Revisiting shape selectivity in liquid chromatography for polycyclic aromatic hydrocarbons (PAHs) - six-ring and seven-ring Cata-condensed PAH isomers of molecular mass 328 Da and 378 Da.

Science.gov (United States)

Oña-Ruales, Jorge O; Sander, Lane C; Wilson, Walter B; Wise, Stephen A

2018-01-01

The relationship of reversed-phase liquid chromatography (RPLC) retention on a polymeric C 18 stationary phase and the shape of polycyclic aromatic hydrocarbons (PAHs) was investigated for three-ring to seven-ring cata-condensed isomers. We report the first RPLC separation for six-ring and seven-ring cata-condensed PAH isomers. Correlations of LC retention and shape parameters (length-to-breath ratio, L/B and thickness, T) were investigated for 2 three-ring isomers (molecular mass 178 Da), 5 four-ring isomers (molecular mass 228 Da), 11 five-ring isomers (molecular mass 278 Da), 17 six-ring isomers (molecular mass 328 Da), and 20 seven-ring isomers (molecular mass 378 Da). Significant linear correlations were found for all isomer groups (r = 0.71 to 0.94). Nonplanarity of the PAH isomers was found to influence retention (i.e., nonplanar isomers eluting earlier than expected based on L/B) and linear correlations of retention vs. T for isomer groups containing nonplanar isomers were significant (r = 0.71 to 0.86). Graphical abstract.

Classical molecular dynamics simulation of electronically non-adiabatic processes.

Science.gov (United States)

Miller, William H; Cotton, Stephen J

2016-12-22

Both classical and quantum mechanics (as well as hybrids thereof, i.e., semiclassical approaches) find widespread use in simulating dynamical processes in molecular systems. For large chemical systems, however, which involve potential energy surfaces (PES) of general/arbitrary form, it is usually the case that only classical molecular dynamics (MD) approaches are feasible, and their use is thus ubiquitous nowadays, at least for chemical processes involving dynamics on a single PES (i.e., within a single Born-Oppenheimer electronic state). This paper reviews recent developments in an approach which extends standard classical MD methods to the treatment of electronically non-adiabatic processes, i.e., those that involve transitions between different electronic states. The approach treats nuclear and electronic degrees of freedom (DOF) equivalently (i.e., by classical mechanics, thereby retaining the simplicity of standard MD), and provides "quantization" of the electronic states through a symmetrical quasi-classical (SQC) windowing model. The approach is seen to be capable of treating extreme regimes of strong and weak coupling between the electronic states, as well as accurately describing coherence effects in the electronic DOF (including the de-coherence of such effects caused by coupling to the nuclear DOF). A survey of recent applications is presented to illustrate the performance of the approach. Also described is a newly developed variation on the original SQC model (found universally superior to the original) and a general extension of the SQC model to obtain the full electronic density matrix (at no additional cost/complexity).

Low-field spin dynamics of Cr7Ni and Cr7Ni-Cu -Cr 7Ni molecular rings as detected by μ SR

Science.gov (United States)

Sanna, S.; Arosio, P.; Bordonali, L.; Adelnia, F.; Mariani, M.; Garlatti, E.; Baines, C.; Amato, A.; Sabareesh, K. P. V.; Timco, G.; Winpenny, R. E. P.; Blundell, S. J.; Lascialfari, A.

2017-11-01

Muon spin rotation measurements were used to investigate the spin dynamics of heterometallic Cr7Ni and Cr7Ni -Cu-Cr7Ni molecular clusters. In Cr7Ni the magnetic ions are arranged in a quasiplanar ring and interact via an antiferromagnetic exchange coupling constant J , while Cr7Ni -Cu-Cr7Ni is composed of two Cr7Ni linked by a bridging moiety containing one Cu ion, that induces an inter-ring ferromagnetic interaction J'≪J . The longitudinal muon relaxation rate λ collected at low magnetic fields μ0H BPP)-like heuristic fitting model that takes into account of a distribution of electronic spin characteristic times for T >5 K, while the shoulder presented by Cr7Ni can be reproduced by a BPP function that incorporates a single electronic characteristic time theoretically predicted to dominate for T <5 K. The flattening of λ (T ) in Cr7Ni -Cu-Cr7Ni occurring at very low temperature can be tentatively attributed to field-dependent quantum effects and/or to an inelastic term in the spectral density of the electronic spin fluctuations.

Temperature dependence of the anisotropy of fluorescence in ring molecular systems

International Nuclear Information System (INIS)

Herman, Pavel; Barvik, Ivan

2007-01-01

The time dependence of the anisotropy of fluorescence after an impulsive excitation in the molecular ring (resembling the B850 ring of the purple bacterium Rhodopseudomonas acidophila) is calculated. Fast fluctuations of the environment are simulated by dynamic disorder and slow fluctuations by uncorrelated static disorder. Without dynamic disorder modest degrees of static disorder are sufficient to cause the experimentally found initial drop of the anisotropy on a sub-100 fs time scale. In the present investigation we are comparing results for the time-dependent optical anisotropy of the molecular ring for four models of the uncorrelated static disorder: Gaussian disorder in the local energies (model A), Gaussian disorder in the transfer integrals (model B), Gaussian disorder in radial positions of molecules (model C) and Gaussian disorder in angular positions of molecules (model D). Both types of disorder-static and dynamic-are taken into account simultaneously

Clinicopathologic and Molecular Features of Colorectal Adenocarcinoma with Signet-Ring Cell Component.

Directory of Open Access Journals (Sweden)

Qing Wei

Full Text Available We performed a retrospective study to assess the clinicopathological characters, molecular alterations and multigene mutation profiles in colorectal cancer patients with signet-ring cell component.Between November 2008 and January 2015, 61 consecutive primary colorectal carcinomas with signet-ring cell component were available for pathological confirmation. RAS/BRAF status was performed by direct sequencing. 14 genes associated with hereditary cancer syndromes were analyzed by targeted gene sequencing.A slight male predominance was detected in these patients (59.0%. Colorectal carcinomas with signet-ring cell component were well distributed along the large intestine. A frequently higher TNM stage at the time of diagnosis was observed, compared with the conventional adenocarcinoma. Family history of malignant tumor was remarkable with 49.2% in 61 cases. The median OS time of stage IV patients in our study was 14 months. RAS mutations were detected in 22.2% (12/54 cases with KRAS mutations in 16.7% (9/54 cases and Nras mutations in 5.4%(3/54 cases. BRAF V600E mutation was detected in 3.7% (2/54 cases. As an exploration, we analyzed 14 genes by targeted gene sequencing. These genes were selected based on their biological role in association with hereditary cancer syndromes. 79.6% cases carried at least one pathogenic mutation. Finally, the patients were classified by the percentage of signet-ring cell. 39 (63.9% cases were composed of ≥50% signet-ring cells; 22 (36.1% cases were composed of <50% signet-ring cells. We compared clinical parameters, molecular and genetic alterations between the two groups and found no significant differences.Colorectal adenocarcinoma with signet-ring cell component is characterized by advanced stage at diagnosis with remarkable family history of malignant tumor. It is likely a negative prognostic factor and tends to affect male patients with low rates of RAS /BRAF mutation. Colorectal patients with any component of

Young's moduli of carbon materials investigated by various classical molecular dynamics schemes

Science.gov (United States)

Gayk, Florian; Ehrens, Julian; Heitmann, Tjark; Vorndamme, Patrick; Mrugalla, Andreas; Schnack, Jürgen

2018-05-01

For many applications classical carbon potentials together with classical molecular dynamics are employed to calculate structures and physical properties of such carbon-based materials where quantum mechanical methods fail either due to the excessive size, irregular structure or long-time dynamics. Although such potentials, as for instance implemented in LAMMPS, yield reasonably accurate bond lengths and angles for several carbon materials such as graphene, it is not clear how accurate they are in terms of mechanical properties such as for instance Young's moduli. We performed large-scale classical molecular dynamics investigations of three carbon-based materials using the various potentials implemented in LAMMPS as well as the EDIP potential of Marks. We show how the Young's moduli vary with classical potentials and compare to experimental results. Since classical descriptions of carbon are bound to be approximations it is not astonishing that different realizations yield differing results. One should therefore carefully check for which observables a certain potential is suited. Our aim is to contribute to such a clarification.

QM/MM and classical molecular dynamics simulation of histidine-tagged peptide immobilization on nickel surface

Energy Technology Data Exchange (ETDEWEB)

Yang Zhenyu [State Key Laboratory of Nonlinear Mechanics (LNM), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100080(China); Zhao Yapu [State Key Laboratory of Nonlinear Mechanics (LNM), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100080 (China)]. E-mail: yzhao@lnm.imech.ac.cn

2006-05-15

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by 'GAMESS', and the rest atoms are treated as MM part calculated by 'TINKER'. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with the QM part with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.

Faithfully quadratic rings

CERN Document Server

Dickmann, M

2015-01-01

In this monograph the authors extend the classical algebraic theory of quadratic forms over fields to diagonal quadratic forms with invertible entries over broad classes of commutative, unitary rings where -1 is not a sum of squares and 2 is invertible. They accomplish this by: (1) Extending the classical notion of matrix isometry of forms to a suitable notion of T-isometry, where T is a preorder of the given ring, A, or T = A^2. (2) Introducing in this context three axioms expressing simple properties of (value) representation of elements of the ring by quadratic forms, well-known to hold in

Energy conservation in molecular dynamics simulations of classical systems

DEFF Research Database (Denmark)

Toxværd, Søren; Heilmann, Ole; Dyre, J. C.

2012-01-01

Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...

Inter professionalization and the breakaway from classic concepts

DEFF Research Database (Denmark)

Borgnakke, Karen; Nielsen, Cathrine Sand

2014-01-01

to explore and describe how the perspective of InBetween can help to strengthen and develop the individual, inter-professional and (inter)organisational learning generating new knowledge of: - the contributions of InBetween to the quality of future health professional education and to the future healthcare...

[Molecular cytogenetic analysis of a case with ring chromosome 3 syndrome].

Science.gov (United States)

Zhang, Kaihui; Song, Fengling; Zhang, Dongdong; Zhang, Haiyan; Wang, Ying; Dong, Rui; Zhang, Yufeng; Liu, Yi; Gai, Zhongtao

2016-12-10

To investigate the genetic cause for a child with developmental delay and congenital heart disease through molecular cytogenetic analysis. G-banded karyotyping and chromosomal microarray analysis (CMA) were performed for the patient and his parents. The proband's karyotype was detected as ring chromosome 3, and a 3q26.3-25.3 deletion encompassing 45 genes has been found with CMA. Testing of both parents was normal. Clinical phenotype of the patient with ring chromosome 3 mainly depends on the involved genes. It is necessary to combine CMA and karyotyping for the diagnosis of ring chromosome, as CMA can provide more accurate information for variations of the genome.

Topological ring currents in the "empty" ring of benzo-annelated perylenes.

Science.gov (United States)

Dickens, Timothy K; Mallion, Roger B

2011-01-27

Cyclic conjugation in benzo-annelated perylenes is examined by means of the topological π-electron ring currents calculated for each of their constituent rings, in a study that is an exact analogy of a recent investigation by Gutman et al. based on energy-effect values for the corresponding rings in each of these structures. "Classical" approaches, such as Kekulé structures, Clar "sextet" formulas, and circuits of conjugation, predict that the central ring in perylene is "empty" and thus contributes negligibly to cyclic conjugation. However, conclusions from the present calculations of topological ring currents agree remarkably with those arising from the earlier study involving energy-effect values in that, contrary to what would be predicted from the classical approaches, rings annelated in an angular fashion relative to the central ring of these perylene structures materially increase the extent of that ring's involvement in cyclic conjugation. It is suggested that such close quantitative agreement between the predictions of these two superficially very different indices (energy effect and topological ring current) might be due to the fact that, ultimately, both depend, albeit in ostensibly quite different ways, only on an adjacency matrix that contains information about the carbon-carbon connectivity of the conjugated system in question.

Vertically coupled double quantum rings at zero magnetic field

OpenAIRE

Malet, Francesc; Barranco, Manuel; Lipparini, Enrico; Pi, Ricardo Mayol Martí; Climente, Juan Ignacio; Planelles, Josep

2006-01-01

Within local-spin-density functional theory, we have investigated the `dissociation' of few-electron circular vertical semiconductor double quantum ring artificial molecules at zero magnetic field as a function of inter-ring distance. In a first step, the molecules are constituted by two identical quantum rings. When the rings are quantum mechanically strongly coupled, the electronic states are substantially delocalized, and the addition energy spectra of the artificial molecule resemble thos...

Mechanistic insights into Mg2+-independent prenylation by CloQ from classical molecular mechanics and hybrid quantum mechanics/molecular mechanics molecular dynamics simulations.

Science.gov (United States)

Bayse, Craig A; Merz, Kenneth M

2014-08-05

Understanding the mechanism of prenyltransferases is important to the design of engineered proteins capable of synthesizing derivatives of naturally occurring therapeutic agents. CloQ is a Mg(2+)-independent aromatic prenyltransferase (APTase) that transfers a dimethylallyl group to 4-hydroxyphenylpyruvate in the biosynthetic pathway for clorobiocin. APTases consist of a common ABBA fold that defines a β-barrel containing the reaction cavity. Positively charged basic residues line the inside of the β-barrel of CloQ to activate the pyrophosphate leaving group to replace the function of the Mg(2+) cofactor in other APTases. Classical molecular dynamics simulations of CloQ, its E281G and F68S mutants, and the related NovQ were used to explore the binding of the 4-hydroxyphenylpyruvate (4HPP) and dimethylallyl diphosphate substrates in the reactive cavity and the role of various conserved residues. Hybrid quantum mechanics/molecular mechanics potential of mean force (PMF) calculations show that the effect of the replacement of the Mg(2+) cofactor with basic residues yields a similar activation barrier for prenylation to Mg(2+)-dependent APTases like NphB. The topology of the binding pocket for 4HPP is important for selective prenylation at the ortho position of the ring. Methylation at this position alters the conformation of the substrate for O-prenylation at the phenol group. Further, a two-dimensional PMF scan shows that a "reverse" prenylation product may be a possible target for protein engineering.

Mechanism of the Glycosidic Bond Cleavage of Mismatched Thymine in Human Thymine DNA Glycosylase Revealed by Classical Molecular Dynamics and Quantum Mechanical/Molecular Mechanical Calculations.

Science.gov (United States)

Kanaan, Natalia; Crehuet, Ramon; Imhof, Petra

2015-09-24

Base excision of mismatched or damaged nucleotides catalyzed by glycosylase enzymes is the first step of the base excision repair system, a machinery preserving the integrity of DNA. Thymine DNA glycosylase recognizes and removes mismatched thymine by cleaving the C1'-N1 bond between the base and the sugar ring. Our quantum mechanical/molecular mechanical calculations of this reaction in human thymine DNA glycosylase reveal a requirement for a positive charge in the active site to facilitate C1'-N1 bond scission: protonation of His151 significantly lowers the free energy barrier for C1'-N1 bond dissociation compared to the situation with neutral His151. Shuttling a proton from His151 to the thymine base further reduces the activation free energy for glycosidic bond cleavage. Classical molecular dynamics simulations of the H151A mutant suggest that the mutation to the smaller, neutral, residue increases the water accessibility of the thymine base, rendering direct proton transfer from the bulk feasible. Quantum mechanical/molecular mechanical calculations of the glycosidic bond cleavage reaction in the H151A mutant show that the activation free energy is slightly lower than in the wild-type enzyme, explaining the experimentally observed higher reaction rates in this mutant.

Molecular architecture of the N-type ATPase rotor ring from Burkholderia pseudomallei.

Science.gov (United States)

Schulz, Sarah; Wilkes, Martin; Mills, Deryck J; Kühlbrandt, Werner; Meier, Thomas

2017-04-01

The genome of the highly infectious bacterium Burkholderia pseudomallei harbors an atp operon that encodes an N-type rotary ATPase, in addition to an operon for a regular F-type rotary ATPase. The molecular architecture of N-type ATPases is unknown and their biochemical properties and cellular functions are largely unexplored. We studied the B. pseudomallei N 1 N o -type ATPase and investigated the structure and ion specificity of its membrane-embedded c-ring rotor by single-particle electron cryo-microscopy. Of several amphiphilic compounds tested for solubilizing the complex, the choice of the low-density, low-CMC detergent LDAO was optimal in terms of map quality and resolution. The cryoEM map of the c-ring at 6.1 Å resolution reveals a heptadecameric oligomer with a molecular mass of ~141 kDa. Biochemical measurements indicate that the c 17 ring is H + specific, demonstrating that the ATPase is proton-coupled. The c 17 ring stoichiometry results in a very high ion-to-ATP ratio of 5.7. We propose that this N-ATPase is a highly efficient proton pump that helps these melioidosis-causing bacteria to survive in the hostile, acidic environment of phagosomes. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

FUZZY RINGS AND ITS PROPERTIES

Directory of Open Access Journals (Sweden)

Karyati Karyati

2017-01-01

  One of algebraic structure that involves a binary operation is a group that is defined  an un empty set (classical with an associative binary operation, it has identity elements and each element has an inverse. In the structure of the group known as the term subgroup, normal subgroup, subgroup and factor group homomorphism and its properties. Classical algebraic structure is developed to algebraic structure fuzzy by the researchers as an example semi group fuzzy and fuzzy group after fuzzy sets is introduced by L. A. Zadeh at 1965. It is inspired of writing about semi group fuzzy and group of fuzzy, a research on the algebraic structure of the ring is held with reviewing ring fuzzy, ideal ring fuzzy, homomorphism ring fuzzy and quotient ring fuzzy with its properties. The results of this study are obtained fuzzy properties of the ring, ring ideal properties fuzzy, properties of fuzzy ring homomorphism and properties of fuzzy quotient ring by utilizing a subset of a subset level  and strong level  as well as image and pre-image homomorphism fuzzy ring.   Keywords: fuzzy ring, subset level, homomorphism fuzzy ring, fuzzy quotient ring

Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. I. Statics

Science.gov (United States)

Halverson, Jonathan D.; Lee, Won Bo; Grest, Gary S.; Grosberg, Alexander Y.; Kremer, Kurt

2011-05-01

Molecular dynamics simulations were conducted to investigate the structural properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest rings were composed of N = 1600 monomers per chain which corresponds to roughly 57 entanglement lengths for comparable linear polymers. For the rings, the radius of gyration squared, , was found to scale as N4/5 for an intermediate regime and N2/3 for the larger rings indicating an overall conformation of a crumpled globule. However, almost all beads of the rings are "surface beads" interacting with beads of other rings, a result also in agreement with a primitive path analysis performed in the next paper [J. D. Halverson, W. Lee, G. S. Grest, A. Y. Grosberg, and K. Kremer, J. Chem. Phys. 134, 204905 (2011)], 10.1063/1.3587138. Details of the internal conformational properties of the ring and linear polymers as well as their packing are analyzed and compared to current theoretical models.

Spin dynamics at level crossing in molecular AF rings probed by NMR

International Nuclear Information System (INIS)

Lascialfari, A.; Borsa, F.; Julien, M.-H.; Micotti, E.; Furukawa, Y.; Jang, Z.H.; Cornia, A.; Gatteschi, D.; Horvatic, M.; Van Slageren, J.

2004-01-01

The low-temperature spin dynamics in molecular rings with a finite number (N≤10) of magnetic ions was studied by means of 1 H NMR. When an external magnetic field (B) induces a crossing between energy levels, peaks are observed in the spin-lattice relaxation rate of protons, 1/T 1 (B), at constant temperature. We discuss similarities and differences in the data from three different rings: Fe10, Fe6:Li and Cr8

RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics

KAUST Repository

Suleimanov, Yu.V.

2013-03-01

We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH 4, OH+CH4 and H+C2H6 reactions. © 2012 Elsevier B.V. All rights reserved.

RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics

KAUST Repository

Suleimanov, Yu.V.; Allen, J.W.; Green, W.H.

2013-01-01

We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH 4, OH+CH4 and H+C2H6 reactions. © 2012 Elsevier B.V. All rights reserved.

Photoswitchable Molecular Rings for Solar-Thermal Energy Storage.

Science.gov (United States)

Durgun, E; Grossman, Jeffrey C

2013-03-21

Solar-thermal fuels reversibly store solar energy in the chemical bonds of molecules by photoconversion, and can release this stored energy in the form of heat upon activation. Many conventional photoswichable molecules could be considered as solar thermal fuels, although they suffer from low energy density or short lifetime in the photoinduced high-energy metastable state, rendering their practical use unfeasible. We present a new approach to the design of chemistries for solar thermal fuel applications, wherein well-known photoswitchable molecules are connected by different linker agents to form molecular rings. This approach allows for a significant increase in both the amount of stored energy per molecule and the stability of the fuels. Our results suggest a range of possibilities for tuning the energy density and thermal stability as a function of the type of the photoswitchable molecule, the ring size, or the type of linkers.

Three-stage classical molecular dynamics model for simulation of heavy-ion fusion

Directory of Open Access Journals (Sweden)

Godre Subodh S.

2015-01-01

Full Text Available A three-stage Classical Molecular Dynamics (3S-CMD approach for heavy-ion fusion is developed. In this approach the Classical Rigid-Body Dynamics simulation for heavy-ion collision involving light deformed nucleus is initiated on their Rutherford trajectories at very large initial separation. Collision simulation is then followed by relaxation of the rigid-body constrains for one or both the colliding nuclei at distances close to the barrier when the trajectories of all the nucleons are obtained in a Classical Molecular Dynamics approach. This 3S-CMD approach explicitly takes into account not only the long range Coulomb reorientation of the deformed collision partner but also the internal vibrational excitations of one or both the nuclei at distances close to the barrier. The results of the dynamical simulation for 24Mg+208Pb collision show significant modification of the fusion barrier and calculated fusion cross sections due to internal excitations.

Spin dynamics at level crossing in molecular AF rings probed by NMR

Energy Technology Data Exchange (ETDEWEB)

Lascialfari, A. E-mail: lascialfari@fisicavolta.unipv.it; Borsa, F.; Julien, M.-H.; Micotti, E.; Furukawa, Y.; Jang, Z.H.; Cornia, A.; Gatteschi, D.; Horvatic, M.; Van Slageren, J

2004-05-01

The low-temperature spin dynamics in molecular rings with a finite number (N{<=}10) of magnetic ions was studied by means of {sup 1}H NMR. When an external magnetic field (B) induces a crossing between energy levels, peaks are observed in the spin-lattice relaxation rate of protons, 1/T{sub 1}(B), at constant temperature. We discuss similarities and differences in the data from three different rings: Fe10, Fe6:Li and Cr8.

Classical molecular dynamics simulations of fusion and fragmentation in fullerene-fullerene collisions

International Nuclear Information System (INIS)

Verkhovtsev, A.; Korol, A.V.; Solovyov, A.V.

2017-01-01

We present the results of classical molecular dynamics simulations of collision-induced fusion and fragmentation of C 60 fullerenes, performed by means of the MBN Explorer software package. The simulations provide information on structural differences of the fused compound depending on kinematics of the collision process. The analysis of fragmentation dynamics at different initial conditions shows that the size distributions of produced molecular fragments are peaked for dimers, which is in agreement with a well-established mechanism of C 60 fragmentation via preferential C 2 emission. Atomic trajectories of the colliding particles are analyzed and different fragmentation patterns are observed and discussed. On the basis of the performed simulations, characteristic time of C 2 emission is estimated as a function of collision energy. The results are compared with experimental time-of-flight distributions of molecular fragments and with earlier theoretical studies. Considering the widely explored case study of C 60 -C 60 collisions, we demonstrate broad capabilities of the MBN Explorer software, which can be utilized for studying collisions of a broad variety of nano-scale and bio-molecular systems by means of classical molecular dynamics. (authors)

Groups, rings, modules

CERN Document Server

Auslander, Maurice

2014-01-01

This classic monograph is geared toward advanced undergraduates and graduate students. The treatment presupposes some familiarity with sets, groups, rings, and vector spaces. The four-part approach begins with examinations of sets and maps, monoids and groups, categories, and rings. The second part explores unique factorization domains, general module theory, semisimple rings and modules, and Artinian rings. Part three's topics include localization and tensor products, principal ideal domains, and applications of fundamental theorem. The fourth and final part covers algebraic field extensions

Molecular dynamics simulations of classical sound absorption in a monatomic gas

Science.gov (United States)

Ayub, M.; Zander, A. C.; Huang, D. M.; Cazzolato, B. S.; Howard, C. Q.

2018-05-01

Sound wave propagation in argon gas is simulated using molecular dynamics (MD) in order to determine the attenuation of acoustic energy due to classical (viscous and thermal) losses at high frequencies. In addition, a method is described to estimate attenuation of acoustic energy using the thermodynamic concept of exergy. The results are compared against standing wave theory and the predictions of the theory of continuum mechanics. Acoustic energy losses are studied by evaluating various attenuation parameters and by comparing the changes in behavior at three different frequencies. This study demonstrates acoustic absorption effects in a gas simulated in a thermostatted molecular simulation and quantifies the classical losses in terms of the sound attenuation constant. The approach can be extended to further understanding of acoustic loss mechanisms in the presence of nanoscale porous materials in the simulation domain.

Protocol for classical molecular dynamics simulations of nano-junctions in solution

KAUST Repository

Gkionis, Konstantinos; Rungger, Ivan; Sanvito, Stefano; Schwingenschlö gl, Udo

2012-01-01

Modeling of nanoscale electronic devices in water requires the evaluation of the transport properties averaged over the possible configurations of the solvent. They can be obtained from classical molecular dynamics for water confined in the device. A series of classical molecular dynamics simulations is performed to establish a methodology for estimating the average number of water molecules N confined between two static and semi-infinite goldelectrodes. Variations in key parameters of the simulations, as well as simulations with non-static infinite goldsurfaces of constant area and with anisotropically fluctuating cell dimensions lead to less than 1% discrepancies in the calculated N. Our approach is then applied to a carbon nanotube placed between the goldelectrodes. The atomic density profile along the axis separating the slabs shows the typical pattern of confined liquids, irrespective of the presence of the nanotube, while parallel to the slabs the nanotube perturbs the obtained profile.

Protocol for classical molecular dynamics simulations of nano-junctions in solution

KAUST Repository

Gkionis, Konstantinos

2012-10-19

Modeling of nanoscale electronic devices in water requires the evaluation of the transport properties averaged over the possible configurations of the solvent. They can be obtained from classical molecular dynamics for water confined in the device. A series of classical molecular dynamics simulations is performed to establish a methodology for estimating the average number of water molecules N confined between two static and semi-infinite goldelectrodes. Variations in key parameters of the simulations, as well as simulations with non-static infinite goldsurfaces of constant area and with anisotropically fluctuating cell dimensions lead to less than 1% discrepancies in the calculated N. Our approach is then applied to a carbon nanotube placed between the goldelectrodes. The atomic density profile along the axis separating the slabs shows the typical pattern of confined liquids, irrespective of the presence of the nanotube, while parallel to the slabs the nanotube perturbs the obtained profile.

Modulated spin waves and robust quasi-solitons in classical Heisenberg rings

International Nuclear Information System (INIS)

Schmidt, Heinz-Juergen; Schroeder, Christian; Luban, Marshall

2011-01-01

We investigate the dynamical behavior of finite rings of classical spin vectors interacting via nearest-neighbor isotropic exchange in an external magnetic field. Our approach is to utilize the solutions of a continuum version of the discrete spin equations of motion (EOM) which we derive by assuming continuous modulations of spin wave solutions of the EOM for discrete spins. This continuum EOM reduces to the Landau-Lifshitz equation in a particular limiting regime. The usefulness of the continuum EOM is demonstrated by the fact that the time-evolved numerical solutions of the discrete spin EOM closely track the corresponding time-evolved solutions of the continuum equation. It is of special interest that our continuum EOM possesses soliton solutions, and we find that these characteristics are also exhibited by the corresponding solutions of the discrete EOM. The robustness of solitons is demonstrated by considering cases where initial states are truncated versions of soliton states and by numerical simulations of the discrete EOM equations when the spins are coupled to a heat bath at finite temperatures. (paper)

Intra-molecular selectivity of muonium towards chlorinated aromatic compounds

International Nuclear Information System (INIS)

Venkateswaran, K.; Stadlbauer, J.M.; Laing, M.E.; Klugkist, J.; Chong, D.P.; Porter, G.B.; Walker, D.C.

1994-01-01

Muon resonance studies show that muonium atoms (Mu) in ethanol add selectively to certain C-sites of aromatic compounds containing -Cl and -OH substituents. The sites chosen seem to be those carrying the lowest electron density. This helps to characterize Mu as a nucleophile in addition reactions and, in this respect, Mu differs from ordinary H-atoms. The study shows no apparent inter-molecular selectivity between a pair of aromatic solutes in an equimolar mixture, but strong intra-molecular selectivity in an ether composed of those two aromatic rings. This difference between intra- and inter-molecular selectivity is interpreted as kinetic in origin - arising from the 'caging effect' of the solvent and peculiar to reactions close to the diffusion-controlled limit. (orig.)

Classical electron ionization mass spectra in gas chromatography/mass spectrometry with supersonic molecular beams.

