graphs with a block-regular structure, is studied, for which analytical results can be obtained. In particular, the spectral density of this ensemble is computed exactly for a modular and bipartite structure. Kesten-McKay's law for random regular graphs is found analytically to apply also for modular and bipartite structures when blocks are homogeneous. An exact solution to graph partitioning for two equal-sized communities is proposed and verified numerically, and a conjecture on the absence of an efficient recovery detectability transition in equitable graphs is suggested. A final discussion summarizes results and outlines their relevance for the solution of graph partitioning problems in other graph ensembles, in particular for the study of detectability thresholds and resolution limits in stochastic block models.

Spectral partitioning in equitable graphs

NASA Astrophysics Data System (ADS)

Barucca, Paolo

2017-06-01

Graph partitioning problems emerge in a wide variety of complex systems, ranging from biology to finance, but can be rigorously analyzed and solved only for a few graph ensembles. Here, an ensemble of equitable graphs, i.e., random graphs with a block-regular structure, is studied, for which analytical results can be obtained. In particular, the spectral density of this ensemble is computed exactly for a modular and bipartite structure. Kesten-McKay's law for random regular graphs is found analytically to apply also for modular and bipartite structures when blocks are homogeneous. An exact solution to graph partitioning for two equal-sized communities is proposed and verified numerically, and a conjecture on the absence of an efficient recovery detectability transition in equitable graphs is suggested. A final discussion summarizes results and outlines their relevance for the solution of graph partitioning problems in other graph ensembles, in particular for the study of detectability thresholds and resolution limits in stochastic block models.

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.

Quantum entanglement between an optical photon and a solid-state spin qubit.

PubMed

Togan, E; Chu, Y; Trifonov, A S; Jiang, L; Maze, J; Childress, L; Dutt, M V G; Sørensen, A S; Hemmer, P R; Zibrov, A S; Lukin, M D

2010-08-05

Quantum entanglement is among the most fascinating aspects of quantum theory. Entangled optical photons are now widely used for fundamental tests of quantum mechanics and applications such as quantum cryptography. Several recent experiments demonstrated entanglement of optical photons with trapped ions, atoms and atomic ensembles, which are then used to connect remote long-term memory nodes in distributed quantum networks. Here we realize quantum entanglement between the polarization of a single optical photon and a solid-state qubit associated with the single electronic spin of a nitrogen vacancy centre in diamond. Our experimental entanglement verification uses the quantum eraser technique, and demonstrates that a high degree of control over interactions between a solid-state qubit and the quantum light field can be achieved. The reported entanglement source can be used in studies of fundamental quantum phenomena and provides a key building block for the solid-state realization of quantum optical networks.

North Atlantic winter eddy-driven jet and atmospheric blocking variability in the Community Earth System Model version 1 Large Ensemble simulations

NASA Astrophysics Data System (ADS)

Kwon, Young-Oh; Camacho, Alicia; Martinez, Carlos; Seo, Hyodae

2018-01-01

The atmospheric jet and blocking distributions, especially in the North Atlantic sector, have been challenging features for a climate model to realistically reproduce. This study examines climatological distributions of winter (December-February) daily jet latitude and blocking in the North Atlantic from the 40-member Community Earth System Model version 1 Large Ensemble (CESM1LE) simulations. This analysis aims at examining whether a broad range of internal climate variability encompassed by a large ensemble of simulations results in an improved representation of the jet latitude distributions and blocking days in CESM1LE. In the historical runs (1951-2005), the daily zonal wind at 850 hPa exhibits three distinct preferred latitudes for the eddy-driven jet position as seen in the reanalysis datasets, which represents a significant improvement from the previous version of the same model. However, the meridional separations between the three jet latitudes are much smaller than those in the reanalyses. In particular, the jet rarely migrates to the observed southernmost position around 37°N. This leads to the bias in blocking frequency that is too low over Greenland and too high over the Azores. These features are shown to be remarkably stable across the 40 ensemble members with negligible member-to-member spread. This result implies the range of internal variability of winter jet latitude and blocking frequency within the 55-year segment from each ensemble member is comparable to that represented by the full large ensemble. Comparison with 2046-2100 from the RCP8.5 future projection runs suggests that the daily jet position is projected to maintain the same three preferred latitudes, with a slightly higher frequency of occurrence over the central latitude around 50°N, instead of shifting poleward in the future as documented in some previous studies. In addition, the daily jet speed is projected not to change significantly between 1951-2005 and 2046-2100. On the other hand, the climatological mean jet is projected to become slightly more elongated and stronger on its southern flank, and the blocking frequency over the Azores is projected to decrease.

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.

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.

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.

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.

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.

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.

Evaluation of blocking performance in ensemble seasonal integrations

NASA Astrophysics Data System (ADS)

Casado, M. J.; Doblas-Reyes, F. J.; Pastor, M. A.

2003-04-01

EVALUATION OF BLOCKING PERFOMANCE IN ENSEMBLE SEASONAL INTEGRATIONS M. J. Casado (1), F. J. Doblas-Reyes (2), A. Pastor (1) (1) I Instituto Nacional de Meteorología, c/Leonardo Prieto Castro,8,28071 ,Madrid,Spain, mjcasado@inm.es (2) ECMWF, Shinfield Park,RG2 9AX, Reading, UK, f.doblas-reyes@ecmwf.int Climate models have shown a robust inability to reliably predict blocking onset and frequency. This systematic error has been evaluated using multi-model ensemble seasonal integrations carried out in the framework of the Prediction Of climate Variations On Seasonal and interanual Timescales (PROVOST) project and compared to a blocking features assessment of the NCEP re-analyses. The PROVOST GCMs are able to adequately reproduce the spatial NCEP teleconnection patterns over the Northern Hemisphere, being notorious the great spatial correlation coefficient with some of the corresponding NCEP patterns. In spite of that, the different models show a consistent underestimation of blocking frequency which may impact on the ability to predict the seasonal amplitude of the leading modes of variability over the Northern Hemisphere.

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.

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.

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

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.

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

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.

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.

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.

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.

Field-theoretic simulations of block copolymer nanocomposites in a constant interfacial tension ensemble.

PubMed

Koski, Jason P; Riggleman, Robert A

2017-04-28

Block copolymers, due to their ability to self-assemble into periodic structures with long range order, are appealing candidates to control the ordering of functionalized nanoparticles where it is well-accepted that the spatial distribution of nanoparticles in a polymer matrix dictates the resulting material properties. The large parameter space associated with block copolymer nanocomposites makes theory and simulation tools appealing to guide experiments and effectively isolate parameters of interest. We demonstrate a method for performing field-theoretic simulations in a constant volume-constant interfacial tension ensemble (nVγT) that enables the determination of the equilibrium properties of block copolymer nanocomposites, including when the composites are placed under tensile or compressive loads. Our approach is compatible with the complex Langevin simulation framework, which allows us to go beyond the mean-field approximation. We validate our approach by comparing our nVγT approach with free energy calculations to determine the ideal domain spacing and modulus of a symmetric block copolymer melt. We analyze the effect of numerical and thermodynamic parameters on the efficiency of the nVγT ensemble and subsequently use our method to investigate the ideal domain spacing, modulus, and nanoparticle distribution of a lamellar forming block copolymer nanocomposite. We find that the nanoparticle distribution is directly linked to the resultant domain spacing and is dependent on polymer chain density, nanoparticle size, and nanoparticle chemistry. Furthermore, placing the system under tension or compression can qualitatively alter the nanoparticle distribution within the block copolymer.

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

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

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.

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.

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.

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.

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.

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.

Ensemble methods with simple features for document zone classification

NASA Astrophysics Data System (ADS)

Obafemi-Ajayi, Tayo; Agam, Gady; Xie, Bingqing

2012-01-01

Document layout analysis is of fundamental importance for document image understanding and information retrieval. It requires the identification of blocks extracted from a document image via features extraction and block classification. In this paper, we focus on the classification of the extracted blocks into five classes: text (machine printed), handwriting, graphics, images, and noise. We propose a new set of features for efficient classifications of these blocks. We present a comparative evaluation of three ensemble based classification algorithms (boosting, bagging, and combined model trees) in addition to other known learning algorithms. Experimental results are demonstrated for a set of 36503 zones extracted from 416 document images which were randomly selected from the tobacco legacy document collection. The results obtained verify the robustness and effectiveness of the proposed set of features in comparison to the commonly used Ocropus recognition features. When used in conjunction with the Ocropus feature set, we further improve the performance of the block classification system to obtain a classification accuracy of 99.21%.

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

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

The random coding bound is tight for the average code.

NASA Technical Reports Server (NTRS)

Gallager, R. G.

1973-01-01

The random coding bound of information theory provides a well-known upper bound to the probability of decoding error for the best code of a given rate and block length. The bound is constructed by upperbounding the average error probability over an ensemble of codes. The bound is known to give the correct exponential dependence of error probability on block length for transmission rates above the critical rate, but it gives an incorrect exponential dependence at rates below a second lower critical rate. Here we derive an asymptotic expression for the average error probability over the ensemble of codes used in the random coding bound. The result shows that the weakness of the random coding bound at rates below the second critical rate is due not to upperbounding the ensemble average, but rather to the fact that the best codes are much better than the average at low rates.

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.

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.

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

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.

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

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.

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%.

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

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.

Simple and Efficient Single Photon Filter for a Rb-based Quantum Memory

NASA Astrophysics Data System (ADS)

Stack, Daniel; Li, Xiao; Quraishi, Qudsia

2015-05-01

Distribution of entangled quantum states over significant distances is important to the development of future quantum technologies such as long-distance cryptography, networks of atomic clocks, distributed quantum computing, etc. Long-lived quantum memories and single photons are building blocks for systems capable of realizing such applications. The ability to store and retrieve quantum information while filtering unwanted light signals is critical to the operation of quantum memories based on neutral-atom ensembles. We report on an efficient frequency filter which uses a glass cell filled with 85Rb vapor to attenuate noise photons by an order of magnitude with little loss to the single photons associated with the operation of our cold 87Rb quantum memory. An Ar buffer gas is required to differentiate between signal and noise photons or similar statement. Our simple, passive filter requires no optical pumping or external frequency references and provides an additional 18 dB attenuation of our pump laser for every 1 dB loss of the single photon signal. We observe improved non-classical correlations and our data shows that the addition of a frequency filter increases the non-classical correlations and readout efficiency of our quantum memory by ~ 35%.

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.

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.

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.

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.

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.

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.

Hartree and Exchange in Ensemble Density Functional Theory: Avoiding the Nonuniqueness Disaster.

PubMed

Gould, Tim; Pittalis, Stefano

2017-12-15

Ensemble density functional theory is a promising method for the efficient and accurate calculation of excitations of quantum systems, at least if useful functionals can be developed to broaden its domain of practical applicability. Here, we introduce a guaranteed single-valued "Hartree-exchange" ensemble density functional, E_{Hx}[n], in terms of the right derivative of the universal ensemble density functional with respect to the coupling constant at vanishing interaction. We show that E_{Hx}[n] is straightforwardly expressible using block eigenvalues of a simple matrix [Eq. (14)]. Specialized expressions for E_{Hx}[n] from the literature, including those involving superpositions of Slater determinants, can now be regarded as originating from the unifying picture presented here. We thus establish a clear and practical description for Hartree and exchange in ensemble systems.

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.

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.

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

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.

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.

A molecular fragment cheminformatics roadmap for mesoscopic simulation.

PubMed

Truszkowski, Andreas; Daniel, Mirco; Kuhn, Hubert; Neumann, Stefan; Steinbeck, Christoph; Zielesny, Achim; Epple, Matthias

2014-12-01

Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even larger molecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix (array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformatics approach tackles these problems and provides solutions for a considerably enhanced accessibility. This study aims at outlining a complete cheminformatics roadmap that frames a mesoscopic Molecular Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application. The molecular fragment cheminformatics roadmap consists of four consecutive building blocks: An adequate fragment structure representation (1), defined operations on these fragment structures (2), the description of compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of a whole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like line notation (denoted f SMILES) with connected molecular fragments to represent a molecular structure. The f SMILES notation and the following concepts and methods for building blocks 2-4 are outlined with examples and practical usage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existing open-source cheminformatics software. Mesoscopic simulation techniques like MFD may be considerably alleviated and broadened for practical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and conceptual usage hurdles. Molecular Fragment Cheminformatics may be regarded as a crucial accelerator to propagate MFD and similar mesoscopic simulation techniques in the molecular sciences. Graphical abstractA molecular fragment cheminformatics roadmap for mesoscopic simulation.

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.

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.

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.

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.

Time-dependent generalized Gibbs ensembles in open quantum systems

NASA Astrophysics Data System (ADS)

Lange, Florian; Lenarčič, Zala; Rosch, Achim

2018-04-01

Generalized Gibbs ensembles have been used as powerful tools to describe the steady state of integrable many-particle quantum systems after a sudden change of the Hamiltonian. Here, we demonstrate numerically that they can be used for a much broader class of problems. We consider integrable systems in the presence of weak perturbations which break both integrability and drive the system to a state far from equilibrium. Under these conditions, we show that the steady state and the time evolution on long timescales can be accurately described by a (truncated) generalized Gibbs ensemble with time-dependent Lagrange parameters, determined from simple rate equations. We compare the numerically exact time evolutions of density matrices for small systems with a theory based on block-diagonal density matrices (diagonal ensemble) and a time-dependent generalized Gibbs ensemble containing only a small number of approximately conserved quantities, using the one-dimensional Heisenberg model with perturbations described by Lindblad operators as an example.

MVL spatiotemporal analysis for model intercomparison in EPS: application to the DEMETER multi-model ensemble

NASA Astrophysics Data System (ADS)

Fernández, J.; Primo, C.; Cofiño, A. S.; Gutiérrez, J. M.; Rodríguez, M. A.

2009-08-01

In a recent paper, Gutiérrez et al. (Nonlinear Process Geophys 15(1):109-114, 2008) introduced a new characterization of spatiotemporal error growth—the so called mean-variance logarithmic (MVL) diagram—and applied it to study ensemble prediction systems (EPS); in particular, they analyzed single-model ensembles obtained by perturbing the initial conditions. In the present work, the MVL diagram is applied to multi-model ensembles analyzing also the effect of model formulation differences. To this aim, the MVL diagram is systematically applied to the multi-model ensemble produced in the EU-funded DEMETER project. It is shown that the shared building blocks (atmospheric and ocean components) impose similar dynamics among different models and, thus, contribute to poorly sampling the model formulation uncertainty. This dynamical similarity should be taken into account, at least as a pre-screening process, before applying any objective weighting method.

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.

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.

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.

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.

The interplay between cooperativity and diversity in model threshold ensembles

PubMed Central

Cervera, Javier; Manzanares, José A.; Mafe, Salvador

2014-01-01

The interplay between cooperativity and diversity is crucial for biological ensembles because single molecule experiments show a significant degree of heterogeneity and also for artificial nanostructures because of the high individual variability characteristic of nanoscale units. We study the cross-effects between cooperativity and diversity in model threshold ensembles composed of individually different units that show a cooperative behaviour. The units are modelled as statistical distributions of parameters (the individual threshold potentials here) characterized by central and width distribution values. The simulations show that the interplay between cooperativity and diversity results in ensemble-averaged responses of interest for the understanding of electrical transduction in cell membranes, the experimental characterization of heterogeneous groups of biomolecules and the development of biologically inspired engineering designs with individually different building blocks. PMID:25142516

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.

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).

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.

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.

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.

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.

Protograph based LDPC codes with minimum distance linearly growing with block size

NASA Technical Reports Server (NTRS)

Divsalar, Dariush; Jones, Christopher; Dolinar, Sam; Thorpe, Jeremy

2005-01-01

We propose several LDPC code constructions that simultaneously achieve good threshold and error floor performance. Minimum distance is shown to grow linearly with block size (similar to regular codes of variable degree at least 3) by considering ensemble average weight enumerators. Our constructions are based on projected graph, or protograph, structures that support high-speed decoder implementations. As with irregular ensembles, our constructions are sensitive to the proportion of degree-2 variable nodes. A code with too few such nodes tends to have an iterative decoding threshold that is far from the capacity threshold. A code with too many such nodes tends to not exhibit a minimum distance that grows linearly in block length. In this paper we also show that precoding can be used to lower the threshold of regular LDPC codes. The decoding thresholds of the proposed codes, which have linearly increasing minimum distance in block size, outperform that of regular LDPC codes. Furthermore, a family of low to high rate codes, with thresholds that adhere closely to their respective channel capacity thresholds, is presented. Simulation results for a few example codes show that the proposed codes have low error floors as well as good threshold SNFt performance.

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.

The interplay between cooperativity and diversity in model threshold ensembles.

PubMed

Cervera, Javier; Manzanares, José A; Mafe, Salvador

2014-10-06

The interplay between cooperativity and diversity is crucial for biological ensembles because single molecule experiments show a significant degree of heterogeneity and also for artificial nanostructures because of the high individual variability characteristic of nanoscale units. We study the cross-effects between cooperativity and diversity in model threshold ensembles composed of individually different units that show a cooperative behaviour. The units are modelled as statistical distributions of parameters (the individual threshold potentials here) characterized by central and width distribution values. The simulations show that the interplay between cooperativity and diversity results in ensemble-averaged responses of interest for the understanding of electrical transduction in cell membranes, the experimental characterization of heterogeneous groups of biomolecules and the development of biologically inspired engineering designs with individually different building blocks. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

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

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

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.

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

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.

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

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.

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.

Application of low energy ion blocking for adsorption site determination of Na Atoms on a Cu(111) surface

NASA Astrophysics Data System (ADS)

Zhang, R.; Makarenko, B.; Bahrim, B.; Rabalais, J. W.

2010-07-01

Ion blocking in the low keV energy range is demonstrated to be a sensitive method for probing surface adsorption sites by means of the technique of time-of-flight scattering and recoiling spectroscopy (TOF-SARS). Adsorbed atoms can block the nearly isotropic backscattering of primary ions from surface atoms in the outmost layers of a crystal. The relative adsorption site position can be derived unambiguously by simple geometrical constructs between the adsorbed atom site and the surface atom sites. Classical ion trajectory simulations using the scattering and recoiling imaging code (SARIC) and molecular dynamics (MD) simulations provide the detailed ion trajectories. Herein we present a quantitative analysis of the blocking effects produced by sub-monolayer Na adsorbed on a Cu(111) surface at room temperature. The results show that the Na adsorption site preferences are different at different Na coverages. At a coverage θ = 0.25 monolayer, Na atoms preferentially populate the fcc threefold surface sites with a height of 2.7 ± 0.1 Å above the 1st layer Cu atoms. At a lower coverage of θ = 0.10 monolayer, there is no adsorption site preference for the Na atoms on the Cu(111) surface.

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).

Rubidium atomic frequency standards for GPS Block IIR

NASA Technical Reports Server (NTRS)

Riley, William J.

1990-01-01

The Rubidium Atomic Frequency Standards (RAFS) were provided for the GPS Block IIR NAVSTAR satellites. These satellites will replenish and upgrade the space segment of the Global Positioning System in the mid 1990s. The GPS RAFS Rb clocks are the latest generation of the high-performance rubidium frequency standards. They offer an aging rate in the low pp 10(exp 14)/day range and a drift-corrected 1-day stability in the low pp 10(exp 14) range. The Block IIR version of these devices will have improved performance, higher reliability, smaller size, and greater radiation hardness. The GPS Block IIR atomic clocks have a natural frequency configuration whereby they output a frequency of about 13.4 MHz that is a submultiple of the atomic resonance of Rb (or Cs). The RAFS operates at a low, fixed C-field for increased stability. The GPS Block IIR RAFS design, including the changes and improvements made, and the test results obtained are described.

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.

Ion blocking dip shape analysis around a LaAlO3/SrTiO3 interface

NASA Astrophysics Data System (ADS)

Jalabert, D.; Zaid, H.; Berger, M. H.; Fongkaew, I.; Lambrecht, W. R. L.; Sehirlioglu, A.

2018-05-01

We present an analysis of the widths of the blocking dips obtained in MEIS ion blocking experiments of two LaAlO3/SrTiO3 heterostructures differing in their LaAlO3 layer thicknesses. In the LaAlO3 layers, the observed blocking dips are larger than expected. This enlargement is the result of the superposition of individual dips at slightly different angular positions revealing a local disorder in the atomic alignment, i.e., layer buckling. By contrast, in the SrTiO3 substrate, just below the interface, the obtained blocking dips are thinner than expected. This thinning indicates that the blocking atoms stand at a larger distance from the scattering center than expected. This is attributed to an accumulation of Sr vacancies at the layer/substrate interface which induces lattice distortions shifting the atoms off the scattering plane.

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

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.

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.

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.

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

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

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

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.

Compressed sensing of hyperspectral images based on scrambled block Hadamard ensemble

NASA Astrophysics Data System (ADS)

Wang, Li; Feng, Yan

2016-11-01

A fast measurement matrix based on scrambled block Hadamard ensemble for compressed sensing (CS) of hyperspectral images (HSI) is investigated. The proposed measurement matrix offers several attractive features. First, the proposed measurement matrix possesses Gaussian behavior, which illustrates that the matrix is universal and requires a near-optimal number of samples for exact reconstruction. In addition, it could be easily implemented in the optical domain due to its integer-valued elements. More importantly, the measurement matrix only needs small memory for storage in the sampling process. Experimental results on HSIs reveal that the reconstruction performance of the proposed measurement matrix is comparable or better than Gaussian matrix and Bernoulli matrix using different reconstruction algorithms while consuming less computational time. The proposed matrix could be used in CS of HSI, which would save the storage memory on board, improve the sampling efficiency, and ameliorate the reconstruction quality.

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.

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.

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.

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.

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.

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.

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.

Photoionization of Atoms and Ions: Application of Time-Dependent Response Method within the Density Functional Theory.

DTIC Science & Technology

1987-10-13

AD-A±95 686 PHOTOIONIZATION OF ATOMS AND IONS: APPLICATION OF III TIME-DEPENDENT RESPONSE..(U) NAVAL RESEARCH LAB WASHINGTON DC U GUPTA ET AL. 13 OCT...on revere if ncemy and idmntify by block number) FIELD GROUP SUBGROUP Photoionization Density functional Atoms Time dependent 1 S. (Continue on...reverse if necenary and identify by block numnbw) The photoionization cross-section of several atoms (AT, Xe, Rn, Cs) and ions (Ne-like Ar, H-like and Li

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.

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.

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

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.

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.

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

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.

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.

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.

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.

Living olefin polymerization processes

DOEpatents

Schrock, Richard R.; Baumann, Robert

1999-01-01

Processes for the living polymerization of olefin monomers with terminal carbon-carbon double bonds are disclosed. The processes employ initiators that include a metal atom and a ligand having two group 15 atoms and a group 16 atom or three group 15 atoms. The ligand is bonded to the metal atom through two anionic or covalent bonds and a dative bond. The initiators are particularly stable under reaction conditions in the absence of olefin monomer. The processes provide polymers having low polydispersities, especially block copolymers having low polydispersities. It is an additional advantage of these processes that, during block copolymer synthesis, a relatively small amount of homopolymer is formed.

Living olefin polymerization processes

DOEpatents

Schrock, R.R.; Baumann, R.

1999-03-30

Processes for the living polymerization of olefin monomers with terminal carbon-carbon double bonds are disclosed. The processes employ initiators that include a metal atom and a ligand having two group 15 atoms and a group 16 atom or three group 15 atoms. The ligand is bonded to the metal atom through two anionic or covalent bonds and a dative bond. The initiators are particularly stable under reaction conditions in the absence of olefin monomer. The processes provide polymers having low polydispersities, especially block copolymers having low polydispersities. It is an additional advantage of these processes that, during block copolymer synthesis, a relatively small amount of homopolymer is formed.