Science.gov (United States)

Gordin, Alexander; Fialkov, Alexander B; Amirav, Aviv

2008-09-01

A major benefit of gas chromatography/mass spectrometry (GC/MS) with a supersonic molecular beam (SMB) interface and its fly-through ion source is the ability to obtain electron ionization of vibrationally cold molecules (cold EI), which show enhanced molecular ions. However, GC/MS with an SMB also has the flexibility to perform 'classical EI' mode of operation which provides mass spectra to mimic those in commercial 70 eV electron ionization MS libraries. Classical EI in SMB is obtained through simple reduction of the helium make-up gas flow rate, which reduces the SMB cooling efficiency; hence the vibrational temperatures of the molecules are similar to those in traditional EI ion sources. In classical EI-SMB mode, the relative abundance of the molecular ion can be tuned and, as a result, excellent identification probabilities and very good matching factors to the NIST MS library are obtained. Classical EI-SMB with the fly-through dual cage ion source has analyte sensitivity similar to that of the standard EI ion source of a basic GC/MS system. The fly-through EI ion source in combination with the SMB interface can serve for cold EI, classical EI-SMB, and cluster chemical ionization (CCI) modes of operation, all easily exchangeable through a simple and quick change (not involving hardware). Furthermore, the fly-through ion source eliminates sample scattering from the walls of the ion source, and thus it offers full sample inertness, tailing-free operation, and no ion-molecule reaction interferences. It is also robust and enables increased column flow rate capability without affecting the sensitivity.

Molecular Diagnosis of Classical Rabies Virus in Polar Foxes in Greeenland

DEFF Research Database (Denmark)

Rasmussen, Thomas Bruun; Strandbygaard, Bertel

Classical rabies virus continues to circulate in polar foxes in Greenland. Within the last 5 years more than 30 animals, mainly polar foxes have been tested positive for rabies. In this study, brain samples from this period were assessed for the presence of rabies viral RNA using molecular...

Physics with colder molecular ions: The Heidelberg Cryogenic Storage Ring CSR

International Nuclear Information System (INIS)

Zajfman, D; Wolf, A; Schwalm, D; Orlov, D A; Grieser, M; Hahn, R von; Welsch, C P; Lopez-Urrutia, J R Crespo; Schroeter, C D; Urbain, X; Ullrich, J

2005-01-01

A novel cryogenic electrostatic storage ring is planned to be built at the Max-Planck Institute for Nuclear Physics in Heidelberg. The machine is expected to operate at low temperatures (∼2K) and to store beams with kinetic energies between 20 to 300 keV. An electron target based on cooled photocathode technology will serve as a major tool for the study of reactions between molecular ions and electrons. Moreover, atomic beams can be merged and crossed with the stored ion beams allowing for atom molecular-ion collision studies at very low up to high relative energies. The proposed experimental program, centered around the physics of cold molecular ions, is shortly outlined

Spin flip in single quantum ring with Rashba spin–orbit interation

Science.gov (United States)

Liu, Duan-Yang; Xia, Jian-Bai

2018-03-01

We theoretically investigate spin transport in the elliptical ring and the circular ring with Rashba spin–orbit interaction. It is shown that when Rashba spin–orbit interaction is relatively weak, a single circular ring can not realize spin flip, however an elliptical ring may work as a spin-inverter at this time, and the influence of the defect of the geometry is not obvious. Howerver if a giant Rashba spin–orbit interaction strength has been obtained, a circular ring can work as a spin-inverter with a high stability. Project supported by the National Natural Science Foundation of China (Grant No. 11504016).

Level crossing in a molecular Cr8 ring

International Nuclear Information System (INIS)

Affronte, M.; Guidi, T.; Caciuffo, R.; Carretta, S.; Amoretti, G.; Hinderer, J.; Sheikin, I.; Smith, A.A.; Winpenny, R.E.P.; Slageren, J. van; Gatteschi, D.

2004-01-01

The heat capacity of a molecular Cr 8 ring was measured as a function of temperature and magnetic field in order to follow the evolution of the Schottky anomaly through the first (S=0 to |1,-1>) level crossing occurring at B c1 =6.9 T. The results are interpreted within the framework of a spin Hamiltonian approach and they nicely fit the pattern of the energy levels derived by inelastic neutron spectroscopy. At B c1 , the Schottky anomaly almost vanishes suggesting that a true crossing occurs in Cr 8 in contrast to what was observed for ferric wheels

Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. II. Dynamics

Science.gov (United States)

Halverson, Jonathan D.; Lee, Won Bo; Grest, Gary S.; Grosberg, Alexander Y.; Kremer, Kurt

2011-05-01

Molecular dynamics simulations were conducted to investigate the dynamic properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest rings were composed of N = 1600 monomers per chain which corresponds to roughly 57 entanglement lengths for comparable linear polymers. The ring melts were found to diffuse faster than their linear counterparts, with both architectures approximately obeying a D ˜ N-2.4 scaling law for large N. The mean-square displacement of the center-of-mass of the rings follows a sub-diffusive behavior for times and distances beyond the ring extension , neither compatible with the Rouse nor the reptation model. The rings relax stress much faster than linear polymers, and the zero-shear viscosity was found to vary as η0 ˜ N1.4 ± 0.2 which is much weaker than the N3.4 behavior of linear chains, not matching any commonly known model for polymer dynamics when compared to the observed mean-square displacements. These findings are discussed in view of the conformational properties of the rings presented in the preceding paper [J. D. Halverson, W. Lee, G. S. Grest, A. Y. Grosberg, and K. Kremer, J. Chem. Phys. 134, 204904 (2011)], 10.1063/1.3587137.

Simulation of molecular transitions using classical trajectories

Energy Technology Data Exchange (ETDEWEB)

Donoso, A.; Martens, C. C. [University of California, California (United States)

2001-03-01

In the present work, we describe the implementation of a semiclassical method to study physical-chemical processes in molecular systems where electronic state transitions and quantum coherence play a dominant role. The method is based on classical trajectory propagation on the underlying coupled electronic surfaces and is derived from the semiclassical limit of the quantum Liouville equation. Unlike previous classical trajectory-based methods, quantum electronic coherence are treated naturally within this approach as complex weighted trajectory ensembles propagating on the average electronic surfaces. The method is tested on a model problem consisting of one-dimensional motion on two crossing electronic surfaces. Excellent agreement is obtained when compared to the exact results obtained by wave packet propagation. The method is applied to model quantum wave packet interferometry, where two wave packets, differing only in a relative phase, collide in the region where the two electronic surfaces cross. The dependence of the resulting population transfer on the initial relative phase of the wave packets is perfectly captured by our classical trajectory method. Comparison with an alternative method, surface hopping, shows that our approach is appropriate for modelling quantum interference phenomena. [Spanish] En este trabajo se describe la implementacion de un metodo semiclasico para estudiar procesos fisicos-quimicos en sistemas moleculares donde las transiciones entre estados electronicos y las coherencias cuanticas juegan un papel predominante. El metodo se basa en la propagacion de trayectorias clasicas sobre las correspondientes superficies electronicas acopladas y se deriva a partir del limite semiclasico de la ecuacion cuantica de Liouville. A diferencia de metodos previos basados en trayectoria clasica, dentro de este esquema, las coherencias electronicas cuanticas son tratadas de manera natural como ensamble de trayectorias con pesos complejos, moviendose en

First-principles and classical molecular dynamics study of threshold displacement energy in beryllium

Energy Technology Data Exchange (ETDEWEB)

Vladimirov, P.V. [Institute for Applied Materials – Applied Materials Physics, Karlsruhe Institute of Technology, P.O. Box 3640, 76021 Karlsruhe (Germany); Borodin, V.A., E-mail: Borodin_VA@nrcki.ru [National Research Center “Kurchatov Institute”, 123182 Moscow (Russian Federation); NRNU MEPhI, 115409 Moscow (Russian Federation)

2017-02-15

Highlights: • Beryllium is a functional material of future fusion reactors. • The threshold displacement energy by fast particles is studied. • Classical and first principles simulations are used. - Abstract: Beryllium selected as a neutron multiplier material for the tritium breeding blanket of fusion reactor should withstand high doses of fast neutron irradiation. The damage produced by irradiation is usually evaluated assuming that the number of atomic displacements to the threshold displacement energy, E{sub d}, which is considered as an intrinsic material parameter. In this work the value of E{sub d} for hcp beryllium is estimated simultaneously from classical and first-principles molecular dynamics simulations. Quite similar quantitative pictures of defect production are observed in both simulation types, though the predicted displacement threshold values seem to be approximately two times higher in the first-principles approach. We expect that, after more detailed first-principles investigations, this approach can be used for scaling the damage prediction predictions by classical molecular dynamics, opening a way for more consistent calculations of displacement damage in materials.

Quantum Fourier Transform Over Galois Rings

OpenAIRE

Zhang, Yong

2009-01-01

Galois rings are regarded as "building blocks" of a finite commutative ring with identity. There have been many papers on classical error correction codes over Galois rings published. As an important warm-up before exploring quantum algorithms and quantum error correction codes over Galois rings, we study the quantum Fourier transform (QFT) over Galois rings and prove it can be efficiently preformed on a quantum computer. The properties of the QFT over Galois rings lead to the quantum algorit...

Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps

KAUST Repository

Oliva, Romina; Chermak, Edrisse; Cavallo, Luigi

2015-01-01

In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions.

Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps

KAUST Repository

Oliva, Romina

2015-07-01

In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions.

(Z)-N,N-Dimethyl-2-[phen­yl(pyridin-2-yl)methyl­idene]hydrazinecarbothio­amide

Science.gov (United States)

Jayakumar, K.; Sithambaresan, M.; Prathapachandra Kurup, M. R.

2011-01-01

The title compound, C15H16N4S, exists in the Z conformation with the thionyl S atom lying cis to the azomethine N atom. The shortening of the N—N distance [1.3697 (17) Å] is due to extensive delocalization with the pyridine ring. The hydrazine–carbothio­amide unit is almost planar, with a maximum deviation of 0.013 (2) Å for the amide N atom. The stability of this conformation is favoured by the formation of an intra­molecular N—H⋯N hydrogen bond. The packing of the mol­ecules involves no classical inter­molecular hydrogen-bonding inter­actions; however, a C—H⋯π inter­action occurs. PMID:22199715

Site-specific 13C content by quantitative isotopic 13C Nuclear Magnetic Resonance spectrometry: A pilot inter-laboratory study

International Nuclear Information System (INIS)

Chaintreau, Alain; Fieber, Wolfgang; Sommer, Horst; Gilbert, Alexis; Yamada, Keita; Yoshida, Naohiro; Pagelot, Alain; Moskau, Detlef; Moreno, Aitor; Schleucher, Jürgen; Reniero, Fabiano; Holland, Margaret; Guillou, Claude; Silvestre, Virginie; Akoka, Serge; Remaud, Gérald S.

2013-01-01

Graphical abstract: -- Highlights: •First ring test on isotopic 13 C NMR spectrometry. •Evaluation of the intra- and inter-variability of the NMR spectrometers used. •Definition of a protocol for qualification of the performance of the spectrometer. -- Abstract: Isotopic 13 C NMR spectrometry, which is able to measure intra-molecular 13 C composition, is of emerging demand because of the new information provided by the 13 C site-specific content of a given molecule. A systematic evaluation of instrumental behaviour is of importance to envisage isotopic 13 C NMR as a routine tool. This paper describes the first collaborative study of intra-molecular 13 C composition by NMR. The main goals of the ring test were to establish intra- and inter-variability of the spectrometer response. Eight instruments with different configuration were retained for the exercise on the basis of a qualification test. Reproducibility at the natural abundance of isotopic 13 C NMR was then assessed on vanillin from three different origins associated with specific δ 13 C i profiles. The standard deviation was, on average, between 0.9 and 1.2‰ for intra-variability. The highest standard deviation for inter-variability was 2.1‰. This is significantly higher than the internal precision but could be considered good in respect of a first ring test on a new analytical method. The standard deviation of δ 13 C i in vanillin was not homogeneous over the eight carbons, with no trend either for the carbon position or for the configuration of the spectrometer. However, since the repeatability for each instrument was satisfactory, correction factors for each carbon in vanillin could be calculated to harmonize the results

Classical molecular dynamics simulation of nuclear fuels

International Nuclear Information System (INIS)

Devanathan, R.; Krack, M.; Bertolus, M.

2015-01-01

Molecular dynamics simulation using forces calculated from empirical potentials, commonly called classical molecular dynamics, is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermomechanical properties. This enables one to obtain insights into fundamental mechanisms governing the behaviour of nuclear fuel, as well as parameters that can be used as inputs for mesoscale models. The interaction potentials used for the force calculations are generated by fitting properties of interest to experimental data and electronic structure calculations (see Chapter 12). We present here the different types of potentials currently available for UO 2 and illustrations of applications to the description of the behaviour of this material under irradiation. The results obtained from the present generation of potentials for UO 2 are qualitatively similar, but quantitatively different. There is a need to refine these existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, develop models that are equipped to handle deviations from stoichiometry, and validate the models and assumptions used. (authors)

Discovery of energetic molecular ions (NO+ and O2+) in the storm time ring current

International Nuclear Information System (INIS)

Klecker, B.; Moebius, E.; Hovestadt, D.; Scholer, M.; Gloeckler, G.; Ipavich, F.M.

1986-01-01

A few hours after the onset of a large geomagnetic storm on September 4, 1984, energetic molecular ions in the mass range 28--32, predminantly NO + and O 2 + , have been discovered in the outer ring current at L--7. The data have been obtained with the time-of-flight spectrometer SULEICA on the AMPTE/IRM spacecraft. We find at 160 keV/e a mean abundance ratio of the molecular ions relative to O + ions of 0.031 +- 0.004. During quiet times no molecular ions are observed, the 1 sigma upper limit of the ratio derived by averaging over several quiet periods is 0.003. The observations demonstrate the injection of ionospheric plasma into the storm time ring current and the subsequent acceleration to energies of several hundred keV on a time scale of a few hours after the onset of the magnetic storm

Inter-laboratory ring trial to evaluate real-time reverse transcription polymerase chain reaction methods used for detection of infectious pancreatic necrosis virus in Chile

Directory of Open Access Journals (Sweden)

David Tapia

2017-07-01

Conclusions: Overall, the ring trial showed high values of sensitivity and specificity, with some problems of repeatability and inter-laboratory variability. This last issue needs to be addressed in order to allow harmonized diagnostic of IPNV within the country. We recommend the use of the NRL methods as validated and reliable qRT-PCR protocols for the detection of IPNV.

Fusion Rings for Quantum Groups

DEFF Research Database (Denmark)

Andersen, Henning Haahr; Stroppel, Catharina

2014-01-01

We study the fusion rings of tilting modules for a quantum group at a root of unity modulo the tensor ideal of negligible tilting modules. We identify them in type A with the combinatorial rings from Korff, C., Stroppel, C.: The sl(ˆn)k-WZNW fusion ring: a combinato-rial construction...... and a realisation as quotient of quantum cohomology. Adv. Math. 225(1), 200–268, (2010) and give a similar description of the sp2n-fusion ring in terms of non-commutative symmetric functions. Moreover we give a presentation of all fusion rings in classical types as quotients of polynomial rings. Finally we also...... compute the fusion rings for type G2....

Comparative classical and 'ab initio' molecular dynamics study of molten and glassy germanium dioxide

International Nuclear Information System (INIS)

Hawlitzky, M; Horbach, J; Binder, K; Ispas, S; Krack, M

2008-01-01

A molecular dynamics (MD) study of the static and dynamic properties of molten and glassy germanium dioxide is presented. The interactions between the atoms are modeled by the classical pair potential proposed by Oeffner and Elliott (OE) (1998 Phys. Rev. B 58 14791). We compare our results to experiments and previous simulations. In addition, an 'ab initio' method, the so-called Car-Parrinello molecular dynamics (CPMD), is applied to check the accuracy of the structural properties, as obtained by the classical MD simulations with the OE potential. As in a similar study for SiO 2 , the structure predicted by CPMD is only slightly softer than that resulting from the classical MD. In contrast to earlier simulations, both the static structure and dynamic properties are in very good agreement with pertinent experimental data. MD simulations with the OE potential are also used to study the relaxation dynamics. As previously found for SiO 2 , for high temperatures the dynamics of molten GeO 2 is compatible with a description in terms of mode coupling theory

Classical molecular dynamics simulation of weakly-bound projectile heavy-ion reactions

Directory of Open Access Journals (Sweden)

Morker Mitul R.

2015-01-01

Full Text Available A 3-body classical molecular dynamics approach for heavy-ion reactions involving weakly bound projectiles is developed. In this approach a weakly bound projectile is constructed as a two-body cluster of the constituent tightly bound nuclei in a configuration corresponding to the observed breakup energy. This 3-body system with their individual nucleon configuration in their ground state is dynamically evolved for given initial conditions using the three-stage classical molecular dynamics approach (3S-CMD. Various levels of rigidbody constraints on the projectile constituents and the target are considered at appropriate stages. This 3-dimensional approach explicitly takes into account not only the long range Coulomb reorientation of the deformed collision partner but internal excitations and breakup probabilities at distances close to the barrier also. Dynamical simulations of 6Li+209Bi show all the possible reaction mechanism like complete fusion, incomplete fusion, scattering and breakup scattering. Complete fusion cross sections of 6Li+209Bi and 7Li+209Bi reactions are calculated in this approach with systematic relaxations of the rigid-body constraints on one or more constituent nuclei.

How to remove the spurious resonances from ring polymer molecular dynamics

Energy Technology Data Exchange (ETDEWEB)

Rossi, Mariana; Manolopoulos, David E. [Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ (United Kingdom); Ceriotti, Michele [Laboratory of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne (Switzerland)

2014-06-21

Two of the most successful methods that are presently available for simulating the quantum dynamics of condensed phase systems are centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD). Despite their conceptual differences, practical implementations of these methods differ in just two respects: the choice of the Parrinello-Rahman mass matrix and whether or not a thermostat is applied to the internal modes of the ring polymer during the dynamics. Here, we explore a method which is halfway between the two approximations: we keep the path integral bead masses equal to the physical particle masses but attach a Langevin thermostat to the internal modes of the ring polymer during the dynamics. We justify this by showing analytically that the inclusion of an internal mode thermostat does not affect any of the established features of RPMD: thermostatted RPMD is equally valid with respect to everything that has actually been proven about the method as RPMD itself. In particular, because of the choice of bead masses, the resulting method is still optimum in the short-time limit, and the transition state approximation to its reaction rate theory remains closely related to the semiclassical instanton approximation in the deep quantum tunneling regime. In effect, there is a continuous family of methods with these properties, parameterised by the strength of the Langevin friction. Here, we explore numerically how the approximation to quantum dynamics depends on this friction, with a particular emphasis on vibrational spectroscopy. We find that a broad range of frictions approaching optimal damping give similar results, and that these results are immune to both the resonance problem of RPMD and the curvature problem of CMD.

How to remove the spurious resonances from ring polymer molecular dynamics

International Nuclear Information System (INIS)

Rossi, Mariana; Manolopoulos, David E.; Ceriotti, Michele

2014-01-01

Two of the most successful methods that are presently available for simulating the quantum dynamics of condensed phase systems are centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD). Despite their conceptual differences, practical implementations of these methods differ in just two respects: the choice of the Parrinello-Rahman mass matrix and whether or not a thermostat is applied to the internal modes of the ring polymer during the dynamics. Here, we explore a method which is halfway between the two approximations: we keep the path integral bead masses equal to the physical particle masses but attach a Langevin thermostat to the internal modes of the ring polymer during the dynamics. We justify this by showing analytically that the inclusion of an internal mode thermostat does not affect any of the established features of RPMD: thermostatted RPMD is equally valid with respect to everything that has actually been proven about the method as RPMD itself. In particular, because of the choice of bead masses, the resulting method is still optimum in the short-time limit, and the transition state approximation to its reaction rate theory remains closely related to the semiclassical instanton approximation in the deep quantum tunneling regime. In effect, there is a continuous family of methods with these properties, parameterised by the strength of the Langevin friction. Here, we explore numerically how the approximation to quantum dynamics depends on this friction, with a particular emphasis on vibrational spectroscopy. We find that a broad range of frictions approaching optimal damping give similar results, and that these results are immune to both the resonance problem of RPMD and the curvature problem of CMD

Proof of concept Laplacian estimate derived for noninvasive tripolar concentric ring electrode with incorporated radius of the central disc and the widths of the concentric rings.

Science.gov (United States)

Makeyev, Oleksandr; Lee, Colin; Besio, Walter G

2017-07-01

Tripolar concentric ring electrodes are showing great promise in a range of applications including braincomputer interface and seizure onset detection due to their superiority to conventional disc electrodes, in particular, in accuracy of surface Laplacian estimation. Recently, we proposed a general approach to estimation of the Laplacian for an (n + 1)-polar electrode with n rings using the (4n + 1)-point method for n ≥ 2 that allows cancellation of all the truncation terms up to the order of 2n. This approach has been used to introduce novel multipolar and variable inter-ring distances concentric ring electrode configurations verified using finite element method. The obtained results suggest their potential to improve Laplacian estimation compared to currently used constant interring distances tripolar concentric ring electrodes. One of the main limitations of the proposed (4n + 1)-point method is that the radius of the central disc and the widths of the concentric rings are not included and therefore cannot be optimized. This study incorporates these two parameters by representing the central disc and both concentric rings as clusters of points with specific radius and widths respectively as opposed to the currently used single point and concentric circles. A proof of concept Laplacian estimate is derived for a tripolar concentric ring electrode with non-negligible radius of the central disc and non-negligible widths of the concentric rings clearly demonstrating how both of these parameters can be incorporated into the (4n + 1)-point method.

Molecular mechanism in the formation of a human ring chromosome 21

International Nuclear Information System (INIS)

Wong, C.; Kazazian, H.H. Jr.; Stetten, G.; Earnshaw, W.C.; Antonarakis, S.E.; Van Keuren, M.L.

1989-01-01

The authors have characterized the structural rearrangements of a chromosome 21 that led to the de novo formation of a human ring chromosome 21 [r(21)]. Molecular cloning and chromosomal localization of the DNA regions flanking the ring junction provide evidence for a long arm to long arm fusion in formation of the r(21). In addition, the centromere and proximal long arm region of a maternal chromosome 21 are duplicated in the r(21). Therefore, the mechanism in formation of the r(21) was complex involving two sequential chromosomal rearrangements. (i) Duplication of the centromere and long arm of one maternal chromosome 21 occurred forming a rearranged intermediate. (ii) Chromosomal breaks in both the proximal and telomeric long arm regions on opposite arms of this rearranged chromosome occurred with subsequent reunion producing the r(21)

(4S)-4-(3,4-Dichloro?phen?yl)-1?-methyl-4?-phenyl-3,4-dihydronaphthalene-2-spiro-3?-pyrrolidine-2?-spiro-1??-acenaphthyl?ene-1,2??(2H,1??H)-dione

OpenAIRE

Murugan, R.; Gunasekaran, B.; Narayanan, S. Sriman; Manivannan, V.

2008-01-01

In the title compound, C37H27Cl2NO2, the 3,4-dichloro?phenyl ring makes a dihedral angle of 46.66?(6)? with the phenyl ring. The mol?ecular structure is stabilized by weak intra?molecular C?H?O inter?actions and the crystal structure is stabilized by weak inter?molecular C?H?O inter?actions. The C?C?C?C?C five-membered ring is planar, while the C?C?C?C?N five-membered ring adopts a half-chair conformation.

Level crossing in a molecular Cr{sub 8} ring

Energy Technology Data Exchange (ETDEWEB)

Affronte, M. E-mail: affronte@unimore.it; Guidi, T.; Caciuffo, R.; Carretta, S.; Amoretti, G.; Hinderer, J.; Sheikin, I.; Smith, A.A.; Winpenny, R.E.P.; Slageren, J. van; Gatteschi, D

2004-05-01

The heat capacity of a molecular Cr{sub 8} ring was measured as a function of temperature and magnetic field in order to follow the evolution of the Schottky anomaly through the first (S=0 to |1,-1>) level crossing occurring at B{sub c1}=6.9 T. The results are interpreted within the framework of a spin Hamiltonian approach and they nicely fit the pattern of the energy levels derived by inelastic neutron spectroscopy. At B{sub c1}, the Schottky anomaly almost vanishes suggesting that a true crossing occurs in Cr{sub 8} in contrast to what was observed for ferric wheels.

Polymorphic Ring-Shaped Molecular Clusters Made of Shape-Variable Building Blocks

Directory of Open Access Journals (Sweden)

Keitel Cervantes-Salguero

2015-02-01

Full Text Available Self-assembling molecular building blocks able to dynamically change their shapes, is a concept that would offer a route to reconfigurable systems. Although simulation studies predict novel properties useful for applications in diverse fields, such kinds of building blocks, have not been implemented thus far with molecules. Here, we report shape-variable building blocks fabricated by DNA self-assembly. Blocks are movable enough to undergo shape transitions along geometrical ranges. Blocks connect to each other and assemble into polymorphic ring-shaped clusters via the stacking of DNA blunt-ends. Reconfiguration of the polymorphic clusters is achieved by the surface diffusion on mica substrate in response to a monovalent salt concentration. This work could inspire novel reconfigurable self-assembling systems for applications in molecular robotics.

A derivation of the Derbenev-Kondratenko formula using semi-classical electrodynamics

International Nuclear Information System (INIS)

Mane, S.R.

1985-11-01

We present a detailed exposition of the mechanism for the build-up of polarization in electron storage rings. A semi-classical approach is used to derive the rate of growth and asymptotic degree of polarization in an electron storage ring (the Derbenev-Kondratenko formula). Statistical mechanical concepts used to obtain as classical an understanding as possible of this phenomenon. (orig.)

Calculation of inter-plane thermal resistance of few-layer graphene from equilibrium molecular dynamics simulations

International Nuclear Information System (INIS)

Ni, Y; Chalopin, Y; Volz, S

2012-01-01

Inter-plane thermal resistance in 5-layer graphene is calculated from equilibrium molecular dynamics (EMD) by calculating the autocorrelation function of temperature difference. Our simulated inter-plane resistance for 5-layer graphene is 4.83 × 10 −9 m 2 K/W. This data is in the same order of magnitude with the reported values from NEMD simulations and Debye model calculations, and the possible reasons for the slight differences are discussed in details. The inter-plane resistance is not dependent on temperature, according to the results of the EMD simulation. Phonon density of states (DOSs) were plotted to better understand the mechanism behind the obtained values. These results provide a better insight in the heat transfer across a few layer graphene and yield useful information on the design of graphene based thermal materials.

Change Ringing - communicating climate change through contemporary classical music

Science.gov (United States)

Kapur, Ravi; Osborn, Laurence; Shenai, Peter

2016-04-01

Change Ringing is a collaborative artwork by artist Peter Shenai and composer Laurence Osborn that forms around a playable sculpture and a large-scale composition. The sculpture incorporates a set of six bronze bells designed and cast by artist Peter Shenai. Their shapes are mathematically derived from graphic statistical representations of summer temperatures at seventeen-year intervals over the course of the twentieth century. Arranged according to the chronology of their corresponding data sets and struck in order, the bells voice a series of inharmonic spectra that communicate sonically the story of climate change during the twentieth century. This series forms the basis for Laurence Osborn's twenty-five minute composition, scored for string orchestra and the bells themselves. In Change Ringing, an artwork that combines music, sculpture, performance, and ritual, we want to move audiences and, in doing so, facilitate their engagement with ideas that are highly relevant today. We believe that the medium of musically organized sound, so often wrongly dismissed as "abstract" and non-referential, can be a more than adequate reflection of lived human experience in the 21st Century, and we work in the hope that Change Ringing will connect with contemporary audiences on the most fundamental level.

Site-specific {sup 13}C content by quantitative isotopic {sup 13}C Nuclear Magnetic Resonance spectrometry: A pilot inter-laboratory study

Energy Technology Data Exchange (ETDEWEB)

Chaintreau, Alain; Fieber, Wolfgang; Sommer, Horst [Firmenich SA, Corporate R and D Division, P.O. Box 239, 1211 Geneva 8 (Switzerland); Gilbert, Alexis; Yamada, Keita [Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503 (Japan); Yoshida, Naohiro [Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503 (Japan); Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo 152-8551 (Japan); Pagelot, Alain [Bruker Biospin SAS, 34 rue de l‘Industrie, 67166 Wissembourg Cedex (France); Moskau, Detlef; Moreno, Aitor [Bruker Biospin AG, Industriestrasse 26, 8117 Fällanden (Switzerland); Schleucher, Jürgen [Department of Medical Biochemistry and Biophysics, Umeå University, S-90187 Umeå (Sweden); Reniero, Fabiano; Holland, Margaret; Guillou, Claude [European Commission, Joint Research Centre – Institute for Health and Consumer Protection, via E. Fermi 2749, I-21027 Ispra (Italy); Silvestre, Virginie; Akoka, Serge [EBSI team, Interdisciplinary Chemistry: Synthesis, Analysis, Modelling (CEISAM), University of Nantes-CNRS UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 Nantes cedex 3 (France); Remaud, Gérald S., E-mail: gerald.remaud@univ-nantes.fr [EBSI team, Interdisciplinary Chemistry: Synthesis, Analysis, Modelling (CEISAM), University of Nantes-CNRS UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 Nantes cedex 3 (France)

2013-07-25

Graphical abstract: -- Highlights: •First ring test on isotopic {sup 13}C NMR spectrometry. •Evaluation of the intra- and inter-variability of the NMR spectrometers used. •Definition of a protocol for qualification of the performance of the spectrometer. -- Abstract: Isotopic {sup 13}C NMR spectrometry, which is able to measure intra-molecular {sup 13}C composition, is of emerging demand because of the new information provided by the {sup 13}C site-specific content of a given molecule. A systematic evaluation of instrumental behaviour is of importance to envisage isotopic {sup 13}C NMR as a routine tool. This paper describes the first collaborative study of intra-molecular {sup 13}C composition by NMR. The main goals of the ring test were to establish intra- and inter-variability of the spectrometer response. Eight instruments with different configuration were retained for the exercise on the basis of a qualification test. Reproducibility at the natural abundance of isotopic {sup 13}C NMR was then assessed on vanillin from three different origins associated with specific δ{sup 13}C{sub i} profiles. The standard deviation was, on average, between 0.9 and 1.2‰ for intra-variability. The highest standard deviation for inter-variability was 2.1‰. This is significantly higher than the internal precision but could be considered good in respect of a first ring test on a new analytical method. The standard deviation of δ{sup 13}C{sub i} in vanillin was not homogeneous over the eight carbons, with no trend either for the carbon position or for the configuration of the spectrometer. However, since the repeatability for each instrument was satisfactory, correction factors for each carbon in vanillin could be calculated to harmonize the results.

Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory.

Science.gov (United States)

Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex; Niklasson, Anders M N; Head-Gordon, Teresa; Skylaris, Chris-Kriton

2017-03-28

Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities are treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes-in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.

Interring Gas Dynamic Analysis of Piston in a Diesel Engine considering the Thermal Effect

Directory of Open Access Journals (Sweden)

Wanyou Li

2015-01-01

Full Text Available Understanding the interaction between ring dynamics and gas transport in ring pack systems is crucial and needs to be imperatively studied. The present work features detailed interring gas dynamics of piston ring pack behavior in internal combustion engines. The model is developed for a ring pack with four rings. The dynamics of ring pack are simulated. Due to the fact that small changes in geometry of the grooves and lands would have a significant impact on the interring gas dynamics, the thermal deformation of piston has been considered during the ring pack motion analysis in this study. In order to get the temperature distribution of piston head more quickly and accurately, an efficient method utilizing the concept of inverse heat conduction is presented. Moreover, a sensitive analysis based on the analysis of partial regression coefficients is presented to investigate the effect of groove parameters on blowby.

Well-defined polyethylene molecular brushes by polyhomologation and ring opening metathesis polymerization

KAUST Repository

Zhang, Hefeng; Gnanou, Yves; Hadjichristidis, Nikolaos

2014-01-01

A novel strategy using polyhomologation and ring opening metathesis polymerization (ROMP) has been developed for the synthesis of well-defined polyethylene (PE) molecular brushes. Polyhomologation was used to afford an OH-terminated PE, which after transformation to the norbornyl PE macromonomer was subjected to ROMP. Kinetics of ROMP of the PE macromonomer was studied by in situ1H NMR monitoring. The brush structure was proved from HT-GPC, 1H NMR and DSC results.

Thomson's Jumping Ring over a Long Coil

Science.gov (United States)

Jeffery, Rondo N.; Amiri, Farhang

2018-01-01

The classic jumping ring apparatus consists of a coil with an iron core that extends out of the coil. A copper or aluminum ring placed over the iron core jumps upward when AC power is applied to the coil. In this paper we will examine a modified design of the jumping ring apparatus, called the "long-coil design." It allows the ring to…

Molecular cytogenetic analysis and clinical manifestations of a case with de novo mosaic ring chromosome 7

Directory of Open Access Journals (Sweden)

Fang Jye-Siung

2011-02-01

Full Text Available Abstract Aim Clinical and molecular cytogenetic investigations of a newborn girl exhibiting facial dysmorphism with developmental delay. Methods Phenotypic evaluation was first applied to examine the proband's developmental status. Computed tomography and colour transcranial Doppler were used then to investigate her brain structure and function. Subsequently, chromosomal abnormalities were examined by karyotyping and fluorescent in situ hybridization was performed to investigate size of fragments lost at the two distal ends of the ring chromosome 7. In addition, multicolour banding was applied to rule out structural rearrangement occurs in between the ring chromosome 7. Results The proband was born with mosaic supernumerary ring chromosome 7, without a normal karyotype detected in the peripheral blood lymphocytes. The distal arm of chromosome 7p (at least 255 kb from the telomere was part of an extra ring chromosome 7. In addition, the distal arm of 7q, at least 8 kb from the telomere, was missing. There was no other chromosomal rearrangement detected by multicolour banding. Interpretation This is the 19th reported case of complete ring chromosome 7 mosaicism and the first survived case with mosaic supernumerary ring 7 without a normal karyotype detected in the peripheral lymphocytes.

Modeling of nuclear glasses by classical and ab initio molecular dynamics

International Nuclear Information System (INIS)

Ganster, P.

2004-01-01

A calcium aluminosilicate glass of molar composition 67 % SiO 2 - 12 % Al 2 O 3 - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri-coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminum atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author) [fr

Modelling of nuclear glasses by classical and ab initio molecular dynamics

International Nuclear Information System (INIS)

Ganster, P.

2004-10-01

A calcium aluminosilicate glass of molar composition 67 % SiO 2 - 12 % Al 2 O 3 - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminium atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)

Energetic disorder and exciton states of individual molecular rings

International Nuclear Information System (INIS)

Herman, Pavel; Barvik, Ivan; Zapletal, David

2006-01-01

Exciton states in molecular rings (resembling, e.g. the B850 ring from LH2 complexes of purple bacterium Rhodopseudomonas acidophila) with strong intermolecular interaction are still a question of interest [V. Sundstrom, T. Pullerits, R. van Grondelle, J. Phys. Chem. B 103 (1999) 2327]. In our theoretical model we use the ring of two-level systems, simulating, e.g., the bacteriochlorophylls B850. The dynamical aspects in ensemble of rings are reflected in optical line shapes of electronic transitions. The observed linewidths reflect the combined influence of different types of static and dynamic disorder. To avoid the broadening of lines due to ensemble averaging one uses the single-molecule spectroscopy technique to obtain a fluorescence-excitation spectrum. For zero disorder the exciton manifold features two non-degenerate and eight pairwise degenerate states. In the presence of energetic disorder the degeneracy of the exciton states is lifted and oscillator strength is redistributed among the exciton states. A satisfactory understanding of the nature of static disorder in light-harvesting systems has not been reached [S. Jang, S.F. Dempster, R.J. Silbey, J. Phys. Chem. B 105 (2001) 6655]. In the local site basis, there can be present static disorder in both diagonal and off-diagonal Hamiltonian matrix elements. Silbey et al. [J. Phys. Chem. B 105 (2001) 6655] pointed out several questions: is former enough or the latter should be included as well? If both are considered, then there remains a question about whether they are independent or correlated. The distribution of the energetic separation E(k=+/-1) and relative orientation of the transition-dipole moments has been recently investigated [S. Jang, et al., J. Phys. Chem. B 105 (2001) 6655; C. Hofmann, T.J. Aartsma, J. Koehler, Chem. Phys. Lett. 395 (2004) 373]. In our present contribution we have extended such a type of investigation to four models of noncorrelated static disorder: (A) Gaussian disorder in the

Molecular cytogenetic and phenotypic characterization of ring chromosome 13 in three unrelated patients

Science.gov (United States)

Abdallah-Bouhjar, Inesse B.; Mougou-Zerelli, Soumaya; Hannachi, Hanene; Gmidène, Abir; Labalme, Audrey; Soyah, Najla; Sanlaville, Damien; Saad, Ali; Elghezal, Hatem

2013-01-01

We report on the cytogenetic and molecular investigations of constitutional de-novo ring chromosome 13s in three unrelated patients for better understanding and delineation of the phenotypic variability characterizing this genomic rearrangement. The patient’s karyotypes were as follows: 46,XY,r(13)(p11q34) dn for patients 1 and 2 and 46,XY,r(13)(p11q14) dn for patient 3, as a result of the deletion in the telomeric regions of chromosome 13. The patients were, therefore, monosomic for the segment 13q34 → 13qter; in addition, for patient 3, the deletion was larger, encompassing the segment 13q14 → 13qter. Fluorescence in situ hybridization confirmed these rearrangement and array CGH technique showed the loss of at least 2.9 Mb on the short arm and 4.7 Mb on the long arm of the chromosome 13 in patient 2. Ring chromosome 13 (r(13)) is associated with several phenotypic features like intellectual disability, marked short stature, brain and heart defects, microcephaly and genital malformations in males, including undescended testes and hypospadias. However, the hearing loss and speech delay that were found in our three patients have rarely been reported with ring chromosome 13. Although little is known about its etiology, there is interesting evidence for a genetic cause for the ring chromosome 13. We thus performed a genotype-phenotype correlation analysis to ascertain the contribution of ring chromosome 13 to the clinical features of our three cases. PMID:27625853

Supra-molecular hydrogen-bonding patterns in the N(9)-H protonated and N(7)-H tautomeric form of an N(6) -benzoyl-adenine salt: N (6)-benzoyl-adeninium nitrate.

Science.gov (United States)

Karthikeyan, Ammasai; Jeeva Jasmine, Nithianantham; Thomas Muthiah, Packianathan; Perdih, Franc

2016-02-01

In the title molecular salt, C12H10N5O(+)·NO3 (-), the adenine unit has an N (9)-protonated N(7)-H tautomeric form with non-protonated N(1) and N(3) atoms. The dihedral angle between the adenine ring system and the phenyl ring is 51.10 (10)°. The typical intra-molecular N(7)-H⋯O hydrogen bond with an S(7) graph-set motif is also present. The benzoyl-adeninium cations also form base pairs through N-H⋯O and C-H⋯N hydrogen bonds involving the Watson-Crick face of the adenine ring and the C and O atoms of the benzoyl ring of an adjacent cation, forming a supra-molecular ribbon with R 2 (2)(9) rings. Benzoyl-adeninum cations are also bridged by one of the oxygen atoms of the nitrate anion, which acts as a double acceptor, forming a pair of N-H⋯O hydrogen bonds to generate a second ribbon motif. These ribbons together with π-π stacking inter-actions between the phenyl ring and the five- and six-membered adenine rings of adjacent mol-ecules generate a three-dimensional supra-molecular architecture.

Reproducing Quantum Probability Distributions at the Speed of Classical Dynamics: A New Approach for Developing Force-Field Functors.

Science.gov (United States)

Sundar, Vikram; Gelbwaser-Klimovsky, David; Aspuru-Guzik, Alán

2018-04-05

Modeling nuclear quantum effects is required for accurate molecular dynamics (MD) simulations of molecules. The community has paid special attention to water and other biomolecules that show hydrogen bonding. Standard methods of modeling nuclear quantum effects like Ring Polymer Molecular Dynamics (RPMD) are computationally costlier than running classical trajectories. A force-field functor (FFF) is an alternative method that computes an effective force field that replicates quantum properties of the original force field. In this work, we propose an efficient method of computing FFF using the Wigner-Kirkwood expansion. As a test case, we calculate a range of thermodynamic properties of Neon, obtaining the same level of accuracy as RPMD, but with the shorter runtime of classical simulations. By modifying existing MD programs, the proposed method could be used in the future to increase the efficiency and accuracy of MD simulations involving water and proteins.

Thermal quantum time-correlation functions from classical-like dynamics

Science.gov (United States)

Hele, Timothy J. H.

2017-07-01

Thermal quantum time-correlation functions are of fundamental importance in quantum dynamics, allowing experimentally measurable properties such as reaction rates, diffusion constants and vibrational spectra to be computed from first principles. Since the exact quantum solution scales exponentially with system size, there has been considerable effort in formulating reliable linear-scaling methods involving exact quantum statistics and approximate quantum dynamics modelled with classical-like trajectories. Here, we review recent progress in the field with the development of methods including centroid molecular dynamics , ring polymer molecular dynamics (RPMD) and thermostatted RPMD (TRPMD). We show how these methods have recently been obtained from 'Matsubara dynamics', a form of semiclassical dynamics which conserves the quantum Boltzmann distribution. We also apply the Matsubara formalism to reaction rate theory, rederiving t → 0+ quantum transition-state theory (QTST) and showing that Matsubara-TST, like RPMD-TST, is equivalent to QTST. We end by surveying areas for future progress.

Rings in drugs.

Science.gov (United States)

Taylor, Richard D; MacCoss, Malcolm; Lawson, Alastair D G

2014-07-24

We have analyzed the rings, ring systems, and frameworks in drugs listed in the FDA Orange Book to understand the frequency, timelines, molecular property space, and the application of these rings in different therapeutic areas and target classes. This analysis shows that there are only 351 ring systems and 1197 frameworks in drugs that came onto the market before 2013. Furthermore, on average six new ring systems enter drug space each year and approximately 28% of new drugs contain a new ring system. Moreover, it is very unusual for a drug to contain more than one new ring system and the majority of the most frequently used ring systems (83%) were first used in drugs developed prior to 1983. These observations give insight into the chemical novelty of drugs and potentially efficient ways to assess compound libraries and develop compounds from hit identification to lead optimization and beyond.

Lattice constants of pure methane and carbon dioxide hydrates at low temperatures. Implementing quantum corrections to classical molecular dynamics studies

Energy Technology Data Exchange (ETDEWEB)

Costandy, Joseph; Michalis, Vasileios K.; Economou, Ioannis G., E-mail: i.tsimpanogiannis@qatar.tamu.edu, E-mail: ioannis.economou@qatar.tamu.edu [Chemical Engineering Program, Texas A& M University at Qatar, P.O. Box 23874, Doha (Qatar); Tsimpanogiannis, Ioannis N., E-mail: i.tsimpanogiannis@qatar.tamu.edu, E-mail: ioannis.economou@qatar.tamu.edu [Chemical Engineering Program, Texas A& M University at Qatar, P.O. Box 23874, Doha (Qatar); Environmental Research Laboratory, National Center for Scientific Research NCSR “Demokritos,” 15310 Aghia Paraskevi, Attikis (Greece); Stubos, Athanassios K. [Environmental Research Laboratory, National Center for Scientific Research NCSR “Demokritos,” 15310 Aghia Paraskevi, Attikis (Greece)

2016-03-28

We introduce a simple correction to the calculation of the lattice constants of fully occupied structure sI methane or carbon dioxide pure hydrates that are obtained from classical molecular dynamics simulations using the TIP4PQ/2005 water force field. The obtained corrected lattice constants are subsequently used in order to obtain isobaric thermal expansion coefficients of the pure gas hydrates that exhibit a trend that is significantly closer to the experimental behavior than previously reported classical molecular dynamics studies.

Stability of molecular dynamics simulations of classical systems

DEFF Research Database (Denmark)

Toxværd, Søren

2012-01-01

The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... for the limit of stability h ⩽ 2/ω. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD...

The classical limit of W-algebras

International Nuclear Information System (INIS)

Figueroa-O'Farrill, J.M.; Ramos, E.

1992-01-01

We define and compute explicitly the classical limit of the realizations of W n appearing as hamiltonian structures of generalized KdV hierarchies. The classical limit is obtained by taking the commutative limit of the ring of pseudodifferential operators. These algebras - denoted w n - have free field realizations in which the generators are given by the elementary symmetric polynomials in the free fields. We compute the algebras explicitly and we show that they are all reductions of a new algebra w KP , which is proposed as the universal classical W-algebra for the w n series. As a deformation of this algebra we also obtain w 1+∞ , the classical limit of W 1+∞ . (orig.)

On the nonlinear modeling of ring oscillators

KAUST Repository

Elwakil, Ahmed S.

2009-06-01

We develop higher-order nonlinear models of three-stage and five-stage ring oscillators based on a novel inverter model. The oscillation condition and oscillation frequency are derived and compared to classical linear model analysis. Two important special cases for five-stage ring oscillators are also studied. Numerical simulations are shown. © 2009 World Scientific Publishing Company.

On the nonlinear modeling of ring oscillators

KAUST Repository

Elwakil, Ahmed S.; Salama, Khaled N.

2009-01-01

We develop higher-order nonlinear models of three-stage and five-stage ring oscillators based on a novel inverter model. The oscillation condition and oscillation frequency are derived and compared to classical linear model analysis. Two important special cases for five-stage ring oscillators are also studied. Numerical simulations are shown. © 2009 World Scientific Publishing Company.

Potassium (2,2'-bipyridine-κN,N')bis-(carbonato-κO,O')cobaltate(III) dihydrate.

Science.gov (United States)

Wang, Jian-Fei; Lin, Jian-Li

2010-09-30

In the title compound, K[Co(CO(3))(2)(C(10)H(8)N(2))]·2H(2)O, the Co(III) atom is coordinated by two bipyridine N atoms and four O atoms from two bidentate chelating carbonate anions, and thus adopts a distorted octa-hedral N(2)O(4) environment. The [Co(bipy)(CO(3))(2)](-) (bipy is 2,2'-bipyridine) -units are stacked along [100] via π-π stacking inter-actions, with inter-planar distances between the bipyridine rings of 3.36 (4) and 3.44 (6) Å, forming chains. Classical O-H⋯O hydrogen-bonding inter-actions link the chains, forming channels along (100) in which the K(+) ions reside and leading to a three-dimensional supra-molecular architecture.

A Step Forward in Molecular Diagnostics of Lyssaviruses – Results of a Ring Trial among European Laboratories

DEFF Research Database (Denmark)

Fischer, Melina; Wernike, Kerstin; Freuling, Conrad M.

2013-01-01

Rabies is a lethal and notifiable zoonotic disease for which diagnostics have to meet the highest standards. In recent years, an evolution was especially seen in molecular diagnostics with a wide variety of different detection methods published. Therefore, a first international ring trial...... participants were asked to investigate a panel of defined lyssavirus RNAs, consisting of Rabies virus (RABV) and European bat lyssavirus 1 and 2 (EBLV-1 and -2) RNA samples, with systems available in their laboratory. The ring trial allowed the important conclusion that conventional RT-PCR assays were really...

Algebras, rings and modules

CERN Document Server

Hazewinkel, Michiel; Kirichenko, V V

Provides both the classical aspects of the theory of groups and their representations as well as a general introduction to the modern theory of representations, including the representations of quivers and finite partially ordered sets. This volume provides the theory of semiprime Noetherian semiperfect and semidistributive rings.

Topology of classical molecular optimal control landscapes for multi-target objectives

Energy Technology Data Exchange (ETDEWEB)

Joe-Wong, Carlee [Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544-1000 (United States); Ho, Tak-San; Rabitz, Herschel, E-mail: hrabitz@princeton.edu [Department of Chemistry, Princeton University, Princeton, New Jersey 08544-1009 (United States); Wu, Rebing [Department of Automation, Tsinghua University, Beijing (China)

2015-04-21

This paper considers laser-driven optimal control of an ensemble of non-interacting molecules whose dynamics lie in classical phase space. The molecules evolve independently under control to distinct final states. We consider a control landscape defined in terms of multi-target (MT) molecular states and analyze the landscape as a functional of the control field. The topology of the MT control landscape is assessed through its gradient and Hessian with respect to the control. Under particular assumptions, the MT control landscape is found to be free of traps that could hinder reaching the objective. The Hessian associated with an optimal control field is shown to have finite rank, indicating an inherent degree of robustness to control noise. Both the absence of traps and rank of the Hessian are shown to be analogous to the situation of specifying multiple targets for an ensemble of quantum states. Numerical simulations are presented to illustrate the classical landscape principles and further characterize the system behavior as the control field is optimized.

Classical, Semi-classical and Quantum Noise

CERN Document Server

Poor, H; Scully, Marlan

2012-01-01

David Middleton was a towering figure of 20th Century engineering and science and one of the founders of statistical communication theory. During the second World War, the young David Middleton, working with Van Fleck, devised the notion of the matched filter, which is the most basic method used for detecting signals in noise. Over the intervening six decades, the contributions of Middleton have become classics. This collection of essays by leading scientists, engineers and colleagues of David are in his honor and reflect the wide  influence that he has had on many fields. Also included is the introduction by Middleton to his forthcoming book, which gives a wonderful view of the field of communication, its history and his own views on the field that he developed over the past 60 years. Focusing on classical noise modeling and applications, Classical, Semi-Classical and Quantum Noise includes coverage of statistical communication theory, non-stationary noise, molecular footprints, noise suppression, Quantum e...

Initial Reactivity of Linkages and Monomer Rings in Lignin Pyrolysis Revealed by ReaxFF Molecular Dynamics.

Science.gov (United States)

Zhang, Tingting; Li, Xiaoxia; Guo, Li

2017-10-24

The initial conversion pathways of linkages and their linked monomer units in lignin pyrolysis were investigated comprehensively by ReaxFF MD simulations facilitated by the unique VARxMD for reaction analysis. The simulated molecular model contains 15 920 atoms and was constructed on the basis of Adler's softwood lignin model. The simulations uncover the initial conversion ratio of various linkages and their linked aryl monomers. For linkages and their linked monomer aryl rings of α-O-4, β-O-4 and α-O-4 & β-5, the C α /C β ether bond cracking dominates the initial pathway accounting for at least up to 80% of their consumption. For the linkage of β-β & γ-O-α, both the C α -O ether bond cracking and its linked monomer aryl ring opening are equally important. Ring-opening reactions dominate the initial consumption of other 4-O-5, 5-5, β-1, β-2, and β-5 linkages and their linked monomers. The ether bond cracking of C α -O and C β -O occurs at low temperature, and the aryl ring-opening reactions take place at relatively high temperature. The important intermediates leading to the stable aryl ring opening are the phenoxy radicals, the bridged five-membered and three-membered rings and the bridged six-membered and three-membered rings. In addition, the reactivity of a linkage and its monomer aryl ring may be affected by other linkages. The ether bond cracking of α-O-4 and β-O-4 linkages can activate its neighboring linkage or monomer ring through the formed phenoxy radicals as intermediates. The important intermediates revealed in this article should be of help in deepening the understanding of the controlling mechanism for producing aromatic chemicals from lignin pyrolysis.

Ring-Opening Polymerization of N-Carboxyanhydrides for Preparation of Polypeptides and Polypeptide-Based Hybrid Materials with Various Molecular Architectures

KAUST Repository

Pahovnik, David; Hadjichristidis, Nikolaos

2015-01-01

Different synthetic approaches utilizing ring-opening polymerization of N-carboxyanhydrides for preparation of polypeptide and polypeptide-based hybrid materials with various molecular architectures are described. An overview of polymerization

A Step Forward in Molecular Diagnostics of Lyssaviruses – Results of a Ring Trial among European Laboratories

NARCIS (Netherlands)

Fischer, M.; Wernike, K.; Freuling, C.M.; Müller, T.; Aylan, O.; Brochier, B.; Cliquet, F.; Vázquez-Morón, S.; Hostnik, P.; Huovilainen, A.; Isaksson, M.; Kooi, E.A.

2013-01-01

Rabies is a lethal and notifiable zoonotic disease for which diagnostics have to meet the highest standards. In recent years, an evolution was especially seen in molecular diagnostics with a wide variety of different detection methods published. Therefore, a first international ring trial

Calculation of the inter-nuclei separation of HD+

International Nuclear Information System (INIS)

Zhu Zhousen; Shi Miangong; Tang Ayou; Yang Baifang; Miao Jingwei

1993-01-01

With the Ritz variational principle, the authors calculate the inter nuclei separation of the HD + molecular ion, and introduces a method to calculate the inter nuclei separations of other simple non-symmetry two-atom molecular ions. One way to work out the trial wave function is provided

The crystal structures of three pyrazine-2,5-dicarb-oxamides: three-dimensional supra-molecular structures.

Science.gov (United States)

Cati, Dilovan S; Stoeckli-Evans, Helen

2017-05-01

The complete mol-ecules of the title compounds, N 2 , N 5 -bis-(pyridin-2-ylmeth-yl)pyrazine-2,5-dicarboxamide, C 18 H 16 N 6 O 2 (I), 3,6-dimethyl- N 2 , N 5 -bis-(pyridin-2-yl-meth-yl)pyrazine-2,5-dicarboxamide, C 20 H 20 N 6 O 2 (II), and N 2 , N 5 -bis-(pyridin-4-ylmeth-yl)pyrazine-2,5-dicarboxamide, C 18 H 16 N 6 O 2 (III), are generated by inversion symmetry, with the pyrazine rings being located about centres of inversion. Each mol-ecule has an extended conformation with the pyridine rings inclined to the pyrazine ring by 89.17 (7)° in (I), 75.83 (8)° in (II) and by 82.71 (6)° in (III). In the crystal of (I), mol-ecules are linked by N-H⋯N hydrogen bonds, forming layers lying parallel to the bc plane. The layers are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. In the crystal of (II), mol-ecules are also linked by N-H⋯N hydrogen bonds, forming layers lying parallel to the (10-1) plane. As in (I), the layers are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. In the crystal of (III), mol-ecules are again linked by N-H⋯N hydrogen bonds, but here form corrugated sheets lying parallel to the bc plane. Within the sheets, neighbouring pyridine rings are linked by offset π-π inter-actions [inter-centroid distance = 3.739 (1) Å]. The sheets are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. Compound (I) crystallizes in the monoclinic space group P 2 1 / c . Another monoclinic polymorph, space group C 2/ c , has been reported on by Cockriel et al. [ Inorg. Chem. Commun. (2008), 11 , 1-4]. The mol-ecular structures of the two polymorphs are compared.

Pathogenic Chlamydia Lack a Classical Sacculus but Synthesize a Narrow, Mid-cell Peptidoglycan Ring, Regulated by MreB, for Cell Division.

Science.gov (United States)

Liechti, George; Kuru, Erkin; Packiam, Mathanraj; Hsu, Yen-Pang; Tekkam, Srinivas; Hall, Edward; Rittichier, Jonathan T; VanNieuwenhze, Michael; Brun, Yves V; Maurelli, Anthony T

2016-05-01

The peptidoglycan (PG) cell wall is a peptide cross-linked glycan polymer essential for bacterial division and maintenance of cell shape and hydrostatic pressure. Bacteria in the Chlamydiales were long thought to lack PG until recent advances in PG labeling technologies revealed the presence of this critical cell wall component in Chlamydia trachomatis. In this study, we utilize bio-orthogonal D-amino acid dipeptide probes combined with super-resolution microscopy to demonstrate that four pathogenic Chlamydiae species each possess a ≤ 140 nm wide PG ring limited to the division plane during the replicative phase of their developmental cycles. Assembly of this PG ring is rapid, processive, and linked to the bacterial actin-like protein, MreB. Both MreB polymerization and PG biosynthesis occur only in the intracellular form of pathogenic Chlamydia and are required for cell enlargement, division, and transition between the microbe's developmental forms. Our kinetic, molecular, and biochemical analyses suggest that the development of this limited, transient, PG ring structure is the result of pathoadaptation by Chlamydia to an intracellular niche within its vertebrate host.

Pathogenic Chlamydia Lack a Classical Sacculus but Synthesize a Narrow, Mid-cell Peptidoglycan Ring, Regulated by MreB, for Cell Division.

Directory of Open Access Journals (Sweden)

George Liechti

2016-05-01

Full Text Available The peptidoglycan (PG cell wall is a peptide cross-linked glycan polymer essential for bacterial division and maintenance of cell shape and hydrostatic pressure. Bacteria in the Chlamydiales were long thought to lack PG until recent advances in PG labeling technologies revealed the presence of this critical cell wall component in Chlamydia trachomatis. In this study, we utilize bio-orthogonal D-amino acid dipeptide probes combined with super-resolution microscopy to demonstrate that four pathogenic Chlamydiae species each possess a ≤ 140 nm wide PG ring limited to the division plane during the replicative phase of their developmental cycles. Assembly of this PG ring is rapid, processive, and linked to the bacterial actin-like protein, MreB. Both MreB polymerization and PG biosynthesis occur only in the intracellular form of pathogenic Chlamydia and are required for cell enlargement, division, and transition between the microbe's developmental forms. Our kinetic, molecular, and biochemical analyses suggest that the development of this limited, transient, PG ring structure is the result of pathoadaptation by Chlamydia to an intracellular niche within its vertebrate host.

Quantum Mechanics/Molecular Mechanics Simulations Identify the Ring-Opening Mechanism of Creatininase.

Science.gov (United States)

Jitonnom, Jitrayut; Mujika, Jon I; van der Kamp, Marc W; Mulholland, Adrian J

2017-12-05

Creatininase catalyzes the conversion of creatinine (a biosensor for kidney function) to creatine via a two-step mechanism: water addition followed by ring opening. Water addition is common to other known cyclic amidohydrolases, but the precise mechanism for ring opening is still under debate. The proton donor in this step is either His178 or a water molecule bound to one of the metal ions, and the roles of His178 and Glu122 are unclear. Here, the two possible reaction pathways have been fully examined by means of combined quantum mechanics/molecular mechanics simulations at the SCC-DFTB/CHARMM22 level of theory. The results indicate that His178 is the main catalytic residue for the whole reaction and explain its role as proton shuttle during the ring-opening step. In the first step, His178 provides electrostatic stabilization to the gem-diolate tetrahedral intermediate. In the second step, His178 abstracts the hydroxyl proton of the intermediate and delivers it to the cyclic amide nitrogen, leading to ring opening. The latter is the rate-limiting step with a free energy barrier of 18.5 kcal/mol, in agreement with the experiment. We find that Glu122 must be protonated during the enzyme reaction, so that it can form a stable hydrogen bond with its neighboring water molecule. Simulations of the E122Q mutant showed that this replacement disrupts the H-bond network formed by three conserved residues (Glu34, Ser78, and Glu122) and water, increasing the energy barrier. Our computational studies provide a comprehensive explanation for previous structural and kinetic observations, including why the H178A mutation causes a complete loss of activity but the E122Q mutation does not.

A molecular recombination map of Antirrhinum majus

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Hudson Andrew

2010-12-01

Full Text Available Abstract Background Genetic recombination maps provide important frameworks for comparative genomics, identifying gene functions, assembling genome sequences and for breeding. The molecular recombination map currently available for the model eudicot Antirrhinum majus is the result of a cross with Antirrhinum molle, limiting its usefulness within A. majus. Results We created a molecular linkage map of A. majus based on segregation of markers in the F2 population of two inbred lab strains of A. majus. The resulting map consisted of over 300 markers in eight linkage groups, which could be aligned with a classical recombination map and the A. majus karyotype. The distribution of recombination frequencies and distorted transmission of parental alleles differed from those of a previous inter-species hybrid. The differences varied in magnitude and direction between chromosomes, suggesting that they had multiple causes. The map, which covered an estimated of 95% of the genome with an average interval of 2 cM, was used to analyze the distribution of a newly discovered family of MITE transposons and tested for its utility in positioning seven mutations that affect aspects of plant size. Conclusions The current map has an estimated interval of 1.28 Mb between markers. It shows a lower level of transmission ratio distortion and a longer length than the previous inter-species map, making it potentially more useful. The molecular recombination map further indicates that the IDLE MITE transposons are distributed throughout the genome and are relatively stable. The map proved effective in mapping classical morphological mutations of A. majus.