Living olefin polymerization processes

DOEpatents

Schrock, Richard R.; Baumann, Robert

2003-08-26

Processes for the living polymerization of olefin monomers with terminal carbon-carbon double bonds are disclosed. The processes employ initiators that include a metal atom and a ligand having two group 15 atoms and a group 16 atom or three group 15 atoms. The ligand is bonded to the metal atom through two anionic or covalent bonds and a dative bond. The initiators are particularly stable under reaction conditions in the absence of olefin monomer. The processes provide polymers having low polydispersities, especially block copolymers having low polydispersities. It is an additional advantage of these processes that, during block copolymer synthesis, a relatively small amount of homopolymer is formed.

Living olefin polymerization processes

DOEpatents

Schrock, Richard R.; Bauman, Robert

2006-11-14

Processes for the living polymerization of olefin monomers with terminal carbon-carbon double bonds are disclosed. The processes employ initiators that include a metal atom and a ligand having two group 15 atoms and a group 16 atom or three group 15 atoms. The ligand is bonded to the metal atom through two anionic or covalent bonds and a dative bond. The initiators are particularly stable under reaction conditions in the absence of olefin monomer. The processes provide polymers having low polydispersities, especially block copolymers having low polydispersities. It is an additional advantage of these processes that, during block copolymer synthesis, a relatively small amount of homopolymer is formed.

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.

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.

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.

Rain radar measurement error estimation using data assimilation in an advection-based nowcasting system

NASA Astrophysics Data System (ADS)

Merker, Claire; Ament, Felix; Clemens, Marco

2017-04-01

The quantification of measurement uncertainty for rain radar data remains challenging. Radar reflectivity measurements are affected, amongst other things, by calibration errors, noise, blocking and clutter, and attenuation. Their combined impact on measurement accuracy is difficult to quantify due to incomplete process understanding and complex interdependencies. An improved quality assessment of rain radar measurements is of interest for applications both in meteorology and hydrology, for example for precipitation ensemble generation, rainfall runoff simulations, or in data assimilation for numerical weather prediction. Especially a detailed description of the spatial and temporal structure of errors is beneficial in order to make best use of the areal precipitation information provided by radars. Radar precipitation ensembles are one promising approach to represent spatially variable radar measurement errors. We present a method combining ensemble radar precipitation nowcasting with data assimilation to estimate radar measurement uncertainty at each pixel. This combination of ensemble forecast and observation yields a consistent spatial and temporal evolution of the radar error field. We use an advection-based nowcasting method to generate an ensemble reflectivity forecast from initial data of a rain radar network. Subsequently, reflectivity data from single radars is assimilated into the forecast using the Local Ensemble Transform Kalman Filter. The spread of the resulting analysis ensemble provides a flow-dependent, spatially and temporally correlated reflectivity error estimate at each pixel. We will present first case studies that illustrate the method using data from a high-resolution X-band radar network.

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

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

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.

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.

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

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.

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.

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.

Stable statistical representations facilitate visual search.

PubMed

Corbett, Jennifer E; Melcher, David

2014-10-01

Observers represent the average properties of object ensembles even when they cannot identify individual elements. To investigate the functional role of ensemble statistics, we examined how modulating statistical stability affects visual search. We varied the mean and/or individual sizes of an array of Gabor patches while observers searched for a tilted target. In "stable" blocks, the mean and/or local sizes of the Gabors were constant over successive displays, whereas in "unstable" baseline blocks they changed from trial to trial. Although there was no relationship between the context and the spatial location of the target, observers found targets faster (as indexed by faster correct responses and fewer saccades) as the global mean size became stable over several displays. Building statistical stability also facilitated scanning the scene, as measured by larger saccadic amplitudes, faster saccadic reaction times, and shorter fixation durations. These findings suggest a central role for peripheral visual information, creating context to free resources for detailed processing of salient targets and maintaining the illusion of visual stability.

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.

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

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

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.

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.

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

The Elephant in the Room

ERIC Educational Resources Information Center

Williams, David A.

2011-01-01

Practically all teenagers find pleasure in music, yet the majority are not involved in traditional school music ensembles. College requirements, the quest for high grade point averages, scheduling conflicts, uncooperative counselors, block schedules, students with too many competing interests, or the need to work may limit participation in music…

Coupling an Ensemble of Electrons on Superfluid Helium to a Superconducting Circuit

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

Yang, Ge; Fragner, A.; Koolstra, G.

2016-03-01

The quantized lateral motional states and the spin states of electrons trapped on the surface of superfluid helium have been proposed as basic building blocks of a scalable quantum computer. Circuit quantum electrodynamics allows strong dipole coupling between electrons and a high-Q superconducting microwave resonator, enabling such sensitive detection and manipulation of electron degrees of freedom. Here, we present the first realization of a hybrid circuit in which a large number of electrons are trapped on the surface of superfluid helium inside a coplanar waveguide resonator. The high finesse of the resonator allows us to observe large dispersive shifts thatmore » are many times the linewidth and make fast and sensitive measurements on the collective vibrational modes of the electron ensemble, as well as the superfluid helium film underneath. Furthermore, a large ensemble coupling is observed in the dispersive regime during experiment, and it shows excellent agreement with our numeric model. The coupling strength of the ensemble to the cavity is found to be approximate to 1 MHz per electron, indicating the feasibility of achieving single electron strong coupling.« less

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

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.

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.

Atomic layer deposition of ultrathin blocking layer for low-temperature solid oxide fuel cell on nanoporous substrate

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

Yu, Wonjong; Cho, Gu Young; Noh, Seungtak

2015-01-15

An ultrathin yttria-stabilized zirconia (YSZ) blocking layer deposited by atomic layer deposition (ALD) was utilized for improving the performance and reliability of low-temperature solid oxide fuel cells (SOFCs) supported by an anodic aluminum oxide substrate. Physical vapor-deposited YSZ and gadolinia-doped ceria (GDC) electrolyte layers were deposited by a sputtering method. The ultrathin ALD YSZ blocking layer was inserted between the YSZ and GDC sputtered layers. To investigate the effects of an inserted ultrathin ALD blocking layer, SOFCs with and without an ultrathin ALD blocking layer were electrochemically characterized. The open circuit voltage (1.14 V) of the ALD blocking-layered SOFC was visiblymore » higher than that (1.05 V) of the other cell. Furthermore, the ALD blocking layer augmented the power density and improved the reproducibility.« less

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

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.

CELES: CUDA-accelerated simulation of electromagnetic scattering by large ensembles of spheres

NASA Astrophysics Data System (ADS)

Egel, Amos; Pattelli, Lorenzo; Mazzamuto, Giacomo; Wiersma, Diederik S.; Lemmer, Uli

2017-09-01

CELES is a freely available MATLAB toolbox to simulate light scattering by many spherical particles. Aiming at high computational performance, CELES leverages block-diagonal preconditioning, a lookup-table approach to evaluate costly functions and massively parallel execution on NVIDIA graphics processing units using the CUDA computing platform. The combination of these techniques allows to efficiently address large electrodynamic problems (>104 scatterers) on inexpensive consumer hardware. In this paper, we validate near- and far-field distributions against the well-established multi-sphere T-matrix (MSTM) code and discuss the convergence behavior for ensembles of different sizes, including an exemplary system comprising 105 particles.

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.

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.

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.

Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Keller, D. A.; Ornstein, R. L.; Rein, R.

1993-01-01

The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.

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.

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.

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.

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

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.

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.

The seasonal predictability of blocking frequency in two seasonal prediction systems (CMCC, Met-Office) and the associated representation of low-frequency variability.

NASA Astrophysics Data System (ADS)

Athanasiadis, Panos; Gualdi, Silvio; Scaife, Adam A.; Bellucci, Alessio; Hermanson, Leon; MacLachlan, Craig; Arribas, Alberto; Materia, Stefano; Borelli, Andrea

2014-05-01

Low-frequency variability is a fundamental component of the atmospheric circulation. Extratropical teleconnections, the occurrence of blocking and the slow modulation of the jet streams and storm tracks are all different aspects of low-frequency variability. Part of the latter is attributed to the chaotic nature of the atmosphere and is inherently unpredictable. On the other hand, primarily as a response to boundary forcings, tropospheric low-frequency variability includes components that are potentially predictable. Seasonal forecasting faces the difficult task of predicting these components. Particularly referring to the extratropics, the current generation of seasonal forecasting systems seem to be approaching this target by realistically initializing most components of the climate system, using higher resolution and utilizing large ensemble sizes. Two seasonal prediction systems (Met-Office GloSea and CMCC-SPS-v1.5) are analyzed in terms of their representation of different aspects of extratropical low-frequency variability. The current operational Met-Office system achieves unprecedented high scores in predicting the winter-mean phase of the North Atlantic Oscillation (NAO, corr. 0.74 at 500 hPa) and the Pacific-N. American pattern (PNA, corr. 0.82). The CMCC system, considering its small ensemble size and course resolution, also achieves good scores (0.42 for NAO, 0.51 for PNA). Despite these positive features, both models suffer from biases in low-frequency variance, particularly in the N. Atlantic. Consequently, it is found that their intrinsic variability patterns (sectoral EOFs) differ significantly from the observed, and the known teleconnections are underrepresented. Regarding the representation of N. hemisphere blocking, after bias correction both systems exhibit a realistic climatology of blocking frequency. In this assessment, instantaneous blocking and large-scale persistent blocking events are identified using daily geopotential height fields at 500 hPa. Given a documented strong relationship between high-latitude N. Atlantic blocking and the NAO, one would expect a predictive skill for the seasonal frequency of blocking comparable to that of the NAO. However, this remains elusive. Future efforts should be in the direction of reducing model biases not only in the mean but also in variability (band-passed variances).

Atmospheric blocking in the Climate SPHINX simulations: the role of orography and resolution

NASA Astrophysics Data System (ADS)

Davini, Paolo; Corti, Susanna; D'Andrea, Fabio; Riviere, Gwendal; von Hardenberg, Jost

2017-04-01

The representation of atmospheric blocking in numerical simulations, especially over the Euro-Atlantic region, still represents a main concern for the climate modelling community. We here discuss the Northern Hemisphere winter atmospheric blocking representation in a set of 30-year simulations which has been performed in the framework of the PRACE project "Climate SPHINX". Simulations were run using the EC-Earth Global Climate Model with several ensemble members at 5 different horizontal resolutions (ranging from 125 km to 16 km). Results show that the negative bias in blocking frequency over Europe becomes negligible at resolutions of about 40 km and finer. However, the blocking duration is still underestimated by 1-2 days, suggesting that the correct blocking frequencies are achieved with an overestimation of the number of blocking onsets. The reasons leading to such improvements are then discussed, highlighting the role of orography in shaping the Atlantic jet stream: at higher resolution the jet is weaker and less penetrating over Europe, favoring the breaking of synoptic Rossby waves over the Atlantic stationary ridge and thus increasing the simulated blocking frequency.

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

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.

Supramolecular chemistry-general principles and selected examples from anion recognition and metallosupramolecular chemistry.

PubMed

Albrecht, Markus

2007-12-01

This review gives an introduction into supramolecular chemistry describing in the first part general principles, focusing on terms like noncovalent interaction, molecular recognition, self-assembly, and supramolecular function. In the second part those will be illustrated by simple examples from our laboratories. Supramolecular chemistry is the science that bridges the gap between the world of molecules and nanotechnology. In supramolecular chemistry noncovalent interactions occur between molecular building blocks, which by molecular recognition and self-assembly form (functional) supramolecular entities. It is also termed the "chemistry of the noncovalent bond." Molecular recognition is based on geometrical complementarity based on the "key-and-lock" principle with nonshape-dependent effects, e.g., solvatization, being also highly influential. Self-assembly leads to the formation of well-defined aggregates. Hereby the overall structure of the target ensemble is controlled by the symmetry features of the certain building blocks. Finally, the aggregates can possess special properties or supramolecular functions, which are only found in the ensemble but not in the participating molecules. This review gives an introduction on supramolecular chemistry and illustrates the fundamental principles by recent examples from our group.

PREPARATION OF BLOCK COPOLYMERS OF POLY(STYRENE) AND POLY(T-BUTYL ACRYLATE) OF VARIOUS MOLECULAR WEIGHTS AND ARCHITECTURES BY ATOM TRANSFER RADICAL POLYMERIZATION. (R826735)

EPA Science Inventory

Block copolymers of polystyrene and poly(t-butyl acrylate) were prepared using atom transfer radical polymerization techniques. These polymers were synthesized with a CuBr/N,N,N,NInteractive vs. Non-Interactive Multi-Model Ensembles

NASA Astrophysics Data System (ADS)

Duane, G. S.

2013-12-01

If the members of an ensemble of different models are allowed to interact with one another in run time, predictive skill can be improved as compared to that of any individual model or any average of indvidual model outputs. Inter-model connections in such an interactive ensemble can be trained, using historical data, so that the resulting ``supermodel' synchronizes with reality when used in weather-prediction mode, where the individual models perform data assimilation from each other (with trainable inter-model 'observation error') as well as from real observations. In climate-projection mode, parameters of the individual models are changed, as might occur from an increase in GHG levels, and one obtains relevant statistical properties of the new supermodel attractor. In simple cases, it has been shown that training of the inter-model connections with the old parameter values gives a supermodel that is still predictive when the parameter values are changed. Here we inquire as to the circumstances under which supermodel performance can be expected to exceed that of the customary weighted average of model outputs. We consider a supermodel formed from quasigeostrophic (QG) channel models with different forcing coefficients, and introduce an effective training scheme for the inter-model connections. We show that the blocked-zonal index cycle is reproduced better by the supermodel than by any non-interactive ensemble in the extreme case where the forcing coefficients of the different models are very large or very small. With realistic differences in forcing coefficients, as would be representative of actual differences among IPCC-class models, the usual linearity assumption is justified and a weighted average of model outputs is adequate. It is therefore hypothesized that supermodeling is likely to be useful in situations where there are qualitative model differences, as arising from sub-gridscale parameterizations, that affect overall model behavior. Otherwise the usual ex post facto averaging will probably suffice. The advantage of supermodeling is seen in statistics such as anticorrelation between blocking activity in the Atlantic and Pacific sectors, in the case of the QG channel model, rather than in overall blocking frequency. Likewise in climate models, the advantage of supermodeling is typically manifest in higher-order statistics rather than in quantities such as mean temperature.

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.

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.

Sequential updating of multimodal hydrogeologic parameter fields using localization and clustering techniques

NASA Astrophysics Data System (ADS)

Sun, Alexander Y.; Morris, Alan P.; Mohanty, Sitakanta

2009-07-01

Estimated parameter distributions in groundwater models may contain significant uncertainties because of data insufficiency. Therefore, adaptive uncertainty reduction strategies are needed to continuously improve model accuracy by fusing new observations. In recent years, various ensemble Kalman filters have been introduced as viable tools for updating high-dimensional model parameters. However, their usefulness is largely limited by the inherent assumption of Gaussian error statistics. Hydraulic conductivity distributions in alluvial aquifers, for example, are usually non-Gaussian as a result of complex depositional and diagenetic processes. In this study, we combine an ensemble Kalman filter with grid-based localization and a Gaussian mixture model (GMM) clustering techniques for updating high-dimensional, multimodal parameter distributions via dynamic data assimilation. We introduce innovative strategies (e.g., block updating and dimension reduction) to effectively reduce the computational costs associated with these modified ensemble Kalman filter schemes. The developed data assimilation schemes are demonstrated numerically for identifying the multimodal heterogeneous hydraulic conductivity distributions in a binary facies alluvial aquifer. Our results show that localization and GMM clustering are very promising techniques for assimilating high-dimensional, multimodal parameter distributions, and they outperform the corresponding global ensemble Kalman filter analysis scheme in all scenarios considered.

Gibbs Ensemble Simulations of the Solvent Swelling of Polymer Films

NASA Astrophysics Data System (ADS)

Gartner, Thomas; Epps, Thomas, III; Jayaraman, Arthi

Solvent vapor annealing (SVA) is a useful technique to tune the morphology of block polymer, polymer blend, and polymer nanocomposite films. Despite SVA's utility, standardized SVA protocols have not been established, partly due to a lack of fundamental knowledge regarding the interplay between the polymer(s), solvent, substrate, and free-surface during solvent annealing and evaporation. An understanding of how to tune polymer film properties in a controllable manner through SVA processes is needed. Herein, the thermodynamic implications of the presence of solvent in the swollen polymer film is explored through two alternative Gibbs ensemble simulation methods that we have developed and extended: Gibbs ensemble molecular dynamics (GEMD) and hybrid Monte Carlo (MC)/molecular dynamics (MD). In this poster, we will describe these simulation methods and demonstrate their application to polystyrene films swollen by toluene and n-hexane. Polymer film swelling experiments, Gibbs ensemble molecular simulations, and polymer reference interaction site model (PRISM) theory are combined to calculate an effective Flory-Huggins χ (χeff) for polymer-solvent mixtures. The effects of solvent chemistry, solvent content, polymer molecular weight, and polymer architecture on χeff are examined, providing a platform to control and understand the thermodynamics of polymer film swelling.

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.

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.

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.

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

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

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.

Total Scattering Analysis of Disordered Nanosheet Materials

NASA Astrophysics Data System (ADS)

Metz, Peter C.

Two dimensional materials are of increasing interest as building blocks for functional coatings, catalysts, and electrochemical devices. While increasingly sophisticated processing routes have been designed to obtain high-quality exfoliated nanosheets and controlled, self-assembled mesostructures, structural characterization of these materials remains challenging. This work presents a novel method of analyzing pair distribution function (PDF) data for disordered nanosheet ensembles, where supercell stacking models are used to infer atom correlations over as much as 50 A. Hierarchical models are used to reduce the parameter space of the refined model and help eliminate strongly correlated parameters. Three data sets for restacked nanosheet assemblies with stacking disorder are analyzed using these methods: simulated data for graphene-like layers, experimental data for 1 nm thick perovskite layers, and experimental data for highly defective delta-MnO2 layers. In each case, the sensitivity of the PDF to the real-space distribution of layer positions is demonstrated by exploring the fit residual as a function of stacking vectors. The refined models demonstrate that nanosheets tend towards local interlayer ordering, which is hypothesized to be driven by the electrostatic potential of the layer surfaces. Correctly accounting for interlayer atom correlations permits more accurate refinement of local structural details including local structure perturbations and defect site occupancies. In the delta-MnO2 nanosheet material, the new modeling approach identified 14% Mn vacancies while application of 3D periodic crystalline models to the < 7 A PDF region suggests a 25% vacancy concentration. In contrast, the perovskite nanosheet material is demonstrated to exhibit almost negligible structural relaxation in contrast with the bulk crystalline material from which it is derived.

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.

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.

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.

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

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.

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.

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.

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.

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.

The Effects of Technology on the Sight-Reading Achievement of Beginning Choir Students

ERIC Educational Resources Information Center

Petty, Colleen; Henry, Michele L.

2014-01-01

The ultimate goal for many choral directors is to develop independent musicians within the ensemble. The ability to sing a series of pitches and rhythms at first sight is widely understood to be a fundamental building block of independent musicianship. Yet sight-reading is not simply a holistic skill. There are separate components of…

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

The Design, Fabrication and Characterization of a Transparent Atom Chip

PubMed Central

Chuang, Ho-Chiao; Huang, Chia-Shiuan; Chen, Hung-Pin; Huang, Chi-Sheng; Lin, Yu-Hsin

2014-01-01

This study describes the design and fabrication of transparent atom chips for atomic physics experiments. A fabrication process was developed to define the wire patterns on a transparent glass substrate to create the desired magnetic field for atom trapping experiments. An area on the chip was reserved for the optical access, so that the laser light can penetrate directly through the glass substrate for the laser cooling process. Furthermore, since the thermal conductivity of the glass substrate is poorer than other common materials for atom chip substrate, for example silicon, silicon carbide, aluminum nitride. Thus, heat dissipation copper blocks are designed on the front and back of the glass substrate to improve the electrical current conduction. The testing results showed that a maximum burnout current of 2 A was measured from the wire pattern (with a width of 100 μm and a height of 20 μm) without any heat dissipation design and it can increase to 2.5 A with a heat dissipation design on the front side of the atom chips. Therefore, heat dissipation copper blocks were designed and fabricated on the back of the glass substrate just under the wire patterns which increases the maximum burnout current to 4.5 A. Moreover, a maximum burnout current of 6 A was achieved when the entire backside glass substrate was recessed and a thicker copper block was electroplated, which meets most requirements of atomic physics experiments. PMID:24922456

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.

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

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.

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.

Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks.

PubMed

Saravanan, Chandra; Shao, Yihan; Baer, Roi; Ross, Philip N; Head-Gordon, Martin

2003-04-15

A sparse matrix multiplication scheme with multiatom blocks is reported, a tool that can be very useful for developing linear-scaling methods with atom-centered basis functions. Compared to conventional element-by-element sparse matrix multiplication schemes, efficiency is gained by the use of the highly optimized basic linear algebra subroutines (BLAS). However, some sparsity is lost in the multiatom blocking scheme because these matrix blocks will in general contain negligible elements. As a result, an optimal block size that minimizes the CPU time by balancing these two effects is recovered. In calculations on linear alkanes, polyglycines, estane polymers, and water clusters the optimal block size is found to be between 40 and 100 basis functions, where about 55-75% of the machine peak performance was achieved on an IBM RS6000 workstation. In these calculations, the blocked sparse matrix multiplications can be 10 times faster than a standard element-by-element sparse matrix package. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 618-622, 2003

New thiol-responsive mono-cleavable block copolymer micelles labeled with single disulfides.

PubMed

Sourkohi, Behnoush Khorsand; Schmidt, Rolf; Oh, Jung Kwon

2011-10-18

Thiol-responsive symmetric triblock copolymers having single disulfide linkages in the middle blocks (called mono-cleavable block copolymers, ss-ABP(2)) were synthesized by atom transfer radical polymerization in the presence of a disulfide-labeled difunctional Br-initiator. These brush-like triblock copolymers consist of a hydrophobic polyacrylate block having pendent oligo(propylene oxide) and a hydrophilic polymethacrylate block having pendent oligo(ethylene oxide). Gel permeation chromatography and (1)H NMR results confirmed the synthesis of well-defined mono-cleavable block copolymers and revealed that polymerizations were well controlled. Because of amphiphilic nature, these copolymers self-assembled to form colloidally stable micelles above critical micellar concentration of 0.032 mg · mL(-1). In response to reductive reactions, disulfides in thiol-responsive micelles were cleaved. Atomic force microscopy and dynamic light scattering analysis suggested that the cleavage of disulfides caused dissociation of micelles to smaller-sized assembled structures in water. Moreover, in a biomedical perspective, the mono-cleavable block copolymer micelles are not cytotoxic and thus biocompatible. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

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.

Molecular Building Block-Based Electronic Charges for High-Throughput Screening of Metal-Organic Frameworks for Adsorption Applications.