Fano resonance and persistent current of a quantum ring

International Nuclear Information System (INIS)

Xiong Yongjian; Liang Xianting

2004-01-01

We investigate electron transport and persistent current of a quantum ring weakly attached to current leads. Assuming there is direct coupling (weakly or strongly) between two leads, electrons can transmit by the inter-lead coupling or tunneling through the quantum ring. The interference between the two paths yields asymmetric Fano line shape for conductance. In presence of interior magnetic flux, there is persistent current along the ring with narrow resonance peaks. The positions of the conductance resonances and the persistent current peaks correspond to the quasibound levels of the closed ring. This feature is helpful to determine the energy spectrum of the quantum ring. Our results show that the proposed setup provides a tunable Fano system

Perspective: Ring-polymer instanton theory

Science.gov (United States)

Richardson, Jeremy O.

2018-05-01

Since the earliest explorations of quantum mechanics, it has been a topic of great interest that quantum tunneling allows particles to penetrate classically insurmountable barriers. Instanton theory provides a simple description of these processes in terms of dominant tunneling pathways. Using a ring-polymer discretization, an efficient computational method is obtained for applying this theory to compute reaction rates and tunneling splittings in molecular systems. Unlike other quantum-dynamics approaches, the method scales well with the number of degrees of freedom, and for many polyatomic systems, the method may provide the most accurate predictions which can be practically computed. Instanton theory thus has the capability to produce useful data for many fields of low-temperature chemistry including spectroscopy, atmospheric and astrochemistry, as well as surface science. There is however still room for improvement in the efficiency of the numerical algorithms, and new theories are under development for describing tunneling in nonadiabatic transitions.

PREFACE: Special section on vortex rings Special section on vortex rings

Science.gov (United States)

Fukumoto, Yasuhide

2009-10-01

This special section of Fluid Dynamics Research includes five articles on vortex rings in both classical and quantum fluids. The leading scientists of the field describe the trends in and the state-of-the-art development of experiments, theories and numerical simulations of vortex rings. The year 2008 was the 150th anniversary of 'vortex motion' since Hermann von Helmholtz opened up this field. In 1858, Helmholtz published a paper in Crelle's Journal which put forward the concept of 'vorticity' and made the first analysis of vortex motion. Fluid mechanics before that was limited to irrotational motion. In the absence of vorticity, the motion of an incompressible homogeneous fluid is virtually equivalent to a rigid-body motion in the sense that the fluid motion is determined once the boundary configuration is specified. Helmholtz proved, among other things, that, without viscosity, a vortex line is frozen into the fluid. This Helmholtz's law immediately implies the preservation of knots and links of vortex lines and its implication is enormous. One of the major trends of fluid mechanics since the latter half of the 20th century is to clarify the topological meaning of Helmholtz's law and to exploit it to develop theoretical and numerical methods to find the solutions of the Euler equations and to develop experimental techniques to gain an insight into fluid motion. Vortex rings are prominent coherent structures in a variety of fluid motions from the microscopic scale, through human and mesoscale to astrophysical scales, and have attracted people's interest. The late professor Philip G Saffman (1981) emphasized the significance of studies on vortex rings. One particular motion exemplifies the whole range of problems of vortex motion and is also a commonly known phenomenon, namely the vortex ring or smoke ring. Vortex rings are easily produced by dropping drops of one liquid into another, or by puffing fluid out of a hole, or by exhaling smoke if one has the skill

A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems

Science.gov (United States)

Kruse, Holger; Grimme, Stefan

2012-04-01

A semi-empirical counterpoise-type correction for basis set superposition error (BSSE) in molecular systems is presented. An atom pair-wise potential corrects for the inter- and intra-molecular BSSE in supermolecular Hartree-Fock (HF) or density functional theory (DFT) calculations. This geometrical counterpoise (gCP) denoted scheme depends only on the molecular geometry, i.e., no input from the electronic wave-function is required and hence is applicable to molecules with ten thousands of atoms. The four necessary parameters have been determined by a fit to standard Boys and Bernadi counterpoise corrections for Hobza's S66×8 set of non-covalently bound complexes (528 data points). The method's target are small basis sets (e.g., minimal, split-valence, 6-31G*), but reliable results are also obtained for larger triple-ζ sets. The intermolecular BSSE is calculated by gCP within a typical error of 10%-30% that proves sufficient in many practical applications. The approach is suggested as a quantitative correction in production work and can also be routinely applied to estimate the magnitude of the BSSE beforehand. The applicability for biomolecules as the primary target is tested for the crambin protein, where gCP removes intramolecular BSSE effectively and yields conformational energies comparable to def2-TZVP basis results. Good mutual agreement is also found with Jensen's ACP(4) scheme, estimating the intramolecular BSSE in the phenylalanine-glycine-phenylalanine tripeptide, for which also a relaxed rotational energy profile is presented. A variety of minimal and double-ζ basis sets combined with gCP and the dispersion corrections DFT-D3 and DFT-NL are successfully benchmarked on the S22 and S66 sets of non-covalent interactions. Outstanding performance with a mean absolute deviation (MAD) of 0.51 kcal/mol (0.38 kcal/mol after D3-refit) is obtained at the gCP-corrected HF-D3/(minimal basis) level for the S66 benchmark. The gCP-corrected B3LYP-D3/6-31G* model

A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems.

Science.gov (United States)

Kruse, Holger; Grimme, Stefan

2012-04-21

A semi-empirical counterpoise-type correction for basis set superposition error (BSSE) in molecular systems is presented. An atom pair-wise potential corrects for the inter- and intra-molecular BSSE in supermolecular Hartree-Fock (HF) or density functional theory (DFT) calculations. This geometrical counterpoise (gCP) denoted scheme depends only on the molecular geometry, i.e., no input from the electronic wave-function is required and hence is applicable to molecules with ten thousands of atoms. The four necessary parameters have been determined by a fit to standard Boys and Bernadi counterpoise corrections for Hobza's S66×8 set of non-covalently bound complexes (528 data points). The method's target are small basis sets (e.g., minimal, split-valence, 6-31G*), but reliable results are also obtained for larger triple-ζ sets. The intermolecular BSSE is calculated by gCP within a typical error of 10%-30% that proves sufficient in many practical applications. The approach is suggested as a quantitative correction in production work and can also be routinely applied to estimate the magnitude of the BSSE beforehand. The applicability for biomolecules as the primary target is tested for the crambin protein, where gCP removes intramolecular BSSE effectively and yields conformational energies comparable to def2-TZVP basis results. Good mutual agreement is also found with Jensen's ACP(4) scheme, estimating the intramolecular BSSE in the phenylalanine-glycine-phenylalanine tripeptide, for which also a relaxed rotational energy profile is presented. A variety of minimal and double-ζ basis sets combined with gCP and the dispersion corrections DFT-D3 and DFT-NL are successfully benchmarked on the S22 and S66 sets of non-covalent interactions. Outstanding performance with a mean absolute deviation (MAD) of 0.51 kcal/mol (0.38 kcal/mol after D3-refit) is obtained at the gCP-corrected HF-D3/(minimal basis) level for the S66 benchmark. The gCP-corrected B3LYP-D3/6-31G* model

Magnetic properties of a classical XY spin dimer in a “planar” magnetic field

Energy Technology Data Exchange (ETDEWEB)

Ciftja, Orion, E-mail: ogciftja@pvamu.edu [Department of Physics, Prairie View A& M University, Prairie View, TX 77446 (United States); Prenga, Dode [Department of Physics, Faculty of Natural Sciences, University of Tirana, Bul. Zog I, Tirana (Albania)

2016-10-15

Single-molecule magnetism originates from the strong intra-molecular magnetic coupling of a small number of interacting spins. Such spins generally interact very weakly with the neighboring spins in the other molecules of the compound, therefore, inter-molecular spin couplings are negligible. In certain cases the number of magnetically coupled spins is as small as a dimer, a system that can be considered the smallest nanomagnet capable of storing non-trivial magnetic information on the molecular level. Additional interesting patterns arise if the spin motion is confined to a two-dimensional space. In such a scenario, clusters consisting of spins with large-spin values are particularly attractive since their magnetic interactions can be described well in terms of classical Heisenberg XY spins. In this work we calculate exactly the magnetic properties of a nanomagnetic dimer of classical XY spins in a “planar” external magnetic field. The problem is solved by employing a mathematical approach whose idea is the introduction of auxiliary spin variables into the starting expression of the partition function. Results for the total internal energy, total magnetic moment, spin–spin correlation function and zero-field magnetic susceptibility can serve as a basis to understand the magnetic properties of large-spin dimer building blocks. - Highlights: • Exact magnetic properties of a dimer system of classical XY spins in magnetic field. • Partition function in nonzero magnetic field obtained in closed-form. • Novel exact analytic results are important for spin models in a magnetic field. • Result provides benchmarks to gauge the accuracy of computational techniques.

A canonical eight-dimensional formalism for linear and non-linear classical spin-orbit motion in storage rings

International Nuclear Information System (INIS)

Barber, D.P.; Heinemann, K.; Ripken, G.

1991-05-01

In the following report we begin to reformulate work by Derbenev on the behaviour of coupled quantized spin-orbit motion. To this end we present a classical symplectic treatment of linear and non-linear spin-orbit motion for storage rings using a fully coupled eight-dimensional formalism which generalizes earlier investigations of coupled synchro-betatron oscillations by introducing two additional canonical spin variables which behave, in a small-angle limit, like those already used in linearised spin theory. Thus in addition to the usual x-z-s couplings, both the spin to orbit and orbit to spin coupling are described canonically. Since the spin Hamiltonian can be expanded in a Taylor series in canonical variables, the formalism is convenient for use in 8-dimensional symplectic tracking calculations with the help, for example, of Lie algebra or differential algebra for the study of chaotic spin motion, for construction of spin normal forms and for the study of the effect of Stern-Gerlach forces. (orig.)

New insights into the by-product fatigue mechanism of the photo-induced ring-opening in diarylethenes.

Science.gov (United States)

Mendive-Tapia, David; Perrier, Aurélie; Bearpark, Michael J; Robb, Michael A; Lasorne, Benjamin; Jacquemin, Denis

2014-09-14

The photochromic properties of diarylethenes, some of the most studied class of molecular switches, are known to be controlled by non-adiabatic decay at a conical intersection seam. Nevertheless, as their fatigue-reaction mechanism - leading to non-photochromic products - is yet to be understood, we investigate the photo-chemical formation of the so-called by-product isomer using three complementary computational methods (MMVB, CASSCF and CASPT2) on three model systems of increasing complexity. We show that for the ring-opening reaction a transition state on S1(2A) involving bond breaking of the penta-ring leads to a low energy S1(2A)/S0(1A) conical intersection seam, which lies above one of the transition states leading to the by-product isomer on the ground state. Therefore, radiationless decay and subsequent side-product formation can take place explaining the photo-degradation responsible for the by-product generation in diarylethene-type molecules. The effect of dynamic electron correlation and the possible role of inter-system crossing along the penta-ring opening coordinate are discussed as well.

Study of inter species diversity and population structure by molecular genetic method in Iranian Artemia

OpenAIRE

Hajirostamloo, Mahbobeh

2005-01-01

Artemia is a small crustacean that adapted to live in brine water and has been seen in different brine water sources in Iran. Considering the importance of genetic studies manifest inter population differences in species, to estimate genetic structure, detect difference at molecular level and separate different Artemia populations of Iran, also study of phylogenic relationships among them, samples of Artemia were collected from nine region: Urmia lake in West Azerbaijan, Sh...

Plasma properties of quasi-one-dimensional ring

CERN Document Server

Shmelev, G M

2001-01-01

The plasma properties of the quasi-one-dimensional ring in the threshold cases of low and high frequencies, corresponding to the plasma oscillations and dielectric relaxation are studied within the frames of the classical approach. The plasma oscillations spectrum and the electron dielectric relaxation frequency in the quasi-one-dimensional ring are calculated. The plasmons spectrum equidistance is identified. It is shown , that in contrast to the three-dimensional case there takes place the dielectric relaxation dispersion, wherefrom there follows the possibility of studying the carriers distribution in the quasi-one-dimensional rings through the method of the dielectric relaxation spectroscopy

Ring-opening polymerization of 19-electron [2]cobaltocenophanes: a route to high-molecular-weight, water-soluble polycobaltocenium polyelectrolytes.

Science.gov (United States)

Mayer, Ulrich F J; Gilroy, Joe B; O'Hare, Dermot; Manners, Ian

2009-08-05

Water-soluble, high-molecular-weight polycobaltocenium polyelectrolytes have been prepared by ring-opening polymerization (ROP) techniques. Anionic polymerization of a strained 19-electron dicarba[2]cobaltocenophane followed by oxidation in the presence of ammonium chloride resulted in the formation of oligomers with up to nine repeat units. Thermal ROP of dicarba[2]cobaltocenophane followed by oxidation in the presence of ammonium nitrate resulted in the formation of high-molecular-weight polycobaltocenium nitrate, a redox-active cobalt-containing polyelectrolyte.

Inhomogeneous molecular ring around the B[e] supergiant LHA 120-S 73

Science.gov (United States)

Kraus, M.; Cidale, L. S.; Arias, M. L.; Maravelias, G.; Nickeler, D. H.; Torres, A. F.; Borges Fernandes, M.; Aret, A.; Curé, M.; Vallverdú, R.; Barbá, R. H.

2016-10-01

Context. B[e] supergiants are evolved massive stars, enshrouded in a dense wind and surrounded by a molecular and dusty disk. The mechanisms that drive phases of enhanced mass loss and mass ejections, responsible for the shaping of the circumstellar material of these objects, are still unclear. Aims: We aim to improve our knowledge on the structure and dynamics of the circumstellar disk of the Large Magellanic Cloud B[e] supergiant LHA 120-S 73. Methods: High-resolution optical and near-infrared spectroscopic data were obtained over a period of 16 and 7 yr, respectively. The spectra cover the diagnostic emission lines from [Ca II] and [O I], as well as the CO bands. These features trace the disk at different distances from the star. We analyzed the kinematics of the individual emission regions by modeling their emission profiles. A low-resolution mid-infrared spectrum was obtained as well, which provides information on the composition of the dusty disk. Results: All diagnostic emission features display double-peaked line profiles, which we interpret as due to Keplerian rotation. We find that the profile of each forbidden line contains contributions from two spatially clearly distinct rings. In total, we find that LHA 120-S 73 is surrounded by at least four individual rings of material with alternating densities (or by a disk with strongly non-monotonic radial density distribution). Moreover, we find that the molecular ring must have gaps or at least strong density inhomogeneities, or in other words, a clumpy structure. The optical spectra additionally display a broad emission feature at 6160-6180 Å, which we interpret as molecular emission from TiO. The mid-infrared spectrum displays features of oxygen- and carbon-rich grain species, which indicates a long-lived, stable dusty disk. We cannot confirm the previously reported high value for the stellar rotation velocity. He I λ 5876 is the only clearly detectable pure atmospheric absorption line in our data. Its

In silico predictions of LH2 ring sizes from the crystal structure of a single subunit using molecular dynamics simulations.

Science.gov (United States)

Janosi, Lorant; Keer, Harindar; Cogdell, Richard J; Ritz, Thorsten; Kosztin, Ioan

2011-07-01

Most of the currently known light-harvesting complexes 2 (LH2) rings are formed by 8 or 9 subunits. As of now, questions like "what factors govern the LH2 ring size?" and "are there other ring sizes possible?" remain largely unanswered. Here, we investigate by means of molecular dynamics (MD) simulations and stochastic modeling the possibility of predicting the size of an LH2 ring from the sole knowledge of the high resolution crystal structure of a single subunit. Starting with single subunits of two LH2 rings with known size, that is, an 8-ring from Rs. moliscianum (MOLI) and a 9-ring from Rps. acidophila (ACI), and one with unknown size (referred to as X), we build atomic models of subunit dimers corresponding to assumed 8-, 9-, and 10-ring geometries. After inserting each of the dimers into a lipid-water environment, we determine the preferred angle between the corresponding subunits by three methods: (1) energy minimization, (2) free MD simulations, and (3) potential of mean force calculations. We find that the results from all three methods are consistent with each other, and when taken together, it allows one to predict with reasonable level of confidence the sizes of the corresponding ring structures. One finds that X and ACI very likely form a 9-ring, while MOLI is more likely to form an 8-ring than a 9-ring. Finally, we discuss both the merits and limitations of all three prediction methods. Copyright © 2011 Wiley-Liss, Inc.

Thermodynamics of Small Alkali Metal Halide Cluster Ions: Comparison of Classical Molecular Simulations with Experiment and Quantum Chemistry

Czech Academy of Sciences Publication Activity Database

Vlček, L.; Uhlík, F.; Moučka, F.; Nezbeda, Ivo; Chialvo, L.

2015-01-01

Roč. 119, č. 3 (2015), s. 488-500 ISSN 1089-5639 Institutional support: RVO:67985858 Keywords : monte-carlo simulations * molecular-dynamic simulations * classical drude oscillators Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.883, year: 2015

Entanglement of distant superconducting quantum interference device rings

International Nuclear Information System (INIS)

Zukarnain, Z Ahmad; Konstadopoulou, A; Vourdas, A; Migliore, R; Messina, A

2005-01-01

We consider two distant mesoscopic SQUID rings, approximated with two-level systems, interacting with two-mode microwaves. The Hamiltonian of the system is used to calculate its time evolution. The cases with microwaves which at t = 0 are in separable states (classically correlated) or entangled states (quantum mechanically correlated) are studied. It is shown that the Josephson currents in the two SQUID rings are also correlated

Magnetic forces and localized resonances in electron transfer through quantum rings.

Science.gov (United States)

Poniedziałek, M R; Szafran, B

2010-11-24

We study the current flow through semiconductor quantum rings. In high magnetic fields the current is usually injected into the arm of the ring preferred by classical magnetic forces. However, for narrow magnetic field intervals that appear periodically on the magnetic field scale the current is injected into the other arm of the ring. We indicate that the appearance of the anomalous-non-classical-current circulation results from Fano interference involving localized resonant states. The identification of the Fano interference is based on the comparison of the solution of the scattering problem with the results of the stabilization method. The latter employs the bound-state type calculations and allows us to extract both the energy of metastable states localized within the ring and the width of resonances by analysis of the energy spectrum of a finite size system as a function of its length. The Fano resonances involving states of anomalous current circulation become extremely narrow on both the magnetic field and energy scales. This is consistent with the orientation of the Lorentz force that tends to keep the electron within the ring and thus increases the lifetime of the electron localization within the ring. Absence of periodic Fano resonances in electron transfer probability through a quantum ring containing an elastic scatterer is also explained.

Two-slit experiment: quantum and classical probabilities

International Nuclear Information System (INIS)

Khrennikov, Andrei

2015-01-01

Inter-relation between quantum and classical probability models is one of the most fundamental problems of quantum foundations. Nowadays this problem also plays an important role in quantum technologies, in quantum cryptography and the theory of quantum random generators. In this letter, we compare the viewpoint of Richard Feynman that the behavior of quantum particles cannot be described by classical probability theory with the viewpoint that quantum–classical inter-relation is more complicated (cf, in particular, with the tomographic model of quantum mechanics developed in detail by Vladimir Man'ko). As a basic example, we consider the two-slit experiment, which played a crucial role in quantum foundational debates at the beginning of quantum mechanics (QM). In particular, its analysis led Niels Bohr to the formulation of the principle of complementarity. First, we demonstrate that in complete accordance with Feynman's viewpoint, the probabilities for the two-slit experiment have the non-Kolmogorovian structure, since they violate one of basic laws of classical probability theory, the law of total probability (the heart of the Bayesian analysis). However, then we show that these probabilities can be embedded in a natural way into the classical (Kolmogorov, 1933) probability model. To do this, one has to take into account the randomness of selection of different experimental contexts, the joint consideration of which led Feynman to a conclusion about the non-classicality of quantum probability. We compare this embedding of non-Kolmogorovian quantum probabilities into the Kolmogorov model with well-known embeddings of non-Euclidean geometries into Euclidean space (e.g., the Poincaré disk model for the Lobachvesky plane). (paper)

Vibrational Spectra of β″-Type BEDT-TTF Salts: Relationship between Conducting Property, Time-Averaged Site Charge and Inter-Molecular Distance

Directory of Open Access Journals (Sweden)

Takashi Yamamoto

2012-07-01

Full Text Available The relationship between the conducting behavior and the degree of charge fluctuation in the β″-type BEDT-TTF salts is reviewed from the standpoints of vibrational spectroscopy and crystal structure. A group of β″-type ET salts demonstrates the best model compounds for achieving the above relationship because the two-dimensional structure is simple and great diversity in conducting behavior is realized under ambient pressure. After describing the requirement for the model compound, the methodology for analyzing the results of the vibrational spectra is presented. Vibrational spectroscopy provides the time-averaged molecular charge, the charge distribution in the two-dimensional layer, and the inter-molecular interactions, etc. The experimental results applied to 2/3-filled and 3/4-filled β″-type ET salts are reported. These experimental results suggest that the conducting property, the difference in the time-averaged molecular charges between the ionic and neutral-like sites, the alternation in the inter-molecular distances and the energy levels in the charge distributions are relevant to one another. The difference in the time-averaged molecular charges, ∆ρ, is a useful criterion for indicating conducting behavior. All superconductors presented in this review are characterized as small but finite ∆ρ.

Second-order Monte Carlo wave-function approach to the relaxation effects on ringing revivals in a molecular system interacting with a strongly squeezed coherent field

International Nuclear Information System (INIS)

Nakano, Masayoshi; Kishi, Ryohei; Nitta, Tomoshige; Yamaguchi, Kizashi

2004-01-01

We investigate the relaxation effects on the quantum dynamics in a two-state molecular system interacting with a single-mode strongly amplitude-squeezed coherent field using the second-order Monte Carlo wave-function method. The molecular population inversion (collapse-revival behavior of Rabi oscillations) is known to show the echoes after each revival, which are referred to as ringing revivals, in the case of strongly squeezed coherent fields with oscillatory photon-number distributions due to the phase-space interference effect. Two types of relaxation effects, i.e., cavity relaxation (the dissipation of an internal single mode to outer mode) and molecular coherent (phase) relaxation caused by nuclear vibrations on ringing revivals are investigated from the viewpoint of the quantum-phase dynamics using the quasiprobability (Q function) distribution of a single-mode field and the off-diagonal molecular density matrix ρ elec1,2 (t). It turns out that the molecular phase relaxation attenuates both the entire revival-collapse behavior and the increase in ρ elec1,2 (t) during the quiescent region, whereas a very slight cavity relaxation particularly suppresses the echoes in ringing revivals more significantly than the first revival but hardly changes a primary variation in envelope of ρ elec1,2 (t) in the nonrelaxation case

Double Rashba Quantum Dots Ring as a Spin Filter

Directory of Open Access Journals (Sweden)

Chi Feng

2008-01-01

Full Text Available AbstractWe theoretically propose a double quantum dots (QDs ring to filter the electron spin that works due to the Rashba spin–orbit interaction (RSOI existing inside the QDs, the spin-dependent inter-dot tunneling coupling and the magnetic flux penetrating through the ring. By varying the RSOI-induced phase factor, the magnetic flux and the strength of the spin-dependent inter-dot tunneling coupling, which arises from a constant magnetic field applied on the tunneling junction between the QDs, a 100% spin-polarized conductance can be obtained. We show that both the spin orientations and the magnitude of it can be controlled by adjusting the above-mentioned parameters. The spin filtering effect is robust even in the presence of strong intra-dot Coulomb interactions and arbitrary dot-lead coupling configurations.

Molecular machines operating on the nanoscale: from classical to quantum

Directory of Open Access Journals (Sweden)

Igor Goychuk

2016-03-01

Full Text Available The main physical features and operating principles of isothermal nanomachines in the microworld, common to both classical and quantum machines, are reviewed. Special attention is paid to the dual, constructive role of dissipation and thermal fluctuations, the fluctuation–dissipation theorem, heat losses and free energy transduction, thermodynamic efficiency, and thermodynamic efficiency at maximum power. Several basic models are considered and discussed to highlight generic physical features. This work examines some common fallacies that continue to plague the literature. In particular, the erroneous beliefs that one should minimize friction and lower the temperature for high performance of Brownian machines, and that the thermodynamic efficiency at maximum power cannot exceed one-half are discussed. The emerging topic of anomalous molecular motors operating subdiffusively but very efficiently in the viscoelastic environment of living cells is also discussed.

Storage Rings

International Nuclear Information System (INIS)

Fischer, W.

2010-01-01

Storage rings are circular machines that store particle beams at a constant energy. Beams are stored in rings without acceleration for a number of reasons (Tab. 1). Storage rings are used in high-energy, nuclear, atomic, and molecular physics, as well as for experiments in chemistry, material and life sciences. Parameters for storage rings such as particle species, energy, beam intensity, beam size, and store time vary widely depending on the application. The beam must be injected into a storage ring but may not be extracted (Fig. 1). Accelerator rings such as synchrotrons are used as storage rings before and after acceleration. Particles stored in rings include electrons and positrons; muons; protons and anti-protons; neutrons; light and heavy, positive and negative, atomic ions of various charge states; molecular and cluster ions, and neutral polar molecules. Spin polarized beams of electrons, positrons, and protons were stored. The kinetic energy of the stored particles ranges from 10 -6 eV to 3.5 x 10 12 eV (LHC, 7 x 10 12 eV planned), the number of stored particles from one (ESR) to 1015 (ISR). To store beam in rings requires bending (dipoles) and transverse focusing (quadrupoles). Higher order multipoles are used to correct chromatic aberrations, to suppress instabilities, and to compensate for nonlinear field errors of dipoles and quadrupoles. Magnetic multipole functions can be combined in magnets. Beams are stored bunched with radio frequency systems, and unbunched. The magnetic lattice and radio frequency system are designed to ensure the stability of transverse and longitudinal motion. New technologies allow for better storage rings. With strong focusing the beam pipe dimensions became much smaller than previously possible. For a given circumference superconducting magnets make higher energies possible, and superconducting radio frequency systems allow for efficient replenishment of synchrotron radiation losses of large current electron or positron beams

The Hopf algebra structure of the character rings of classical groups

International Nuclear Information System (INIS)

Fauser, Bertfried; Jarvis, Peter D; King, Ronald C

2013-01-01

The character ring Char-GL of covariant irreducible tensor representations of the general linear group admits a Hopf algebra structure isomorphic to the Hopf algebra Symm-Λ of symmetric functions. Here we study the character rings Char-O and Char-Sp of the orthogonal and symplectic subgroups of the general linear group within the same framework of symmetric functions. We show that Char-O and Char-Sp also admit natural Hopf algebra structures that are isomorphic to that of Char-GL, and hence to Symm-Λ. The isomorphisms are determined explicitly, along with the specification of standard bases for Char-O and Char-Sp analogous to those used for Symm-Λ. A major structural change arising from the adoption of these bases is the introduction of new orthogonal and symplectic Schur–Hall scalar products. Significantly, the adjoint with respect to multiplication no longer coincides, as it does in the Char-GL case, with a Foulkes derivative or skew operation. The adjoint and Foulkes derivative now require separate definitions, and their properties are explored here in the orthogonal and symplectic cases. Moreover, the Hopf algebras Char-O and Char-Sp are not self-dual. The dual Hopf algebras Char-O * and Char-Sp are identified. Finally, the Hopf algebra of the universal rational character ring Char-GLrat of mixed irreducible tensor representations of the general linear group is introduced and its structure maps identified. (paper)

Dopamine and Caffeine Encapsulation within Boron Nitride (14,0) Nanotubes: Classical Molecular Dynamics and First Principles Calculations.

Science.gov (United States)

García-Toral, Dolores; González-Melchor, Minerva; Rivas-Silva, Juan F; Meneses-Juárez, Efraín; Cano-Ordaz, José; H Cocoletzi, Gregorio

2018-06-07

Classical molecular dynamics (MD) and density functional theory (DFT) calculations are developed to investigate the dopamine and caffeine encapsulation within boron nitride (BN) nanotubes (NT) with (14,0) chirality. Classical MD studies are done at canonical and isobaric-isothermal conditions at 298 K and 1 bar in explicit water. Results reveal that both molecules are attracted by the nanotube; however, only dopamine is able to enter the nanotube, whereas caffeine moves in its vicinity, suggesting that both species can be transported: the first by encapsulation and the second by drag. Findings are analyzed using the dielectric behavior, pair correlation functions, diffusion of the species, and energy contributions. The DFT calculations are performed according to the BLYP approach and applying the atomic base of the divided valence 6-31g(d) orbitals. The geometry optimization uses the minimum-energy criterion, accounting for the total charge neutrality and multiplicity of 1. Adsorption energies in the dopamine encapsulation indicate physisorption, which induces the highly occupied molecular orbital-lower unoccupied molecular orbital gap reduction yielding a semiconductor behavior. The charge redistribution polarizes the BNNT/dopamine and BNNT/caffeine structures. The work function decrease and the chemical potential values suggest the proper transport properties in these systems, which may allow their use in nanobiomedicine.

The classical theory of the bumpy torus relativistic annulus

International Nuclear Information System (INIS)

Hamasaki, S.; Krall, N.A.; Sperling, J.L.

1983-01-01

The relativistic electron annulus is a critical component of the bumpy torus magnetic fusion concept. An analysis of the annulus is presented in which the ring steady state is determined by the explicit balance of quasi-linear heating and classical losses, i.e. collisions and synchrotron radiation. Both anisotropy and loss-cone effects are included in the formalism. It is demonstrated that a large number of electron cyclotron harmonics, not just the first and second, contribute in an appreciable way to annulus steady state and power balance. Without a loss cone, the analysis reproduces the relativistic passing electron population observed in bumpy tori on confined drift surfaces near the centre of the bumpy torus cross-section. Loss-cone effects permit an annulus population with large perpendicular pressure to exist. It is shown that the balance between quasi-linear heating and the classical losses cannot account for the experimental scaling of bumpy torus annulus temperature; therefore, processes not included in the classical ring power balance model must contribute in a non-trivial way to observed annulus properties. (author)

Bernstein instability driven by thermal ring distribution

Energy Technology Data Exchange (ETDEWEB)

Yoon, Peter H., E-mail: yoonp@umd.edu [Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742 (United States); School of Space Research, Kyung Hee University, Yongin-Si, Gyeonggi-Do 446-701 (Korea, Republic of); Hadi, Fazal; Qamar, Anisa [Institute of Physics and Electronics, University of Peshawar, Peshawar 25000 (Pakistan)

2014-07-15

The classic Bernstein waves may be intimately related to banded emissions detected in laboratory plasmas, terrestrial, and other planetary magnetospheres. However, the customary discussion of the Bernstein wave is based upon isotropic thermal velocity distribution function. In order to understand how such waves can be excited, one needs an emission mechanism, i.e., an instability. In non-relativistic collision-less plasmas, the only known Bernstein wave instability is that associated with a cold perpendicular velocity ring distribution function. However, cold ring distribution is highly idealized. The present Brief Communication generalizes the cold ring distribution model to include thermal spread, so that the Bernstein-ring instability is described by a more realistic electron distribution function, with which the stabilization by thermal spread associated with the ring distribution is demonstrated. The present findings imply that the excitation of Bernstein waves requires a sufficiently high perpendicular velocity gradient associated with the electron distribution function.

Bernstein instability driven by thermal ring distribution

International Nuclear Information System (INIS)

Yoon, Peter H.; Hadi, Fazal; Qamar, Anisa

2014-01-01

The classic Bernstein waves may be intimately related to banded emissions detected in laboratory plasmas, terrestrial, and other planetary magnetospheres. However, the customary discussion of the Bernstein wave is based upon isotropic thermal velocity distribution function. In order to understand how such waves can be excited, one needs an emission mechanism, i.e., an instability. In non-relativistic collision-less plasmas, the only known Bernstein wave instability is that associated with a cold perpendicular velocity ring distribution function. However, cold ring distribution is highly idealized. The present Brief Communication generalizes the cold ring distribution model to include thermal spread, so that the Bernstein-ring instability is described by a more realistic electron distribution function, with which the stabilization by thermal spread associated with the ring distribution is demonstrated. The present findings imply that the excitation of Bernstein waves requires a sufficiently high perpendicular velocity gradient associated with the electron distribution function

Nonequilibrium molecular dynamics study of ring polymer melts under shear and elongation flows: A comparison with their linear analogs

Energy Technology Data Exchange (ETDEWEB)

Yoon, Jeongha; Kim, Jinseong; Baig, Chunggi, E-mail: cbaig@unist.ac.kr [Department of Chemical Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798 (Korea, Republic of)

2016-07-15

We present detailed results for the structural and rheological properties of unknotted and unconcatenated ring polyethylene (PE) melts under shear and elongation flows via direct atomistic nonequilibrium molecular dynamics simulations. Short (C{sub 78}H{sub 156}) and long (C{sub 400}H{sub 800}) ring PE melts were subjected to planar Couette flow (PCF) and planar elongational flow (PEF) across a wide range of strain rates from linear to highly nonlinear flow regimes. The results are analyzed in detail through a direct comparison with those of the corresponding linear polymers. We found that, in comparison to their linear analogs, ring melts possess rather compact chain structures at or near the equilibrium state and exhibit a considerably lesser degree of structural deformation with respect to the applied flow strength under both PCF and PEF. The large structural resistance of ring polymers against an external flow field is attributed to the intrinsic closed-loop configuration of the ring and the topological constraint of nonconcatenation between ring chains in the melt. As a result, there appears to be a substantial discrepancy between ring and linear systems in terms of their structural and rheological properties such as chain orientation, the distribution of chain dimensions, viscosity, flow birefringence, hydrostatic pressure, the pair correlation function, and potential interaction energies. The findings and conclusions drawn in this work would be a useful guide in future exploration of the characteristic dynamical and relaxation mechanisms of ring polymers in bulk or confined systems under flowing conditions.

Dynamical coupling of plasmons and molecular excitations by hybrid quantum/classical calculations: time-domain approach

International Nuclear Information System (INIS)

Sakko, Arto; Rossi, Tuomas P; Nieminen, Risto M

2014-01-01

The presence of plasmonic material influences the optical properties of nearby molecules in untrivial ways due to the dynamical plasmon-molecule coupling. We combine quantum and classical calculation schemes to study this phenomenon in a hybrid system that consists of a Na 2 molecule located in the gap between two Au/Ag nanoparticles. The molecule is treated quantum-mechanically with time-dependent density-functional theory, and the nanoparticles with quasistatic classical electrodynamics. The nanoparticle dimer has a plasmon resonance in the visible part of the electromagnetic spectrum, and the Na 2 molecule has an electron-hole excitation in the same energy range. Due to the dynamical interaction of the two subsystems the plasmon and the molecular excitations couple, creating a hybridized molecular-plasmon excited state. This state has unique properties that yield e.g. enhanced photoabsorption compared to the freestanding Na 2 molecule. The computational approach used enables decoupling of the mutual plasmon-molecule interaction, and our analysis verifies that it is not legitimate to neglect the backcoupling effect when describing the dynamical interaction between plasmonic material and nearby molecules. Time-resolved analysis shows nearly instantaneous formation of the coupled state, and provides an intuitive picture of the underlying physics. (paper)

Potassium (2,2′-bipyridine-κ2 N,N′)bis­(carbonato-κ2 O,O′)cobaltate(III) dihydrate

Science.gov (United States)

Wang, Jian-Fei; Lin, Jian-Li

2010-01-01

In the title compound, K[Co(CO3)2(C10H8N2)]·2H2O, the Co(III) atom is coordinated by two bipyridine N atoms and four O atoms from two bidentate chelating carbonate anions, and thus adopts a distorted octa­hedral N2O4 environment. The [Co(bipy)(CO3)2]− (bipy is 2,2′-bipyridine) ­units are stacked along [100] via π–π stacking inter­actions, with inter­planar distances between the bipyridine rings of 3.36 (4) and 3.44 (6) Å, forming chains. Classical O—H⋯O hydrogen-bonding inter­actions link the chains, forming channels along (100) in which the K+ ions reside and leading to a three-dimensional supra­molecular architecture. PMID:21587447

The derivation of the conventional basis for the classical Lie algebra generators

International Nuclear Information System (INIS)

Karadayi, H.R.

1982-01-01

The explicit construction of the classical Lie algebra generators in the conventional Gell-Mann basis is derived for all irreducible unitary representations of all classical groups. The main framework is based on a description of the simple roots of the classical Lie algebras such that the inter-relations implied by the Cartan matrix of the group among these simple roots are explicit within this description. (author)

Carbon Nanotube Based Molecular Electronics and Motors: A View from Classical and Quantum Dynamics Simulations

Science.gov (United States)

Srivastava, Deepak; Saini, Subhash (Technical Monitor)

1998-01-01

The tubular forms of fullerenes popularly known as carbon nanotubes are experimentally produced as single-, multiwall, and rope configurations. The nanotubes and nanoropes have shown to exhibit unusual mechanical and electronic properties. The single wall nanotubes exhibit both semiconducting and metallic behavior. In short undefected lengths they are the known strongest fibers which are unbreakable even when bent in half. Grown in ropes their tensile strength is approximately 100 times greater than steel at only one sixth the weight. Employing large scale classical and quantum molecular dynamics simulations we will explore the use of carbon nanotubes and carbon nanotube junctions in 2-, 3-, and 4-point molecular electronic device components, dynamic strength characterization for compressive, bending and torsional strains, and chemical functionalization for possible use in a nanoscale molecular motor. The above is an unclassified material produced for non-competitive basic research in the nanotechnology area.

Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

International Nuclear Information System (INIS)

Carnevale, V.; Raugei, S.

2009-01-01

Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

A classical Ehlers-Danlos syndrome family with incomplete presentation diagnosed by molecular testing.

Science.gov (United States)

Colombi, Marina; Dordoni, Chiara; Cinquina, Valeria; Venturini, Marina; Ritelli, Marco

2018-01-01

The 2017 EDS revised nosology indicates that minimal criteria suggestive for classical Ehlers-Danlos syndrome (cEDS) are skin hyperextensibility plus atrophic scarring together with either generalized joint hypermobility (gJHM) and/or at least three minor criteria that include cutaneous features and gJHM complications. Confirmatory molecular testing is obligatory to reach a final diagnosis. Although the large majority of the patients presents with these clinical features, some do not and might remain undiagnosed or misdiagnosed. Here we describe a family with 2 affected members, a 23-year-old proposita and her 51-year-old mother, who presented subtle cutaneous signs, including a variable degree of skin hyperextensibility without extensive widened atrophic scars that apparently better fitted with the overlapping hypermobile EDS. The proposita also presented gastrointestinal symptoms secondary to aberrant mast cells mediators release, making the clinical picture even more puzzling. Both patients were diagnosed by molecular testing that revealed a COL5A1 splice mutation. This report highlights the relevance of molecular analysis in patients presenting rather mild signs of EDS, especially in familial cases, and the importance of clinical expertise to make such a diagnosis. Copyright © 2017. Published by Elsevier Masson SAS.

Physics of quantum rings

International Nuclear Information System (INIS)

Fomin, Vladimir M.

2014-01-01

Presents the new class of materials of quantum rings. Provides an elemental basis for low-cost high-performance devices promising for electronics, optoelectronics, spintronics and quantum information processing. Explains the physical properties of quantum rings to cover a gap in scientific literature. Presents the application of most advanced nanoengineering and nanocharacterization techniques. This book deals with a new class of materials, quantum rings. Innovative recent advances in experimental and theoretical physics of quantum rings are based on the most advanced state-of-the-art fabrication and characterization techniques as well as theoretical methods. The experimental efforts allow to obtain a new class of semiconductor quantum rings formed by capping self-organized quantum dots grown by molecular beam epitaxy. Novel optical and magnetic properties of quantum rings are associated with non-trivial topologies at the nanoscale. An adequate characterization of quantum rings is possible on the basis of modern characterization methods of nanostructures, such as Scanning Tunneling Microscopy. A high level of complexity is demonstrated to be needed for a dedicated theoretical model to adequately represent the specific features of quantum rings. The findings presented in this book contribute to develop low-cost high-performance electronic, spintronic, optoelectronic and information processing devices based on quantum rings.

First molecular identification and characterization of classical swine fever virus isolates from Nepal.

Science.gov (United States)

Postel, Alexander; Jha, Vijay C; Schmeiser, Stefanie; Becher, Paul

2013-01-01

Classical swine fever (CSF) is a major constraint to pig production worldwide, and in many developing countries, the epidemiological status is unknown. Here, for the first time, molecular identification and characterization of CSFV isolates from two recent outbreaks in Nepal are presented. Analysis of full-length E2-encoding sequences revealed that these isolates belonged to CSFV subgenotype 2.2 and had highest genetic similarity to isolates from India. Hence, for CSFV, Nepal and India should be regarded as one epidemiological unit. Both Nepalese isolates exhibited significant sequence differences, excluding a direct epidemiological connection and suggesting that CSFV is endemic in that country.

Safety assessment of inter-channel / inter-system digital communications: A defensive measures approach

International Nuclear Information System (INIS)

Thuy, N. N. Q.

2006-01-01

Inappropriately designed inter-channel and inter-system digital communications could initiate common cause failure of multiple channels or multiple systems. Defensive measures were introduced in EPRI report TR-1002835 (Guideline for Performing Defense-in-Depth and Diversity Assessments for Digital Upgrades) to assess, on a deterministic basis, the susceptibility of digital systems architectures to common-cause failures. This paper suggests how this approach could be applied to assess inter-channel and inter-system digital communications from a safety standpoint. The first step of the approach is to systematically identify the so called 'influence factors' that one end of the data communication path can have on the other. Potential factors to be considered would typically include data values, data volumes and data rates. The second step of the approach is to characterize the ways possible failures of a given end of the communication path could affect these influence factors (e.g., incorrect data values, excessive data rates, time-outs, incorrect data volumes). The third step is to analyze the designed-in measures taken to guarantee independence of the other end. In addition to classical error detection and correction codes, typical defensive measures are one-way data communication, fixed-rate data communication, fixed-volume data communication, validation of data values. (authors)

Olive tree-ring problematic dating: a comparative analysis on Santorini (Greece.

Directory of Open Access Journals (Sweden)

Paolo Cherubini

Full Text Available Olive trees are a classic component of Mediterranean environments and some of them are known historically to be very old. In order to evaluate the possibility to use olive tree-rings for dendrochronology, we examined by various methods the reliability of olive tree-rings identification. Dendrochronological analyses of olive trees growing on the Aegean island Santorini (Greece show that the determination of the number of tree-rings is impossible because of intra-annual wood density fluctuations, variability in tree-ring boundary structure, and restriction of its cambial activity to shifting sectors of the circumference, causing the tree-ring sequences along radii of the same cross section to differ.

Olive tree-ring problematic dating: a comparative analysis on Santorini (Greece).

Science.gov (United States)

Cherubini, Paolo; Humbel, Turi; Beeckman, Hans; Gärtner, Holger; Mannes, David; Pearson, Charlotte; Schoch, Werner; Tognetti, Roberto; Lev-Yadun, Simcha

2013-01-01

Olive trees are a classic component of Mediterranean environments and some of them are known historically to be very old. In order to evaluate the possibility to use olive tree-rings for dendrochronology, we examined by various methods the reliability of olive tree-rings identification. Dendrochronological analyses of olive trees growing on the Aegean island Santorini (Greece) show that the determination of the number of tree-rings is impossible because of intra-annual wood density fluctuations, variability in tree-ring boundary structure, and restriction of its cambial activity to shifting sectors of the circumference, causing the tree-ring sequences along radii of the same cross section to differ.

Molecular characterization of classical and nonclassical MHC class I genes from the golden pheasant (Chrysolophus pictus).

Science.gov (United States)

Zeng, Q-Q; Zhong, G-H; He, K; Sun, D-D; Wan, Q-H

2016-02-01

Classical major histocompatibility complex (MHC) class I allelic polymorphism is essential for competent antigen presentation. To improve the genotyping efforts in the golden pheasant, it is necessary to differentiate more accurately between classical and nonclassical class I molecules. In our study, all MHC class I genes were isolated from one golden pheasant based on two overlapping PCR amplifications. In total, six full-length class I nucleotide sequences (A-F) were identified, and four were novel. Two (A and C) belonged to the IA1 gene, two (B and D) were alleles derived from the IA2 gene through transgene amplification, and two (E and F) comprised a third novel locus, IA3 that was excluded from the core region of the golden pheasant MHC-B. IA1 and IA2 exhibited the broad expression profiles characteristic of classical loci, while IA3 showed no expression in multiple tissues and was therefore defined as a nonclassical gene. Phylogenetic analysis indicated that the three IA genes in the golden pheasant share a much closer evolutionary relationship than the corresponding sequences in other galliform species. This observation was consistent with high sequence similarity among them, which likely arises from the homogenizing effect of recombination. Our careful distinction between the classical and nonclassical MHC class I genes in the golden pheasant lays the foundation for developing locus-specific genotyping and establishing a good molecular marker system of classical MHC I loci. © 2015 John Wiley & Sons Ltd.

Ring-Expansion/Contraction Radical Crossover Reactions of Cyclic Alkoxyamines: A Mechanism for Ring Expansion-Controlled Radical Polymerization

Directory of Open Access Journals (Sweden)

Atsushi Narumi

2018-06-01

Full Text Available Macrocyclic polymers present an important class of macromolecules, displaying the reduced radius of gyration or impossibility to entangle. A rare approach for their synthesis is the ring expansion-controlled radical “vinyl” polymerization, starting from a cyclic alkoxyamine. We here describe ring-expansion radical crossover reactions of cyclic alkoxyamines which run in parallel to chain-propagation reactions in the polymerization system. The radical crossover reactions extensively occurred at 105–125 °C, eventually producing high molecular weight polymers with multiple inherent dynamic covalent bonds (NOC bonds. A subsequent ring-contraction radical crossover reaction and the second ring-expansion radical crossover reaction are also described. The major products for the respective three stages were shown to possess cyclic morphologies by the molecular weight profiles and the residual ratios for the NOC bonds (φ in %. In particular, the high φ values ranging from ca. 80% to 98% were achieved for this cyclic alkoxyamine system. This result verifies the high availability of this system as a tool demonstrating the ring-expansion “vinyl” polymerization that allows them to produce macrocyclic polymers via a one-step vinyl polymerization.

The classical and quantum dynamics of molecular spins on graphene

Science.gov (United States)

Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

2016-02-01

Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices.

The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid.

Science.gov (United States)

Xu, You; Villa, Alessandra; Nilsson, Lennart

2017-06-05

Locked nucleic acid (LNA), a modified nucleoside which contains a bridging group across the ribose ring, improves the stability of DNA/RNA duplexes significantly, and therefore is of interest in biotechnology and gene therapy applications. In this study, we investigate the free energy change between LNA and DNA nucleosides. The transformation requires the breaking of the bridging group across the ribose ring, a problematic transformation in free energy calculations. To address this, we have developed a 3-step (easy to implement) and a 1-step protocol (more efficient, but more complicated to setup), for single and dual topologies in classical molecular dynamics simulations, using the Bennett Acceptance Ratio method to calculate the free energy. We validate the approach on the solvation free energy difference for the nucleosides thymidine, cytosine, and 5-methyl-cytosine. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Topological orbifold models and quantum cohomology rings

International Nuclear Information System (INIS)

Zaslow, E.

1993-01-01

We discuss the topological sigma model on an orbifold target space. We describe the moduli space of classical minima for computing correlation functions involving twisted operators, and show, through a detailed computation of an orbifold of CP 1 by the dihedral group D 4 , how to compute the complete ring of observables. Through this procedure, we compute all the rings from dihedral CP 1 orbifolds. We then consider CP 2 /D 4 , and show how the techniques of topological-anti-topological fusion might be used to compute twist field correlation functions for nonabelian orbifolds. (orig.)

Remodeling Mitral Annuloplasty Ring Concept with Preserved Dynamics of Annular Height

DEFF Research Database (Denmark)

Skov, Søren N; Røpcke, Diana M; Tjørnild, Marcell J

2017-01-01

BACKGROUND: The configuration of the native annulus changes from nearly flat in the diastolic phase to saddle-shaped in the systolic phase. The present study was conducted to test a novel remodeling annuloplasty ring with built-in septal-lateral fixation and commissural axial flexibility so...... as to maintain the change in annular saddle shape. The study aim was to evaluate the in-vivo biomechanical performance of the novel annuloplasty ring, compared with the native valve and a semi-rigid and rigid annuloplasty ring. METHODS: All measurements were performed in vivo using a porcine model. A total of 28...... pigs (bodyweight ca. 80 kg) were randomized to four groups: (i) with no ring; (ii) with a novel remodeling ring; (iii) with a semi-rigid ring (Physio I Ring, Edwards Lifesciences); and (iv) with a rigid ring (Classic Annuloplasty Ring, Edwards Lifesciences). Force measurements were performed using...

The Structure–Function Relationships of Classical Cannabinoids: CB1/CB2 Modulation

Science.gov (United States)

Bow, Eric W.; Rimoldi, John M.

2016-01-01

The cannabinoids are members of a deceptively simple class of terpenophenolic secondary metabolites isolated from Cannabis sativa highlighted by (−)-Δ9-tetrahydrocannabinol (THC), eliciting distinct pharmacological effects mediated largely by cannabinoid receptor (CB1 or CB2) signaling. Since the initial discovery of THC and related cannabinoids, synthetic and semisynthetic classical cannabinoid analogs have been evaluated to help define receptor binding modes and structure–CB1/CB2 functional activity relationships. This perspective will examine the classical cannabinoids, with particular emphasis on the structure–activity relationship of five regions: C3 side chain, phenolic hydroxyl, aromatic A-ring, pyran B-ring, and cyclohexenyl C-ring. Cumulative structure–activity relationship studies to date have helped define the critical structural elements required for potency and selectivity toward CB1 and CB2 and, more importantly, ushered the discovery and development of contemporary nonclassical cannabinoid modulators with enhanced physicochemical and pharmacological profiles. PMID:27398024

Classical molecular dynamics simulation on the dynamical properties of H2 on silicene layer

Directory of Open Access Journals (Sweden)

Casuyac Miqueas

2016-01-01

Full Text Available This study investigates the diffusion of hydrogen molecule physisorbed on the surface of silicene nanoribbon (SiNRusing the classical molecular dynamic (MD simulation in LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator. The interactions between silicon atoms are modeled using the modified Tersoff potential, the Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO potential for hydrogen – hydrogen interaction and the Lennard – Jones potential for the physisorbed H2 on SiNR. By varying the temperatures (60 K Δ 130 K, we observed that the Δxdisplacement of H2 on the surface SiNR shows a Brownian motion on a Lennard-Jones potential and a Gaussian probability distribution can be plotted describing the diffusion of H2. The calculated mean square displacement (MSD was approximately increasing in time and the activation energy barrier for diffusion has been found to be 43.23meV.

Cleaning graphene: A first quantum/classical molecular dynamics approach

Energy Technology Data Exchange (ETDEWEB)

Delfour, L.; Magaud, L., E-mail: emilie.despiau-pujo@cea.fr, E-mail: laurence.magaud@grenoble.cnrs.fr [Institut Néel, CNRS/Université Grenoble Alpes, 25 Avenue des Martyrs, 38054 Grenoble (France); Davydova, A.; Despiau-Pujo, E., E-mail: emilie.despiau-pujo@cea.fr, E-mail: laurence.magaud@grenoble.cnrs.fr; Cunge, G. [LTM, CNRS/Université Grenoble Alpes/CEA, 17 Avenue des Martyrs, 38054 Grenoble (France); Graves, D. B. [Department of Chemical and Biomolecular Engineering, University of California at Berkeley, Berkeley, California 94720 (United States)

2016-03-28

Graphene outstanding properties created a huge interest in the condensed matter community and unprecedented fundings at the international scale in the hope of application developments. Recently, there have been several reports of incomplete removal of the polymer resists used to transfer as-grown graphene from one substrate to another, resulting in altered graphene transport properties. Finding a large-scale solution to clean graphene from adsorbed residues is highly desirable and one promising possibility would be to use hydrogen plasmas. In this spirit, we couple here quantum and classical molecular dynamics simulations to explore the kinetic energy ranges required by atomic hydrogen to selectively etch a simple residue—a CH{sub 3} group—without irreversibly damaging the graphene. For incident energies in the 2–15 eV range, the CH{sub 3} radical can be etched by forming a volatile CH{sub 4} compound which leaves the surface, either in the CH{sub 4} form or breaking into CH{sub 3} + H fragments, without further defect formation. At this energy, adsorption of H atoms on graphene is possible and further annealing will be required to recover pristine graphene.

Light-Ring Stability for Ultracompact Objects

Science.gov (United States)

Cunha, Pedro V. P.; Berti, Emanuele; Herdeiro, Carlos A. R.

2017-12-01

We prove the following theorem: axisymmetric, stationary solutions of the Einstein field equations formed from classical gravitational collapse of matter obeying the null energy condition, that are everywhere smooth and ultracompact (i.e., they have a light ring) must have at least two light rings, and one of them is stable. It has been argued that stable light rings generally lead to nonlinear spacetime instabilities. Our result implies that smooth, physically and dynamically reasonable ultracompact objects are not viable as observational alternatives to black holes whenever these instabilities occur on astrophysically short time scales. The proof of the theorem has two parts: (i) We show that light rings always come in pairs, one being a saddle point and the other a local extremum of an effective potential. This result follows from a topological argument based on the Brouwer degree of a continuous map, with no assumptions on the spacetime dynamics, and, hence, it is applicable to any metric gravity theory where photons follow null geodesics. (ii) Assuming Einstein's equations, we show that the extremum is a local minimum of the potential (i.e., a stable light ring) if the energy-momentum tensor satisfies the null energy condition.

A method for studying post-fledging survival rates using data from ringing recoveries

NARCIS (Netherlands)

Thomson, D.L.; Baillie, S.R.; Peach, W.J.

1999-01-01

We present a method for studying post-fledging survival rates from data on national ringing recoveries. The approach extends the classical two-age-class models of Brownie et al. (1985) to include a third age-class of birds ringed as nestlings. The models can incorporate age-class-specific and

Representational Realism, Closed Theories and the Quantum to Classical Limit

Science.gov (United States)

de Ronde, Christian

In this chapter, we discuss the representational realist stance as a pluralistontic approach to inter-theoretic relationships. Our stance stresses the fact that physical theories require the necessary consideration of a conceptual level of discourse which determines and configures the specific field of phenomena discussed by each particular theory. We will criticize the orthodox line of research which has grounded the analysis about QM in two (Bohrian) metaphysical presuppositions - accepted in the present as dogmas that all interpretations must follow. We will also examine how the orthodox project of "bridging the gap" between the quantum and the classical domains has constrained the possibilities of research, producing only a limited set of interpretational problems which only focus in the justification of "classical reality" and exclude the possibility of analyzing the possibilities of non-classical conceptual representations of QM. The representational realist stance introduces two new problems, namely, the superposition problem and the contextuality problem, which consider explicitly the conceptual representation of orthodox QM beyond the mere reference to mathematical structures and measurement outcomes. In the final part of the chapter, we revisit, from representational realist perspective, the quantum to classical limit and the orthodox claim that this inter-theoretic relation can be explained through the principle of decoherence.

Evidence of Accretion in Saturn's F Ring (Invited)

Science.gov (United States)

Agnor, C. B.; Buerle, K.; Murray, C. D.; Evans, M. W.; Cooper, N. J.; Williams, G. W.

2010-12-01

Lying slightly outside the classical Roche radius and being strongly perturbed by the adjacent moons Prometheus and Pandora, Saturn's F ring represents a unique astrophysical laboratory for examining the processes of mass accretion and moonlet formation. Recent images from the Cassini spacecraft reveal optically thick clumps, capable of casting shadows, and associated structures in regions of the F ring following close passage by Prometheus. Here we examine the accretion environment of the F ring and Prometheus' role in moonlet formation and evolution. Using the observed structures adjacent to these clumps and dynamical arguments we estimate the masses of these clumps and find them comparable to that of ~10-20-km contiguous moonlets. Further, we show that Prometheus' perturbations on the F ring create regions of enhanced density and low relative velocity that may accelerate the accretion of clumps and moonlets.

Nonlinear dynamics aspects of modern storage rings

International Nuclear Information System (INIS)

Helleman, R.H.G.; Kheifets, S.A.

1986-01-01

It is argued that the nonlinearity of storage rings becomes an essential problem as the design parameters of each new machine are pushed further and further. Yet the familiar methods of classical mechanics do not allow determination of single particle orbits over reasonable lengths of time. It is also argued that the single particle dynamics of a storage ring is possibly one of the cleanest and simplest nonlinear dynamical systems available with very few degrees of freedom. Hence, reasons are found for accelerator physicists to be interested in nonlinear dynamics and for researchers in nonlinear dynamics to be interested in modern storage rings. The more familiar methods of treating nonlinear systems routinely used in acclerator theory are discussed, pointing out some of their limitations and pitfalls. 39 refs., 1 fig

Parameterization of the prosthetic redox centers of the bacterial cytochrome bc(1) complex for atomistic molecular dynamics simulations

DEFF Research Database (Denmark)

Kaszuba, K.; Postila, P. A.; Cramariuc, O.

2013-01-01

studied in large-scale classical molecular dynamics (MD) simulations. In part, this is due to lack of suitable force field parameters, centered atomic point charges in particular, for the complex's prosthetic redox centers. Accurate redox center charges are needed to depict realistically the inter-molecular...... interactions at different redox stages of the cyt bc(1) complex. Accordingly, here we present high-precision atomic point charges for the metal centers of the cyt bc(1) complex of Rhodobacter capsulatus derived from extensive density functional theory calculations, fitted using the restrained electrostatic...

Annual rings in a native Hawaiian tree, Sophora chrysophylla, on Maunakea, Hawai‘i

Science.gov (United States)

Kainana S. Francisco; Patrick J. Hart; Jinbao Li; Edward R. Cook; Patrick J. Baker

2015-01-01

Annual rings are not commonly produced in tropical trees because they grow in a relatively aseasonal environment. However, in the subalpine zones of Hawai‘i's highest volcanoes, there is often strong seasonal variability in temperature and rainfall. Using classical dendrochronological methods, annual growth rings were shown to occur in Sophora...

Radar imaging of Saturn's rings

Science.gov (United States)

Nicholson, Philip D.; French, Richard G.; Campbell, Donald B.; Margot, Jean-Luc; Nolan, Michael C.; Black, Gregory J.; Salo, Heikki J.