PubMed

Argueta, Edwin; Shaji, Jeena; Gopalan, Arun; Liao, Peilin; Snurr, Randall Q; Gómez-Gualdrón, Diego A

2018-01-09

Metal-organic frameworks (MOFs) are porous crystalline materials with attractive properties for gas separation and storage. Their remarkable tunability makes it possible to create millions of MOF variations but creates the need for fast material screening to identify promising structures. Computational high-throughput screening (HTS) is a possible solution, but its usefulness is tied to accurate predictions of MOF adsorption properties. Accurate adsorption simulations often require an accurate description of electrostatic interactions, which depend on the electronic charges of the MOF atoms. HTS-compatible methods to assign charges to MOF atoms need to accurately reproduce electrostatic potentials (ESPs) and be computationally affordable, but current methods present an unsatisfactory trade-off between computational cost and accuracy. We illustrate a method to assign charges to MOF atoms based on ab initio calculations on MOF molecular building blocks. A library of building blocks with built-in charges is thus created and used by an automated MOF construction code to create hundreds of MOFs with charges "inherited" from the constituent building blocks. The molecular building block-based (MBBB) charges are similar to REPEAT charges-which are charges that reproduce ESPs obtained from ab initio calculations on crystallographic unit cells of nanoporous crystals-and thus similar predictions of adsorption loadings, heats of adsorption, and Henry's constants are obtained with either method. The presented results indicate that the MBBB method to assign charges to MOF atoms is suitable for use in computational high-throughput screening of MOFs for applications that involve adsorption of molecules such as carbon dioxide.

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.

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.

Oligosaccharide/silicon-containing block copolymers with 5 nm features for lithographic applications.

PubMed

Cushen, Julia D; Otsuka, Issei; Bates, Christopher M; Halila, Sami; Fort, Sébastien; Rochas, Cyrille; Easley, Jeffrey A; Rausch, Erica L; Thio, Anthony; Borsali, Redouane; Willson, C Grant; Ellison, Christopher J

2012-04-24

Block copolymers demonstrate potential for use in next-generation lithography due to their ability to self-assemble into well-ordered periodic arrays on the 3-100 nm length scale. The successful lithographic application of block copolymers relies on three critical conditions being met: high Flory-Huggins interaction parameters (χ), which enable formation of <10 nm features, etch selectivity between blocks for facile pattern transfer, and thin film self-assembly control. The present paper describes the synthesis and self-assembly of block copolymers composed of naturally derived oligosaccharides coupled to a silicon-containing polystyrene derivative synthesized by activators regenerated by electron transfer atom transfer radical polymerization. The block copolymers have a large χ and a low degree of polymerization (N) enabling formation of 5 nm feature diameters, incorporate silicon in one block for oxygen reactive ion etch contrast, and exhibit bulk and thin film self-assembly of hexagonally packed cylinders facilitated by a combination of spin coating and solvent annealing techniques. As observed by small angle X-ray scattering and atomic force microscopy, these materials exhibit some of the smallest block copolymer features in the bulk and in thin films reported to date.

On the importance of the heterogeneity assumption in the characterization of reservoir geomechanical properties

NASA Astrophysics Data System (ADS)

Zoccarato, C.; Baù, D.; Bottazzi, F.; Ferronato, M.; Gambolati, G.; Mantica, S.; Teatini, P.

2016-10-01

The geomechanical analysis of a highly compartmentalized reservoir is performed to simulate the seafloor subsidence due to gas production. The available observations over the hydrocarbon reservoir consist of bathymetric surveys carried out before and at the end of a 10-yr production life. The main goal is the calibration of the reservoir compressibility cM, that is, the main geomechanical parameter controlling the surface response. Two conceptual models are considered: in one (i) cM varies only with the depth and the vertical effective stress (heterogeneity due to lithostratigraphic variability); in another (ii) cM varies also in the horizontal plane, that is, it is spatially distributed within the reservoir stratigraphic units. The latter hypothesis accounts for a possible partitioning of the reservoir due to the presence of sealing faults and thrusts that suggests the idea of a block heterogeneous system with the number of reservoir blocks equal to the number of uncertain parameters. The method applied here relies on an ensemble-based data assimilation (DA) algorithm (i.e. the ensemble smoother, ES), which incorporates the information from the bathymetric measurements into the geomechanical model response to infer and reduce the uncertainty of the parameter cM. The outcome from conceptual model (i) indicates that DA is effective in reducing the cM uncertainty. However, the maximum settlement still remains underestimated, while the areal extent of the subsidence bowl is overestimated. We demonstrate that the selection of the heterogeneous conceptual model (ii) allows to reproduce much better the observations thus removing a clear bias of the model structure. DA allows significantly reducing the cM uncertainty in the five blocks (out of the seven) characterized by large volume and large pressure decline. Conversely, the assimilation of land displacements only partially constrains the prior cM uncertainty in the reservoir blocks marginally contributing to the cumulative seafloor subsidence, that is, blocks with low pressure.

29 CFR Appendix E to Subpart L of... - Test Methods for Protective Clothing

Code of Federal Regulations, 2010 CFR

2010-07-01

... test ensemble consisting of the sample unit, the two prepared blocks, a piece of leather outsole 10 to... perpendicular to the 1-inch (2.5 cm) edge. B. Apparatus. (i) Six-ounce (.17 kg) weight tension clamps shall be used so designed that the six ounces (.17 kg) of weight are distributed evenly across the complete...

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.

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.

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.

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.

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.

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.

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.;

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.

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

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.

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.

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

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.

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

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

Neuromuscular blocking properties of some bistropinium esters

PubMed Central

Haining, C. G.; Johnston, R. G.

1962-01-01

The neuromuscular blocking, anti-acetylcholine and ganglion blocking properties of two series of bistropinium esters were examined. The neuromuscular blocking activities of the mandelic acid esters of NN'-polymethylenebis(tropinium halides) were found to depend upon the number of carbon atoms (n) in the linking chain. Potency was enhanced more than 50 times as n was increased from 2 to 7. Compounds in which n equalled 7, 8, 9, 10 and 12 differed little in activity, but were generally more potent than tubocurarine in cats and rabbits. A peak of ganglion blocking action was obtained at the pentamethylene member. Esterification enhanced the feeble neuromuscular blocking properties of NN'-decamethylenebis(tropinium halide), the mandelic acid ester being more effective than the tropic, benzoic or phenylacetic acid esters in cats and rabbits. When two benzoic or mandelic acid esters of tropine were linked through their nitrogen atoms by a phenylenedimethyl grouping (-CH2.C6H4.CH2-), meta substitution was more effective than was ortho or para in producing neuromuscular block. The effectiveness of esterifying acids in m-phenylenedimethyl derivatives decreased in the following order, phenylacetic> tropic or mandelic>benzoic>acetic and diphenylacetic. PMID:13903721

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.

Hydrogen Bonding Stabilized Self-Assembly of Inorganic Nanoparticles: Mechanism and Collective Properties.

PubMed

Yue, Mingli; Li, Yanchun; Hou, Ying; Cao, Wenxin; Zhu, Jiaqi; Han, Jiecai; Lu, Zhongyuan; Yang, Ming

2015-06-23

Developing a simple and efficient method to organize nanoscale building blocks into ordered superstructures, understanding the mechanism for self-assembly and revealing the essential collective properties are crucial steps toward the practical use of nanostructures in nanotechnology-based applications. In this study, we showed that the high-yield formation of ZnO nanoparticle chains with micrometer length can be readily achieved by the variation of solvents from methanol to water. Spectroscopic studies confirmed the solvent effect on the surface properties of ZnO nanoparticles, which were found to be critical for the formation of anisotropic assemblies. Quantum mechanical calculations and all atom molecular dynamic simulations indicated the contribution of hydrogen bonding for stabilizing the structure in water. Dissipative particle dynamics further revealed the importance of solvent-nanoparticle interactions for promoting one-dimensional self-assembly. The branching of chains was found upon aging, resulting in the size increase of the ensembles and network formation. Steady-state and time-resolved luminescent spectroscopes, which probed the variation of defect-related emission, revealed stronger Forster resonance energy transfer (FRET) between nanoparticles when the chain networks were formed. The high efficiency of FRET quenching can be ascribed to the presence of multiple energy transfer channels, as well as the short internanoparticle distances and the dipole alignment.

Layer-by-layer assembly of two-dimensional materials into wafer-scale heterostructures

NASA Astrophysics Data System (ADS)

Kang, Kibum; Lee, Kan-Heng; Han, Yimo; Gao, Hui; Xie, Saien; Muller, David A.; Park, Jiwoong

2017-10-01

High-performance semiconductor films with vertical compositions that are designed to atomic-scale precision provide the foundation for modern integrated circuitry and novel materials discovery. One approach to realizing such films is sequential layer-by-layer assembly, whereby atomically thin two-dimensional building blocks are vertically stacked, and held together by van der Waals interactions. With this approach, graphene and transition-metal dichalcogenides--which represent one- and three-atom-thick two-dimensional building blocks, respectively--have been used to realize previously inaccessible heterostructures with interesting physical properties. However, no large-scale assembly method exists at present that maintains the intrinsic properties of these two-dimensional building blocks while producing pristine interlayer interfaces, thus limiting the layer-by-layer assembly method to small-scale proof-of-concept demonstrations. Here we report the generation of wafer-scale semiconductor films with a very high level of spatial uniformity and pristine interfaces. The vertical composition and properties of these films are designed at the atomic scale using layer-by-layer assembly of two-dimensional building blocks under vacuum. We fabricate several large-scale, high-quality heterostructure films and devices, including superlattice films with vertical compositions designed layer-by-layer, batch-fabricated tunnel device arrays with resistances that can be tuned over four orders of magnitude, band-engineered heterostructure tunnel diodes, and millimetre-scale ultrathin membranes and windows. The stacked films are detachable, suspendable and compatible with water or plastic surfaces, which will enable their integration with advanced optical and mechanical systems.

Layer-by-layer assembly of two-dimensional materials into wafer-scale heterostructures.

PubMed

Kang, Kibum; Lee, Kan-Heng; Han, Yimo; Gao, Hui; Xie, Saien; Muller, David A; Park, Jiwoong

2017-10-12

High-performance semiconductor films with vertical compositions that are designed to atomic-scale precision provide the foundation for modern integrated circuitry and novel materials discovery. One approach to realizing such films is sequential layer-by-layer assembly, whereby atomically thin two-dimensional building blocks are vertically stacked, and held together by van der Waals interactions. With this approach, graphene and transition-metal dichalcogenides-which represent one- and three-atom-thick two-dimensional building blocks, respectively-have been used to realize previously inaccessible heterostructures with interesting physical properties. However, no large-scale assembly method exists at present that maintains the intrinsic properties of these two-dimensional building blocks while producing pristine interlayer interfaces, thus limiting the layer-by-layer assembly method to small-scale proof-of-concept demonstrations. Here we report the generation of wafer-scale semiconductor films with a very high level of spatial uniformity and pristine interfaces. The vertical composition and properties of these films are designed at the atomic scale using layer-by-layer assembly of two-dimensional building blocks under vacuum. We fabricate several large-scale, high-quality heterostructure films and devices, including superlattice films with vertical compositions designed layer-by-layer, batch-fabricated tunnel device arrays with resistances that can be tuned over four orders of magnitude, band-engineered heterostructure tunnel diodes, and millimetre-scale ultrathin membranes and windows. The stacked films are detachable, suspendable and compatible with water or plastic surfaces, which will enable their integration with advanced optical and mechanical systems.

The First Row Anomaly and Recoupled Pair Bonding in the Halides of the Late p-Block Elements

PubMed Central

2012-01-01

The dramatic differences between the properties of molecules formed from the late p-block elements of the first row of the periodic table (N–F) and those of the corresponding elements in subsequent rows is well recognized as the first row anomaly. Certain properties of the atoms, such as the relative energies and spatial extents of the ns and np orbitals, can explain some of these differences, but not others. In this Account, we summarize the results of our recent computational studies of the halides of the late p-block elements. Our studies point to a single underlying cause for many of these differences: the ability of the late p-block elements in the second and subsequent rows of the periodic table to form recoupled pair bonds and recoupled pair bond dyads with very electronegative ligands. Recoupled pair bonds form when an electron in a singly occupied ligand orbital recouples the pair of electrons in a doubly occupied lone pair orbital on the central atom, leading to a central atom-ligand bond. Recoupled pair bond dyads occur when a second ligand forms a bond with the orbital left over from the initial recoupled pair bond. Recoupled pair bonds and recoupled pair bond dyads enable the late p-block elements to form remarkably stable hypervalent compounds such as PF5 and SF6 and lead to unexpected excited states in smaller halides of the late p-block elements such as SF and SF2. Recoupled pair bonding also causes the Fn–1X–F bond energies to oscillate dramatically once the normal valences of the central atoms have been satisfied. In addition, recoupled pair bonding provides a lower-energy pathway for inversion in heavily fluorinated compounds (PF3 and PF2H, but not PH2F and PH3) and leads to unusual intermediates and products in reactions involving halogens and late p-block element compounds, such as (CH3)2S + F2. Although this Account focuses on the halides of the second row, late p-block elements, recoupled pair bonds and recoupled pair bond dyads are important in the chemistry of p-block elements beyond the second row (As, Se, and Br) and for compounds of these elements with other very electronegative ligands, such as OH and O. Knowledge of recoupled pair bonding is thus critical to understanding the properties and reactivity of molecules containing the late p-block elements beyond the first row. PMID:23151313

The first row anomaly and recoupled pair bonding in the halides of the late p-block elements.

PubMed

Dunning, Thom H; Woon, David E; Leiding, Jeff; Chen, Lina

2013-02-19

The dramatic differences between the properties of molecules formed from the late p-block elements of the first row of the periodic table (N-F) and those of the corresponding elements in subsequent rows is well recognized as the first row anomaly. Certain properties of the atoms, such as the relative energies and spatial extents of the ns and np orbitals, can explain some of these differences, but not others. In this Account, we summarize the results of our recent computational studies of the halides of the late p-block elements. Our studies point to a single underlying cause for many of these differences: the ability of the late p-block elements in the second and subsequent rows of the periodic table to form recoupled pair bonds and recoupled pair bond dyads with very electronegative ligands. Recoupled pair bonds form when an electron in a singly occupied ligand orbital recouples the pair of electrons in a doubly occupied lone pair orbital on the central atom, leading to a central atom-ligand bond. Recoupled pair bond dyads occur when a second ligand forms a bond with the orbital left over from the initial recoupled pair bond. Recoupled pair bonds and recoupled pair bond dyads enable the late p-block elements to form remarkably stable hypervalent compounds such as PF(5) and SF(6) and lead to unexpected excited states in smaller halides of the late p-block elements such as SF and SF(2). Recoupled pair bonding also causes the F(n-1)X-F bond energies to oscillate dramatically once the normal valences of the central atoms have been satisfied. In addition, recoupled pair bonding provides a lower-energy pathway for inversion in heavily fluorinated compounds (PF(3) and PF(2)H, but not PH(2)F and PH(3)) and leads to unusual intermediates and products in reactions involving halogens and late p-block element compounds, such as (CH(3))(2)S + F(2). Although this Account focuses on the halides of the second row, late p-block elements, recoupled pair bonds and recoupled pair bond dyads are important in the chemistry of p-block elements beyond the second row (As, Se, and Br) and for compounds of these elements with other very electronegative ligands, such as OH and O. Knowledge of recoupled pair bonding is thus critical to understanding the properties and reactivity of molecules containing the late p-block elements beyond the first row.

Fabrication of Ordered Nanopattern by using ABC Triblock Copolymer with Salt in Toluene.

PubMed

Huang, Hailiang; Zhong, Benbin; Zu, Xihong; Luo, Hongsheng; Lin, Wenjing; Zhang, Minghai; Zhong, Yazhou; Yi, Guobin

2017-08-15

Ordered nanopatterns of triblock copolymer polystyrene-block-poly(2-vinylpyridine)-block- poly (ethylene oxide)(PS-b-P2VP-b-PEO) have been achieved by the addition of lithium chloride (LiCl). The morphological and structural evolution of PS-b-P2VP-b-PEO/LiCl thin films were systematically investigated by varying different experimental parameters, including the treatment for polymer solution after the addition of LiCl, the time scale of ultrasonic treatment and the molar ratio of Li + ions to the total number of oxygen atoms (O) in PEO block and the nitrogen atoms (N) in P2VP block. When toluene was used as the solvent for LiCl, ordered nanopattern with cylinders or nanostripes could be obtained after spin-coating. The mechanism of nanopattern transformation was related to the loading of LiCl in different microdomains.

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.

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.

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

High Infrared Blocking Cellulose Film Based on Amorphous to Anatase Transition of TiO2 via Atomic Layer Deposition.

PubMed

Li, Wenbin; Li, Linfeng; Wu, Xi; Li, Junyu; Jiang, Lang; Yang, Hongjun; Ke, Guizhen; Cao, Genyang; Deng, Bo; Xu, Weilin

2018-06-27

A high IR-blocking cellulose film was designed based on an amorphous to anatase transition of TiO 2 using atomic layer deposition (ALD). This transition was realized at 250 °C, at which the cellulose is thermal stable. Optimized ALD condition of 250 °C and 1200 cycles give us an excellent heat insulator, which could significantly reduce the enclosed space temperature from 59.2 to 51.9 °C after exposure to IR lamp for 5 min.

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.

Mechanics of deformations in terms of scalar variables

NASA Astrophysics Data System (ADS)

Ryabov, Valeriy A.

2017-05-01

Theory of particle and continuous mechanics is developed which allows a treatment of pure deformation in terms of the set of variables "coordinate-momentum-force" instead of the standard treatment in terms of tensor-valued variables "strain-stress." This approach is quite natural for a microscopic description of atomic system, according to which only pointwise forces caused by the stress act to atoms making a body deform. The new concept starts from affine transformation of spatial to material coordinates in terms of the stretch tensor or its analogs. Thus, three principal stretches and three angles related to their orientation form a set of six scalar variables to describe deformation. Instead of volume-dependent potential used in the standard theory, which requires conditions of equilibrium for surface and body forces acting to a volume element, a potential dependent on scalar variables is introduced. A consistent introduction of generalized force associated with this potential becomes possible if a deformed body is considered to be confined on the surface of torus having six genuine dimensions. Strain, constitutive equations and other fundamental laws of the continuum and particle mechanics may be neatly rewritten in terms of scalar variables. Giving a new presentation for finite deformation new approach provides a full treatment of hyperelasticity including anisotropic case. Derived equations of motion generate a new kind of thermodynamical ensemble in terms of constant tension forces. In this ensemble, six internal deformation forces proportional to the components of Irving-Kirkwood stress are controlled by applied external forces. In thermodynamical limit, instead of the pressure and volume as state variables, this ensemble employs deformation force measured in kelvin unit and stretch ratio.

Pt Single Atoms Embedded in the Surface of Ni Nanocrystals as Highly Active Catalysts for Selective Hydrogenation of Nitro Compounds.

PubMed

Peng, Yuhan; Geng, Zhigang; Zhao, Songtao; Wang, Liangbing; Li, Hongliang; Wang, Xu; Zheng, Xusheng; Zhu, Junfa; Li, Zhenyu; Si, Rui; Zeng, Jie

2018-06-13

Single-atom catalysts exhibit high selectivity in hydrogenation due to their isolated active sites, which ensure uniform adsorption configurations of substrate molecules. Compared with the achievement in catalytic selectivity, there is still a long way to go in exploiting the catalytic activity of single-atom catalysts. Herein, we developed highly active and selective catalysts in selective hydrogenation by embedding Pt single atoms in the surface of Ni nanocrystals (denoted as Pt 1 /Ni nanocrystals). During the hydrogenation of 3-nitrostyrene, the TOF numbers based on surface Pt atoms of Pt 1 /Ni nanocrystals reached ∼1800 h -1 under 3 atm of H 2 at 40 °C, much higher than that of Pt single atoms supported on active carbon, TiO 2 , SiO 2 , and ZSM-5. Mechanistic studies reveal that the remarkable activity of Pt 1 /Ni nanocrystals derived from sufficient hydrogen supply because of spontaneous dissociation of H 2 on both Pt and Ni atoms as well as facile diffusion of H atoms on Pt 1 /Ni nanocrystals. Moreover, the ensemble composed of the Pt single atom and nearby Ni atoms in Pt 1 /Ni nanocrystals leads to the adsorption configuration of 3-nitrostyrene favorable for the activation of nitro groups, accounting for the high selectivity for 3-vinylaniline.

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.

Integrative, Dynamic Structural Biology at Atomic Resolution—It’s About Time

PubMed Central

van den Bedem, Henry; Fraser, James S.

2015-01-01

Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, and other techniques are helping us realize the dream of seeing—in atomic detail—how different parts of biomolecules exchange between functional sub-states using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR, and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution. PMID:25825836

Free-energy landscape of the villin headpiece in an all-atom force field.

PubMed

Herges, Thomas; Wenzel, Wolfgang

2005-04-01

We investigate the landscape of the internal free-energy of the 36 amino acid villin headpiece with a modified basin hopping method in the all-atom force field PFF01, which was previously used to predictively fold several helical proteins with atomic resolution. We identify near native conformations of the protein as the global optimum of the force field. More than half of the twenty best simulations started from random initial conditions converge to the folding funnel of the native conformation, but several competing low-energy metastable conformations were observed. From 76,000 independently generated conformations we derived a decoy tree which illustrates the topological structure of the entire low-energy part of the free-energy landscape and characterizes the ensemble of metastable conformations. These emerge as similar in secondary content, but differ in tertiary arrangement.

Deterministic Squeezed States with Collective Measurements and Feedback.

PubMed

Cox, Kevin C; Greve, Graham P; Weiner, Joshua M; Thompson, James K

2016-03-04

We demonstrate the creation of entangled, spin-squeezed states using a collective, or joint, measurement and real-time feedback. The pseudospin state of an ensemble of N=5×10^{4} laser-cooled ^{87}Rb atoms is deterministically driven to a specified population state with angular resolution that is a factor of 5.5(8) [7.4(6) dB] in variance below the standard quantum limit for unentangled atoms-comparable to the best enhancements using only unitary evolution. Without feedback, conditioning on the outcome of the joint premeasurement, we directly observe up to 59(8) times [17.7(6) dB] improvement in quantum phase variance relative to the standard quantum limit for N=4×10^{5}  atoms. This is one of the largest reported entanglement enhancements to date in any system.

PHARAO flight model: optical on ground performance tests

NASA Astrophysics Data System (ADS)

Lévèque, T.; Faure, B.; Esnault, F. X.; Grosjean, O.; Delaroche, C.; Massonnet, D.; Escande, C.; Gasc, Ph.; Ratsimandresy, A.; Béraud, S.; Buffe, F.; Torresi, P.; Larivière, Ph.; Bernard, V.; Bomer, T.; Thomin, S.; Salomon, C.; Abgrall, M.; Rovera, D.; Moric, I.; Laurent, Ph.

2017-11-01

PHARAO (Projet d'Horloge Atomique par Refroidissement d'Atomes en Orbite), which has been developed by CNES, is the first primary frequency standard specially designed for operation in space. PHARAO is the main instrument of the ESA mission ACES (Atomic Clock Ensemble in Space). ACES payload will be installed on-board the International Space Station (ISS) to perform fundamental physics experiments. All the sub-systems of the Flight Model (FM) have now passed the qualification process and the whole FM of the cold cesium clock, PHARAO, is being assembled and will undergo extensive tests. The expected performances in space are frequency accuracy less than 3.10-16 (with a final goal at 10-16) and frequency stability of 10-13 τ-1/2. In this paper, we focus on the laser source performances and the main results on the cold atom manipulation.

Intrinsic Folding Proclivities in Cyclic β-Peptide Building Blocks: Configuration and Heteroatom Effects Analyzed by Conformer-Selective Spectroscopy and Quantum Chemistry.

PubMed

Alauddin, Mohammad; Gloaguen, Eric; Brenner, Valérie; Tardivel, Benjamin; Mons, Michel; Zehnacker-Rentien, Anne; Declerck, Valérie; Aitken, David J

2015-11-09

This work describes the use of conformer-selective laser spectroscopy following supersonic expansion to probe the local folding proclivities of four-membered ring cyclic β-amino acid building blocks. Emphasis is placed on stereochemical effects as well as on the structural changes induced by the replacement of a carbon atom of the cycle by a nitrogen atom. The amide A IR spectra are obtained and interpreted with the help of quantum chemistry structure calculations. Results provide evidence that the building block with a trans-substituted cyclobutane ring has a predilection to form strong C8 hydrogen bonds. Nitrogen-atom substitution in the ring induces the formation of the hydrazino turn, with a related but distinct hydrogen-bonding network: the structure is best viewed as a bifurcated C8/C5 bond with the N heteroatom lone electron pair playing a significant acceptor role, which supports recent observations on the hydrazino turn structure in solution. Surprisingly, this study shows that the cis-substituted cyclobutane ring derivative also gives rise predominantly to a C8 hydrogen bond, although weaker than in the two former cases, a feature that is not often encountered for this building block. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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).

Edge usage, motifs, and regulatory logic for cell cycling genetic networks

NASA Astrophysics Data System (ADS)

Zagorski, M.; Krzywicki, A.; Martin, O. C.

2013-01-01

The cell cycle is a tightly controlled process, yet it shows marked differences across species. Which of its structural features follow solely from the ability to control gene expression? We tackle this question in silico by examining the ensemble of all regulatory networks which satisfy the constraint of producing a given sequence of gene expressions. We focus on three cell cycle profiles coming from baker's yeast, fission yeast, and mammals. First, we show that the networks in each of the ensembles use just a few interactions that are repeatedly reused as building blocks. Second, we find an enrichment in network motifs that is similar in the two yeast cell cycle systems investigated. These motifs do not have autonomous functions, yet they reveal a regulatory logic for cell cycling based on a feed-forward cascade of activating interactions.

Resonant Laser Manipulation of an Atomic Beam

DTIC Science & Technology

2010-07-01

similar species such as alkali metals . 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF PAGES...resonant laser-atom interaction with other rarefied and collisional solvers for similar species such as alkali metals . Keywords: atomic beam, cesium...a target flow over length scales which push the limits of physical manufacture. The ability to create masks, beam blocks, controlling electric

Synthesis of two-dimensional TlxBi1−x compounds and Archimedean encoding of their atomic structure

PubMed Central

Gruznev, Dimitry V.; Bondarenko, Leonid V.; Matetskiy, Andrey V.; Mihalyuk, Alexey N.; Tupchaya, Alexandra Y.; Utas, Oleg A.; Eremeev, Sergey V.; Hsing, Cheng-Rong; Chou, Jyh-Pin; Wei, Ching-Ming; Zotov, Andrey V.; Saranin, Alexander A.

2016-01-01

Crystalline atomic layers on solid surfaces are composed of a single building block, unit cell, that is copied and stacked together to form the entire two-dimensional crystal structure. However, it appears that this is not an unique possibility. We report here on synthesis and characterization of the one-atomic-layer-thick TlxBi1−x compounds which display quite a different arrangement. It represents a quasi-periodic tiling structures that are built by a set of tiling elements as building blocks. Though the layer is lacking strict periodicity, it shows up as an ideally-packed tiling of basic elements without any skips or halting. The two-dimensional TlxBi1−x compounds were formed by depositing Bi onto the Tl-covered Si(111) surface where Bi atoms substitute appropriate amount of Tl atoms. Atomic structure of each tiling element as well as arrangement of TlxBi1−x compounds were established in a detail. Electronic properties and spin texture of the selected compounds having periodic structures were characterized. The shown example demonstrates possibility for the formation of the exotic low-dimensional materials via unusual growth mechanisms. PMID:26781340

All-atom ensemble modeling to analyze small angle X-ray scattering of glycosylated proteins

PubMed Central

Guttman, Miklos; Weinkam, Patrick; Sali, Andrej; Lee, Kelly K.

2013-01-01

Summary The flexible and heterogeneous nature of carbohydrate chains often renders glycoproteins refractory to traditional structure determination methods. Small Angle X-ray scattering (SAXS) can be a useful tool for obtaining structural information of these systems. All-atom modeling of glycoproteins with flexible glycan chains was applied to interpret the solution SAXS data for a set of glycoproteins. For simpler systems (single glycan, with a well defined protein structure), all-atom modeling generates models in excellent agreement with the scattering pattern, and reveals the approximate spatial occupancy of the glycan chain in solution. For more complex systems (several glycan chains, or unknown protein substructure), the approach can still provide insightful models, though the orientations of glycans become poorly determined. Ab initio shape reconstructions appear to capture the global morphology of glycoproteins, but in most cases offer little information about glycan spatial occupancy. The all-atom modeling methodology is available as a webserver at http://modbase.compbio.ucsf.edu/allosmod-foxs. PMID:23473666

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

Keldysh approach for nonequilibrium phase transitions in quantum optics: Beyond the Dicke model in optical cavities

NASA Astrophysics Data System (ADS)

Torre, Emanuele G. Dalla; Diehl, Sebastian; Lukin, Mikhail D.; Sachdev, Subir; Strack, Philipp

2013-02-01

We investigate nonequilibrium phase transitions for driven atomic ensembles interacting with a cavity mode and coupled to a Markovian dissipative bath. In the thermodynamic limit and at low frequencies, we show that the distribution function of the photonic mode is thermal, with an effective temperature set by the atom-photon interaction strength. This behavior characterizes the static and dynamic critical exponents of the associated superradiance transition. Motivated by these considerations, we develop a general Keldysh path-integral approach that allows us to study physically relevant nonlinearities beyond the idealized Dicke model. Using standard diagrammatic techniques, we take into account the leading-order corrections due to the finite number N of atoms. For finite N, the photon mode behaves as a damped classical nonlinear oscillator at finite temperature. For the atoms, we propose a Dicke action that can be solved for any N and correctly captures the atoms’ depolarization due to dissipative dephasing.

Block Copolymers: Synthesis and Applications in Nanotechnology

NASA Astrophysics Data System (ADS)

Lou, Qin

This study is focused on the synthesis and study of (block) copolymers using reversible deactivation radical polymerizations (RDRPs), including atom transfer radical polymerization (ATRP) and reversible addition-fragmentation chain transfer (RAFT) polymerization. In particular, two primary areas of study are undertaken: (1) a proof-of-concept application of lithographic block copolymers, and (2) the mechanistic study of the deposition of titania into block copolymer templates for the production of well-ordered titania nanostructures. Block copolymers have the ability to undergo microphase separation, with an average size of each microphase ranging from tens to hundreds of nanometers. As such, block copolymers have been widely considered for nanotechnological applications over the past two decades. The development of materials for various nanotechnologies has become an increasingly studied area as improvements in many applications, such as those found in the semiconductor and photovoltaic industries are constantly being sought. Significant growth in developments of new synthetic methods ( i.e. RDRPs) has allowed the production of block copolymers with molecular (and sometimes atomic) definition. In turn, this has greatly expanded the use of block copolymers in nanotechnology. Herein, we describe the synthesis of statistical and block copolymers of 193 nm photolithography methacrylate and acrylate resist monomers with norbornyl and adamantyl moieties using RAFT polymerization.. For these resist (block) copolymers, the phase separation behaviors were examined by atomic force microscopy (AFM). End groups were removed from the polymers to avoid complications during the photolithography since RAFT end groups absorb visible light. Poly(glycidyl methacrylate-block-polystyrene) (PGMA-b-PS) was synthesize by ATRP and demonstrated that this block copolymer acts as both a lithographic UV (365 nm) photoresist and a self-assembly material. The PGMA segments can undergo cationic ring-opening crosslinking and can act as a negative-tone photoresist. The PGMA-b-PS thin films were also studied for phase separation with ˜25 nm patterns using transmission electron microscopy (TEM). Poly(styrene-block-4-vinyl pyridine) (PS-b-P4VP) block copolymer thin films are shown to form perpendicular cylinder phase separated structures, and these may be used to template the formation of ordered titania nanostructures with sub-50 nm diameters on either silicon or indium tin oxide (ITO) substrates. A study of the mechanism of TiO2 formation within the P4VP cylinder phase was developed and tested. It was found that the titania nanostructure morphology is affected by pH and deposition temperatures, and successful deposition required the cross-linking of the P4VP phase in order to obtain individual nanostructures.

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.

Soliton Dynamics of an Atomic Spinor Condensate on a Ring Lattice

DTIC Science & Technology

2013-02-22

REPORT Soliton dynamics of an atomic spinor condensate on a Ring Lattice 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: We study the dynamics of...8/98) Prescribed by ANSI Std. Z39.18 - Soliton dynamics of an atomic spinor condensate on a Ring Lattice Report Title ABSTRACT We study the dynamics...Report Number Soliton dynamics of an atomic spinor condensat Block 13: Supplementary Note © 2013 . Published in Physical Review A (accepted), Vol. Ed

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

Superradiance of cold atoms coupled to a superconducting circuit

NASA Astrophysics Data System (ADS)

Braun, Daniel; Hoffman, Jonathan; Tiesinga, Eite

2011-06-01

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

Wavevector multiplexed atomic quantum memory via spatially-resolved single-photon detection.

PubMed

Parniak, Michał; Dąbrowski, Michał; Mazelanik, Mateusz; Leszczyński, Adam; Lipka, Michał; Wasilewski, Wojciech

2017-12-15

Parallelized quantum information processing requires tailored quantum memories to simultaneously handle multiple photons. The spatial degree of freedom is a promising candidate to facilitate such photonic multiplexing. Using a single-photon resolving camera, we demonstrate a wavevector multiplexed quantum memory based on a cold atomic ensemble. Observation of nonclassical correlations between Raman scattered photons is confirmed by an average value of the second-order correlation function [Formula: see text] in 665 separated modes simultaneously. The proposed protocol utilizing the multimode memory along with the camera will facilitate generation of multi-photon states, which are a necessity in quantum-enhanced sensing technologies and as an input to photonic quantum circuits.

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

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.

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.

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.

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 MD simulations restrained via crystallographic data: Accurate structure leads to accurate dynamics

PubMed Central

Xue, Yi; Skrynnikov, Nikolai R

2014-01-01

Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free-energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD simulation of protein crystal is essentially an ensemble simulation involving multiple protein molecules in a crystal unit cell (or a block of unit cells). To ensure that average protein coordinates remain correct during the simulation, we introduced crystallography-based restraints into the MD protocol. Because these restraints are aimed at the ensemble-average structure, they have only minimal impact on conformational dynamics of the individual protein molecules. So long as the average structure remains reasonable, the proteins move in a native-like fashion as dictated by the original force field. To validate this approach, we have used the data from solid-state NMR spectroscopy, which is the orthogonal experimental technique uniquely sensitive to protein local dynamics. The new method has been tested on the well-established model protein, ubiquitin. The ensemble-restrained MD simulations produced lower crystallographic R factors than conventional simulations; they also led to more accurate predictions for crystallographic temperature factors, solid-state chemical shifts, and backbone order parameters. The predictions for 15N R1 relaxation rates are at least as accurate as those obtained from conventional simulations. Taken together, these results suggest that the presented trajectories may be among the most realistic protein MD simulations ever reported. In this context, the ensemble restraints based on high-resolution crystallographic data can be viewed as protein-specific empirical corrections to the standard force fields. PMID:24452989

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

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.

Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble.

PubMed

A Rohrdanz, Mary; Zheng, Wenwei; Lambeth, Bradley; Vreede, Jocelyne; Clementi, Cecilia

2014-10-01

The nature of the optical cycle of photoactive yellow protein (PYP) makes its elucidation challenging for both experiment and theory. The long transition times render conventional simulation methods ineffective, and yet the short signaling-state lifetime makes experimental data difficult to obtain and interpret. Here, through an innovative combination of computational methods, a prediction and analysis of the biological signaling state of PYP is presented. Coarse-grained modeling and locally scaled diffusion map are first used to obtain a rough bird's-eye view of the free energy landscape of photo-activated PYP. Then all-atom reconstruction, followed by an enhanced sampling scheme; diffusion map-directed-molecular dynamics are used to focus in on the signaling-state region of configuration space and obtain an ensemble of signaling state structures. To the best of our knowledge, this is the first time an all-atom reconstruction from a coarse grained model has been performed in a relatively unexplored region of molecular configuration space. We compare our signaling state prediction with previous computational and more recent experimental results, and the comparison is favorable, which validates the method presented. This approach provides additional insight to understand the PYP photo cycle, and can be applied to other systems for which more direct methods are impractical.

Caoxite-hydroxyapatite composition as consolidating material for the chalk stone from Basarabi-Murfatlar churches ensemble

NASA Astrophysics Data System (ADS)

Ion, Rodica-Mariana; Turcanu-Caruţiu, Daniela; Fierăscu, Radu-Claudiu; Fierăscu, Irina; Bunghez, Ioana-Raluca; Ion, Mihaela-Lucia; Teodorescu, Sofia; Vasilievici, Gabriel; Rădiţoiu, Valentin

2015-12-01

The development of new composition for surface conservation of some architectural monuments represents now an important research topic. The Basarabi-Murfatlar Ensemble, recognized as the first religious monument from mediaeval Dobrogea (Romania) (from 9th to 11th century), is one of the most impressive archaeological sites of Europe. This ensemble is built from amorphous calcium carbonate, very sensitive to humidity, frost, salts, etc. The aim of this paper is to test on chalk stone samples a new consolidant - hydroxyapatite (HAp) mixed with calcium oxalate trihydrate (caoxite) (COT). Some specific techniques for evaluation its impact on chalk stone surface are used, as follows: petrographical and physical-chemical techniques: SEM, OM, ICP-AES, TGA, FTIR and Raman spectroscopy, chromatic parameters changes, the accelerated weathering tests: heating, freeze-thaw, and their effects on porosity and capillary water uptake by the chalk surface. All these have been evaluated before and after treatment with COT-HAp, putting into evidence the effect of the new composition on the chalk stone surface. HAp induces COT stabilization, and their joint composition can bind weathered stone blocks providing a substantial reinforcement of chalk surface.

Towards a true protein movie: a perspective on the potential impact of the ensemble-based structure determination using exact NOEs.

PubMed

Vögeli, Beat; Orts, Julien; Strotz, Dean; Chi, Celestine; Minges, Martina; Wälti, Marielle Aulikki; Güntert, Peter; Riek, Roland

2014-04-01

Confined by the Boltzmann distribution of the energies of the states, a multitude of structural states are inherent to biomolecules. For a detailed understanding of a protein's function, its entire structural landscape at atomic resolution and insight into the interconversion between all the structural states (i.e. dynamics) are required. Whereas dedicated trickery with NMR relaxation provides aspects of local dynamics, and 3D structure determination by NMR is well established, only recently have several attempts been made to formulate a more comprehensive description of the dynamics and the structural landscape of a protein. Here, a perspective is given on the use of exact NOEs (eNOEs) for the elucidation of structural ensembles of a protein describing the covered conformational space. Copyright © 2013 Elsevier Inc. All rights reserved.

All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds

PubMed Central

2017-01-01

Recent advances in understanding protein folding have benefitted from coarse-grained representations of protein structures. Empirical energy functions derived from these techniques occasionally succeed in distinguishing native structures from their corresponding ensembles of nonnative folds or decoys which display varying degrees of structural dissimilarity to the native proteins. Here we utilized atomic coordinates of single protein chains, comprising a large diverse training set, to develop and evaluate twelve all-atom four-body statistical potentials obtained by exploring alternative values for a pair of inherent parameters. Delaunay tessellation was performed on the atomic coordinates of each protein to objectively identify all quadruplets of interacting atoms, and atomic potentials were generated via statistical analysis of the data and implementation of the inverted Boltzmann principle. Our potentials were evaluated using benchmarking datasets from Decoys-‘R'-Us, and comparisons were made with twelve other physics- and knowledge-based potentials. Ranking 3rd, our best potential tied CHARMM19 and surpassed AMBER force field potentials. We illustrate how a generalized version of our potential can be used to empirically calculate binding energies for target-ligand complexes, using HIV-1 protease-inhibitor complexes for a practical application. The combined results suggest an accurate and efficient atomic four-body statistical potential for protein structure prediction and assessment. PMID:29119109

Single-Atom Catalysts of Precious Metals for Electrochemical Reactions.

PubMed

Kim, Jiwhan; Kim, Hee-Eun; Lee, Hyunjoo

2018-01-10

Single-atom catalysts (SACs), in which metal atoms are dispersed on the support without forming nanoparticles, have been used for various heterogeneous reactions and most recently for electrochemical reactions. In this Minireview, recent examples of single-atom electrocatalysts used for the oxygen reduction reaction (ORR), hydrogen oxidation reaction (HOR), hydrogen evolution reaction (HER), formic acid oxidation reaction (FAOR), and methanol oxidation reaction (MOR) are introduced. Many density functional theory (DFT) simulations have predicted that SACs may be effective for CO 2 reduction to methane or methanol production while suppressing H 2 evolution, and those cases are introduced here as well. Single atoms, mainly Pt single atoms, have been deposited on TiN or TiC nanoparticles, defective graphene nanosheets, N-doped covalent triazine frameworks, graphitic carbon nitride, S-doped zeolite-templated carbon, and Sb-doped SnO 2 surfaces. Scanning transmission electron microscopy, extended X-ray absorption fine structure measurement, and in situ infrared spectroscopy have been used to detect the single-atom structure and confirm the absence of nanoparticles. SACs have shown high mass activity, minimizing the use of precious metal, and unique selectivity distinct from nanoparticle catalysts owing to the absence of ensemble sites. Additional features that SACs should possess for effective electrochemical applications were also suggested. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Resolution Sensitivity of Northern Hemisphere Blocking in Four 25-km Atmospheric Global Circulation Models

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

Schiemann, Reinhard; Demory, Marie-Estelle; Shaffrey, Len C.

The aim of this study is to investigate if the representation of Northern Hemisphere blocking is sensitive to resolution in current-generation atmospheric global circulation models (AGCMs). An evaluation is thus conducted of how well atmospheric blocking is represented in four AGCMs whose horizontal resolution is increased from a grid spacing of more than 100 km to about 25 km. It is shown that Euro-Atlantic blocking is simulated overall more credibly at higher resolution (i.e., in better agreement with a 50-yr reference blocking climatology created from the reanalyses ERA-40 and ERA-Interim). The improvement seen with resolution depends on the season andmore » to some extent on the model considered. Euro-Atlantic blocking is simulated more realistically at higher resolution in winter, spring, and autumn, and robustly so across the model ensemble. The improvement in spring is larger than that in winter and autumn. Summer blocking is found to be better simulated at higher resolution by one model only, with little change seen in the other three models. The representation of Pacific blocking is not found to systematically depend on resolution. Despite the improvements seen with resolution, the 25-km models still exhibit large biases in Euro-Atlantic blocking. For example, three of the four 25-km models underestimate winter northern European blocking frequency by about one-third. The resolution sensitivity and biases in the simulated blocking are shown to be in part associated with the mean-state biases in the models' midlatitude circulation.« less

The Resolution Sensitivity of Northern Hemisphere Blocking in Four 25-km Atmospheric Global Circulation Models

DOE PAGES

Schiemann, Reinhard; Demory, Marie-Estelle; Shaffrey, Len C.; ...

2016-12-19

The aim of this study is to investigate if the representation of Northern Hemisphere blocking is sensitive to resolution in current-generation atmospheric global circulation models (AGCMs). An evaluation is thus conducted of how well atmospheric blocking is represented in four AGCMs whose horizontal resolution is increased from a grid spacing of more than 100 km to about 25 km. It is shown that Euro-Atlantic blocking is simulated overall more credibly at higher resolution (i.e., in better agreement with a 50-yr reference blocking climatology created from the reanalyses ERA-40 and ERA-Interim). The improvement seen with resolution depends on the season andmore » to some extent on the model considered. Euro-Atlantic blocking is simulated more realistically at higher resolution in winter, spring, and autumn, and robustly so across the model ensemble. The improvement in spring is larger than that in winter and autumn. Summer blocking is found to be better simulated at higher resolution by one model only, with little change seen in the other three models. The representation of Pacific blocking is not found to systematically depend on resolution. Despite the improvements seen with resolution, the 25-km models still exhibit large biases in Euro-Atlantic blocking. For example, three of the four 25-km models underestimate winter northern European blocking frequency by about one-third. The resolution sensitivity and biases in the simulated blocking are shown to be in part associated with the mean-state biases in the models' midlatitude circulation.« less

Atomic solid state energy scale: Universality and periodic trends in oxidation state

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

Pelatt, Brian D.; Kokenyesi, Robert S.; Ravichandran, Ram

2015-11-15

The atomic solid state energy (SSE) scale originates from a plot of the electron affinity (EA) and ionization potential (IP) versus band gap (E{sub G}). SSE is estimated for a given atom by assessing an average EA (for a cation) or an average IP (for an anion) for binary inorganic compounds having that specific atom as a constituent. Physically, SSE is an experimentally-derived average frontier orbital energy referenced to the vacuum level. In its original formulation, 69 binary closed-shell inorganic semiconductors and insulators were employed as a database, providing SSE estimates for 40 elements. In this contribution, EA and IPmore » versus E{sub G} are plotted for an additional 92 compounds, thus yielding SSE estimates for a total of 64 elements from the s-, p-, d-, and f-blocks of the periodic table. Additionally, SSE is refined to account for its dependence on oxidation state. Although most cations within the SSE database are found to occur in a single oxidation state, data are available for nine d-block transition metals and one p-block main group metal in more than one oxidation state. SSE is deeper in energy for a higher cation oxidation state. Two p-block main group non-metals within the SSE database are found to exist in both positive and negative oxidation states so that they can function as a cation or anion. SSEs for most cations are positioned above −4.5 eV with respect to the vacuum level, and SSEs for all anions are positioned below. Hence, the energy −4.5 eV, equal to the hydrogen donor/acceptor ionization energy ε(+/−) or equivalently the standard hydrogen electrode energy, is considered to be an absolute energy reference for chemical bonding in the solid state. - Highlights: • Atomic solid-state energies are estimated for 64 elements from experimental data. • The relationship between atomic SSEs and oxidation state is assessed. • Cations are positioned above and absolute energy of −4.5 eV and anions below.« less

Boosting Contextual Information for Deep Neural Network Based Voice Activity Detection

DTIC Science & Technology

2015-02-01

multi-resolution stacking (MRS), which is a stack of ensemble classifiers. Each classifier in a building block inputs the concatenation of the predictions ...a base classifier in MRS, named boosted deep neural network (bDNN). bDNN first generates multiple base predictions from different contexts of a single...frame by only one DNN and then aggregates the base predictions for a better prediction of the frame, and it is different from computationally

Developing Density of Laser-Cooled Neutral Atoms and Molecules in a Linear Magnetic Trap

NASA Astrophysics Data System (ADS)

Velasquez, Joe, III; Walstrom, Peter; di Rosa, Michael

2013-05-01

In this poster we show that neutral particle injection and accumulation using laser-induced spin flips may be used to form dense ensembles of ultracold magnetic particles, i.e., laser-cooled paramagnetic atoms and molecules. Particles are injected in a field-seeking state, are switched by optical pumping to a field-repelled state, and are stored in the minimum-B trap. The analogous process in high-energy charged-particle accumulator rings is charge-exchange injection using stripper foils. The trap is a linear array of sextupoles capped by solenoids. Particle-tracking calculations and design of our linear accumulator along with related experiments involving 7Li will be presented. We test these concepts first with atoms in preparation for later work with selected molecules. Finally, we present our preliminary results with CaH, our candidate molecule for laser cooling. This project is funded by the LDRD program of Los Alamos National Laboratory.