2005-09-01

We present delay-Doppler images of Saturn's rings based on radar observations made at Arecibo Observatory between 1999 and 2003, at a wavelength of 12.6 cm and at ring opening angles of 20.1°⩽|B|⩽26.7°. The average radar cross-section of the A ring is ˜77% relative to that of the B ring, while a stringent upper limit of 3% is placed on the cross-section of the C ring and 9% on that of the Cassini Division. These results are consistent with those obtained by Ostro et al. [1982, Icarus 49, 367-381] from radar observations at |B|=21.4°, but provide higher resolution maps of the rings' reflectivity profile. The average cross-section of the A and B rings, normalized by their projected unblocked area, is found to have decreased from 1.25±0.31 to 0.74±0.19 as the rings have opened up, while the circular polarization ratio has increased from 0.64±0.06 to 0.77±0.06. The steep decrease in cross-section is at variance with previous radar measurements [Ostro et al., 1980, Icarus 41, 381-388], and neither this nor the polarization variations are easily understood within the framework of either classical, many-particle-thick or monolayer ring models. One possible explanation involves vertical size segregation in the rings, whereby observations at larger elevation angles which see deeper into the rings preferentially see the larger particles concentrated near the rings' mid-plane. These larger particles may be less reflective and/or rougher and thus more depolarizing than the smaller ones. Images from all four years show a strong m=2 azimuthal asymmetry in the reflectivity of the A ring, with an amplitude of ±20% and minima at longitudes of 67±4° and 247±4° from the sub-Earth point. We attribute the asymmetry to the presence of gravitational wakes in the A ring as invoked by Colombo et al. [1976, Nature 264, 344-345] to explain the similar asymmetry long seen at optical wavelengths. A simple radiative transfer model suggests that the enhancement of the azimuthal

Supra-molecular architecture in a co-crystal of the N(7)-H tautomeric form of N (6)-benzoyl-adenine with adipic acid (1/0.5).

Science.gov (United States)

Swinton Darious, Robert; Thomas Muthiah, Packianathan; Perdih, Franc

2016-06-01

The asymmetric unit of the title co-crystal, C12H9N5O·0.5C6H10O4, consists of one mol-ecule of N (6)-benzoyl-adenine (BA) and one half-mol-ecule of adipic acid (AA), the other half being generated by inversion symmetry. The dihedral angle between the adenine and phenyl ring planes is 26.71 (7)°. The N (6)-benzoyl-adenine mol-ecule crystallizes in the N(7)-H tautomeric form with three non-protonated N atoms. This tautomeric form is stabilized by intra-molecular N-H⋯O hydrogen bonding between the carbonyl (C=O) group and the N(7)-H hydrogen atom on the Hoogsteen face of the purine ring, forming an S(7) ring motif. The two carboxyl groups of adipic acid inter-act with the Watson-Crick face of the BA mol-ecules through O-H⋯N and N-H⋯O hydrogen bonds, generating an R 2 (2)(8) ring motif. The latter units are linked by N-H⋯N hydrogen bonds, forming layers parallel to (10-5). A weak C-H⋯O hydrogen bond is also present, linking adipic acid mol-ecules in neighbouring layers, enclosing R (2) 2(10) ring motifs and forming a three-dimensional structure. C=O⋯π and C-H⋯π inter-actions are also present in the structure.

Persistent currents in metallic rings containing a quantum dot

International Nuclear Information System (INIS)

Machura, Lukasz; Łuczka, Jerzy

2015-01-01

Currents in metallic rings with a quantum dot are studied in the framework of a Langevin equation for a magnetic flux passing through the ring. Two scenarios are considered: one in which thermal fluctuations of the dissipative part of the current are modeled by classical Johnson–Nyquist noise and one in which quantum character of thermal fluctuations is taken into account in terms of a quantum Smoluchowski equation. The impact of the amplitude and phase of the transmission coefficient of the electron through a quantum dot on current characteristics is analyzed. In tailored parameter regimes, both scenarios can exhibit the transition from para- to diamagnetic response of the current versus external magnetic flux. The type of response is more robust to changes of the amplitude of the transmission coefficient and more sensitive to changes of the phase around some values. - Highlights: • Langevin dynamics of the magnetic flux for classical and quantum Smoluchowski regimes. • Current-flux characteristics vs the amplitude and phase of the transmission coefficient. • Crucial role of the phase of the transmission coefficient. • Contribution to the development of effective control of current in mesoscopic rings

Post coital penile ring entrapment: A report of a non-surgical extrication method

Directory of Open Access Journals (Sweden)

Agu Thaddeus Chika

2016-01-01

Full Text Available This case report shows how a simple but painstaking method of milking and levering in a slippery field was used to remove a thick metallic ring entrapped at the root of the penis after sexual intercourse. A ring can be removed easily from an organ if the inter-phase is made slippery. However this must be weighed against the handling difficulties posed by a wet slippery surface. With perseverance and the use of unconventional instrument, the ring was successfully extricated as a day case and without a surgical incision.

Comparison of inter-diffusion coefficients for Ni/Cu thin films determined from classical heating analysis and linear temperature ramping analysis by means of profile reconstruction and a numerical solution of Fick's law

International Nuclear Information System (INIS)

Joubert, H.D.; Terblans, J.J.; Swart, H.C.

2009-01-01

Classical inter-diffusion studies assume a constant time of annealing when samples are annealed in a furnace. It is assumed that the sample temperature reaches the annealing temperature immediately after insertion, while the sample temperature immediately drops to room temperature after removal, the annealing time being taken as the time between insertion and removal. Using the above assumption, the diffusion coefficient can be calculated in a number of ways. In reality, the sample temperature does not immediately reach the annealing temperature; instead it rises at a rate governed by several heat transfer mechanisms, depending on the annealing procedure. For short annealing times, the sample temperature may not attain the annealing temperature, while for extended annealing times the sample temperature may reach the annealing temperature only for a fraction of the annealing time. To eliminate the effect of heat transfer mechanisms, a linear temperature ramping regime is proposed. Used in conjunction with a suitable profile reconstructing technique and a numerical solution of Fick's second law, the inter-diffusion parameters obtained from a linear ramping of Ni/Cu thin film samples can be compared to those obtained from calculations performed with the so-called Mixing-Roughness-Information model or any other suitable method used to determine classical diffusion coefficients.

Radiation chemical yields for formation of molecular hydrogen in alcohols based on the cyclohexane ring

International Nuclear Information System (INIS)

Val'ter, A.I.; Kovalev, G.V.

1989-01-01

Within the framework of the general problem of studying the radiolysis mechanism for alcohols based on the cyclohexane ring, we have determined the yields of molecular hydrogen in γ-irradiated cyclohexanol, 1,2-cis- and 1,2-trans-cyclohexanediols, and inositol (cyclohexanehexol). The cyclohexanol and also powders of the polyols were placed into ampuls, deaerated in a vacuum apparatus and irradiated with 60 Co γ-rays at 77 K and 293 K. After irradiation, the samples were heated up to 373 K (the polyol crystals were heated until melting) and the hydrogen evolved from the liquid phase was determined by gas chromatography

Parameter scan for the CLIC Damping rings under the infleunce of intrabeam scattering

OpenAIRE

Antoniou, F; Martini, M; Papaphilippou, Y; Vivoli, A

2010-01-01

Due to the high bunch density, the output emittances of the CLIC Damping Rings (DR) are strongly dominated by the effect of Intrabeam Scattering (IBS). In an attempt to optimize the ring design, the bench-marking of the multiparticle tracking code SIRE with the classical IBS formalisms and approximations is first considered. The scaling of the steady state emittances and IBS growth rates is also studied, with respect to several ring parameters including energy, bunch charge and wiggler charac...

Parameter scan for the CLIC Damping rings under the infleunce of intrabeam scattering

CERN Document Server

Antoniou, F; Papaphilippou, Y; Vivoli, A

2010-01-01

Due to the high bunch density, the output emittances of the CLIC Damping Rings (DR) are strongly dominated by the effect of Intrabeam Scattering (IBS). In an attempt to optimize the ring design, the bench-marking of the multiparticle tracking code SIRE with the classical IBS formalisms and approximations is first considered. The scaling of the steady state emittances and IBS growth rates is also studied, with respect to several ring parameters including energy, bunch charge and wiggler characteristics.

Three-dimensional ordering of cold ion beams in a storage ring: A molecular-dynamics simulation study

Energy Technology Data Exchange (ETDEWEB)

Yuri, Yosuke, E-mail: yuri.yosuke@jaea.go.jp [Takasaki Advanced Radiation Research Institute, Japan Atomic Energy Agency, 1233 Watanuki-machi Takasaki, Gunma 370-1292 Japan (Japan)

2015-06-29

Three-dimensional (3D) ordering of a charged-particle beams circulating in a storage ring is systematically studied with a molecular-dynamics simulation code. An ion beam can exhibit a 3D ordered configuration at ultralow temperature as a result of powerful 3D laser cooling. Various unique characteristics of the ordered beams, different from those of crystalline beams, are revealed in detail, such as the single-particle motion in the transverse and longitudinal directions, and the dependence of the tune depression and the Coulomb coupling constant on the operating points.

Distinct Histopathologic and Molecular Alterations in Inflammatory Bowel Disease-Associated Intestinal Adenocarcinoma: c-MYC Amplification is Common and Associated with Mucinous/Signet Ring Cell Differentiation.

Science.gov (United States)

Hartman, Douglas J; Binion, David G; Regueiro, Miguel D; Miller, Caitlyn; Herbst, Cameron; Pai, Reetesh K

2018-05-17

Chronic idiopathic inflammatory bowel disease (IBD) is a significant risk factor for the development of intestinal adenocarcinoma. The underlying molecular alterations in IBD-associated intestinal adenocarcinoma remain largely unknown. We compared the clinicopathologic and molecular features of 35 patients with 47 IBD-associated intestinal adenocarcinomas with a consecutive series of 451 patients with sporadic colorectal carcinoma identified at our institution and published data on sporadic colorectal carcinoma. c-MYC amplification was the most frequent molecular alteration identified in 33% of IBD-associated intestinal adenocarcinoma that is a significantly higher frequency than in sporadic colorectal carcinoma (8%) (P = 0.0001). Compared to sporadic colorectal carcinoma, IBD-associated intestinal adenocarcinomas more frequently demonstrated mucinous differentiation (60% vs 25%, P < 0.001) and signet ring cell differentiation (28% vs 4%, P < 0.001). Mucinous and signet ring cell differentiation were significantly associated with the presence of c-MYC amplification (both with P < 0.05). HER2 positivity (11%), KRAS exon 2 or 3 mutation (10%), and IDH1 mutation (7%) were less commonly observed in IBD-associated intestinal adenocarcinoma. There was an association between poor survival and HER2 status with 3 of 4 patients having HER2-positive adenocarcinoma dead of disease at last clinical follow-up; however, no statistically significant survival effect was identified for any of the molecular alterations identified. We demonstrate that IBD-associated intestinal adenocarcinomas have a high frequency of c-MYC amplification that is associated with mucinous and signet ring cell differentiation. Many of the identified molecular alterations have potential therapeutic relevance, including HER2 amplification, IDH1 mutation, and low frequency KRAS mutation.

Reconciling patterns of inter-ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans).

Science.gov (United States)

Buonaccorsi, V P; McDowell, J R; Graves, J E

2001-05-01

Different classes of molecular markers occasionally yield discordant views of population structure within a species. Here, we examine the distribution of molecular variance from 14 polymorphic loci comprising four classes of molecular markers within approximately 400 blue marlin individuals (Makaira nigricans). Samples were collected from the Atlantic and Pacific Oceans over 5 years. Data from five hypervariable tetranucleotide microsatellite loci and restriction fragment length polymorphism (RFLP) analysis of whole molecule mitochondrial DNA (mtDNA) were reported and compared with previous analyses of allozyme and single-copy nuclear DNA (scnDNA) loci. Temporal variance in allele frequencies was nonsignificant in nearly all cases. Mitochondrial and microsatellite loci revealed striking phylogeographic partitioning among Atlantic and Pacific Ocean samples. A large cluster of alleles was present almost exclusively in Atlantic individuals at one microsatellite locus and for mtDNA, suggesting that, if gene flow occurs, it is likely to be unidirectional from Pacific to Atlantic oceans. Mitochondrial DNA inter-ocean divergence (FST) was almost four times greater than microsatellite or combined nuclear divergences including allozyme and scnDNA markers. Estimates of Neu varied by five orders of magnitude among marker classes. Using mathematical and computer simulation approaches, we show that substantially different distributions of FST are expected from marker classes that differ in mode of inheritance and rate of mutation, without influence of natural selection or sex-biased dispersal. Furthermore, divergent FST values can be reconciled by quantifying the balance between genetic drift, mutation and migration. These results illustrate the usefulness of a mitochondrial analysis of population history, and relative precision of nuclear estimates of gene flow based on a mean of several loci.

RENGA: a systems approach to facilitating inter-organizational network development

NARCIS (Netherlands)

Akkermans, H.A.

2001-01-01

This article describes a consulting approach aimed specifically at facilitating development of intra- and inter-organizational networks, a business phenomenon of growing importance. This approach is called Renga, after the classical Japanese style of composing linked verse, with which it is shown to

Classical and quantum analysis of a hetero-triatomic molecular Bose-Einstein condensate model

International Nuclear Information System (INIS)

Tonel, A.P.; Kuhn, C.C.N.; Foerster, A.; Santos, G.; Roditi, I.; Santos, Z.V.T.

2014-11-01

We investigate an integrable Hamiltonian modelling a hetero-triatomic-molecular Bose-Einstein condensate. This model describes a mixture of two species of atoms in different proportions, which can combine to form a triatomic molecule. Beginning with a classical analysis, we determine the fixed points of the system. Bifurcations of these points separate the parameter space into different regions. Three distinct scenarios are found, varying with the atomic population imbalance. This result suggests the ground state properties of the quantum model exhibits a sensitivity on the atomic population imbalance, which is confirmed by a quantum analysis using different approaches, such as the ground-state expectation values, the behaviour of the quantum dynamics, the energy gap and the ground state fidelity. (author)

Proton NMR for Measuring Quantum Level Crossing in the Magnetic Molecular Ring Fe10

International Nuclear Information System (INIS)

Julien, M.; Jang, Z.H.; Borsa, F.; Julien, M.; Lascialfari, A.; Borsa, F.; Horvatic, M.; Caneschi, A.; Gatteschi, D.

1999-01-01

The proton nuclear spin-lattice relaxation rate 1/T 1 has been measured as a function of temperature and magnetic field (up to 15thinspthinspT) in the molecular magnetic ring Fe 10 ( OCH 3 ) 20 (O 2 CCH 2 Cl) 10 (Fe10). Striking enhancement of 1/T 1 is observed around magnetic field values corresponding to a crossing between the ground state and the excited states of the molecule. We propose that this is due to a cross-relaxation effect between the nuclear Zeeman reservoir and the reservoir of the Zeeman levels of the molecule. This effect provides a powerful tool to investigate quantum dynamical phenomena at level crossing. copyright 1999 The American Physical Society

Ion effects in the SLC electron damping ring under exceptionally poor vacuum conditions

International Nuclear Information System (INIS)

Zimmermann, F.; Krejcik, P.; Minty, M.; Pritzkau, D.; Raubenheimer, T.; Ross, M.; Woodley, M.

1997-10-01

In 1996, due to a catastrophic kicker chamber failure in the SLC electron damping ring, the ring vacuum system was contamianted for several months. During this time, the vertical emittance of the beam extracted from the ring was increased by a large factor (4--20). The emittance slowly decreased as the vacuum pressure gradually improved. At the same time, an intermittent vertical instability was observed. Both the emittance blow-up and the instability behavior depended strongly on beam current, ring pressure, number of bunches in the ring (1 or 2), duty cycle, store time and betatron tunes. In this report, the authors describe the observations, and compare them with predictions from classical ion-trapping and ion-instability theories

Manipulating molecular quantum states with classical metal atom inputs: demonstration of a single molecule NOR logic gate.

Science.gov (United States)

Soe, We-Hyo; Manzano, Carlos; Renaud, Nicolas; de Mendoza, Paula; De Sarkar, Abir; Ample, Francisco; Hliwa, Mohamed; Echavarren, Antonio M; Chandrasekhar, Natarajan; Joachim, Christian

2011-02-22

Quantum states of a trinaphthylene molecule were manipulated by putting its naphthyl branches in contact with single Au atoms. One Au atom carries 1-bit of classical information input that is converted into quantum information throughout the molecule. The Au-trinaphthylene electronic interactions give rise to measurable energy shifts of the molecular electronic states demonstrating a NOR logic gate functionality. The NOR truth table of the single molecule logic gate was characterized by means of scanning tunnelling spectroscopy.

Classic and Golli Myelin Basic Protein have distinct developmental trajectories in human visual cortex.

Science.gov (United States)

Siu, Caitlin R; Balsor, Justin L; Jones, David G; Murphy, Kathryn M

2015-01-01

Traditionally, myelin is viewed as insulation around axons, however, more recent studies have shown it also plays an important role in plasticity, axonal metabolism, and neuroimmune signaling. Myelin is a complex multi-protein structure composed of hundreds of proteins, with Myelin Basic Protein (MBP) being the most studied. MBP has two families: Classic-MBP that is necessary for activity driven compaction of myelin around axons, and Golli-MBP that is found in neurons, oligodendrocytes, and T-cells. Furthermore, Golli-MBP has been called a "molecular link" between the nervous and immune systems. In visual cortex specifically, myelin proteins interact with immune processes to affect experience-dependent plasticity. We studied myelin in human visual cortex using Western blotting to quantify Classic- and Golli-MBP expression in post-mortem tissue samples ranging in age from 20 days to 80 years. We found that Classic- and Golli-MBP have different patterns of change across the lifespan. Classic-MBP gradually increases to 42 years and then declines into aging. Golli-MBP has early developmental changes that are coincident with milestones in visual system sensitive period, and gradually increases into aging. There are three stages in the balance between Classic- and Golli-MBP expression, with Golli-MBP dominating early, then shifting to Classic-MBP, and back to Golli-MBP in aging. Also Golli-MBP has a wave of high inter-individual variability during childhood. These results about cortical MBP expression are timely because they compliment recent advances in MRI techniques that produce high resolution maps of cortical myelin in normal and diseased brain. In addition, the unique pattern of Golli-MBP expression across the lifespan suggests that it supports high levels of neuroimmune interaction in cortical development and in aging.

Genotyping and Molecular Identification of Date Palm Cultivars Using Inter-Simple Sequence Repeat (ISSR) Markers.

Science.gov (United States)

Ayesh, Basim M

2017-01-01

Molecular markers are credible for the discrimination of genotypes and estimation of the extent of genetic diversity and relatedness in a set of genotypes. Inter-simple sequence repeat (ISSR) markers rapidly reveal high polymorphic fingerprints and have been used frequently to determine the genetic diversity among date palm cultivars. This chapter describes the application of ISSR markers for genotyping of date palm cultivars. The application involves extraction of genomic DNA from the target cultivars with reliable quality and quantity. Subsequently the extracted DNA serves as a template for amplification of genomic regions flanked by inverted simple sequence repeats using a single primer. The similarity of each pair of samples is measured by calculating the number of mono- and polymorphic bands revealed by gel electrophoresis. Matrices constructed for similarity and genetic distance are used to build a phylogenetic tree and cluster analysis, to determine the molecular relatedness of cultivars. The protocol describes 3 out of 9 tested primers consistently amplified 31 loci in 6 date palm cultivars, with 28 polymorphic loci.

Crystal structures of 4-meth-oxy-N-(4-methyl-phenyl)benzene-sulfonamide and N-(4-fluoro-phenyl)-4-meth-oxy-benzene-sulfonamide.

Science.gov (United States)

Rodrigues, Vinola Z; Preema, C P; Naveen, S; Lokanath, N K; Suchetan, P A

2015-11-01

Crystal structures of two N-(ar-yl)aryl-sulfonamides, namely, 4-meth-oxy-N-(4-methyl-phen-yl)benzene-sulfonamide, C14H15NO3S, (I), and N-(4-fluoro-phen-yl)-4-meth-oxy-benzene-sulfonamide, C13H12FNO3S, (II), were determined and analyzed. In (I), the benzene-sulfonamide ring is disordered over two orientations, in a 0.516 (7):0.484 (7) ratio, which are inclined to each other at 28.0 (1)°. In (I), the major component of the sulfonyl benzene ring and the aniline ring form a dihedral angle of 63.36 (19)°, while in (II), the planes of the two benzene rings form a dihedral angle of 44.26 (13)°. In the crystal structure of (I), N-H⋯O hydrogen bonds form infinite C(4) chains extended in [010], and inter-molecular C-H⋯πar-yl inter-actions link these chains into layers parallel to the ab plane. The crystal structure of (II) features N-H⋯O hydrogen bonds forming infinite one dimensional C(4) chains along [001]. Further, a pair of C-H⋯O inter-molecular inter-actions consolidate the crystal packing of (II) into a three-dimensional supra-molecular architecture.

Genetic plasticity of the Shigella virulence plasmid is mediated by intra- and inter-molecular events between insertion sequences.

Science.gov (United States)

Pilla, Giulia; McVicker, Gareth; Tang, Christoph M

2017-09-01

Acquisition of a single copy, large virulence plasmid, pINV, led to the emergence of Shigella spp. from Escherichia coli. The plasmid encodes a Type III secretion system (T3SS) on a 30 kb pathogenicity island (PAI), and is maintained in a bacterial population through a series of toxin:antitoxin (TA) systems which mediate post-segregational killing (PSK). The T3SS imposes a significant cost on the bacterium, and strains which have lost the plasmid and/or genes encoding the T3SS grow faster than wild-type strains in the laboratory, and fail to bind the indicator dye Congo Red (CR). Our aim was to define the molecular events in Shigella flexneri that cause loss of Type III secretion (T3S), and to examine whether TA systems exert positional effects on pINV. During growth at 37°C, we found that deletions of regions of the plasmid including the PAI lead to the emergence of CR-negative colonies; deletions occur through intra-molecular recombination events between insertion sequences (ISs) flanking the PAI. Furthermore, by repositioning MvpAT (which belongs to the VapBC family of TA systems) near the PAI, we demonstrate that the location of this TA system alters the rearrangements that lead to loss of T3S, indicating that MvpAT acts both globally (by reducing loss of pINV through PSK) as well as locally (by preventing loss of adjacent sequences). During growth at environmental temperatures, we show for the first time that pINV spontaneously integrates into different sites in the chromosome, and this is mediated by inter-molecular events involving IS1294. Integration leads to reduced PAI gene expression and impaired secretion through the T3SS, while excision of pINV from the chromosome restores T3SS function. Therefore, pINV integration provides a reversible mechanism for Shigella to circumvent the metabolic burden imposed by pINV. Intra- and inter-molecular events between ISs, which are abundant in Shigella spp., mediate plasticity of S. flexneri pINV.

Rings of Molecular Line Emission in the Disk Orbiting the Young, Close Binary V4046 Sgr

Science.gov (United States)

Dickson-Vandervelde, Dorothy; Kastner, Joel H.; Qi, C.; Forveille, Thierry; Hily-Blant, Pierre; Oberg, Karin; Wilner, David; Andrews, Sean; Gorti, Uma; Rapson, Valerie; Sacco, Germano; Principe, David

2018-01-01

We present analysis of a suite of subarcsecond ALMA Band 6 (1.1 - 1.4 mm) molecular line images of the circumbinary, protoplanetary disk orbiting V4046 Sgr. The ~20 Myr-old V4046 Sgr system, which lies a mere ~73 pc from Earth, consists of a close (separation ~10 Rsun) pair of roughly solar-mass stars that are orbited by a gas-rich crcumbinary disk extending to ~350 AU in radius. The ALMA images reveal that the molecules CO and HCN and their isotopologues display centrally peaked surface brightness morphologies, whereas the cyanide group molecules (HC3N, CH3CN), deuterated molecules (DCN, DCO+), hydrocarbons (as traced by C2H), and potential CO ice line tracers (N2H+, and H2CO) appear as a sequence of sharp and diffuse rings of increasing radii. The characteristic sizes of these molecular emission rings, which range from ~25 to >100 AU in radius, are evident in radial emission-line surface brightness profiles extracted from the deprojected disk images. We find that emission from 13CO emission transitions from optically thin to thick within ~50 AU, whereas C18O emission remains optically thin within this radius. We summarize the insight into the physical and chemical processes within this evolved protoplanetary disk that can be obtained from comparisons of the various emission-line morphologies with each other and with that of the continuum (large-grain) emission on size scales of tens of AU.This research is supported by NASA Exoplanets program grant NNX16AB43G to RIT

(2RS)-2-(2,4-Difluoro-phen-yl)-1-[(4-iodo-benz-yl)(meth-yl)amino]-3-(1H-1,2,4-tri-azol-1-yl)propan-2-ol.

Science.gov (United States)

Xiong, Hui-Ping; Gao, Shou-Hong; Li, Chun-Tong; Wu, Zhi-Jun

2012-08-01

IN THE TITLE COMPOUND (COMMON NAME: iodiconazole), C(19)H(19)F(2)IN(4)O, there is an intra-molecular O-H⋯N hydrogen bond and mol-ecules are linked by weak inter-actions only, namely C-H⋯N, C-H⋯O and C-H⋯F hydrogen bonds, and π-electron ring-π-electron ring inter-actions between the triazole rings with centroid-centroid distances of 3.725 (3) Å.

Crystal structure of [(2R,3R,4S)-3,4-bis(acet-yloxy)-5-iodo-3,4-di-hydro-2H-pyran-2-yl]methyl acetate.

Science.gov (United States)

Zukerman-Schpector, Julio; Caracelli, Ignez; Stefani, Hélio A; Shamim, Anwar; Tiekink, Edward R T

2015-01-01

In the title compound, C12H15IO7, the 3,4-di-hydro-2H-pyran ring is in a distorted half-boat conformation with the atom bearing the acet-yloxy group adjacent to the C atom bearing the methyl-acetate group lying 0.633 (6) Å above the plane of the remaining ring atoms (r.m.s. deviation = 0.0907 Å). In the crystal, mol-ecules are linked into a supra-molecular chain along the a axis through two C-H⋯O inter-actions to the same acceptor carbonyl O atom; these chains pack with no specific inter-molecular inter-actions between them.

Insights into structural and dynamical features of water at halloysite interfaces probed by DFT and classical molecular dynamics simulations.

Science.gov (United States)

Presti, Davide; Pedone, Alfonso; Mancini, Giordano; Duce, Celia; Tiné, Maria Rosaria; Barone, Vincenzo

2016-01-21

Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension. The first technique allowed us to accurately describe the structure of the tetrahedral-octahedral slab of kaolinite in vacuum and in interaction with water molecules and to assess the performance of two widely employed empirical force fields to model water/clay interfaces. Classical molecular dynamics simulations were used to study the hydrogen bond network structure and dynamics of water adsorbed on kaolinite surfaces and confined in the halloysite interlayer. The results are in nice agreement with the few experimental data available in the literature, showing a pronounced ordering and reduced mobility of water molecules at the hydrophilic octahedral surfaces of kaolinite and confined in the halloysite interlayer, with respect to water interacting with the hydrophobic tetrahedral surfaces and in the bulk. Finally, this investigation provides new atomistic insights into the structural and dynamical properties of water-clay interfaces, which are of fundamental importance for both natural processes and industrial applications.

The Cryogenic Storage Ring CSR

OpenAIRE

von Hahn, Robert; Becker, Arno; Berg, Felix; Blaum, Klaus; Breitenfeldt, Christian; Fadil, Hisham; Fellenberger, Florian; Froese, Michael; George, Sebastian; Göck, Jürgen; Grieser, Manfred; Grussie, Florian; Guerin, Elisabeth A.; Heber, Oded; Herwig, Philipp

2016-01-01

An electrostatic cryogenic storage ring, CSR, for beams of anions and cations with up to 300 keV kinetic energy per unit charge has been designed, constructed, and put into operation. With a circumference of 35 m, the ion-beam vacuum chambers and all beam optics are in a cryostat and cooled by a closed-cycle liquid helium system. At temperatures as low as (5.5 ± 1) K inside the ring, storage time constants of several minutes up to almost an hour were observed for atomic and molecular, anion a...

UV-laser microdissection system - A novel approach for the preparation of high-resolution stable isotope records (δ13C/δ18O) from tree rings

Science.gov (United States)

Schollaen, Karina; Helle, Gerhard

2013-04-01

Intra-annual stable isotope (δ13C and δ18O) studies of tree rings at various incremental resolutions have been attempting to extract valuable seasonal climatic and environmental information or assessing plant ecophysiological processes. For preparing high-resolution isotope samples normally wood segments or cores are mechanically divided in radial direction or cut in tangential direction. After mechanical dissection, wood samples are ground to a fine powder and either cellulose is extracted or bulk wood samples are analyzed. Here, we present a novel approach for the preparation of high-resolution stable isotope records from tree rings using an UV-laser microdissection system. Firstly, tree-ring cellulose is directly extracted from wholewood cross-sections largely leaving the wood anatomical structure intact and saving time as compared to the classical procedure. Secondly, micro-samples from cellulose cross-sections are dissected with an UV-Laser dissection microscope. Tissues of interest from cellulose cross-sections are identified and marked precisely with a screen-pen and dissected via an UV-laser beam. Dissected cellulose segments were automatically collected in capsules and are prepared for stable isotope (δ13C and δ18O) analysis. The new techniques facilitate inter- and intra-annual isotope analysis on tree-ring and open various possibilities for comparisons with wood anatomy in plant eco-physiological studies. We describe the design and the handling of this novel methodology and discuss advantages and constraints given by the example of intra-annual oxygen isotope analysis on tropical trees.

Classical and quantum ordering of protons in cold solid hydrogen under megabar pressures.