Entanglement-Enhanced Phase Estimation without Prior Phase Information

NASA Astrophysics Data System (ADS)

Colangelo, G.; Martin Ciurana, F.; Puentes, G.; Mitchell, M. W.; Sewell, R. J.

2017-06-01

We study the generation of planar quantum squeezed (PQS) states by quantum nondemolition (QND) measurement of an ensemble of Rb 87 atoms with a Poisson distributed atom number. Precise calibration of the QND measurement allows us to infer the conditional covariance matrix describing the Fy and Fz components of the PQS states, revealing the dual squeezing characteristic of PQS states. PQS states have been proposed for single-shot phase estimation without prior knowledge of the likely values of the phase. We show that for an arbitrary phase, the generated PQS states can give a metrological advantage of at least 3.1 dB relative to classical states. The PQS state also beats, for most phase angles, single-component-squeezed states generated by QND measurement with the same resources and atom number statistics. Using spin squeezing inequalities, we show that spin-spin entanglement is responsible for the metrological advantage.

The ACES mission: scientific objectives and present status

NASA Astrophysics Data System (ADS)

Cacciapuoti, L.; Dimarcq, N.; Salomon, C.

2017-11-01

"Atomic Clock Ensemble in Space" (ACES) is a mission in fundamental physics that will operate a new generation of atomic clocks in the microgravity environment of the International Space Station (ISS). The ACES clock signal will combine the medium term frequency stability of a space hydrogen maser (SHM) and the long term stability and accuracy of a frequency standard based on cold cesium atoms (PHARAO). Fractional frequency stability and accuracy of few parts in 1016 will be achieved. The on-board time base distributed on Earth via a microwave link (MWL) will be used to test fundamental laws of physics (Einstein's theories of Special and General Relativity, Standard Model Extension, string theories…) and to develop applications in time and frequency metrology, universal time scales, global positioning and navigation, geodesy and gravimetry. After a general overview on the mission concept and its scientific objectives, the present status of ACES instruments and sub-systems will be discussed.

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

Revealing the distinct folding phases of an RNA three-helix junction.

PubMed

Plumridge, Alex; Katz, Andrea M; Calvey, George D; Elber, Ron; Kirmizialtin, Serdal; Pollack, Lois

2018-05-14

Remarkable new insight has emerged into the biological role of RNA in cells. RNA folding and dynamics enable many of these newly discovered functions, calling for an understanding of RNA self-assembly and conformational dynamics. Because RNAs pass through multiple structures as they fold, an ensemble perspective is required to visualize the flow through fleetingly populated sets of states. Here, we combine microfluidic mixing technology and small angle X-ray scattering (SAXS) to measure the Mg-induced folding of a small RNA domain, the tP5abc three helix junction. Our measurements are interpreted using ensemble optimization to select atomically detailed structures that recapitulate each experimental curve. Structural ensembles, derived at key stages in both time-resolved studies and equilibrium titrations, reproduce the features of known intermediates, and more importantly, offer a powerful new structural perspective on the time-progression of folding. Distinct collapse phases along the pathway appear to be orchestrated by specific interactions with Mg ions. These key interactions subsequently direct motions of the backbone that position the partners of tertiary contacts for later bonding, and demonstrate a remarkable synergy between Mg and RNA across numerous time-scales.

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

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

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

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.

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.

Precipitation of energetic neutral atoms and induced non-thermal escape fluxes from the Martian atmosphere

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

Lewkow, N. R.; Kharchenko, V.

2014-08-01

The precipitation of energetic neutral atoms, produced through charge exchange collisions between solar wind ions and thermal atmospheric gases, is investigated for the Martian atmosphere. Connections between parameters of precipitating fast ions and resulting escape fluxes, altitude-dependent energy distributions of fast atoms and their coefficients of reflection from the Mars atmosphere, are established using accurate cross sections in Monte Carlo (MC) simulations. Distributions of secondary hot (SH) atoms and molecules, induced by precipitating particles, have been obtained and applied for computations of the non-thermal escape fluxes. A new collisional database on accurate energy-angular-dependent cross sections, required for description of themore » energy-momentum transfer in collisions of precipitating particles and production of non-thermal atmospheric atoms and molecules, is reported with analytic fitting equations. Three-dimensional MC simulations with accurate energy-angular-dependent cross sections have been carried out to track large ensembles of energetic atoms in a time-dependent manner as they propagate into the Martian atmosphere and transfer their energy to the ambient atoms and molecules. Results of the MC simulations on the energy-deposition altitude profiles, reflection coefficients, and time-dependent atmospheric heating, obtained for the isotropic hard sphere and anisotropic quantum cross sections, are compared. Atmospheric heating rates, thermalization depths, altitude profiles of production rates, energy distributions of SH atoms and molecules, and induced escape fluxes have been determined.« less

Phasic and tonic neuron ensemble codes for stimulus-environment conjunctions in the lateral entorhinal cortex.

PubMed

Pilkiw, Maryna; Insel, Nathan; Cui, Younghua; Finney, Caitlin; Morrissey, Mark D; Takehara-Nishiuchi, Kaori

2017-07-06

The lateral entorhinal cortex (LEC) is thought to bind sensory events with the environment where they took place. To compare the relative influence of transient events and temporally stable environmental stimuli on the firing of LEC cells, we recorded neuron spiking patterns in the region during blocks of a trace eyeblink conditioning paradigm performed in two environments and with different conditioning stimuli. Firing rates of some neurons were phasically selective for conditioned stimuli in a way that depended on which room the rat was in; nearly all neurons were tonically selective for environments in a way that depended on which stimuli had been presented in those environments. As rats moved from one environment to another, tonic neuron ensemble activity exhibited prospective information about the conditioned stimulus associated with the environment. Thus, the LEC formed phasic and tonic codes for event-environment associations, thereby accurately differentiating multiple experiences with overlapping features.

An Ensemble of Atomic Fountains

DTIC Science & Technology

2012-05-01

1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 ph as e (n s) 56000559005580055700 MJD 8 10-16 2 4 6 8 10-15 2 4 ov er la pp in g Al la n de vi at io n 104... Metrologia 49, 49-56 (2012). [3] N. Ashby et al., Phys. Rev. Lett. 98, 070802 (2007). [4] S. J. Ferrell, et al., Phys. Rev. A 76, 062104 (2007). [5] T. M

WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis

PubMed Central

Zwier, Matthew C.; Adelman, Joshua L.; Kaus, Joseph W.; Pratt, Adam J.; Wong, Kim F.; Rego, Nicholas B.; Suárez, Ernesto; Lettieri, Steven; Wang, David W.; Grabe, Michael; Zuckerman, Daniel M.; Chong, Lillian T.

2015-01-01

The weighted ensemble (WE) path sampling approach orchestrates an ensemble of parallel calculations with intermittent communication to enhance the sampling of rare events, such as molecular associations or conformational changes in proteins or peptides. Trajectories are replicated and pruned in a way that focuses computational effort on under-explored regions of configuration space while maintaining rigorous kinetics. To enable the simulation of rare events at any scale (e.g. atomistic, cellular), we have developed an open-source, interoperable, and highly scalable software package for the execution and analysis of WE simulations: WESTPA (The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis). WESTPA scales to thousands of CPU cores and includes a suite of analysis tools that have been implemented in a massively parallel fashion. The software has been designed to interface conveniently with any dynamics engine and has already been used with a variety of molecular dynamics (e.g. GROMACS, NAMD, OpenMM, AMBER) and cell-modeling packages (e.g. BioNetGen, MCell). WESTPA has been in production use for over a year, and its utility has been demonstrated for a broad set of problems, ranging from atomically detailed host-guest associations to non-spatial chemical kinetics of cellular signaling networks. The following describes the design and features of WESTPA, including the facilities it provides for running WE simulations, storing and analyzing WE simulation data, as well as examples of input and output. PMID:26392815

Atomic Basic Blocks

NASA Astrophysics Data System (ADS)

Scheler, Fabian; Mitzlaff, Martin; Schröder-Preikschat, Wolfgang

Die Entscheidung, einen zeit- bzw. ereignisgesteuerten Ansatz für ein Echtzeitsystem zu verwenden, ist schwierig und sehr weitreichend. Weitreichend vor allem deshalb, weil diese beiden Ansätze mit äußerst unterschiedlichen Kontrollflussabstraktionen verknüpft sind, die eine spätere Migration zum anderen Paradigma sehr schwer oder gar unmöglich machen. Wir schlagen daher die Verwendung einer Zwischendarstellung vor, die unabhängig von der jeweils verwendeten Kontrollflussabstraktion ist. Für diesen Zweck verwenden wir auf Basisblöcken basierende Atomic Basic Blocks (ABB) und bauen darauf ein Werkzeug, den Real-Time Systems Compiler (RTSC) auf, der die Migration zwischen zeit- und ereignisgesteuerten Systemen unterstützt.

Inertial rotation measurement with atomic spins: From angular momentum conservation to quantum phase theory

NASA Astrophysics Data System (ADS)

Zhang, C.; Yuan, H.; Tang, Z.; Quan, W.; Fang, J. C.

2016-12-01

Rotation measurement in an inertial frame is an important technology for modern advanced navigation systems and fundamental physics research. Inertial rotation measurement with atomic spin has demonstrated potential in both high-precision applications and small-volume low-cost devices. After rapid development in the last few decades, atomic spin gyroscopes are considered a promising competitor to current conventional gyroscopes—from rate-grade to strategic-grade applications. Although it has been more than a century since the discovery of the relationship between atomic spin and mechanical rotation by Einstein [Naturwissenschaften, 3(19) (1915)], research on the coupling between spin and rotation is still a focus point. The semi-classical Larmor precession model is usually adopted to describe atomic spin gyroscope measurement principles. More recently, the geometric phase theory has provided a different view of the rotation measurement mechanism via atomic spin. The theory has been used to describe a gyroscope based on the nuclear spin ensembles in diamond. A comprehensive understanding of inertial rotation measurement principles based on atomic spin would be helpful for future applications. This work reviews different atomic spin gyroscopes and their rotation measurement principles with a historical overlook. In addition, the spin-rotation coupling mechanism in the context of the quantum phase theory is presented. The geometric phase is assumed to be the origin of the measurable rotation signal from atomic spins. In conclusion, with a complete understanding of inertial rotation measurements using atomic spin and advances in techniques, wide application of high-performance atomic spin gyroscopes is expected in the near future.

Characterization of AlN/AlGaN/GaN:C heterostructures grown on Si(111) using atom probe tomography, secondary ion mass spectrometry, and vertical current-voltage measurements

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

Huber, Martin, E-mail: martin.huberVIH@infineon.com; Daumiller, Ingo; Andreev, Andrei

2016-03-28

Complementary studies of atom probe tomography, secondary ion mass spectrometry, and vertical current-voltage measurements are carried out in order to unravel the influence of C-doping of GaN on the vertical leakage current of AlN/AlGaN/GaN:C heterostructures. A systematic increment of the vertical blocking voltage at a given current density is observed in the structures, when moving from the nominally undoped conditions—corresponding to a residual C-background of ∼10{sup 17 }cm{sup −3}—to a C-content of ∼10{sup 19 }cm{sup −3} in the GaN layer. The value of the vertical blocking voltage saturates for C concentrations higher than ∼10{sup 19 }cm{sup −3}. Atom probe tomography confirms the homogeneitymore » of the GaN:C layers, demonstrating that there is no clustering at C-concentrations as high as 10{sup 20 }cm{sup −3}. It is inferred that the vertical blocking voltage saturation is not likely to be related to C-clustering.« less

Block copolymer libraries: modular versatility of the macromolecular Lego system.

PubMed

Lohmeijer, Bas G G; Wouters, Daan; Yin, Zhihui; Schubert, Ulrich S

2004-12-21

The synthesis and characterization of a new 4 x 4 library of block copolymers based on polystyrene and poly(ethylene oxide) connected by an asymmetrical octahedral bis(terpyridine) ruthenium complex at the block junction are described, while initial studies on the thin film morphology of the components of the library are presented by the use of Atomic Force Microscopy, demonstrating the impact of a library approach to derive structure-property relationships.

Response of rotation-translation blocked proteins using Langevin dynamics on a locally harmonic landscape.

PubMed

Manson, Anthony C; Coalson, Rob D

2012-10-11

Langevin dynamics is used to compute the time evolution of the nonequilibrium motion of the atomic coordinates of a protein in response to ligand dissociation. The protein potential energy surface (PES) is approximated by a harmonic basin about the minimum of the unliganded state. Upon ligand dissociation, the protein undergoes relaxation from the bound to the unbound state. A coarse graining scheme based on rotation translation blocks (RTB) is applied to the relaxation of the two domain iron transport protein, ferric binding protein. This scheme provides a natural and efficient way to freeze out the small amplitude, high frequency motions within each rigid fragment, thereby allowing for the number of dynamical degrees of freedom to be reduced. The results obtained from all flexible atom (constraint free) dynamics are compared to those obtained using RTB-Langevin dynamics. To assess the impact of the assumed rigid fragment clustering on the temporal relaxation dynamics of the protein molecule, three distinct rigid block decompositions were generated and their responses compared. Each of the decompositions was a variant of the one-block-per-residue grouping, with their force and friction matrices being derived from their fully flexible counterpart. Monitoring the time evolution of the distance separating a selected pair of amino acids, the response curves of the blocked decompositions were similar in shape to each other and to the control system in which all atomic degrees of freedom are fully independent. The similar shape of the blocked responses showed that the variations in grouping had only a minor impact on the kinematics. Compared with the all atom responses, however, the blocked responses were faster as a result of the instantaneous transmission of force throughout each rigid block. This occurred because rigid blocking does not permit any intrablock deformation that could store or divert energy. It was found, however, that this accelerated response could be successfully corrected by scaling each eigenvalue in the appropriate propagation matrix by the least-squares fitted slope of the blocked vs nonblocked eigenvalue spectra. The RTB responses for each test system were dominated by small eigenvalue overdamped Langevin modes. The large eigenvalue members of each response dissipated within the first 5 ps, after which the long time response was dominated by a modest set of low energy, overdamped normal modes, that were characterized by highly cooperative, functionally relevant displacements. The response assuming that the system is in the overdamped limit was compared to the full phase space Langevin dynamics results. The responses after the first 5 ps were nearly identical, confirming that the inertial components were significant only in the initial stages of the relaxation. Since the propagator matrix in the overdamped formulation is real-symmetric and does not require the inertial component in the propagator, the computation time and memory footprint was reduced by 1 order of magnitude.

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.

Breaking Quantum and Thermal Limits on Precision Measurements

NASA Astrophysics Data System (ADS)

Thompson, James K.

2016-05-01

I will give an overview of our efforts to use correlations and entanglement between many atoms to overcome quantum and thermal limits on precision measurements. In the first portion of my talk, I will present a path toward a 10000 times reduced sensitivity to the thermal mirror motion that limits the linewidth of today's best lasers. By utilizing narrow atomic transitions, the laser's phase information is primarily stored in the atomic gain medium rather than in the vibration-sensitive cavity field. To this end, I will present the first observation of lasing based on the mHz linewidth optical-clock transition in a laser-cooled ensemble of strontium atoms. In the second portion of my talk, I will describe how we use collective measurements to surpass the standard quantum limit on phase estimation 1 /√{ N} for N unentangled atoms. We achieve a directly observed reduction in phase variance relative to the standard quantum limit of as much as 17.7(6) dB. Supported by DARPA QuASAR, NIST, ARO, and NSF PFC. This material is based upon work supported by the National Science Foundation under Grant Number 1125844 Physics Frontier Center.

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

Coherence Measurements for Excited to Excited State Transitions in Barium

NASA Technical Reports Server (NTRS)

Trajmar, S.; Kanik, I.; Karaganov, V.; Zetner, P. W.; Csanak, G.

2000-01-01

Experimental studies concerning elastic and inelastic electron scattering by coherently ensembles of Ba (...6s6p (sub 1)P(sub 1)) atoms with various degrees of alignment will be described. An in-plane, linearly-polarized laser beam was utilized to prepare these target ensembles and the electron scattering signal as a function of polarization angle was measured for several laser geometries at fixed impact energies and scattering angles. From these measurements, we derived cross sections and electron-impact coherence parameters associated with the electron scattering process which is time reverse of the actual experimentally studied process. This interpretation of the experiment is based on the theory of Macek and Herte. The experimental results were also interpreted in terms of cross sections and collision parameters associated with the actual experimental processes. Results obtained so far will be presented and plans for further studies will be discussed.

Microcanonical fluctuations of the condensate in weakly interacting Bose gases

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

Idziaszek, Zbigniew

2005-05-15

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

High temperature phonon dispersion in graphene using classical molecular dynamics

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

Anees, P., E-mail: anees@igcar.gov.in; Panigrahi, B. K.; Valsakumar, M. C., E-mail: anees@igcar.gov.in

2014-04-24

Phonon dispersion and phonon density of states of graphene are calculated using classical molecular dynamics simulations. In this method, the dynamical matrix is constructed based on linear response theory by computing the displacement of atoms during the simulations. The computed phonon dispersions show excellent agreement with experiments. The simulations are done in both NVT and NPT ensembles at 300 K and found that the LO/TO modes are getting hardened at the Γ point. The NPT ensemble simulations capture the anharmonicity of the crystal accurately and the hardening of LO/TO modes is more pronounced. We also found that at 300 Kmore » the C-C bond length reduces below the equilibrium value and the ZA bending mode frequency becomes imaginary close to Γ along K-Γ direction, which indicates instability of the flat 2D graphene sheets.« less

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.

Horizon in random matrix theory, the Hawking radiation, and flow of cold atoms.

PubMed

Franchini, Fabio; Kravtsov, Vladimir E

2009-10-16

We propose a Gaussian scalar field theory in a curved 2D metric with an event horizon as the low-energy effective theory for a weakly confined, invariant random matrix ensemble (RME). The presence of an event horizon naturally generates a bath of Hawking radiation, which introduces a finite temperature in the model in a nontrivial way. A similar mapping with a gravitational analogue model has been constructed for a Bose-Einstein condensate (BEC) pushed to flow at a velocity higher than its speed of sound, with Hawking radiation as sound waves propagating over the cold atoms. Our work suggests a threefold connection between a moving BEC system, black-hole physics and unconventional RMEs with possible experimental applications.

Quantum trajectory phase transitions in the micromaser.

PubMed

Garrahan, Juan P; Armour, Andrew D; Lesanovsky, Igor

2011-08-01

We study the dynamics of the single-atom maser, or micromaser, by means of the recently introduced method of thermodynamics of quantum jump trajectories. We find that the dynamics of the micromaser displays multiple space-time phase transitions, i.e., phase transitions in ensembles of quantum jump trajectories. This rich dynamical phase structure becomes apparent when trajectories are classified by dynamical observables that quantify dynamical activity, such as the number of atoms that have changed state while traversing the cavity. The space-time transitions can be either first order or continuous, and are controlled not just by standard parameters of the micromaser but also by nonequilibrium "counting" fields. We discuss how the dynamical phase behavior relates to the better known stationary-state properties of the micromaser.

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.

Vacuum-induced quantum memory in an opto-electromechanical system

NASA Astrophysics Data System (ADS)

Qin, Li-Guo; Wang, Zhong-Yang; Wu, Shi-Chao; Gong, Shang-Qing; Ma, Hong-Yang; Jing, Jun

2018-03-01

We propose a scheme to implement electrically controlled quantum memory based on vacuum-induced transparency (VIT) in a high-Q tunable cavity, which is capacitively coupled to a mechanically variable capacitor by a charged mechanical cavity mirror as an interface. We analyze the changes of the cavity photons arising from vacuum-induced-Raman process and discuss VIT in an atomic ensemble trapped in the cavity. By slowly adjusting the voltage on the capacitor, the VIT can be adiabatically switched on or off, meanwhile, the transfer between the probe photon state and the atomic spin state can be electrically and adiabatically modulated. Therefore, we demonstrate a vacuum-induced quantum memory by electrically manipulating the mechanical mirror of the cavity based on electromagnetically induced transparency mechanism.

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.

Chemically directing d-block heterometallics to nanocrystal surfaces as molecular beacons of surface structure

DOE PAGES

Rosen, Evelyn L.; Gilmore, Keith; Sawvel, April M.; ...

2015-07-28

Our understanding of structure and bonding in nanoscale materials is incomplete without knowledge of their surface structure. Needed are better surveying capabilities responsive not only to different atoms at the surface, but also their respective coordination environments. We report here that d-block organometallics, when placed at nanocrystal surfaces through heterometallic bonds, serve as molecular beacons broadcasting local surface structure in atomic detail. This unique ability stems from their elemental specificity and the sensitivity of their d-orbital level alignment to local coordination environment, which can be assessed spectroscopically. Re-surfacing cadmium and lead chalcogenide nanocrystals with iron- or ruthenium-based molecular beacons ismore » readily accomplished with trimethylsilylated cyclopentadienyl metal carbonyls. For PbSe nanocrystals with iron-based beacons, we show how core-level X-ray spectroscopies and DFT calculations enrich our understanding of both charge and atomic reorganization at the surface when beacons are bound.« less

First-Principles Molecular Dynamics Study of a Deep Eutectic Solvent: Choline Chloride/Urea and Its Mixture with Water

DOE PAGES

Fetisov, Evgenii O.; Harwood, David B.; Kuo, I-Feng William; ...

2017-12-07

First-principles molecular dynamics simulations in the canonical ensemble at temperatures of 333 and 363 K and at the corresponding experimental densities are carried out to investigate the behavior of the 1:2 choline chloride/urea (reline) deep eutectic solvent and its equimolar mixture with water. Analysis of atom–atom radial and spatial distribution functions and of the H-bond network reveals the microheterogeneous structure of these complex liquid mixtures. In neat reline, the structure is governed by strong H-bonds of the trans- and cis-H atoms of urea to the chloride ion. In hydrous reline, water competes for the anions, and the H atoms ofmore » urea have similar propensities to bond to the chloride ions and the O atoms of urea and water. Finally, the vibrational spectra exhibit relatively broad peaks reflecting the heterogeneity of the environment. Although the 100 ps trajectories allow only for a qualitative assessment of transport properties, the simulations indicate that water is more mobile than the other species and its addition also fosters faster motion of urea.« less

3-D Observation of dopant distribution at NAND flash memory floating gate using Atom probe tomography

NASA Astrophysics Data System (ADS)

Lee, Ji-hyun; Chae, Byeong-Kyu; Kim, Joong-Jeong; Lee, Sun Young; Park, Chan Gyung

2015-01-01

Dopant control becomes more difficult and critical as silicon devices become smaller. We observed the dopant distribution in a thermally annealed polysilicon gate using Transmission Electron Microscopy (TEM) and Atom probe tomography (APT). Phosphorus was doped at the silicon-nitride-diffusion-barrier-layer-covered polycrystalline silicon gate. Carbon also incorporated at the gate for the enhancement of operation uniformity. The impurity distribution was observed using atom probe tomography. The carbon atoms had segregated at grain boundaries and suppressed silicon grain growth. Phosphorus atoms, on the other hand, tended to pile-up at the interface. A 1-nm-thick diffusion barrier effectively blocked P atom out-diffusion. [Figure not available: see fulltext.