Science.gov (United States)

Li, Xin-Zheng; Walker, Brent; Probert, Matthew I J; Pickard, Chris J; Needs, Richard J; Michaelides, Angelos

2013-02-27

A combination of state-of-the-art theoretical methods has been used to obtain an atomic-level picture of classical and quantum ordering of protons in cold high-pressure solid hydrogen. We focus mostly on phases II and III of hydrogen, exploring the effects of quantum nuclear motion on certain features of these phases (through a number of ab initio path integral molecular dynamics (PIMD) simulations at particular points on the phase diagram). We also examine the importance of van der Waals forces in this system by performing calculations using the optB88-vdW density functional, which accounts for non-local correlations. Our calculations reveal that the transition between phases I and II is strongly quantum in nature, resulting from a competition between anisotropic inter-molecular interactions that restrict molecular rotation and thermal plus quantum fluctuations of the nuclear positions that facilitate it. The transition from phase II to III is more classical because quantum nuclear motion plays only a secondary role and the transition is determined primarily by the underlying potential energy surface. A structure of P2(1)/c symmetry with 24 atoms in the primitive unit cell is found to be stable when anharmonic quantum nuclear vibrational motion is included at finite temperatures using the PIMD method. This structure gives a good account of the infra-red and Raman vibron frequencies of phase II. We find additional support for a C2/c structure as a strong candidate for phase III, since it remains transparent up to 300 GPa, even when quantum nuclear effects are included. Finally, we find that accounting for van der Waals forces improves the agreement between experiment and theory for the parts of the phase diagram considered, when compared to previous work which employed the widely-used Perdew-Burke-Ernzerhof exchange-correlation functional.

Classical and quantum ordering of protons in cold solid hydrogen under megabar pressures

International Nuclear Information System (INIS)

Li Xinzheng; Walker, Brent; Michaelides, Angelos; Probert, Matthew I J; Pickard, Chris J; Needs, Richard J

2013-01-01

A combination of state-of-the-art theoretical methods has been used to obtain an atomic-level picture of classical and quantum ordering of protons in cold high-pressure solid hydrogen. We focus mostly on phases II and III of hydrogen, exploring the effects of quantum nuclear motion on certain features of these phases (through a number of ab initio path integral molecular dynamics (PIMD) simulations at particular points on the phase diagram). We also examine the importance of van der Waals forces in this system by performing calculations using the optB88-vdW density functional, which accounts for non-local correlations. Our calculations reveal that the transition between phases I and II is strongly quantum in nature, resulting from a competition between anisotropic inter-molecular interactions that restrict molecular rotation and thermal plus quantum fluctuations of the nuclear positions that facilitate it. The transition from phase II to III is more classical because quantum nuclear motion plays only a secondary role and the transition is determined primarily by the underlying potential energy surface. A structure of P2 1 /c symmetry with 24 atoms in the primitive unit cell is found to be stable when anharmonic quantum nuclear vibrational motion is included at finite temperatures using the PIMD method. This structure gives a good account of the infra-red and Raman vibron frequencies of phase II. We find additional support for a C2/c structure as a strong candidate for phase III, since it remains transparent up to 300 GPa, even when quantum nuclear effects are included. Finally, we find that accounting for van der Waals forces improves the agreement between experiment and theory for the parts of the phase diagram considered, when compared to previous work which employed the widely-used Perdew–Burke–Ernzerhof exchange–correlation functional. (paper)

A step forward in molecular diagnostics of lyssaviruses--results of a ring trial among European laboratories.

Directory of Open Access Journals (Sweden)

Melina Fischer

Full Text Available Rabies is a lethal and notifiable zoonotic disease for which diagnostics have to meet the highest standards. In recent years, an evolution was especially seen in molecular diagnostics with a wide variety of different detection methods published. Therefore, a first international ring trial specifically designed on the use of reverse transcription polymerase chain reaction (RT-PCR for detection of lyssavirus genomic RNA was organized. The trial focussed on assessment and comparison of the performance of conventional and real-time assays. In total, 16 European laboratories participated. All participants were asked to investigate a panel of defined lyssavirus RNAs, consisting of Rabies virus (RABV and European bat lyssavirus 1 and 2 (EBLV-1 and -2 RNA samples, with systems available in their laboratory. The ring trial allowed the important conclusion that conventional RT-PCR assays were really robust assays tested with a high concordance between different laboratories and assays. The real-time RT-PCR system by Wakeley et al. (2005 in combination with an intercalating dye, and the combined version by Hoffmann and co-workers (2010 showed good sensitivity for the detection of all RABV samples included in this test panel. Furthermore, all used EBLV-specific assays, real-time RT-PCRs as well as conventional RT-PCR systems, were shown to be suitable for a reliable detection of EBLVs. It has to be mentioned that differences were seen in the performance between both the individual RT-PCR systems and the laboratories. Laboratories which used more than one molecular assay for testing the sample panel always concluded a correct sample result. Due to the markedly high genetic diversity of lyssaviruses, the application of different assays in diagnostics is needed to achieve a maximum of diagnostic accuracy. To improve the knowledge about the diagnostic performance proficiency testing at an international level is recommended before using lyssavirus molecular

Phase behaviour of polyethylene knotted ring chains

International Nuclear Information System (INIS)

Wen Xiao-Hui; Xia A-Gen; Chen Hong-Ping; Zhang Lin-Xi

2011-01-01

The phase behaviour of polyethylene knotted ring chains is investigated by using molecular dynamics simulations. In this paper, we focus on the collapse of the polyethylene knotted ring chain, and also present the results of linear and ring chains for comparison. At high temperatures, a fully extensive knot structure is observed. The mean-square radius of gyration per bond (S 2 )/(Nb 2 ) and the shape factor (δ*) depend on not only the chain length but also the knot type. With temperature decreasing, chain collapse is observed, and the collapse temperature decreases with the chain length increasing. The actual collapse transition can be determined by the specific heat capacity C v , and the knotted ring chain undergoes gas—liquid—solid-like transition directly. The phase transition of a knotted ring chain is only one-stage collapse, which is different from the polyethylene linear and ring chains. This investigation can provide some insights into the statistical properties of knotted polymer chains. (condensed matter: structural, mechanical, and thermal properties)

THE INTER-ERUPTION TIMESCALE OF CLASSICAL NOVAE FROM EXPANSION OF THE Z CAMELOPARDALIS SHELL

International Nuclear Information System (INIS)

Shara, Michael M.; Mizusawa, Trisha; Zurek, David; Martin, Christopher D.; Neill, James D.; Seibert, Mark

2012-01-01

The dwarf nova Z Camelopardalis is surrounded by the largest known classical nova shell. This shell demonstrates that at least some dwarf novae must have undergone classical nova eruptions in the past, and that at least some classical novae become dwarf novae long after their nova thermonuclear outbursts. The current size of the shell, its known distance, and the largest observed nova ejection velocity set a lower limit to the time since Z Cam's last outburst of 220 years. The radius of the brightest part of Z Cam's shell is currently ∼880 arcsec. No expansion of the radius of the brightest part of the ejecta was detected, with an upper limit of ≤0.17 arcsec yr –1 . This suggests that the last Z Cam eruption occurred ≥5000 years ago. However, including the important effect of deceleration as the ejecta sweeps up interstellar matter in its snowplow phase reduces the lower limit to 1300 years. This is the first strong test of the prediction of nova thermonuclear runaway theory that the interoutburst times of classical novae are longer than 1000 years. The intriguing suggestion that Z Cam was a bright nova, recorded by Chinese imperial astrologers in October-November 77 B.C.E., is consistent with our measurements. If Z Cam was indeed the nova of 77 B.C.E. we predict that its ejecta are currently expanding at 85 km s –1 , or 0.11 arcsec yr –1 . Detection and measurement of this rate of expansion should be possible in just a few years.

Phenylene ring dynamics in bisphenol-A-polysulfone by neutron scattering

International Nuclear Information System (INIS)

Arrese-Igor, S.; Arbe, A.; Alegria, A.; Colmenero, J.; Frick, B.

2004-01-01

We have investigated the dynamics of phenylene rings in a glassy polysulfone (bisphenol-A-polysulfone) by means of quasielastic neutron scattering. Nowadays it is well known that these molecular motions are directly connected with the mechanical properties of engineering thermoplastics in general. The particular system investigated by us has the advantage that by selective deuteration of the methyl groups, the neutron scattering measured is dominated by the incoherent contribution from the protons in the phenylene rings. In this way, the dynamics of such molecular groups can be experimentally isolated. Two different types of neutron spectrometers: time of flight and backscattering, were used in order to cover a wide dynamic range, which extends from microscopic (10 -13 s) to mesoscopic (10 -9 s) times. Moreover, neutron diffraction experiments with polarization analysis were also carried out in order to characterize the structural features of the sample investigated. Fast oscillations of increasing amplitude with temperature and π-flips are identified for phenylene rings motions. Due to the structural disorder characteristic of the amorphous state, both molecular motions display a broad distribution of relaxation times, which spreads over several orders of magnitude. Based on the results obtained, we propose a model for phenylene rings dynamics, which combines the two kinds of molecular motions identified. This model nicely describes the neutron scattering results in the whole dynamic range investigated

Propagator formalism and computer simulation of restricted diffusion behaviors of inter-molecular multiple-quantum coherences

International Nuclear Information System (INIS)

Cai Congbo; Chen Zhong; Cai Shuhui; Zhong Jianhui

2005-01-01

In this paper, behaviors of single-quantum coherences and inter-molecular multiple-quantum coherences under restricted diffusion in nuclear magnetic resonance experiments were investigated. The propagator formalism based on the loss of spin phase memory during random motion was applied to describe the diffusion-induced signal attenuation. The exact expression of the signal attenuation under the short gradient pulse approximation for restricted diffusion between two parallel plates was obtained using this propagator method. For long gradient pulses, a modified formalism was proposed. The simulated signal attenuation under the effects of gradient pulses of different width based on the Monte Carlo method agrees with the theoretical predictions. The propagator formalism and computer simulation can provide convenient, intuitive and precise methods for the study of the diffusion behaviors

Dissociative recombination and excitation in ion storage rings

International Nuclear Information System (INIS)

Larsson, Mats

2000-01-01

The application of ion storage rings to the study of electron-molecular ion interaction has led to an experimental breakthrough. The development since the first experiments with molecular ions in storage rings about seven years ago, which in themselves represented a big leap forward, has been striking, and was impossible to envision at the outset. The development has been driven by advances in accelerator physics, detector technology, challenging applications in astrophysics and atmospheric physics, and by a close interplay with theory. Despite the remarkable progress, many important questions remain unanswered. For example, even for someone with a good knowledge of molecular physics it may come as a surprise that it is far from understood how the simplest polyatomic molecule H 3 + recombines with electrons, and it remains an experimental controversy at what rate it recombines

Classical simulations of heavy-ion fusion reactions and weakly

Indian Academy of Sciences (India)

2014-04-30

Apr 30, 2014 ... Heavy-ion collision simulations in various classical models are discussed. ... are also simulated in a 3-stage classical molecular dynamics (3S-CMD) ... considered as a weakly-bound cluster of deuteron and 4He nuclei, thus, ...

A new storage-ring light source

Energy Technology Data Exchange (ETDEWEB)

Chao, Alex [SLAC National Accelerator Lab., Menlo Park, CA (United States)

2015-06-01

A recently proposed technique in storage ring accelerators is applied to provide potential high-power sources of photon radiation. The technique is based on the steady-state microbunching (SSMB) mechanism. As examples of this application, one may consider a high-power DUV photon source for research in atomic and molecular physics or a high-power EUV radiation source for industrial lithography. A less challenging proof-of-principle test to produce IR radiation using an existing storage ring is also considered.

Virtual Exploration of the Ring Systems Chemical Universe.

Science.gov (United States)

Visini, Ricardo; Arús-Pous, Josep; Awale, Mahendra; Reymond, Jean-Louis

2017-11-27

Here, we explore the chemical space of all virtually possible organic molecules focusing on ring systems, which represent the cyclic cores of organic molecules obtained by removing all acyclic bonds and converting all remaining atoms to carbon. This approach circumvents the combinatorial explosion encountered when enumerating the molecules themselves. We report the chemical universe database GDB4c containing 916 130 ring systems up to four saturated or aromatic rings and maximum ring size of 14 atoms and GDB4c3D containing the corresponding 6 555 929 stereoisomers. Almost all (98.6%) of these ring systems are unknown and represent chiral 3D-shaped macrocycles containing small rings and quaternary centers reminiscent of polycyclic natural products. We envision that GDB4c can serve to select new ring systems from which to design analogs of such natural products. The database is available for download at www.gdb.unibe.ch together with interactive visualization and search tools as a resource for molecular design.

Heat conduction in chain polymer liquids: molecular dynamics study on the contributions of inter- and intramolecular energy transfer.

Science.gov (United States)

Ohara, Taku; Yuan, Tan Chia; Torii, Daichi; Kikugawa, Gota; Kosugi, Naohiro

2011-07-21

In this paper, the molecular mechanisms which determine the thermal conductivity of long chain polymer liquids are discussed, based on the results observed in molecular dynamics simulations. Linear n-alkanes, which are typical polymer molecules, were chosen as the target of our studies. Non-equilibrium molecular dynamics simulations of bulk liquid n-alkanes under a constant temperature gradient were performed. Saturated liquids of n-alkanes with six different chain lengths were examined at the same reduced temperature (0.7T(c)), and the contributions of inter- and intramolecular energy transfer to heat conduction flux, which were identified as components of heat flux by the authors' previous study [J. Chem. Phys. 128, 044504 (2008)], were observed. The present study compared n-alkane liquids with various molecular lengths at the same reduced temperature and corresponding saturated densities, and found that the contribution of intramolecular energy transfer to the total heat flux, relative to that of intermolecular energy transfer, increased with the molecular length. The study revealed that in long chain polymer liquids, thermal energy is mainly transferred in the space along the stiff intramolecular bonds. This finding implies a connection between anisotropic thermal conductivity and the orientation of molecules in various organized structures with long polymer molecules aligned in a certain direction, which includes confined polymer liquids and self-organized structures such as membranes of amphiphilic molecules in water.

An algorithm and a Tool for Wavelength Allocation in OMS-SP Ring Architecture

DEFF Research Database (Denmark)

Riaz, Muhammad Tahir; Pedersen, Jens Myrup; Madsen, Ole Brun

2006-01-01

OMS-SP ring is one of the well known architectures in Wavelength Division Multiplexing based optical fiber networks. The architecture supports a restorable full mesh in an optical fiber ring using multiple light wavelengths. The paper presents an algorithm to allocate wavelengths in the OMS-SP ri...... architecture. A tool is also introduced which implements the algorithm and assigns wavelengths. The proposed algorithm uses fewer number of wavelengths than the classical allocation method. The algorithm is described and results are presented.......OMS-SP ring is one of the well known architectures in Wavelength Division Multiplexing based optical fiber networks. The architecture supports a restorable full mesh in an optical fiber ring using multiple light wavelengths. The paper presents an algorithm to allocate wavelengths in the OMS-SP ring...

Molecular Studies of Complex Soil Organic Matter Interactions with Metal Ions and Mineral Surfaces using Classical Molecular Dynamics and Quantum Chemistry Methods

Science.gov (United States)

Andersen, A.; Govind, N.; Laskin, A.

2017-12-01

Mineral surfaces have been implicated as potential protectors of soil organic matter (SOM) against decomposition and ultimate mineralization to small molecules which can provide nutrients for plants and soil microbes and can also contribute to the Earth's elemental cycles. SOM is a complex mixture of organic molecules of biological origin at varying degrees of decomposition and can, itself, self-assemble in such a way as to expose some biomolecule types to biotic and abiotic attack while protecting other biomolecule types. The organization of SOM and SOM with mineral surfaces and solvated metal ions is driven by an interplay of van der Waals and electrostatic interactions leading to partitioning of hydrophilic (e.g. sugars) and hydrophobic (e.g., lipids) SOM components that can be bridged with amphiphilic molecules (e.g., proteins). Classical molecular dynamics simulations can shed light on assemblies of organic molecules alone or complexation with mineral surfaces. The role of chemical reactions is also an important consideration in potential chemical changes of the organic species such as oxidation/reduction, degradation, chemisorption to mineral surfaces, and complexation with solvated metal ions to form organometallic systems. For the study of chemical reactivity, quantum chemistry methods can be employed and combined with structural insight provided by classical MD simulations. Moreover, quantum chemistry can also simulate spectroscopic signatures based on chemical structure and is a valuable tool in interpreting spectra from, notably, x-ray absorption spectroscopy (XAS). In this presentation, we will discuss our classical MD and quantum chemistry findings on a model SOM system interacting with mineral surfaces and solvated metal ions.

Solid state synthesis, structural, physicochemical and optical properties of an inter-molecular compound: 2-hydroxy-1, 2-diphenylethanone-4-nitro-o-phenylenediamine system

Science.gov (United States)

Rai, U. S.; Singh, Manjeet; Rai, R. N.

2017-09-01

The phase diagram of 2-hydroxy-1, 2-diphenylethanone (HDPE)-4-nitro-o-phenylenediamine (NOPDA) system, determined by the thaw-melt method, gives two eutectics E1 (m p = 66.0 °C) and E2 (m p = 155.0 °C) with 0.30 and 0.55 mol fractions of NOPDA, respectively, and an 1:1 inter-molecular compound (IMC) (m p 162.0 °C). This IMC was synthesized by adopting the green synthetic method of solid state reaction. While its formation and structure were confirmed by the X-ray diffraction and spectroscopic methods, the ORTEP view gives mode of crystal packing, C‒H…O, C‒H…N, π-π stacking and the inter-molecular hydrogen bonding in the compound. The single crystal of the IMC shows 53% transmission and emits significantly higher dual fluorescence, and the band gap was computed to be 3.04 eV. The values of solubility of the IMC, measured in the temperature range 304-322 K, satisfy the mole fraction (X) and temperature equation: Xeq= 5.1324 × 10-7 e 0.01356T.

Vortex-ring-fractal Structure of Atom and Molecule

International Nuclear Information System (INIS)

Osmera, Pavel

2010-01-01

This chapter is an attempt to attain a new and profound model of the nature's structure using a vortex-ring-fractal theory (VRFT). Scientists have been trying to explain some phenomena in Nature that have not been explained so far. The aim of this paper is the vortex-ring-fractal modeling of elements in the Mendeleev's periodic table, which is not in contradiction to the known laws of nature. We would like to find some acceptable structure model of the hydrogen as a vortex-fractal-coil structure of the proton and a vortex-fractal-ring structure of the electron. It is known that planetary model of the hydrogen atom is not right, the classical quantum model is too abstract. Our imagination is that the hydrogen is a levitation system of the proton and the electron. Structures of helium, oxygen, and carbon atoms and a hydrogen molecule are presented too.

Optimal control theory for quantum-classical systems: Ehrenfest molecular dynamics based on time-dependent density-functional theory

International Nuclear Information System (INIS)

Castro, A; Gross, E K U

2014-01-01

We derive the fundamental equations of an optimal control theory for systems containing both quantum electrons and classical ions. The system is modeled with Ehrenfest dynamics, a non-adiabatic variant of molecular dynamics. The general formulation, that needs the fully correlated many-electron wavefunction, can be simplified by making use of time-dependent density-functional theory. In this case, the optimal control equations require some modifications that we will provide. The abstract general formulation is complemented with the simple example of the H 2 + molecule in the presence of a laser field. (paper)

Damping in accelerators due to classical radiation

International Nuclear Information System (INIS)

Mills, F.E.

1962-01-01

The rates of change of the magnitudes of the adiabatic invariants is calculated in the case of a Hamiltonian system subjected to generalized non conservative forces. These results are applied to the case of the classical radiation of electrons in an accelerator or storage ring. The resulting expressions for the damping rates of three independent oscillation modes suggest structures which are damping in all three modes, while at the same time allowing 'strong focussing' and the attendant strong momentum compaction. (author)

CLASSICAL AND MOLECULAR CYTOGENETIC STUDIES FOR BREEDING AND SELECTION OF TULIPS

Directory of Open Access Journals (Sweden)

Aurel Popescu

2012-12-01

Full Text Available Due to their extreme popularity as fresh cut flowers and garden plants, and being used extensively for landscaping, tulips undergone a continuous process of selective breeding. For almost nine decades, classical cytogenetic studies, mainly the chromosome counts, have been an important part in the breeding programme for polyploid tulips. The efficiency of breeding is greatly aided by a thorough knowledge of the occurrence of polyploidy in the plant material. While the traditional cytogenetic approaches are still highly useful in selecting polyploids and aneuploids arising from crosses involving (most often parents of different ploidy or from the material subjected to ploidy manipulation, the new strategies for inducing polyploidy in tulips, either in vivo or in vitro, and advances in molecular cytogenetics are expected to allow a significant increase in breeding efficiency. Together with the shortening of breeding cycle, major genetic improvements could be made for specific traits. In this we review the development of cytogenetic studies in tulips, and the most relevant achievements so far, providing an overview of what we consider to be valuable tools for the processes of selective breeding .

Visceral Leishmaniasis: Advancements in vaccine development via classical and molecular approaches

Directory of Open Access Journals (Sweden)

Sumit eJoshi

2014-08-01

Full Text Available Visceral Leishmaniasis (VL or kala-azar, a vector-borne protozoan disease, shows endemicity in larger areas of the tropical, subtropical and the Mediterranean countries. WHO report suggested that nearly 500,000 new cases of VL occur annually, including 100,000 cases from India itself. Treatment with available anti-leishmanial drugs are not cost effective, with varied efficacies and higher relapse rate, which poses a major challenge to current kala-azar control program in Indian subcontinent. Therefore, a vaccine against VL is imperative and knowing the fact that recovered individuals developed lifelong immunity against re-infection, it is feasible. Vaccine development program, though time taking, has recently gained momentum with the emergence of omic era i.e. from genomics to immunomics. Classical as well as molecular methodologies has been overtaken with alternative strategies wherein proteomics based knowledge combined with computational techniques (immunoinformatics speed up the identification and detailed characterization of new antigens for potential vaccine candidates. This may eventually help in the designing of polyvalent synthetic and recombinant chimeric vaccines as an effective intervention measures to control the disease in endemic areas. This review focuses on such newer approaches being utilized for vaccine development against VL.

Molecular diversity analysis of Tetradium ruticarpum (WuZhuYu) in China based on inter-primer binding site (iPBS) markers and inter-simple sequence repeat (ISSR) markers.

Science.gov (United States)

Xu, Jing-Yuan; Zhu, Yan; Yi, Ze; Wu, Gang; Xie, Guo-Yong; Qin, Min-Jian

2018-01-01

"Wu zhu yu", which is obtained from the dried unripe fruits of Tetradium ruticarpum (A. Jussieu) T. G. Hartley, has been used as a traditional Chinese medicine for treatment of headaches, abdominal colic, and hypertension for thousands of years. The present study was designed to assess the molecular genetic diversity among 25 collected accessions of T. ruticarpum (Wu zhu yu in Chinese) from different areas of China, based on inter-primer binding site (iPBS) markers and inter-simple sequence repeat (ISSR) markers. Thirteen ISSR primers generated 151 amplification bands, of which 130 were polymorphic. Out of 165 bands that were amplified using 10 iPBS primers, 152 were polymorphic. The iPBS markers displayed a higher proportion of polymorphic loci (PPL = 92.5%) than the ISSR markers (PPL = 84.9%). The results showed that T. ruticarpum possessed high loci polymorphism and genetic differentiation occurred in this plant. The combined data of iPBS and ISSR markers scored on 25 accessions produced five clusters that approximately matched the geographic distribution of the species. The results indicated that both iPBS and ISSR markers were reliable and effective tools for analyzing the genetic diversity in T. ruticarpum. Copyright © 2018 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.

Optimal fold symmetry of LH2 rings on a photosynthetic membrane.

Science.gov (United States)

Cleary, Liam; Chen, Hang; Chuang, Chern; Silbey, Robert J; Cao, Jianshu

2013-05-21

An intriguing observation of photosynthetic light-harvesting systems is the N-fold symmetry of light-harvesting complex 2 (LH2) of purple bacteria. We calculate the optimal rotational configuration of N-fold rings on a hexagonal lattice and establish two related mechanisms for the promotion of maximum excitation energy transfer (EET). (i) For certain fold numbers, there exist optimal basis cells with rotational symmetry, extendable to the entire lattice for the global optimization of the EET network. (ii) The type of basis cell can reduce or remove the frustration of EET rates across the photosynthetic network. We find that the existence of a basis cell and its type are directly related to the number of matching points S between the fold symmetry and the hexagonal lattice. The two complementary mechanisms provide selection criteria for the fold number and identify groups of consecutive numbers. Remarkably, one such group consists of the naturally occurring 8-, 9-, and 10-fold rings. By considering the inter-ring distance and EET rate, we demonstrate that this group can achieve minimal rotational sensitivity in addition to an optimal packing density, achieving robust and efficient EET. This corroborates our findings i and ii and, through their direct relation to S, suggests the design principle of matching the internal symmetry with the lattice order.

New developments in ultrasonic inspection of retaining rings on generators in operation

International Nuclear Information System (INIS)

Koch-Mathian, A.

1990-01-01

The ultrasonic inspection of retaining rings of operating generators has been operational since 1986. The aim of this presentation is to outline the experience acquired on many retaining rings on different types of generators. In-situ inspections have made it possible to detect more exactly the different shape echoes for the various elements located beneath the retaining ring such as rotor teeth, damping and epoxy insulation. Various methods of identifying these parts are currently being developed. Investigation on corroded retaining rings has made it possible to demonstrate the close correlation between the transverse beam detection and the presence of actual cracks identified by micrograph. The specific facies of these cracks precludes the use of classic dimensioning techniques, but a method based on longitudinal wave detection has already given encouraging results

Disentangling the Circumnuclear Environs of Centaurus A. III. An Inner Molecular Ring, Nuclear Shocks, and the CO to Warm H{sub 2} Interface

Energy Technology Data Exchange (ETDEWEB)

Espada, D.; Miura, R. E.; Iono, D. [National Astronomical Observatory of Japan, 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan); Matsushita, S. [Academia Sinica, Institute of Astronomy and Astrophysics, P.O. Box 23-141, Taipei 10617, Taiwan (China); Israel, F. P. [Sterrewacht Leiden, Leiden University, P.O. Box 9513, 2300 RA, Leiden (Netherlands); Neumayer, N. [Max Planck Institute for Astronomy (MPIA), Königstuhl 17, D-69121 Heidelberg (Germany); Martin, S. [Joint ALMA Observatory, Alonso de Córdova, 3107, Vitacura, Santiago 763-0355 (Chile); Henkel, C. [Max-Planck-Institut für Radioastronomie, Auf dem Hügel 69, D-53121, Bonn (Germany); Izumi, T.; Kohno, K. [Institute of Astronomy, School of Science, The University of Tokyo, 2-21-1 Osawa, Mitaka, Tokyo 181-0015 (Japan); Aalto, S. [Department of Earth and Space Sciences, Chalmers University (Sweden); Ott, J. [National Radio Astronomy Observatory, Socorro, NM (United States); Peck, A. B. [Gemini Observatory, 670 N’Aohoku Pl, Hilo 96720-2700, Hawaii, HI (United States); Quillen, A. C. [Department of Physics and Astronomy, University of Rochester, Rochester, NY 14627 (United States)

2017-07-10

We present the distribution and kinematics of the molecular gas in the circumnuclear disk (CND; 400 pc × 200 pc) of Centaurus A with resolutions of ∼5 pc (0.″3) and shed light onto the mechanism feeding the active galactic nucleus (AGN) using CO(3–2), HCO{sup +}(4–3), HCN(4–3), and CO(6–5) observations obtained with ALMA. Multiple filaments or streamers of tens to a hundred parsec scale exist within the CND, which form a ring-like structure with an unprojected diameter of 9″ × 6″ (162 pc × 108 pc) and a position angle P.A. ≃ 155°. Inside the nuclear ring, there are two leading and straight filamentary structures with lengths of about 30–60 pc at P.A. ≃ 120° on opposite sides of the AGN, with a rotational symmetry of 180° and steeper position–velocity diagrams, which are interpreted as nuclear shocks due to non-circular motions. Along the filaments, and unlike other nearby AGNs, several dense molecular clumps present low HCN/HCO{sup +}(4–3) ratios (≲0.5). The filaments abruptly end in the probed transitions at r ≃ 20 pc from the AGN, but previous near-IR H{sub 2}( J = 1–0)S(1) maps show that they continue in an even warmer gas phase ( T ∼ 1000 K), winding up in the form of nuclear spirals, and forming an inner ring structure with another set of symmetric filaments along the N–S direction and within r ≃ 10 pc. The molecular gas is governed primarily by non-circular motions, being the successive shock fronts at different scales where loss of angular momentum occurs, a mechanism that may feed efficiently powerful radio galaxies down to parsec scales.

Structural variations in aromatic 2π-electron three-membered rings ...

Indian Academy of Sciences (India)

Abstract. Structural variations of different 2π-aromatic three-membered ring systems of main group ele- ments, especially group 14 and 13 elements as compared to the classical description of cyclopropenyl cation has been reviewed in this article. The structures of heavier analogues as well as group 13 analogues of cyclo-.

Miscibility phase diagram of ring-polymer blends: A topological effect.

Science.gov (United States)

Sakaue, Takahiro; Nakajima, Chihiro H

2016-04-01

The miscibility of polymer blends, a classical problem in polymer science, may be altered, if one or both of the component do not have chain ends. Based on the idea of topological volume, we propose a mean-field theory to clarify how the topological constraints in ring polymers affect the phase behavior of the blends. While the large enhancement of the miscibility is expected for ring-linear polymer blends, the opposite trend toward demixing, albeit comparatively weak, is predicted for ring-ring polymer blends. Scaling formulas for the shift of critical point for both cases are derived. We discuss the valid range of the present theory, and the crossover to the linear polymer blends behaviors, which is expected for short chains. These analyses put forward a view that the topological constraints could be represented as an effective excluded-volume effects, in which the topological length plays a role of the screening factor.

On Sagnac frequency splitting in a solid-state ring Raman laser.

Science.gov (United States)

Liang, Wei; Savchenkov, Anatoliy; Ilchenko, Vladimir; Griffith, Robert; De Cuir, Edwin; Kim, Steven; Matsko, Andrey; Maleki, Lute

2017-11-15

We report on an accurate measurement of the frequency splitting of an optical rotating ring microcavity made out of calcium fluoride. By measuring the frequencies of the clockwise and counter-clockwise coherent Raman emissions confined in the cavity modes, we show that the frequency splitting is inversely proportional to the refractive index of the cavity host material. The measurement has an accuracy of 1% and unambiguously confirms the classical theoretical prediction based on special theory of relativity. This Letter also demonstrates the usefulness of the ring Raman microlaser for rotation measurements.