Climate model biases in jet streams, blocking and storm tracks resulting from missing orographic drag

NASA Astrophysics Data System (ADS)

Pithan, Felix; Shepherd, Theodore G.; Zappa, Giuseppe; Sandu, Irina

2016-07-01

State-of-the art climate models generally struggle to represent important features of the large-scale circulation. Common model deficiencies include an equatorward bias in the location of the midlatitude westerlies and an overly zonal orientation of the North Atlantic storm track. Orography is known to strongly affect the atmospheric circulation and is notoriously difficult to represent in coarse-resolution climate models. Yet how the representation of orography affects circulation biases in current climate models is not understood. Here we show that the effects of switching off the parameterization of drag from low-level orographic blocking in one climate model resemble the biases of the Coupled Model Intercomparison Project Phase 5 ensemble: An overly zonal wintertime North Atlantic storm track and less European blocking events, and an equatorward shift in the Southern Hemispheric jet and increase in the Southern Annular Mode time scale. This suggests that typical circulation biases in coarse-resolution climate models may be alleviated by improved parameterizations of low-level drag.

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.

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

PubMed Central

Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; Wall, Michael E.; Jackson, Colin J.; Sauter, Nicholas K.; Adams, Paul D.; Urzhumtsev, Alexandre; Fraser, James S.

2015-01-01

Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier’s equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophos­phodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis. PMID:26249347

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering.

PubMed

Wall, Michael E

2018-03-01

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.

A Metascalable Computing Framework for Large Spatiotemporal-Scale Atomistic Simulations

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

Nomura, K; Seymour, R; Wang, W

2009-02-17

A metascalable (or 'design once, scale on new architectures') parallel computing framework has been developed for large spatiotemporal-scale atomistic simulations of materials based on spatiotemporal data locality principles, which is expected to scale on emerging multipetaflops architectures. The framework consists of: (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms for high complexity problems; (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, while introducing multiple parallelization axes; and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these O(N) algorithms onto a multicore cluster based onmore » hybrid implementation combining message passing and critical section-free multithreading. The EDC-STEP-HCD framework exposes maximal concurrency and data locality, thereby achieving: (1) inter-node parallel efficiency well over 0.95 for 218 billion-atom molecular-dynamics and 1.68 trillion electronic-degrees-of-freedom quantum-mechanical simulations on 212,992 IBM BlueGene/L processors (superscalability); (2) high intra-node, multithreading parallel efficiency (nanoscalability); and (3) nearly perfect time/ensemble parallel efficiency (eon-scalability). The spatiotemporal scale covered by MD simulation on a sustained petaflops computer per day (i.e. petaflops {center_dot} day of computing) is estimated as NT = 2.14 (e.g. N = 2.14 million atoms for T = 1 microseconds).« less

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

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

Wall, Michael E.

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structuremore » to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.« less

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

DOE PAGES

Wall, Michael E.

2018-01-25

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structuremore » to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.« less

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

DOE PAGES

Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; ...

2015-07-28

Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier'smore » equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. In addition, these methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.« less

Learning surface molecular structures via machine vision

NASA Astrophysics Data System (ADS)

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-01

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (`read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

Bioelectrical Signals and Ion Channels in the Modeling of Multicellular Patterns and Cancer Biophysics.

PubMed

Cervera, Javier; Alcaraz, Antonio; Mafe, Salvador

2016-02-04

Bioelectrical signals and ion channels are central to spatial patterns in cell ensembles, a problem of fundamental interest in positional information and cancer processes. We propose a model for electrically connected cells based on simple biological concepts: i) the membrane potential of a single cell characterizes its electrical state; ii) the long-range electrical coupling of the multicellular ensemble is realized by a network of gap junction channels between neighboring cells; and iii) the spatial distribution of an external biochemical agent can modify the conductances of the ion channels in a cell membrane and the multicellular electrical state. We focus on electrical effects in small multicellular ensembles, ignoring slow diffusional processes. The spatio-temporal patterns obtained for the local map of cell electric potentials illustrate the normalization of regions with abnormal cell electrical states. The effects of intercellular coupling and blocking of specific channels on the electrical patterns are described. These patterns can regulate the electrically-induced redistribution of charged nanoparticles over small regions of a model tissue. The inclusion of bioelectrical signals provides new insights for the modeling of cancer biophysics because collective multicellular states show electrical coupling mechanisms that are not readily deduced from biochemical descriptions at the individual cell level.

Bioelectrical Signals and Ion Channels in the Modeling of Multicellular Patterns and Cancer Biophysics

PubMed Central

Cervera, Javier; Alcaraz, Antonio; Mafe, Salvador

2016-01-01

Bioelectrical signals and ion channels are central to spatial patterns in cell ensembles, a problem of fundamental interest in positional information and cancer processes. We propose a model for electrically connected cells based on simple biological concepts: i) the membrane potential of a single cell characterizes its electrical state; ii) the long-range electrical coupling of the multicellular ensemble is realized by a network of gap junction channels between neighboring cells; and iii) the spatial distribution of an external biochemical agent can modify the conductances of the ion channels in a cell membrane and the multicellular electrical state. We focus on electrical effects in small multicellular ensembles, ignoring slow diffusional processes. The spatio-temporal patterns obtained for the local map of cell electric potentials illustrate the normalization of regions with abnormal cell electrical states. The effects of intercellular coupling and blocking of specific channels on the electrical patterns are described. These patterns can regulate the electrically-induced redistribution of charged nanoparticles over small regions of a model tissue. The inclusion of bioelectrical signals provides new insights for the modeling of cancer biophysics because collective multicellular states show electrical coupling mechanisms that are not readily deduced from biochemical descriptions at the individual cell level. PMID:26841954

Bioelectrical Signals and Ion Channels in the Modeling of Multicellular Patterns and Cancer Biophysics

NASA Astrophysics Data System (ADS)

Cervera, Javier; Alcaraz, Antonio; Mafe, Salvador

2016-02-01

Bioelectrical signals and ion channels are central to spatial patterns in cell ensembles, a problem of fundamental interest in positional information and cancer processes. We propose a model for electrically connected cells based on simple biological concepts: i) the membrane potential of a single cell characterizes its electrical state; ii) the long-range electrical coupling of the multicellular ensemble is realized by a network of gap junction channels between neighboring cells; and iii) the spatial distribution of an external biochemical agent can modify the conductances of the ion channels in a cell membrane and the multicellular electrical state. We focus on electrical effects in small multicellular ensembles, ignoring slow diffusional processes. The spatio-temporal patterns obtained for the local map of cell electric potentials illustrate the normalization of regions with abnormal cell electrical states. The effects of intercellular coupling and blocking of specific channels on the electrical patterns are described. These patterns can regulate the electrically-induced redistribution of charged nanoparticles over small regions of a model tissue. The inclusion of bioelectrical signals provides new insights for the modeling of cancer biophysics because collective multicellular states show electrical coupling mechanisms that are not readily deduced from biochemical descriptions at the individual cell level.

eHive: an artificial intelligence workflow system for genomic analysis.

PubMed

Severin, Jessica; Beal, Kathryn; Vilella, Albert J; Fitzgerald, Stephen; Schuster, Michael; Gordon, Leo; Ureta-Vidal, Abel; Flicek, Paul; Herrero, Javier

2010-05-11

The Ensembl project produces updates to its comparative genomics resources with each of its several releases per year. During each release cycle approximately two weeks are allocated to generate all the genomic alignments and the protein homology predictions. The number of calculations required for this task grows approximately quadratically with the number of species. We currently support 50 species in Ensembl and we expect the number to continue to grow in the future. We present eHive, a new fault tolerant distributed processing system initially designed to support comparative genomic analysis, based on blackboard systems, network distributed autonomous agents, dataflow graphs and block-branch diagrams. In the eHive system a MySQL database serves as the central blackboard and the autonomous agent, a Perl script, queries the system and runs jobs as required. The system allows us to define dataflow and branching rules to suit all our production pipelines. We describe the implementation of three pipelines: (1) pairwise whole genome alignments, (2) multiple whole genome alignments and (3) gene trees with protein homology inference. Finally, we show the efficiency of the system in real case scenarios. eHive allows us to produce computationally demanding results in a reliable and efficient way with minimal supervision and high throughput. Further documentation is available at: http://www.ensembl.org/info/docs/eHive/.

DART: A Community Facility Providing State-of-the-Art, Efficient Ensemble Data Assimilation for Large (Coupled) Geophysical Models

NASA Astrophysics Data System (ADS)

Hoar, T. J.; Anderson, J. L.; Collins, N.; Kershaw, H.; Hendricks, J.; Raeder, K.; Mizzi, A. P.; Barré, J.; Gaubert, B.; Madaus, L. E.; Aydogdu, A.; Raeder, J.; Arango, H.; Moore, A. M.; Edwards, C. A.; Curchitser, E. N.; Escudier, R.; Dussin, R.; Bitz, C. M.; Zhang, Y. F.; Shrestha, P.; Rosolem, R.; Rahman, M.

2016-12-01

Strongly-coupled ensemble data assimilation with multiple high-resolution model components requires massive state vectors which need to be efficiently stored and accessed throughout the assimilation process. Supercomputer architectures are tending towards increasing the number of cores per node but have the same or less memory per node. Recent advances in the Data Assimilation Research Testbed (DART), a freely-available community ensemble data assimilation facility that works with dozens of large geophysical models, have addressed the need to run with a smaller memory footprint on a higher node count by utilizing MPI-2 one-sided communication to do non-blocking asynchronous access of distributed data. DART runs efficiently on many computational platforms ranging from laptops through thousands of cores on the newest supercomputers. Benefits of the new DART implementation will be shown. In addition, overviews of the most recently supported models will be presented: CAM-CHEM, WRF-CHEM, CM1, OpenGGCM, FESOM, ROMS, CICE5, TerrSysMP (COSMO, CLM, ParFlow), JULES, and CABLE. DART provides a comprehensive suite of software, documentation, and tutorials that can be used for ensemble data assimilation research, operations, and education. Scientists and software engineers at NCAR are available to support DART users who want to use existing DART products or develop their own applications. Current DART users range from university professors teaching data assimilation, to individual graduate students working with simple models, through national laboratories and state agencies doing operational prediction with large state-of-the-art models.

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.

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.

Global Weirding? - Using Very Large Ensembles and Extreme Value Theory to assess Changes in Extreme Weather Events Today

NASA Astrophysics Data System (ADS)

Otto, F. E. L.; Mitchell, D.; Sippel, S.; Black, M. T.; Dittus, A. J.; Harrington, L. J.; Mohd Saleh, N. H.

2014-12-01

A shift in the distribution of socially-relevant climate variables such as daily minimum winter temperatures and daily precipitation extremes, has been attributed to anthropogenic climate change for various mid-latitude regions. However, while there are many process-based arguments suggesting also a change in the shape of these distributions, attribution studies demonstrating this have not currently been undertaken. Here we use a very large initial condition ensemble of ~40,000 members simulating the European winter 2013/2014 using the distributed computing infrastructure under the weather@home project. Two separate scenarios are used:1. current climate conditions, and 2. a counterfactual scenario of "world that might have been" without anthropogenic forcing. Specifically focusing on extreme events, we assess how the estimated parameters of the Generalized Extreme Value (GEV) distribution vary depending on variable-type, sampling frequency (daily, monthly, …) and geographical region. We find that the location parameter changes for most variables but, depending on the region and variables, we also find significant changes in scale and shape parameters. The very large ensemble allows, furthermore, to assess whether such findings in the fitted GEV distributions are consistent with an empirical analysis of the model data, and whether the most extreme data still follow a known underlying distribution that in a small sample size might otherwise be thought of as an out-lier. The ~40,000 member ensemble is simulated using 12 different SST patterns (1 'observed', and 11 best guesses of SSTs with no anthropogenic warming). The range in SSTs, along with the corresponding changings in the NAO and high-latitude blocking inform on the dynamics governing some of these extreme events. While strong tele-connection patterns are not found in this particular experiment, the high number of simulated extreme events allows for a more thorough analysis of the dynamics than has been performed before. Therefore, combining extreme value theory with very large ensemble simulations allows us to understand the dynamics of changes in extreme events which is not possible just using the former but also shows in which cases statistics combined with smaller ensembles give as valid results as very large initial conditions.

Dependence of present and future European heat waves and cold spells on the location of atmospheric blocking

NASA Astrophysics Data System (ADS)

Brunner, L.; Schaller, N.; Sillmann, J.; Steiner, A. K.

2017-12-01

Atmospheric blocking describes stationary anti-cyclones, which weaken or reverse the climatological flow at mid-latitudes. In the northern hemisphere one of the main blocking regions is located over the North Atlantic and Northern Europe. The link between blocking and European temperature extremes, such as heat waves and cold spells, strongly depends on several aspects like season, longitudinal location of the block, and location of the extremes (particularly Northern Europe versus Southern Europe). We use a 50-member ensemble of the Canadian CanESM2 model to investigate historical (1981-2010) and future (2070-2099) blocking cases and their relationship with European temperature extremes. For the historical period the model results are also compared to those from the ERA-Interim reanalysis. Atmospheric blocking is detected on a daily basis in different 30° longitude windows between 60°W and 60°E, using a standard geopotential height-based detection index. Temperature extremes are defined by the daily Heat/Cold Wave Magnitude Index (HWMId/CWMId). The role of cold advection is found particularly important in winter conditions leading to a more than threefold increase in cold wave occurrence during blocking between 60°W and 0°. During blocking over Northern Europe (0° to 60°E) a split relationship is found with cold wave occurrence being strongly increased in Southern Europe, while it is decreased in Northern Europe. Direct, radiative effects dominate in summer, therefore blocking westward of Europe has a weaker effect, while blocking over Northern Europe leads to an increase of heat waves by at least a factor three at the location of the block and a decrease in cold wave occurrence in almost all of Europe. Comparing the historical and future period we find the link between blocking and temperature extremes in Europe to be robust, even though blocking frequency and temperatures are changing.

On the representation of atmospheric blocking in EURO-CORDEX control runs

NASA Astrophysics Data System (ADS)

Jury, Martin W.; García, Sixto; Gutiérrez, José M.

2017-04-01

While regional climate models (RCMs) have been shown to yield improved projections, due to better representations of orography and higher resolved scales, impacts on mesoscale phenomena like atmospheric blocking have been hardly addressed. In this study we clarify if the EURO-CORDEX domain is large enough to allow the RCMs to significantly amplify the blocking representation in reference to the underlying driving data. Therefore, we analyzed blocking accompanying anomalies in temperature near the surface (TAS) and precipitation rate (PR) for a set of RCMs. 5 RCMs stem from the ensemble of EURO-CORDEX control runs, while 3 RCMs are WRF models with different nudging realizations, all of them are driven by ERA-Interim. The used blocking detection method detects blockings by localizing high pressure systems between 55°N and 65°N with the use of geopotential height gradients on the 500 hPa level (Z500), and was applied to ERA-Interim and the mentioned RCM data between 1981 and 2010. Detected blockings centers were spatially attributed to three sectors, which have been shown to display distinctive impacts on TAS and PR during blocking episodes. As a reference for TAS and PR we used 86 weather stations across Europe from the ECA&D dataset. Our results indicate, that little improvement can be expected in the representation of Z500 fields by the RCMs. Most of them show less blocking than the driving data, while blocking representation was most in agreement with the driving data for RCMs that have been strongly conditioned to the driving data. Further, in our idealized setting the RCMs were not able to reproduce the anomalies for TAS connected to blocking. Moreover, using the blocking index of the driving data could be considered correct, because the representation of TAS and PR for falsely detected blocking and non-blocking days in the RCMs did not deviate strongly.

WATER-BORNE BLOCK COPOLYMER SYNTHESIS AND A SIMPLE AND EFFECTIVE ONE-POT SYNTHESIS OF ACRYLATE-METHACRYLATE BLOCK COPOLYMERS BY ATOM TRANSFER RADICAL POLYMERIZATION. (R826735)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

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.

Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures

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

Dunn, Nicholas J. H.; Noid, W. G., E-mail: wnoid@chem.psu.edu

This work investigates the promise of a “bottom-up” extended ensemble framework for developing coarse-grained (CG) models that provide predictive accuracy and transferability for describing both structural and thermodynamic properties. We employ a force-matching variational principle to determine system-independent, i.e., transferable, interaction potentials that optimally model the interactions in five distinct heptane-toluene mixtures. Similarly, we employ a self-consistent pressure-matching approach to determine a system-specific pressure correction for each mixture. The resulting CG potentials accurately reproduce the site-site rdfs, the volume fluctuations, and the pressure equations of state that are determined by all-atom (AA) models for the five mixtures. Furthermore, we demonstratemore » that these CG potentials provide similar accuracy for additional heptane-toluene mixtures that were not included their parameterization. Surprisingly, the extended ensemble approach improves not only the transferability but also the accuracy of the calculated potentials. Additionally, we observe that the required pressure corrections strongly correlate with the intermolecular cohesion of the system-specific CG potentials. Moreover, this cohesion correlates with the relative “structure” within the corresponding mapped AA ensemble. Finally, the appendix demonstrates that the self-consistent pressure-matching approach corresponds to minimizing an appropriate relative entropy.« less

Nanoscale Electronic Conditioning for Improvement of Nanowire Light-Emitting-Diode Efficiency.

PubMed

May, Brelon J; Belz, Matthew R; Ahamed, Arshad; Sarwar, A T M G; Selcu, Camelia M; Myers, Roberto C

2018-04-24

Commercial III-Nitride LEDs and lasers spanning visible and ultraviolet wavelengths are based on epitaxial films. Alternatively, nanowire-based III-Nitride optoelectronics offer the advantage of strain compliance and high crystalline quality growth on a variety of inexpensive substrates. However, nanowire LEDs exhibit an inherent property distribution, resulting in uneven current spreading through macroscopic devices that consist of millions of individual nanowire diodes connected in parallel. Despite being electrically connected, only a small fraction of nanowires, sometimes <1%, contribute to the electroluminescence (EL). Here, we show that a population of electrical shorts exists in the devices, consisting of a subset of low-resistance nanowires that pass a large portion of the total current in the ensemble devices. Burn-in electronic conditioning is performed by applying a short-term overload voltage; the nanoshorts experience very high current density, sufficient to render them open circuits, thereby forcing a new current path through more nanowire LEDs in an ensemble device. Current-voltage measurements of individual nanowires are acquired using conductive atomic force microscopy to observe the removal of nanoshorts using burn-in. In macroscopic devices, this results in a 33× increase in peak EL and reduced leakage current. Burn-in conditioning of nanowire ensembles therefore provides a straightforward method to mitigate nonuniformities inherent to nanowire devices.

Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures.

PubMed

Dunn, Nicholas J H; Noid, W G

2016-05-28

This work investigates the promise of a "bottom-up" extended ensemble framework for developing coarse-grained (CG) models that provide predictive accuracy and transferability for describing both structural and thermodynamic properties. We employ a force-matching variational principle to determine system-independent, i.e., transferable, interaction potentials that optimally model the interactions in five distinct heptane-toluene mixtures. Similarly, we employ a self-consistent pressure-matching approach to determine a system-specific pressure correction for each mixture. The resulting CG potentials accurately reproduce the site-site rdfs, the volume fluctuations, and the pressure equations of state that are determined by all-atom (AA) models for the five mixtures. Furthermore, we demonstrate that these CG potentials provide similar accuracy for additional heptane-toluene mixtures that were not included their parameterization. Surprisingly, the extended ensemble approach improves not only the transferability but also the accuracy of the calculated potentials. Additionally, we observe that the required pressure corrections strongly correlate with the intermolecular cohesion of the system-specific CG potentials. Moreover, this cohesion correlates with the relative "structure" within the corresponding mapped AA ensemble. Finally, the appendix demonstrates that the self-consistent pressure-matching approach corresponds to minimizing an appropriate relative entropy.

Single Polymer Chain Elongation by Atomic Force Microscopy.

DTIC Science & Technology

1998-01-01

are designated by PS for polystyrene and P2VP or PVP for poly-2-vinyl-pyridine. Molecular weights of the individual blocks are given after the...In the case of PS - P2VP the difference in interfacial tensions of the two blocks with water are too close to distinguish. Using block copolymers with...Stanford University, 1987. (20) Static light scattering reveals that the CMC of PS - P2VP solutions in toluene is approximately 65ug/ml,19 and as such

An Ensemble-Based Protocol for the Computational Prediction of Helix-Helix Interactions in G Protein-Coupled Receptors using Coarse-Grained Molecular Dynamics.

PubMed

Altwaijry, Nojood A; Baron, Michael; Wright, David W; Coveney, Peter V; Townsend-Nicholson, Andrea

2017-05-09

The accurate identification of the specific points of interaction between G protein-coupled receptor (GPCR) oligomers is essential for the design of receptor ligands targeting oligomeric receptor targets. A coarse-grained molecular dynamics computer simulation approach would provide a compelling means of identifying these specific protein-protein interactions and could be applied both for known oligomers of interest and as a high-throughput screen to identify novel oligomeric targets. However, to be effective, this in silico modeling must provide accurate, precise, and reproducible information. This has been achieved recently in numerous biological systems using an ensemble-based all-atom molecular dynamics approach. In this study, we describe an equivalent methodology for ensemble-based coarse-grained simulations. We report the performance of this method when applied to four different GPCRs known to oligomerize using error analysis to determine the ensemble size and individual replica simulation time required. Our measurements of distance between residues shown to be involved in oligomerization of the fifth transmembrane domain from the adenosine A 2A receptor are in very good agreement with the existing biophysical data and provide information about the nature of the contact interface that cannot be determined experimentally. Calculations of distance between rhodopsin, CXCR4, and β 1 AR transmembrane domains reported to form contact points in homodimers correlate well with the corresponding measurements obtained from experimental structural data, providing an ability to predict contact interfaces computationally. Interestingly, error analysis enables identification of noninteracting regions. Our results confirm that GPCR interactions can be reliably predicted using this novel methodology.

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.

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale.

PubMed

Parton, Daniel L; Grinaway, Patrick B; Hanson, Sonya M; Beauchamp, Kyle A; Chodera, John D

2016-06-01

The rapidly expanding body of available genomic and protein structural data provides a rich resource for understanding protein dynamics with biomolecular simulation. While computational infrastructure has grown rapidly, simulations on an omics scale are not yet widespread, primarily because software infrastructure to enable simulations at this scale has not kept pace. It should now be possible to study protein dynamics across entire (super)families, exploiting both available structural biology data and conformational similarities across homologous proteins. Here, we present a new tool for enabling high-throughput simulation in the genomics era. Ensembler takes any set of sequences-from a single sequence to an entire superfamily-and shepherds them through various stages of modeling and refinement to produce simulation-ready structures. This includes comparative modeling to all relevant PDB structures (which may span multiple conformational states of interest), reconstruction of missing loops, addition of missing atoms, culling of nearly identical structures, assignment of appropriate protonation states, solvation in explicit solvent, and refinement and filtering with molecular simulation to ensure stable simulation. The output of this pipeline is an ensemble of structures ready for subsequent molecular simulations using computer clusters, supercomputers, or distributed computing projects like Folding@home. Ensembler thus automates much of the time-consuming process of preparing protein models suitable for simulation, while allowing scalability up to entire superfamilies. A particular advantage of this approach can be found in the construction of kinetic models of conformational dynamics-such as Markov state models (MSMs)-which benefit from a diverse array of initial configurations that span the accessible conformational states to aid sampling. We demonstrate the power of this approach by constructing models for all catalytic domains in the human tyrosine kinase family, using all available kinase catalytic domain structures from any organism as structural templates. Ensembler is free and open source software licensed under the GNU General Public License (GPL) v2. It is compatible with Linux and OS X. The latest release can be installed via the conda package manager, and the latest source can be downloaded from https://github.com/choderalab/ensembler.

LDPC Codes with Minimum Distance Proportional to Block Size

NASA Technical Reports Server (NTRS)

Divsalar, Dariush; Jones, Christopher; Dolinar, Samuel; Thorpe, Jeremy

2009-01-01

Low-density parity-check (LDPC) codes characterized by minimum Hamming distances proportional to block sizes have been demonstrated. Like the codes mentioned in the immediately preceding article, the present codes are error-correcting codes suitable for use in a variety of wireless data-communication systems that include noisy channels. The previously mentioned codes have low decoding thresholds and reasonably low error floors. However, the minimum Hamming distances of those codes do not grow linearly with code-block sizes. Codes that have this minimum-distance property exhibit very low error floors. Examples of such codes include regular LDPC codes with variable degrees of at least 3. Unfortunately, the decoding thresholds of regular LDPC codes are high. Hence, there is a need for LDPC codes characterized by both low decoding thresholds and, in order to obtain acceptably low error floors, minimum Hamming distances that are proportional to code-block sizes. The present codes were developed to satisfy this need. The minimum Hamming distances of the present codes have been shown, through consideration of ensemble-average weight enumerators, to be proportional to code block sizes. As in the cases of irregular ensembles, the properties of these codes are sensitive to the proportion of degree-2 variable nodes. A code having too few such nodes tends to have an iterative decoding threshold that is far from the capacity threshold. A code having too many such nodes tends not to exhibit a minimum distance that is proportional to block size. Results of computational simulations have shown that the decoding thresholds of codes of the present type are lower than those of regular LDPC codes. Included in the simulations were a few examples from a family of codes characterized by rates ranging from low to high and by thresholds that adhere closely to their respective channel capacity thresholds; the simulation results from these examples showed that the codes in question have low error floors as well as low decoding thresholds. As an example, the illustration shows the protograph (which represents the blueprint for overall construction) of one proposed code family for code rates greater than or equal to 1.2. Any size LDPC code can be obtained by copying the protograph structure N times, then permuting the edges. The illustration also provides Field Programmable Gate Array (FPGA) hardware performance simulations for this code family. In addition, the illustration provides minimum signal-to-noise ratios (Eb/No) in decibels (decoding thresholds) to achieve zero error rates as the code block size goes to infinity for various code rates. In comparison with the codes mentioned in the preceding article, these codes have slightly higher decoding thresholds.

Matterwave interferometric velocimetry of cold Rb atoms

NASA Astrophysics Data System (ADS)

Carey, Max; Belal, Mohammad; Himsworth, Matthew; Bateman, James; Freegarde, Tim

2018-03-01

We consider the matterwave interferometric measurement of atomic velocities, which forms a building block for all matterwave inertial measurements. A theoretical analysis, addressing both the laboratory and atomic frames and accounting for residual Doppler sensitivity in the beamsplitter and recombiner pulses, is followed by an experimental demonstration, with measurements of the velocity distribution within a 20 ?K cloud of rubidium atoms. Our experiments use Raman transitions between the long-lived ground hyperfine states, and allow quadrature measurements that yield the full complex interferometer signal and hence discriminate between positive and negative velocities. The technique is most suitable for measurement of colder samples.

Matterwave interferometric velocimetry of cold Rb atoms

NASA Astrophysics Data System (ADS)

Carey, Max; Belal, Mohammad; Himsworth, Matthew; Bateman, James; Freegarde, Tim

2018-02-01

We consider the matterwave interferometric measurement of atomic velocities, which forms a building block for all matterwave inertial measurements. A theoretical analysis, addressing both the laboratory and atomic frames and accounting for residual Doppler sensitivity in the beamsplitter and recombiner pulses, is followed by an experimental demonstration, with measurements of the velocity distribution within a 20 $\\mu$K cloud of rubidium atoms. Our experiments use Raman transitions between the long-lived ground hyperfine states, and allow quadrature measurements that yield the full complex interferometer signal and hence discriminate between positive and negative velocities. The technique is most suitable for measurement of colder samples.

Fifty years of atomic time-keeping at VNIIFTRI

NASA Astrophysics Data System (ADS)

Domnin, Yu; Gaigerov, B.; Koshelyaevsky, N.; Poushkin, S.; Rusin, F.; Tatarenkov, V.; Yolkin, G.

2005-06-01

Time metrology in Russia in the second half of the twentieth century has been marked, as in other advanced countries, by the rapid development of time and frequency quantum standards and the beginning of atomic time-keeping. This brief review presents the main developments and studies in time and frequency measurement, and the improvement of accuracy and atomic time-keeping at the VNIIFTRI—the National Metrology Institute keeping primary time and frequency standards and ensuring unification of measurement. The milestones along the way have been the ammonia and hydrogen masers, primary caesium beam and fountain standards and laser frequency standards. For many years, VNIIFTRI was the only world laboratory that applied hydrogen-maser clock ensembles for time-keeping. VNIIFTRI's work on international laser standard frequency comparisons and absolute frequency measurements contributed greatly to the adoption by the CIPM of a highly accurate value for the He-Ne/CH4 laser frequency. VNIIFTRI and the VNIIM were the first to establish a united time, frequency and length standard.

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.

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).

Tackling CO Poisoning with Single Atom Alloy Catalysts

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

Liu, Jilei; Lucci, Felicia R.; Yang, Ming

2016-05-01

Platinum (Pt) catalysts are extensively used in the chemical industry and as electrocatalysts in fuel cells. Pt is notorious for its sensitivity to poisoning by strong CO adsorption. Here we demonstrate that the single atom alloy (SAA) strat-egy applied to Pt reduces the binding strength of CO while maintaining catalytic performance. By using surface sensi-tive studies, we accurately determined the binding strength of CO to different Pt ensembles, and this in turn guided the preparation of PtCu alloy nanoparticles. The atomic ratio Pt:Cu = 1:120 yielded a SAA which exhibited excellent CO tolerance in H2 activation, the key elementary stepmore » for hy-drogenation and hydrogen electro-oxidation. As a probe reaction, the selective hydrogenation of acetylene to ethene was performed under flow conditions on the SAA nanopar-ticles supported on alumina without activity loss in the pres-ence of CO. The ability to maintain reactivity in the presence of CO is vital to other industrial reactions including fuel reforming and methanol/ethanol fuel cells.« less

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.

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.

An extensive study of Bose-Einstein condensation in liquid helium using Tsallis statistics

NASA Astrophysics Data System (ADS)

Guha, Atanu; Das, Prasanta Kumar

2018-05-01

Realistic scenario can be represented by general canonical ensemble way better than the ideal one, with proper parameter sets involved. We study the Bose-Einstein condensation phenomena of liquid helium within the framework of Tsallis statistics. With a comparatively high value of the deformation parameter q(∼ 1 . 4) , the theoretically calculated value of the critical temperature (Tc) of the phase transition of liquid helium is found to agree with the experimentally determined value (Tc = 2 . 17 K), although they differs from each other for q = 1 (undeformed scenario). This throws a light on the understanding of the phenomenon and connects temperature fluctuation(non-equilibrium conditions) with the interactions between atoms qualitatively. More interactions between atoms give rise to more non-equilibrium conditions which is as expected.

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.

Horizon in Random Matrix Theory, the Hawking Radiation, and Flow of Cold Atoms

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

Franchini, Fabio; Kravtsov, Vladimir E.

2009-10-16

We propose a Gaussian scalar field theory in a curved 2D metric with an event horizon as the low-energy effective theory for a weakly confined, invariant random matrix ensemble (RME). The presence of an event horizon naturally generates a bath of Hawking radiation, which introduces a finite temperature in the model in a nontrivial way. A similar mapping with a gravitational analogue model has been constructed for a Bose-Einstein condensate (BEC) pushed to flow at a velocity higher than its speed of sound, with Hawking radiation as sound waves propagating over the cold atoms. Our work suggests a threefold connectionmore » between a moving BEC system, black-hole physics and unconventional RMEs with possible experimental applications.« less

Free energy landscape from path-sampling: application to the structural transition in LJ38

NASA Astrophysics Data System (ADS)

Adjanor, G.; Athènes, M.; Calvo, F.

2006-09-01

We introduce a path-sampling scheme that allows equilibrium state-ensemble averages to be computed by means of a biased distribution of non-equilibrium paths. This non-equilibrium method is applied to the case of the 38-atom Lennard-Jones atomic cluster, which has a double-funnel energy landscape. We calculate the free energy profile along the Q4 bond orientational order parameter. At high or moderate temperature the results obtained using the non-equilibrium approach are consistent with those obtained using conventional equilibrium methods, including parallel tempering and Wang-Landau Monte Carlo simulations. At lower temperatures, the non-equilibrium approach becomes more efficient in exploring the relevant inherent structures. In particular, the free energy agrees with the predictions of the harmonic superposition approximation.

Data-Driven Learning of Total and Local Energies in Elemental Boron

NASA Astrophysics Data System (ADS)

Deringer, Volker L.; Pickard, Chris J.; Csányi, Gábor

2018-04-01

The allotropes of boron continue to challenge structural elucidation and solid-state theory. Here we use machine learning combined with random structure searching (RSS) algorithms to systematically construct an interatomic potential for boron. Starting from ensembles of randomized atomic configurations, we use alternating single-point quantum-mechanical energy and force computations, Gaussian approximation potential (GAP) fitting, and GAP-driven RSS to iteratively generate a representation of the element's potential-energy surface. Beyond the total energies of the very different boron allotropes, our model readily provides atom-resolved, local energies and thus deepened insight into the frustrated β -rhombohedral boron structure. Our results open the door for the efficient and automated generation of GAPs, and other machine-learning-based interatomic potentials, and suggest their usefulness as a tool for materials discovery.

Data-Driven Learning of Total and Local Energies in Elemental Boron.

PubMed

Deringer, Volker L; Pickard, Chris J; Csányi, Gábor

2018-04-13

The allotropes of boron continue to challenge structural elucidation and solid-state theory. Here we use machine learning combined with random structure searching (RSS) algorithms to systematically construct an interatomic potential for boron. Starting from ensembles of randomized atomic configurations, we use alternating single-point quantum-mechanical energy and force computations, Gaussian approximation potential (GAP) fitting, and GAP-driven RSS to iteratively generate a representation of the element's potential-energy surface. Beyond the total energies of the very different boron allotropes, our model readily provides atom-resolved, local energies and thus deepened insight into the frustrated β-rhombohedral boron structure. Our results open the door for the efficient and automated generation of GAPs, and other machine-learning-based interatomic potentials, and suggest their usefulness as a tool for materials discovery.

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.

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.

Colloidal Disorder-Order Transition Experiment Probes Particle Interactions in Microgravity

NASA Technical Reports Server (NTRS)

1997-01-01

Everything in the universe is made up of the same basic building blocks - atoms. All physical properties of matter such as weight, hardness, and color are determined by the kind of atoms present and the way they interact with each other. The Colloidal Disorder-Order Transition (CDOT) shuttle flight experiment tested fundamental theories that model atomic interactions. The experiment was part of the Second United States Microgravity Laboratory (USML-2) aboard the Space Shuttle Columbia, which flew from October 20 to November 5, 1995.

One-way EPR steering and genuine multipartite EPR steering

NASA Astrophysics Data System (ADS)

He, Qiongyi; Reid, Margaret D.

2012-11-01

We propose criteria and experimental strategies to realise the Einstein-Podolsky-Rosen (EPR) steering nonlocality. One-way steering can be obtained where there is asymmetry of thermal noise on each system. We also present EPR steering inequalities that act as signatures and suggest how to optimise EPR correlations in specific schemes so that the genuine multipartite EPR steering nonlocality (EPR paradox) can also possibly be realised. The results presented here also apply to the spatially separated macroscopic atomic ensembles.

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.

Bringing diffuse X-ray scattering into focus

DOE PAGES

Wall, Michael E.; Wolff, Alexander M.; Fraser, James S.

2018-02-16

X-ray crystallography is experiencing a renaissance as a method for probing the protein conformational ensemble. The inherent limitations of Bragg analysis, however, which only reveals the mean structure, have given way to a surge in interest in diffuse scattering, which is caused by structure variations. Diffuse scattering is present in all macromolecular crystallography experiments. Recent studies are shedding light on the origins of diffuse scattering in protein crystallography, and provide clues for leveraging diffuse scattering to model protein motions with atomic detail.

Bringing diffuse X-ray scattering into focus

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

Wall, Michael E.; Wolff, Alexander M.; Fraser, James S.

X-ray crystallography is experiencing a renaissance as a method for probing the protein conformational ensemble. The inherent limitations of Bragg analysis, however, which only reveals the mean structure, have given way to a surge in interest in diffuse scattering, which is caused by structure variations. Diffuse scattering is present in all macromolecular crystallography experiments. Recent studies are shedding light on the origins of diffuse scattering in protein crystallography, and provide clues for leveraging diffuse scattering to model protein motions with atomic detail.

High-performance Raman memory with spatio-temporal reversal

NASA Astrophysics Data System (ADS)

Vernaz-Gris, Pierre; Tranter, Aaron D.; Everett, Jesse L.; Leung, Anthony C.; Paul, Karun V.; Campbell, Geoff T.; Lam, Ping Koy; Buchler, Ben C.

2018-05-01

A number of techniques exist to use an ensemble of atoms as a quantum memory for light. Many of these propose to use backward retrieval as a way to improve the storage and recall efficiency. We report on a demonstration of an off-resonant Raman memory that uses backward retrieval to achieve an efficiency of $65\\pm6\\%$ at a storage time of one pulse duration. The memory has a characteristic decay time of 60 $\\mu$s, corresponding to a delay-bandwidth product of $160$.

Thermostatted molecular dynamics: How to avoid the Toda demon hidden in Nose-Hoover dynamics

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

Holian, B.L.; Voter, A.F.; Ravelo, R.

The Nose-Hoover thermostat, which is often used in the hope of modifying molecular dynamics trajectories in order to achieve canonical-ensemble averages, has hidden in it a Toda ``demon,`` which can give rise to unwanted, noncanonical undulations in the instantaneous kinetic temperature. We show how these long-lived oscillations arise from insufficient coupling of the thermostat to the atoms, and give straightforward, practical procedures for avoiding this weak-coupling pathology in isothermal molecular dynamics simulations.

Collection of gravitropic effectors from mucilage of electrotropically-stimulated roots of Zea mays L

NASA Technical Reports Server (NTRS)

Fondren, W. M.; Moore, R.

1987-01-01

We placed agar blocks adjacent to tips of electrotropically stimulated primary roots of Zea mays. Blocks placed adjacent to the anode-side of the roots for 3 h induced significant curvature when subsequently placed asymmetrically on tips of vertically-oriented roots. Curvature was always toward the side of the root unto which the agar block was placed. Agar blocks not contacting roots and blocks placed adjacent to the cathode-side of electrotropically stimulated roots did not induce significant curvature when placed asymmetrically on tips of vertically-oriented roots. Atomic absorption spectrophotometry indicated that blocks adjacent to the anode-side of electrotropically-stimulated roots contained significantly more calcium than (1) blocks not contacting roots, and (2) blocks contacting the cathode-side of roots. These results demonstrate the presence of a gradient of endogenous Ca in mucilage of electrotropically-stimulated roots (i.e. roots undergoing gravitropic-like curvature).

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.

Superimposition of protein structures with dynamically weighted RMSD.

PubMed

Wu, Di; Wu, Zhijun

2010-02-01

In protein modeling, one often needs to superimpose a group of structures for a protein. A common way to do this is to translate and rotate the structures so that the square root of the sum of squares of coordinate differences of the atoms in the structures, called the root-mean-square deviation (RMSD) of the structures, is minimized. While it has provided a general way of aligning a group of structures, this approach has not taken into account the fact that different atoms may have different properties and they should be compared differently. For this reason, when superimposed with RMSD, the coordinate differences of different atoms should be evaluated with different weights. The resulting RMSD is called the weighted RMSD (wRMSD). Here we investigate the use of a special wRMSD for superimposing a group of structures with weights assigned to the atoms according to certain thermal motions of the atoms. We call such an RMSD the dynamically weighted RMSD (dRMSD). We show that the thermal motions of the atoms can be obtained from several sources such as the mean-square fluctuations that can be estimated by Gaussian network model analysis. We show that the superimposition of structures with dRMSD can successfully identify protein domains and protein motions, and that it has important implications in practice, e.g., in aligning the ensemble of structures determined by nuclear magnetic resonance.

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.

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).

Phasic and tonic neuron ensemble codes for stimulus-environment conjunctions in the lateral entorhinal cortex

PubMed Central

Pilkiw, Maryna; Insel, Nathan; Cui, Younghua; Finney, Caitlin; Morrissey, Mark D; Takehara-Nishiuchi, Kaori

2017-01-01

The lateral entorhinal cortex (LEC) is thought to bind sensory events with the environment where they took place. To compare the relative influence of transient events and temporally stable environmental stimuli on the firing of LEC cells, we recorded neuron spiking patterns in the region during blocks of a trace eyeblink conditioning paradigm performed in two environments and with different conditioning stimuli. Firing rates of some neurons were phasically selective for conditioned stimuli in a way that depended on which room the rat was in; nearly all neurons were tonically selective for environments in a way that depended on which stimuli had been presented in those environments. As rats moved from one environment to another, tonic neuron ensemble activity exhibited prospective information about the conditioned stimulus associated with the environment. Thus, the LEC formed phasic and tonic codes for event-environment associations, thereby accurately differentiating multiple experiences with overlapping features. DOI: http://dx.doi.org/10.7554/eLife.28611.001 PMID:28682237

Sulfonated amphiphilic block copolymers : synthesis, self-assembly in water, and application as stabilizer in emulsion polymerization

Treesearch

Jiguang Zhang; Matthew R. Dubay; Carl J. Houtman; Steven J. Severtson

2009-01-01

Described is the synthesis of diblock copolymers generated via sequential atom transfer radical polymerization (ATRP) of poly(n-butyl acrylate) (PnBA) followed by chain augmentation with either sulfonated poly(2-hydroxyethyl methacrylate) (PHEMA) or poly(2-hydroxyethyl acrylate) (PHEA) blocks. ATRP of PHEMA or PHEA from PnBA macroinitiator was conducted in acetone/...

Nanostructures and surface hydrophobicity of self-assembled thermosets involving epoxy resin and poly(2,2,2-trifluoroethyl acrylate)-block-poly(ethylene oxide) amphiphilic diblock copolymer.

PubMed

Yi, Fangping; Zheng, Sixun; Liu, Tianxi

2009-02-19

Poly(2,2,2-trifluoroethyl acrylate)-block-poly(ethylene oxide) (PTFEA-b-PEO) amphiphilic diblock copolymer was synthesized via the reversible addition-fragmentation transfer polymerization of 2,2,2-triffluroethyl acrylate with dithiobenzoyl-terminated poly(ethylene oxide) as a chain-transfer agent. The amphiphilic diblock copolymer was incorporated into epoxy resin to prepare the nanostructured epoxy thermosets. The nanostructures were investigated by means of atomic force microscopy, small-angle X-ray scattering, and dynamic mechanical analysis. In terms of the miscibility of the subchains of the block copolymer with epoxy after and before curing reaction, it is judged that the formation of the nanostructures follows the mechanism of self-assembly. The static contact angle measurements indicate that the nanostructured thermosets containing PTFEA-b-PEO diblock copolymer displayed a significant enhancement in surface hydrophobicity as well as a reduction in surface free energy. The improvement in surface properties was ascribed to the enrichment of the fluorine-containing subchain (i.e., PTFEA block) of the amphiphilic diblock copolymer on the surface of the nanostructured thermosets, which was evidenced by surface atomic force microscopy and energy-dispersive X-ray spectroscopy.

Learning surface molecular structures via machine vision

DOE PAGES

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-10

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (‘read out’) all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds andmore » thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. Here, the method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.« less

Learning surface molecular structures via machine vision

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

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (‘read out’) all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds andmore » thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. Here, the method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.« less

Poly(cyclohexylethylene)- block -Poly(lactide) Oligomers for Ultrasmall Nanopatterning Using Atomic Layer Deposition

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

Yao, Li; Oquendo, Luis E.; Schulze, Morgan W.

2016-03-08

Poly(cyclohexylethylene)-block-poly(lactide) (PCHE–PLA) block polymers were synthesized through a combination of anionic polymerization, heterogeneous catalytic hydrogenation and controlled ring-opening polymerization. Ordered thin films of PCHE–PLA with ultrasmall hexagonally packed cylinders oriented perpendicularly to the substrate surface were prepared by spin-coating and subsequent solvent vapor annealing for use in two distinct templating strategies. In one approach, selective hydrolytic degradation of the PLA domains generated nanoporous PCHE templates with an average pore diameter of 5 ± 1 nm corroborated by atomic force microscopy and grazing incidence small-angle X-ray scattering. Alternatively, sequential infiltration synthesis (SIS) was employed to deposit Al2O3 selectively into the PLAmore » domains of PCHE–PLA thin films. A combination of argon ion milling and O2 reactive ion etching (RIE) enabled the replication of the Al2O3 nanoarray from the PCHE–PLA template on diverse substrates including silicon and gold with feature diameters less than 10 nm.« less

Point-by-point compositional analysis for atom probe tomography.

PubMed

Stephenson, Leigh T; Ceguerra, Anna V; Li, Tong; Rojhirunsakool, Tanaporn; Nag, Soumya; Banerjee, Rajarshi; Cairney, Julie M; Ringer, Simon P

2014-01-01

This new alternate approach to data processing for analyses that traditionally employed grid-based counting methods is necessary because it removes a user-imposed coordinate system that not only limits an analysis but also may introduce errors. We have modified the widely used "binomial" analysis for APT data by replacing grid-based counting with coordinate-independent nearest neighbour identification, improving the measurements and the statistics obtained, allowing quantitative analysis of smaller datasets, and datasets from non-dilute solid solutions. It also allows better visualisation of compositional fluctuations in the data. Our modifications include:.•using spherical k-atom blocks identified by each detected atom's first k nearest neighbours.•3D data visualisation of block composition and nearest neighbour anisotropy.•using z-statistics to directly compare experimental and expected composition curves. Similar modifications may be made to other grid-based counting analyses (contingency table, Langer-Bar-on-Miller, sinusoidal model) and could be instrumental in developing novel data visualisation options.

Invited Article: Autonomous assembly of atomically perfect nanostructures using a scanning tunneling microscope.

PubMed

Celotta, Robert J; Balakirsky, Stephen B; Fein, Aaron P; Hess, Frank M; Rutter, Gregory M; Stroscio, Joseph A

2014-12-01

A major goal of nanotechnology is to develop the capability to arrange matter at will by placing individual atoms at desired locations in a predetermined configuration to build a nanostructure with specific properties or function. The scanning tunneling microscope has demonstrated the ability to arrange the basic building blocks of matter, single atoms, in two-dimensional configurations. An array of various nanostructures has been assembled, which display the quantum mechanics of quantum confined geometries. The level of human interaction needed to physically locate the atom and bring it to the desired location limits this atom assembly technology. Here we report the use of autonomous atom assembly via path planning technology; this allows atomically perfect nanostructures to be assembled without the need for human intervention, resulting in precise constructions in shorter times. We demonstrate autonomous assembly by assembling various quantum confinement geometries using atoms and molecules and describe the benefits of this approach.

Junior High School Students' Ideas about the Shape and Size of the Atom

ERIC Educational Resources Information Center

Cokelez, Aytekin

2012-01-01

The concept of the atom is one of the building blocks of science education. Although the concept is a foundation for students' subsequent learning experiences, it is difficult for students to comprehend because of common misconceptions and its abstractness. The purpose of this study is to examine junior high school students' (ages 12-13) ideas…

And so Ad Infinitum: The Search for Quark and Lepton Substructure

ERIC Educational Resources Information Center

Lincoln, Don

2018-01-01

The saga of the search for the ultimate constituents of matter has long been one of finding a seemingly fundamental structure that, in turn, was found to be made of even smaller building blocks. Matter is made of molecules. Molecules are in turn made of atoms, which are themselves made of electrons and atomic nuclei. The nucleus consists of…

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.

Thermal nanostructure: An order parameter multiscale ensemble approach

NASA Astrophysics Data System (ADS)

Cheluvaraja, S.; Ortoleva, P.

2010-02-01

Deductive all-atom multiscale techniques imply that many nanosystems can be understood in terms of the slow dynamics of order parameters that coevolve with the quasiequilibrium probability density for rapidly fluctuating atomic configurations. The result of this multiscale analysis is a set of stochastic equations for the order parameters whose dynamics is driven by thermal-average forces. We present an efficient algorithm for sampling atomistic configurations in viruses and other supramillion atom nanosystems. This algorithm allows for sampling of a wide range of configurations without creating an excess of high-energy, improbable ones. It is implemented and used to calculate thermal-average forces. These forces are then used to search the free-energy landscape of a nanosystem for deep minima. The methodology is applied to thermal structures of Cowpea chlorotic mottle virus capsid. The method has wide applicability to other nanosystems whose properties are described by the CHARMM or other interatomic force field. Our implementation, denoted SIMNANOWORLD™, achieves calibration-free nanosystem modeling. Essential atomic-scale detail is preserved via a quasiequilibrium probability density while overall character is provided via predicted values of order parameters. Applications from virology to the computer-aided design of nanocapsules for delivery of therapeutic agents and of vaccines for nonenveloped viruses are envisioned.

MODELING GALACTIC EXTINCTION WITH DUST AND 'REAL' POLYCYCLIC AROMATIC HYDROCARBONS

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

Mulas, Giacomo; Casu, Silvia; Cecchi-Pestellini, Cesare

We investigate the remarkable apparent variety of galactic extinction curves by modeling extinction profiles with core-mantle grains and a collection of single polycyclic aromatic hydrocarbons. Our aim is to translate a synthetic description of dust into physically well-grounded building blocks through the analysis of a statistically relevant sample of different extinction curves. All different flavors of observed extinction curves, ranging from the average galactic extinction curve to virtually 'bumpless' profiles, can be described by the present model. We prove that a mixture of a relatively small number (54 species in 4 charge states each) of polycyclic aromatic hydrocarbons can reproducemore » the features of the extinction curve in the ultraviolet, dismissing an old objection to the contribution of polycyclic aromatic hydrocarbons to the interstellar extinction curve. Despite the large number of free parameters (at most the 54 Multiplication-Sign 4 column densities of each species in each ionization state included in the molecular ensemble plus the 9 parameters defining the physical properties of classical particles), we can strongly constrain some physically relevant properties such as the total number of C atoms in all species and the mean charge of the mixture. Such properties are found to be largely independent of the adopted dust model whose variation provides effects that are orthogonal to those brought about by the molecular component. Finally, the fitting procedure, together with some physical sense, suggests (but does not require) the presence of an additional component of chemically different very small carbonaceous grains.« less

Polarization Properties of Semiconductor Nanorod Heterostructures: From Single Particles to the Ensemble.

PubMed

Hadar, Ido; Hitin, Gal B; Sitt, Amit; Faust, Adam; Banin, Uri

2013-02-07

Semiconductor heterostructured seeded nanorods exhibit intense polarized emission, and the degree of polarization is determined by their morphology and dimensions. Combined optical and atomic force microscopy were utilized to directly correlate the emission polarization and the orientation of single seeded nanorods. For both the CdSe/CdS sphere-in-rod (S@R) and rod-in-rod (R@R), the emission was found to be polarized along the nanorod's main axis. Statistical analysis for hundreds of single nanorods shows higher degree of polarization, p, for R@R (p = 0.83), in comparison to S@R (p = 0.75). These results are in good agreement with the values inferred by ensemble photoselection anisotropy measurements in solution, establishing its validity for nanorod samples. On this basis, photoselection photoluminescence excitation anisotropy measurements were carried out providing unique information concerning the symmetry of higher excitonic transitions and allowing for a better distinction between the dielectric and the quantum-mechanical contributions to polarization in nanorods.

Probing the Topology of Density Matrices

NASA Astrophysics Data System (ADS)

Bardyn, Charles-Edouard; Wawer, Lukas; Altland, Alexander; Fleischhauer, Michael; Diehl, Sebastian

2018-01-01

The mixedness of a quantum state is usually seen as an adversary to topological quantization of observables. For example, exact quantization of the charge transported in a so-called Thouless adiabatic pump is lifted at any finite temperature in symmetry-protected topological insulators. Here, we show that certain directly observable many-body correlators preserve the integrity of topological invariants for mixed Gaussian quantum states in one dimension. Our approach relies on the expectation value of the many-body momentum-translation operator and leads to a physical observable—the "ensemble geometric phase" (EGP)—which represents a bona fide geometric phase for mixed quantum states, in the thermodynamic limit. In cyclic protocols, the EGP provides a topologically quantized observable that detects encircled spectral singularities ("purity-gap" closing points) of density matrices. While we identify the many-body nature of the EGP as a key ingredient, we propose a conceptually simple, interferometric setup to directly measure the latter in experiments with mesoscopic ensembles of ultracold atoms.

The Origin of the Elements

ScienceCinema

Murphy, Edward

2018-01-23

The world around us is made of atoms. Did you ever wonder where these atoms came from? How was the gold in our jewelry, the carbon in our bodies, and the iron in our cars made? In this lecture, we will trace the origin of a gold atom from the Big Bang to the present day, and beyond. You will learn how the elements were forged in the nuclear furnaces inside stars, and how, when they die, these massive stars spread the elements into space. You will learn about the origin of the building blocks of matter in the Big Bang, and we will speculate on the future of the atoms around us today.

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.

eHive: An Artificial Intelligence workflow system for genomic analysis

PubMed Central

2010-01-01

Background The Ensembl project produces updates to its comparative genomics resources with each of its several releases per year. During each release cycle approximately two weeks are allocated to generate all the genomic alignments and the protein homology predictions. The number of calculations required for this task grows approximately quadratically with the number of species. We currently support 50 species in Ensembl and we expect the number to continue to grow in the future. Results We present eHive, a new fault tolerant distributed processing system initially designed to support comparative genomic analysis, based on blackboard systems, network distributed autonomous agents, dataflow graphs and block-branch diagrams. In the eHive system a MySQL database serves as the central blackboard and the autonomous agent, a Perl script, queries the system and runs jobs as required. The system allows us to define dataflow and branching rules to suit all our production pipelines. We describe the implementation of three pipelines: (1) pairwise whole genome alignments, (2) multiple whole genome alignments and (3) gene trees with protein homology inference. Finally, we show the efficiency of the system in real case scenarios. Conclusions eHive allows us to produce computationally demanding results in a reliable and efficient way with minimal supervision and high throughput. Further documentation is available at: http://www.ensembl.org/info/docs/eHive/. PMID:20459813

Insights into Inverse Materials Design from Phase Transitions in Shape Space

NASA Astrophysics Data System (ADS)

Cersonsky, Rose; van Anders, Greg; Dodd, Paul M.; Glotzer, Sharon C.

In designing new materials for synthesis, the inverse materials design approach posits that, given a structure, we can predict a building block optimized for self- assembly. How does that building block change as pressure is varied to maintain the same crystal structure? We address this question for entropically stabilized colloidal crystals by working in a generalized statistical thermodynamic ensemble where an alchemical potential variable is fixed and its conjugate variable, particle shape, is allowed to fluctuate. We show that there are multiple regions of shape behavior and phase transitions in shape space between these regions. Furthermore, while past literature has looked towards packing arguments for proposing shape-filling candidate building blocks for structure formation, we show that even at very high pressures, a structure will attain lowest free energy by modifying these space-filling shapes. U.S. Army Research Office under Grant Award No. W911NF-10-1-0518, Emerging Frontiers in Research and Innovation Award EFRI-1240264, National Science Foundation Grant Number ACI- 1053575, XSEDE award DMR 140129, Rackham Merit Fellowship Program.

Statistical mechanical models for dissociative adsorption of O2 on metal(100) surfaces with blocking, steering, and funneling

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

Evans, James W.; Liu, Da-Jiang

We develop statistical mechanical models amenable to analytic treatment for the dissociative adsorption of O2 at hollow sites on fcc(100) metal surfaces. The models incorporate exclusion of nearest-neighbor pairs of adsorbed O. However, corresponding simple site-blocking models, where adsorption requires a large ensemble of available sites, exhibit an anomalously fast initial decrease in sticking. Thus, in addition to blocking, our models also incorporate more facile adsorption via orientational steering and funneling dynamics (features supported by ab initio Molecular Dynamics studies). Behavior for equilibrated adlayers is distinct from those with finite adspecies mobility. We focus on the low-temperature limited-mobility regime wheremore » analysis of the associated master equations readily produces exact results for both short- and long-time behavior. Kinetic Monte Carlo simulation is also utilized to provide a more complete picture of behavior. These models capture both the initial decrease and the saturation of the experimentally observed sticking versus coverage, as well as features of non-equilibrium adlayer ordering as assessed by surface-sensitive diffraction.« less

Statistical mechanical models for dissociative adsorption of O{sub 2} on metal(100) surfaces with blocking, steering, and funneling

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

Evans, James W.; Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011; Liu, Da-Jiang

We develop statistical mechanical models amenable to analytic treatment for the dissociative adsorption of O{sub 2} at hollow sites on fcc(100) metal surfaces. The models incorporate exclusion of nearest-neighbor pairs of adsorbed O. However, corresponding simple site-blocking models, where adsorption requires a large ensemble of available sites, exhibit an anomalously fast initial decrease in sticking. Thus, in addition to blocking, our models also incorporate more facile adsorption via orientational steering and funneling dynamics (features supported by ab initio Molecular Dynamics studies). Behavior for equilibrated adlayers is distinct from those with finite adspecies mobility. We focus on the low-temperature limited-mobility regimemore » where analysis of the associated master equations readily produces exact results for both short- and long-time behavior. Kinetic Monte Carlo simulation is also utilized to provide a more complete picture of behavior. These models capture both the initial decrease and the saturation of the experimentally observed sticking versus coverage, as well as features of non-equilibrium adlayer ordering as assessed by surface-sensitive diffraction.« less

Studying Scientific Discovery by Computer Simulation.

DTIC Science & Technology

1983-03-30

Mendel’s laws of inheritance, the law of Gay- Lussac for gaseous reactions, tile law of Dulong and Petit, the derivation of atomic weights by Avogadro...neceseary mid identify by block number) scientific discovery -ittri sic properties physical laws extensive terms data-driven heuristics intensive...terms theory-driven heuristics conservation laws 20. ABSTRACT (Continue on revere. side It necessary and identify by block number) Scientific discovery

Soft nanoparticles: nano ionic networks of associated ionic polymers

DOE PAGES

Aryal, Dipak; Grest, Gary S.; Perahia, Dvora

2017-01-01

Directing the formation of nanostructures that serve as building blocks of membranes presents an immense step towards engineering controlled polymeric ion transport systems. Here, using the exquisite atomic detail captured by molecular dynamics simulations, we follow the assembly of a co-polymer that consists of polystyrene sulfonate tethered symmetrically to hydrophobic blocks, realizing a new type of long lived solvent-responsive soft nanoparticle.

Functional Perfluoroalkyl Polyhedral Oligomeric Silsesquioxane (F-POSS): Building Blocks for Low Surface Energy Materials

DTIC Science & Technology

2010-10-21

Technical Paper 3. DATES COVERED (From - To) 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Functional Perfluoroalkyl Polyhedral Oligomeric Silsesquioxane (F...long chain fluorinated alkyl groups ranging from 6-12 carbon atoms in length. Herein, a disilanol perfluoroalkyl polyhedral oligomeric...FUNCTIONAL PERFLUOROALKYL POLYHEDRAL OLIGOMERIC SILSESQUIOXANES (F-POSS): BUILDING BLOCKS FOR LOW SURFACE ENERGY MATERIA LS Sean M Rami,.e:, Yvonne Dia

An Ensemble-Based Protocol for the Computational Prediction of Helix–Helix Interactions in G Protein-Coupled Receptors using Coarse-Grained Molecular Dynamics

PubMed Central

2017-01-01

The accurate identification of the specific points of interaction between G protein-coupled receptor (GPCR) oligomers is essential for the design of receptor ligands targeting oligomeric receptor targets. A coarse-grained molecular dynamics computer simulation approach would provide a compelling means of identifying these specific protein–protein interactions and could be applied both for known oligomers of interest and as a high-throughput screen to identify novel oligomeric targets. However, to be effective, this in silico modeling must provide accurate, precise, and reproducible information. This has been achieved recently in numerous biological systems using an ensemble-based all-atom molecular dynamics approach. In this study, we describe an equivalent methodology for ensemble-based coarse-grained simulations. We report the performance of this method when applied to four different GPCRs known to oligomerize using error analysis to determine the ensemble size and individual replica simulation time required. Our measurements of distance between residues shown to be involved in oligomerization of the fifth transmembrane domain from the adenosine A2A receptor are in very good agreement with the existing biophysical data and provide information about the nature of the contact interface that cannot be determined experimentally. Calculations of distance between rhodopsin, CXCR4, and β1AR transmembrane domains reported to form contact points in homodimers correlate well with the corresponding measurements obtained from experimental structural data, providing an ability to predict contact interfaces computationally. Interestingly, error analysis enables identification of noninteracting regions. Our results confirm that GPCR interactions can be reliably predicted using this novel methodology. PMID:28383913

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

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.

Spatial entanglement patterns and Einstein-Podolsky-Rosen steering in Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Fadel, Matteo; Zibold, Tilman; Décamps, Boris; Treutlein, Philipp

2018-04-01

Many-particle entanglement is a fundamental concept of quantum physics that still presents conceptual challenges. Although nonclassical states of atomic ensembles were used to enhance measurement precision in quantum metrology, the notion of entanglement in these systems was debated because the correlations among the indistinguishable atoms were witnessed by collective measurements only. Here, we use high-resolution imaging to directly measure the spin correlations between spatially separated parts of a spin-squeezed Bose-Einstein condensate. We observe entanglement that is strong enough for Einstein-Podolsky-Rosen steering: We can predict measurement outcomes for noncommuting observables in one spatial region on the basis of corresponding measurements in another region with an inferred uncertainty product below the Heisenberg uncertainty bound. This method could be exploited for entanglement-enhanced imaging of electromagnetic field distributions and quantum information tasks.

Quantum State Transfer via Noisy Photonic and Phononic Waveguides

NASA Astrophysics Data System (ADS)

Vermersch, B.; Guimond, P.-O.; Pichler, H.; Zoller, P.

2017-03-01

We describe a quantum state transfer protocol, where a quantum state of photons stored in a first cavity can be faithfully transferred to a second distant cavity via an infinite 1D waveguide, while being immune to arbitrary noise (e.g., thermal noise) injected into the waveguide. We extend the model and protocol to a cavity QED setup, where atomic ensembles, or single atoms representing quantum memory, are coupled to a cavity mode. We present a detailed study of sensitivity to imperfections, and apply a quantum error correction protocol to account for random losses (or additions) of photons in the waveguide. Our numerical analysis is enabled by matrix product state techniques to simulate the complete quantum circuit, which we generalize to include thermal input fields. Our discussion applies both to photonic and phononic quantum networks.

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.

Cluster Beam Studies.

DTIC Science & Technology

1988-04-01

Continue on reverse if necessary and identify by block number) Cluster beams offer a means of depositing high-quality thin films at low...either directly inclustered vapors of nonvolatile materials or Indirectly by bombarding the film duringdeposition with clusters of inert gases. When a...electron volt energy per atom. The suprathermal energy of thej depositing atoms is thought to produce unique thin films (either in quality, or in the ability

Graphene as a flexible template for controlling magnetic interactions between metal atoms.

PubMed

Lee, Sungwoo; Kim, Dongwook; Robertson, Alex W; Yoon, Euijoon; Hong, Suklyun; Ihm, Jisoon; Yu, Jaejun; Warner, Jamie H; Lee, Gun-Do

2017-03-01

Metal-doped graphene produces magnetic moments that have potential application in spintronics. Here we use density function theory computational methods to show how the magnetic interaction between metal atoms doped in graphene can be controlled by the degree of flexure in a graphene membrane. Bending graphene by flexing causes the distance between two substitutional Fe atoms covalently bonded in graphene to gradually increase and these results in the magnetic moment disappearing at a critical strain value. At the critical strain, a carbon atom can enter between the two Fe atoms and blocks the interaction between relevant orbitals of Fe atoms to quench the magnetic moment. The control of interactions between doped atoms by exploiting the mechanical flexibility of graphene is a unique approach to manipulating the magnetic properties and opens up new opportunities for mechanical-magnetic 2D device systems.

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.

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

Nanofiber quantum photonics

NASA Astrophysics Data System (ADS)

Nayak, Kali P.; Sadgrove, Mark; Yalla, Ramachandrarao; Le Kien, Fam; Hakuta, Kohzo

2018-07-01

Recent advances in the coherent control of single quanta of light, photons, is a topic of prime interest, and is discussed under the banner of quantum photonics. In the last decade, the subwavelength diameter waist of a tapered optical fiber, referred to as an optical nanofiber, has opened promising new avenues in the field of quantum optics, paving the way toward a versatile platform for quantum photonics applications. The key feature of the technique is that the optical field can be tightly confined in the transverse direction while propagating over long distances as a guided mode and enabling strong interaction with the surrounding medium in the evanescent region. This feature has led to surprising possibilities to manipulate single atoms and fiber-guided photons, e.g. the efficient channeling of emission from single atoms and solid-state quantum emitters into the fiber-guided modes, high optical depth with a few atoms around the nanofiber, trapping atoms around a nanofiber, and atomic memories for fiber-guided photons. Furthermore, implementing a moderate longitudinal confinement in nanofiber cavities has enabled the strong coupling regime of cavity quantum electrodynamics to be reached, and the long-range dipole–dipole interaction between quantum emitters mediated by the nanofiber offers a platform for quantum nonlinear optics with an ensemble of atoms. In addition, the presence of a longitudinal component of the guided field has led to unique capabilities for chiral light–matter interactions on nanofibers. In this article, we review the key developments of the nanofiber technology toward a vision for quantum photonics on an all-fiber interface.

Optically Controlled Distributed Quantum Computing Using Atomic Ensembles As Qubits

DTIC Science & Technology

2016-02-23

Second, the lithium niobate material has a large nonlinear coefficient (>20 pm V–1) for efficient QFC and a wide transparent window (∼ 350 –5200 nm...for the 1550 nm + 1570 nm 780 nm process. Finally, to implement QFC for the 637 and 780 nm light, one would use a pump at 350 nm and a waveguide QPM...for the 637 nm + 780 nm 350 nm process. Again, the 350 nm laser can be produced adopting successive SHG and SFG processes using a 1050 nm laser

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.

Multimode cavity-assisted quantum storage via continuous phase-matching control

NASA Astrophysics Data System (ADS)

Kalachev, Alexey; Kocharovskaya, Olga

2013-09-01

A scheme for spatial multimode quantum memory is developed such that spatial-temporal structure of a weak signal pulse can be stored and recalled via cavity-assisted off-resonant Raman interaction with a strong angular-modulated control field in an extended Λ-type atomic ensemble. It is shown that effective multimode storage is possible when the Raman coherence spatial grating involves wave vectors with different longitudinal components relative to the paraxial signal field. The possibilities of implementing the scheme in the solid-state materials are discussed.

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.

Hybrid classical/quantum simulation for infrared spectroscopy of water

NASA Astrophysics Data System (ADS)

Maekawa, Yuki; Sasaoka, Kenji; Ube, Takuji; Ishiguro, Takashi; Yamamoto, Takahiro

2018-05-01

We have developed a hybrid classical/quantum simulation method to calculate the infrared (IR) spectrum of water. The proposed method achieves much higher accuracy than conventional classical molecular dynamics (MD) simulations at a much lower computational cost than ab initio MD simulations. The IR spectrum of water is obtained as an ensemble average of the eigenvalues of the dynamical matrix constructed by ab initio calculations, using the positions of oxygen atoms that constitute water molecules obtained from the classical MD simulation. The calculated IR spectrum is in excellent agreement with the experimental IR spectrum.

Late-Paleozoic-Mesozoic deformational and deformation related metamorphic structures of Kuznetsk-Altai region

NASA Astrophysics Data System (ADS)

Zinoviev, Sergei

2014-05-01

Kuznetsk-Altai region is a part of the Central Asian Orogenic Belt. The nature and formation mechanisms of the observed structure of Kuznetsk-Altai region are interpreted by the author as the consequence of convergence of Tuva-Mongolian and Junggar lithospheric block structures and energy of collision interaction between the blocks of crust in Late-Paleozoic-Mesozoic period. Tectonic zoning of Kuznetsk-Altai region is based on the principle of adequate description of geological medium (without methods of 'primary' state recovery). The initial indication of this convergence is the crust thickening in the zone of collision. On the surface the mechanisms of lateral compression form a regional elevation; with this elevation growth the 'mountain roots' start growing. With an approach of blocks an interblock elevation is divided into various fragments, and these fragments interact in the manner of collision. The physical expression of collision mechanisms are periodic pulses of seismic activity. The main tectonic consequence of the block convergence and collision of interblock units is formation of an ensemble of regional structures of the deformation type on the basis of previous 'pre-collision' geological substratum [Chikov et al., 2012]. This ensemble includes: 1) allochthonous and autochthonous blocks of weakly deformed substratum; 2) folded (folded-thrust) systems; 3) dynamic metamorphism zones of regional shears and main faults. Characteristic of the main structures includes: the position of sedimentary, magmatic and PT-metamorphic rocks, the degree of rock dynamometamorphism and variety rock body deformation, as well as the styles and concentrations of mechanic deformations. 1) block terranes have weakly elongated or isometric shape in plane, and they are the systems of block structures of pre-collision substratum separated by the younger zones of interblock deformations. They stand out among the main deformation systems, and the smallest are included into the deformation systems. 2) folded (folded-thrust) deformation systems combine deformation zones with relic lenses of Paleozoid substratum, and predominantly conform systems of the main faults. Despite a high degree of regional deformation the sedimentary-stratified and intrusive-contact relations of geological bodies are stored within the deformation systems, and this differs in the main the collision systems from zones of dynamic metamorphism. 3) regional zones of dynamic metamorphism of Kuznetsk-Altai region are the concentration belts of multiple mechanic deformations and contrast dynamometamorphism of complexes. The formational basis of dynamic metamorphism zones is tectonites of the collision stage. Zones of dynamic metamorphism attract special attention in the structural model of Kuznetsk-Altai region. They not only form the typical tectonic framework of collision sutures, but also contain the main part of ore deposits of this region. Pulse mode of structure formation of Kuznetsk-Altai region is detected. Major collision events in Kuznetsk-Altai region were in the late-Carboniferous-Triassic time (307-310, 295-285, 260-250 and 240-220 Ma). This study was supported by a grant of the Russian Foundation for Basic Research (project nos. 14-05-00117).

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.

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.