Classical altitude training.

Science.gov (United States)

Friedmann-Bette, B

2008-08-01

For more than 40 years, the effects of classical altitude training on sea-level performance have been the subject of many scientific investigations in individual endurance sports. To our knowledge, no studies have been performed in team sports like football. Two well-controlled studies showed that living and training at an altitude of >or=1800-2700 m for 3-4 weeks is superior to equivalent training at sea level in well-trained athletes. Most of the controlled studies with elite athletes did not reveal such an effect. However, the results of some uncontrolled studies indicate that sea-level performance might be enhanced after altitude training also in elite athletes. Whether hypoxia provides an additional stimulus for muscular adaptation, when training is performed with equal intensity compared with sea-level training is not known. There is some evidence for an augmentation of total hemoglobin mass after classical altitude training with duration >or=3 weeks at an altitude >or=2000 m due to altitude acclimatization. Considerable individual variation is observed in the erythropoietic response to hypoxia and in the hypoxia-induced reduction of aerobic performance capacity during training at altitude, both of which are thought to contribute to inter-individual variation in the improvement of sea-level performance after altitude training.

Evolution and molecular epidemiology of classical swine fever virus during a multi-annual outbreak amongst European wild boar.

Science.gov (United States)

Goller, Katja V; Gabriel, Claudia; Dimna, Mireille Le; Le Potier, Marie-Frédérique; Rossi, Sophie; Staubach, Christoph; Merboth, Matthias; Beer, Martin; Blome, Sandra

2016-03-01

Classical swine fever is a viral disease of pigs that carries tremendous socio-economic impact. In outbreak situations, genetic typing is carried out for the purpose of molecular epidemiology in both domestic pigs and wild boar. These analyses are usually based on harmonized partial sequences. However, for high-resolution analyses towards the understanding of genetic variability and virus evolution, full-genome sequences are more appropriate. In this study, a unique set of representative virus strains was investigated that was collected during an outbreak in French free-ranging wild boar in the Vosges-du-Nord mountains between 2003 and 2007. Comparative sequence and evolutionary analyses of the nearly full-length sequences showed only slow evolution of classical swine fever virus strains over the years and no impact of vaccination on mutation rates. However, substitution rates varied amongst protein genes; furthermore, a spatial and temporal pattern could be observed whereby two separate clusters were formed that coincided with physical barriers.

Minimization of the transformer inter-winding parasitic capacitance for modular stacking power supply applications

DEFF Research Database (Denmark)

Nguyen-Duy, Khiem; Ouyang, Ziwei; Knott, Arnold

2014-01-01

In an isolated power supply, the inter-winding parasitic capacitance plays a vital role in the mitigation of common mode noise currents created by fast voltage transient responses. The lower the transformer inter-winding capacitance, the more immune the power supply is to fast voltage transient...... responses. This requirement is even more critical for modular stacking applications in which multiple power supplies are stacked. This paper addresses the issue by presenting a detailed analysis and design of an unconventional isolated power supply that uses a ring core transformer with a very low inter......-winding parasitic capacitance of 10 pF. Considering its output power of 300 W, this approach yields about 0.033 pF/W inter-winding capacitance over output power, approximately thirty times lower than existing approaches in the literature. This makes the converter a suitable solution for modular stacking of fast...

The RING 2.0 web server for high quality residue interaction networks.

Science.gov (United States)

Piovesan, Damiano; Minervini, Giovanni; Tosatto, Silvio C E

2016-07-08

Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico-chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain-domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π-π stacking and π-cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Analysis of the biological and molecular variability of the Polish isolates of Tomato black ring virus (TBRV).

Science.gov (United States)

Rymelska, N; Borodynko, N; Pospieszny, H; Hasiów-Jaroszewska, B

2013-10-01

Tomato black ring virus (TBRV) is an important pathogen infecting many plant species worldwide. The biological and molecular variability of the Polish isolates of TBRV was analyzed. The analysis was performed based on the symptoms induced by various isolates on test plant species as well as on phylogenetic relationships between isolates. Isolates differed in their host range and symptomatology. In addition, genetic variation among isolates was characterized by restriction fragment length polymorphism analysis and confirmed by sequencing. The phylogenetic analysis revealed that the Polish isolates differ from each other and do not form a monophyletic cluster. Finally, we identified and analyzed sequences of defective RNA forms arising from the TBRV genome.

Classical and quantum molecular dynamics in NMR spectra

CERN Document Server

Szymański, Sławomir

2018-01-01

The book provides a detailed account of how condensed-phase molecular dynamics are reflected in the line shapes of NMR spectra. The theories establishing connections between random, time-dependent molecular processes and lineshape effects are exposed in depth. Special emphasis is placed on the theoretical aspects, involving in particular intermolecular processes in solution, and molecular symmetry issues. The Liouville super-operator formalism is briefly introduced and used wherever it is beneficial for the transparency of presentation. The proposed formal descriptions of the discussed problems are sufficiently detailed to be implemented on a computer. Practical applications of the theory in solid- and liquid-phase studies are illustrated with appropriate experimental examples, exposing the potential of the lineshape method in elucidating molecular dynamics NMR-observable molecular phenomena where quantization of the spatial nuclear degrees of freedom is crucial are addressed in the last part of the book. As ...

From Chemical Topology to Molecular Machines (Nobel Lecture).

Science.gov (United States)

Sauvage, Jean-Pierre

2017-09-04

To a large extent, the field of "molecular machines" started after several groups were able to prepare, reasonably easily, interlocking ring compounds (named catenanes for compounds consisting of interlocking rings and rotaxanes for rings threaded by molecular filaments or axes). Important families of molecular machines not belonging to the interlocking world were also designed, prepared, and studied but, for most of them, their elaboration was more recent than that of catenanes or rotaxanes. Since the creation of interlocking ring molecules is so important in relation to the molecular machinery area, we will start with this aspect of our work. The second part will naturally be devoted to the dynamic properties of such systems and to the compounds for which motions can be directed in a controlled manner from the outside, that is, molecular machines. We will restrict our discussion to a very limited number of examples which we consider as particularly representative of the field. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Programmable dispersion on a photonic integrated circuit for classical and quantum applications.

Science.gov (United States)

Notaros, Jelena; Mower, Jacob; Heuck, Mikkel; Lupo, Cosmo; Harris, Nicholas C; Steinbrecher, Gregory R; Bunandar, Darius; Baehr-Jones, Tom; Hochberg, Michael; Lloyd, Seth; Englund, Dirk

2017-09-04

We demonstrate a large-scale tunable-coupling ring resonator array, suitable for high-dimensional classical and quantum transforms, in a CMOS-compatible silicon photonics platform. The device consists of a waveguide coupled to 15 ring-based dispersive elements with programmable linewidths and resonance frequencies. The ability to control both quality factor and frequency of each ring provides an unprecedented 30 degrees of freedom in dispersion control on a single spatial channel. This programmable dispersion control system has a range of applications, including mode-locked lasers, quantum key distribution, and photon-pair generation. We also propose a novel application enabled by this circuit - high-speed quantum communications using temporal-mode-based quantum data locking - and discuss the utility of the system for performing the high-dimensional unitary optical transformations necessary for a quantum data locking demonstration.

Molecular characterization of Fagaceae species using inter-primer binding site (iPBS) markers.

Science.gov (United States)

Coutinho, João Paulo; Carvalho, Ana; Martín, Antonio; Lima-Brito, José

2018-04-01

Retrotransposons (RTNs) contribute for genome evolution, influencing its size and structure. We investigated the utility of the RTN-based markers inter-primer binding site (iPBS) for the molecular characterization of 25 Fagaceae species from genera Castanea, Fagus and Quercus. The assessment of genetic diversity, relationships and structure, as well as taxonomic classification of Fagaceae based on molecular data is important for definition of conservation, forestry management strategies and discrimination among natural hybrids and their parents since natural hybridization may increase with the climate changes. Here, iPBS primers designed by other authors were tested alone and combined. Some of them were discriminative, revealed polymorphism within and among taxa allowing the production of a total of 150 iPBS markers. In addition, several monomorphic iPBS markers were also amplified in each taxon. The UPGMA dendrogram based on the pooled iPBS data revealed 27% of genetic similarity among species. The individuals were clustered per genus and most of the oaks per infrageneric group corroborating the adopted taxonomy. Globally, the iPBS markers demonstrated suitability for DNA fingerprinting, determination of phylogenies and taxonomic discrimination in Fagaceae, and could constitute a useful and alternative tool for germplasm characterization, and for definition of conservation strategies and forestry management. Moreover, these markers would be useful for fingerprinting natural hybrids that share morphological similarities with their parents. Since iPBS markers could also enable insights about RTNs evolution, an eventual correlation among iPBS polymorphism, variability of RTN insertions and/or genome size in Fagaceae is discussed.

Classical many-body theory with retarded interactions: Dynamical irreversibility and determinism without probabilities

Energy Technology Data Exchange (ETDEWEB)

Zakharov, A.Yu., E-mail: Anatoly.Zakharov@novsu.ru; Zakharov, M.A., E-mail: ma_zakharov@list.ru

2016-01-28

The exact equations of motion for microscopic density of classical many-body system with account of inter-particle retarded interactions is derived. It is shown that interactions retardation leads to irreversible behavior of many-body systems. - Highlights: • A new form of equation of motion of classical many-body system is proposed. • Interactions retardation as one of the mechanisms of many-body system irreversibility. • Irreversibility and determinism without probabilities. • The possible way to microscopic foundation of thermodynamics.

Mechanistic Insights into Radical-Mediated Oxidation of Tryptophan from ab Initio Quantum Chemistry Calculations and QM/MM Molecular Dynamics Simulations.

Science.gov (United States)

Wood, Geoffrey P F; Sreedhara, Alavattam; Moore, Jamie M; Wang, John; Trout, Bernhardt L

2016-05-12

An assessment of the mechanisms of (•)OH and (•)OOH radical-mediated oxidation of tryptophan was performed using density functional theory calculations and ab initio plane-wave Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics simulations. For the (•)OH reactions, addition to the pyrrole ring at position 2 is the most favored site with a barrierless reaction in the gas phase. The subsequent degradation of this adduct through a H atom transfer to water was intermittently observed in aqueous-phase molecular dynamics simulations. For the (•)OOH reactions, addition to the pyrrole ring at position 2 is the most favored pathway, in contrast to the situation in the model system ethylene, where concerted addition to the double bond is preferred. From the (•)OOH position 2 adduct QM/MM simulations show that formation of oxy-3-indolanaline occurs readily in an aqueous environment. The observed transformation starts from an initial rupture of the O-O bond followed by a H atom transfer with the accompanying loss of an (•)OH radical to solution. Finally, classical molecular dynamics simulations were performed to equate observed differential oxidation rates of various tryptophan residues in monoclonal antibody fragments. It was found that simple parameters derived from simulation correlate well with the experimental data.

Molecular biomarkers of resistance to anti-EGFR treatment in metastatic colorectal cancer, from classical to innovation.

Science.gov (United States)

Giampieri, Riccardo; Scartozzi, Mario; Del Prete, Michela; Maccaroni, Elena; Bittoni, Alessandro; Faloppi, Luca; Bianconi, Maristella; Cecchini, Luca; Cascinu, Stefano

2013-11-01

Systematic dissection of the EGFR pathway was considered as the best way to identify putative markers of resistance to anti-EGFR therapies. This kind of approach leaves other, less known but by no means less important, putative mechanisms of resistance. We tried to shed some light on these mechanisms of resistance. We performed a research through Pubmed database of all published articles highlighting mechanisms of resistance to Cetuximab and Panitumumab based therapies, published in 2000-2012 period. We reviewed the "classical" molecular factors, extensively analyzed as predictive factors for efficacy to anti-EGFR therapy, such as K-ras, B-raf, and PI3K-mTOR-Akt, focusing on their predictive or prognostic value and on the controversial aspects of the biomarker analysis for clinical practice. On the second part we will then move on to other less known molecular markers, for the future understanding of biological mechanisms underlying anti-EGFR therapy resistance, such as non-canonical heterodimer candidates, microRNA, IGF1-IGF1R, HGF-cMET and secondary mutations of EGFR. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Commissioning of the Cryogenic Plant for the Cryogenic Storage Ring (CSR) at Heidelberg

CERN Document Server

von Hahn, R; Grieser, M; Haberstroh, C; Kaiser, D; Lange, M; Laux, F; Menk, S; Orlov, D A; Repnow, R; Sieber, T; Quack, H; Varju, J; Wolf A

2009-01-01

At the Max-Planck-Institute for Nuclear Physics in Heidelberg a next generation electrostatic storage ring for low velocity atomic and molecular ion beams is under construction. In contrast to existing electrostatic storage rings, the Cryogenic Storage Ring CSR will be cooled down to temperatures below 2 K. Thus acting as a large cryopump it will provide long storage times and, in addition, open a new field of quantum state controlled molecular physics due to a low heat radiation background from space-like environment. A concept for cooling the storage ring has been developed and is presently tested by means of a linear trap as a prototype with a length of 1/10 of the planned ring. A commercial refrigerator with 21 W at 2 K has been successfully commissioned and was connected to the prototype. This paper presents the status of the cryogenic plant after the commissioning and one year of operation.

A note on derivations in semiprime rings

Directory of Open Access Journals (Sweden)

Joso Vukman

2005-01-01

Full Text Available We prove in this note the following result. Let n>1 be an integer and let R be an n!-torsion-free semiprime ring with identity element. Suppose that there exists an additive mapping D:R→R such that D(xn=∑j=1nxn−jD(xxj−1 is fulfilled for all x∈R. In this case, D is a derivation. This research is motivated by the work of Bridges and Bergen (1984. Throughout, R will represent an associative ring with center Z(R. Given an integer n>1, a ring R is said to be n-torsion-free if for x∈R, nx=0 implies that x=0. Recall that a ring R is prime if for a,b∈R, aRb=(0 implies that either a=0 or b=0, and is semiprime in case aRa=(0 implies that a=0. An additive mapping D:R→R is called a derivation if D(xy=D(xy+xD(y holds for all pairs x,y∈R and is called a Jordan derivation in case D(x2=D(xx+xD(x is fulfilled for all x∈R. Every derivation is a Jordan derivation. The converse is in general not true. A classical result of Herstein (1957 asserts that any Jordan derivation on a prime ring with characteristic different from two is a derivation. A brief proof of Herstein's result can be found in 1988 by Brešar and Vukman. Cusack (1975 generalized Herstein's result to 2-torsion-free semiprime rings (see also Brešar (1988 for an alternative proof. For some other results concerning derivations on prime and semiprime rings, we refer to Brešar (1989, Vukman (2005, Vukman and Kosi-Ulbl (2005.

Classical swine fever virus detection: results of a real-time reverse transcription polymerase chain reaction ring trial conducted in the framework of the European network of excellence for epizootic disease diagnosis and control

DEFF Research Database (Denmark)

Hoffmann, Bernd; Blome, Sandra; Bonilauri, Paolo

2011-01-01

and specificity values. Nevertheless, some in-house systems had unspecific reactions or suboptimal sensitivity with only a single CSFV genotype. Follow-up actions involved either improvement of suboptimal assays or replacement of specific laboratory assays with the FLI protocol, with or without modifications......The current study reports on a real-time reverse transcription polymerase chain reaction (real-time RT-PCR) ring trial for the detection of Classical swine fever virus (CSFV) genomic RNA undertaken by 10 European laboratories. All laboratories were asked to use their routine in-house real-time RT...

Electrostatic storage rings for atomic and molecular physics

International Nuclear Information System (INIS)

Schmidt, H T

2015-01-01

A significant number of electrostatic ion-storage rings have been built since the late 1990s or are currently in their construction or commisioning phases. In this short contribution, we attempt to supply an overview of these different facilities, while we also mention a selection of the electrostatic ion-beam traps that has been developed through the same time period and by some of the same research groups. (paper)

Spontaneous actin dynamics in contractile rings

Science.gov (United States)

Kruse, Karsten; Wollrab, Viktoria; Thiagarajan, Raghavan; Wald, Anne; Riveline, Daniel

Networks of polymerizing actin filaments are known to be capable to self-organize into a variety of structures. For example, spontaneous actin polymerization waves have been observed in living cells in a number of circumstances, notably, in crawling neutrophils and slime molds. During later stages of cell division, they can also spontaneously form a contractile ring that will eventually cleave the cell into two daughter cells. We present a framework for describing networks of polymerizing actin filaments, where assembly is regulated by various proteins. It can also include the effects of molecular motors. We show that the molecular processes driven by these proteins can generate various structures that have been observed in contractile rings of fission yeast and mammalian cells. We discuss a possible functional role of each of these patterns. The work was supported by Agence Nationale de la Recherche, France, (ANR-10-LABX-0030-INRT) and by Deutsche Forschungsgemeinschaft through SFB1027.

The anisotropy of fluorescence in ring units II: transfer integral fluctuations

International Nuclear Information System (INIS)

Herman, Pavel; Barvik, Ivan; Reiter, Michal

2005-01-01

The time dependence of the anisotropy of fluorescence after an impulsive excitation in the molecular ring (resembling the B850 ring of the purple bacterium Rhodopseudomonas acidophila) is calculated. Fast fluctuations of the environment are simulated by dynamic disorder and slow fluctuations by static disorder. Without dynamic disorder, modest degrees of static disorder are sufficient to cause the experimentally found initial drop of the anisotropy on a sub-100 fs time scale. In the present investigation we are comparing results for the time-dependent optical anisotropy of the molecular ring for three models of the static disorder: Gaussian disorder in the local energies (Model A), Gaussian disorder in the transfer integrals (Model B) and Gaussian disorder in radial positions of molecules (Model C). Both types of disorder-static and dynamic-are taken into account simultaneously

Classical origins of stabilization in circularly polarized laser fields

International Nuclear Information System (INIS)

Chism, Will; Choi, Dae-Il; Reichl, L. E.

2000-01-01

We investigate the interaction of a two-dimensional model atom with an intense, high-frequency circularly polarized laser pulse. As the laser intensity is increased, the ionization rate initially increases, then decreases dramatically, with the electron wave function developing an asymmetric ring form which rotates with the electric field. We provide evidence that this wave form is due to localization of the electron onto nonlinear classical structures. (c) 2000 The American Physical Society

Ring-Opening Polymerization of N-Carboxyanhydrides for Preparation of Polypeptides and Polypeptide-Based Hybrid Materials with Various Molecular Architectures

KAUST Repository

Pahovnik, David

2015-09-01

Different synthetic approaches utilizing ring-opening polymerization of N-carboxyanhydrides for preparation of polypeptide and polypeptide-based hybrid materials with various molecular architectures are described. An overview of polymerization mechanisms using conventional (various amines) as well as some recently developed initiators (hexamethyldisilazane, N-heterocyclic persistent carbenes, etc.) is presented, and their benefits and drawbacks for preparation of polypeptides with well-defined chain lengths and chain-end functionality are discussed. Recent examples from literature are used to illustrate different possibilities for synthesis of pure polypeptide materials with different molecular architectures bearing various functional groups, which are introduced either by modification of amino acids, before they are transformed into corresponding Ncarboxyanhydrides, or by post-polymerization modifications using protective groups and/or orthogonal functional groups. Different approaches for preparation of polypeptide-based hybrid materials are discussed as well using examples from recent literature. Syntheses of simple block copolymers or copolymers with more complex molecular architectures (graft and star copolymers) as well as modifications of nanoparticles and other surfaces with polypeptides are described.

Immunomodulation of classical and non-classical HLA molecules by ionizing radiation.

Science.gov (United States)

Gallegos, Cristina E; Michelin, Severino; Dubner, Diana; Carosella, Edgardo D

2016-05-01

Radiotherapy has been employed for the treatment of oncological patients for nearly a century, and together with surgery and chemotherapy, radiation oncology constitutes one of the three pillars of cancer therapy. Ionizing radiation has complex effects on neoplastic cells and on tumor microenvironment: beyond its action as a direct cytotoxic agent, tumor irradiation triggers a series of alterations in tumoral cells, which includes the de novo synthesis of particular proteins and the up/down-regulation of cell surface molecules. Additionally, ionizing radiation may induce the release of "danger signals" which may, in turn lead to cellular and molecular responses by the immune system. This immunomodulatory action of ionizing radiation highlights the importance of the combined use (radiotherapy plus immunotherapy) for cancer healing. Major histocompatibility complex antigens (also called Human Leukocyte Antigens, HLA in humans) are one of those molecules whose expression is modulated after irradiation. This review summarizes the modulatory properties of ionizing radiation on the expression of HLA class I (classical and non-classical) and class II molecules, with special emphasis in non-classical HLA-I molecules. Copyright © 2016 Elsevier Inc. All rights reserved.

Conditions for the classicality of the center of mass of many-particle quantum states

International Nuclear Information System (INIS)

Oriols, Xavier; Benseny, Albert

2017-01-01

We discuss the conditions for the classicality of quantum states with a very large number of identical particles. By defining the center of mass from a large set of Bohmian particles, we show that it follows a classical trajectory when the distribution of the Bohmian particle positions in a single experiment is always equal to the marginal distribution of the quantum state in physical space. This result can also be interpreted as a single experiment generalization of the well-known Ehrenfest theorem. We also demonstrate that the classical trajectory of the center of mass is fully compatible with a quantum (conditional) wave function solution of a classical non-linear Schrödinger equation. Our work shows clear evidence for a quantum–classical inter-theory unification, and opens new possibilities for practical quantum computations with decoherence. (paper)

4-[(1E)-3-(2,6-Dichloro-3-fluoro-phen-yl)-3-oxoprop-1-en-1-yl]benzonitrile.

Science.gov (United States)

Praveen, Aletti S; Yathirajan, Hemmige S; Narayana, Badiadka; Gerber, Thomas; Hosten, Eric; Betz, Richard

2012-05-01

In the title mol-ecule, C(16)H(8)Cl(2)FNO, the benzene rings form a dihedral angle of 78.69 (8)°. The F atom is disordered over two positions in a 0.530 (3):0.470 (3) ratio. The crystal packing exhibits π-π inter-actions between dichloro-substituted rings [centroid-centroid distance = 3.6671 (10) Å] and weak inter-molecular C-H⋯F contacts.

Inter-relationships of haplosporidians deduced from ultrastructural studies

NARCIS (Netherlands)

Hine, P.M.; Carnegie, R.B.; Burreson, E.M.; Engelsma, M.Y.

2009-01-01

We reviewed papers reporting haplosporidian ultrastructure to compare inter-relationships based on ultrastructure with those based on molecular data, to identify features that may be important in haplosporidian taxonomy, and to consider parasite taxonomy in relation to host taxonomy. There were

Translucent Radiosity: Efficiently Combining Diffuse Inter-Reflection and Subsurface Scattering.

Science.gov (United States)

Sheng, Yu; Shi, Yulong; Wang, Lili; Narasimhan, Srinivasa G

2014-07-01

It is hard to efficiently model the light transport in scenes with translucent objects for interactive applications. The inter-reflection between objects and their environments and the subsurface scattering through the materials intertwine to produce visual effects like color bleeding, light glows, and soft shading. Monte-Carlo based approaches have demonstrated impressive results but are computationally expensive, and faster approaches model either only inter-reflection or only subsurface scattering. In this paper, we present a simple analytic model that combines diffuse inter-reflection and isotropic subsurface scattering. Our approach extends the classical work in radiosity by including a subsurface scattering matrix that operates in conjunction with the traditional form factor matrix. This subsurface scattering matrix can be constructed using analytic, measurement-based or simulation-based models and can capture both homogeneous and heterogeneous translucencies. Using a fast iterative solution to radiosity, we demonstrate scene relighting and dynamically varying object translucencies at near interactive rates.

(E)-6-Amino-1,3-dimethyl-5-[(pyridin-2-yl-methyl-idene)amino]-pyrimidine-2,4(1H,3H)-dione.

Science.gov (United States)

Booysen, Irvin; Hlela, Thulani; Ismail, Muhammed; Gerber, Thomas; Hosten, Eric; Betz, Richard

2011-09-01

In the title compound, C(12)H(13)N(5)O(2), a Schiff-base-derived chelate ligand, the non-aromatic heterocycle and its substituents essentially occupy one common plane (r.m.s. of fitted non-H atoms = 0.0503 Å). The N=C bond is E-configured. Intra-cyclic angles in the pyridine moiety cover the range 117.6 (2)-124.1 (2)°. Intra- and inter-molecular N-H⋯N and N-H⋯O hydrogen bonds are observed in the crystal structure, as are intra- and inter-molecular C-H⋯O contacts which, in total, connect the mol-ecules into a three-dimensional network. The shortest ring-centroid-to-ring-centroid distance of 3.5831 (14) Å is between the two different types of six-membered rings.

Biophysical mechanisms complementing "classical" cell biology.

Science.gov (United States)

Funk, Richard H W

2018-01-01

This overview addresses phenomena in cell- and molecular biology which are puzzling by their fast and highly coordinated way of organization. Generally, it appears that informative processes probably involved are more on the biophysical than on the classical biochemical side. The coordination problem is explained within the first part of the review by the topic of endogenous electrical phenomena. These are found e.g. in fast tissue organization and reorganization processes like development, wound healing and regeneration. Here, coupling into classical biochemical signaling and reactions can be shown by modern microscopy, electronics and bioinformatics. Further, one can follow the triggered reactions seamlessly via molecular biology till into genetics. Direct observation of intracellular electric processes is very difficult because of e.g. shielding through the cell membrane and damping by other structures. Therefore, we have to rely on photonic and photon - phonon coupling phenomena like molecular vibrations, which are addressed within the second part. Molecules normally possess different charge moieties and thus small electromagnetic (EMF) patterns arise during molecular vibration. These patterns can now be measured best within the optical part of the spectrum - much less in the lower terahertz till kHz and lower Hz part (third part of this review). Finally, EMFs facilitate quantum informative processes in coherent domains of molecular, charge and electron spin motion. This helps to coordinate such manifold and intertwined processes going on within cells, tissues and organs (part 4). Because the phenomena described in part 3 and 4 of the review still await really hard proofs we need concerted efforts and a combination of biophysics, molecular biology and informatics to unravel the described mysteries in "physics of life".

Inchworm movement of two rings switching onto a thread by biased Brownian diffusion represent a three-body problem.

Science.gov (United States)

Benson, Christopher R; Maffeo, Christopher; Fatila, Elisabeth M; Liu, Yun; Sheetz, Edward G; Aksimentiev, Aleksei; Singharoy, Abhishek; Flood, Amar H

2018-05-07

The coordinated motion of many individual components underpins the operation of all machines. However, despite generations of experience in engineering, understanding the motion of three or more coupled components remains a challenge, known since the time of Newton as the "three-body problem." Here, we describe, quantify, and simulate a molecular three-body problem of threading two molecular rings onto a linear molecular thread. Specifically, we use voltage-triggered reduction of a tetrazine-based thread to capture two cyanostar macrocycles and form a [3]pseudorotaxane product. As a consequence of the noncovalent coupling between the cyanostar rings, we find the threading occurs by an unexpected and rare inchworm-like motion where one ring follows the other. The mechanism was derived from controls, analysis of cyclic voltammetry (CV) traces, and Brownian dynamics simulations. CVs from two noncovalently interacting rings match that of two covalently linked rings designed to thread via the inchworm pathway, and they deviate considerably from the CV of a macrocycle designed to thread via a stepwise pathway. Time-dependent electrochemistry provides estimates of rate constants for threading. Experimentally derived parameters (energy wells, barriers, diffusion coefficients) helped determine likely pathways of motion with rate-kinetics and Brownian dynamics simulations. Simulations verified intercomponent coupling could be separated into ring-thread interactions for kinetics, and ring-ring interactions for thermodynamics to reduce the three-body problem to a two-body one. Our findings provide a basis for high-throughput design of molecular machinery with multiple components undergoing coupled motion.

Hybrid classical/quantum simulation for infrared spectroscopy of water

Science.gov (United States)

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.

Molecular insights into the evolutionary pathway of Vibrio cholerae O1 atypical El Tor variants.

Science.gov (United States)

Kim, Eun Jin; Lee, Dokyung; Moon, Se Hoon; Lee, Chan Hee; Kim, Sang Jun; Lee, Jae Hyun; Kim, Jae Ouk; Song, Manki; Das, Bhabatosh; Clemens, John D; Pape, Jean William; Nair, G Balakrish; Kim, Dong Wook

2014-09-01

Pandemic V. cholerae strains in the O1 serogroup have 2 biotypes: classical and El Tor. The classical biotype strains of the sixth pandemic, which encode the classical type cholera toxin (CT), have been replaced by El Tor biotype strains of the seventh pandemic. The prototype El Tor strains that produce biotype-specific cholera toxin are being replaced by atypical El Tor variants that harbor classical cholera toxin. Atypical El Tor strains are categorized into 2 groups, Wave 2 and Wave 3 strains, based on genomic variations and the CTX phage that they harbor. Whole-genome analysis of V. cholerae strains in the seventh cholera pandemic has demonstrated gradual changes in the genome of prototype and atypical El Tor strains, indicating that atypical strains arose from the prototype strains by replacing the CTX phages. We examined the molecular mechanisms that effected the emergence of El Tor strains with classical cholera toxin-carrying phage. We isolated an intermediary V. cholerae strain that carried two different CTX phages that encode El Tor and classical cholera toxin, respectively. We show here that the intermediary strain can be converted into various Wave 2 strains and can act as the source of the novel mosaic CTX phages. These results imply that the Wave 2 and Wave 3 strains may have been generated from such intermediary strains in nature. Prototype El Tor strains can become Wave 3 strains by excision of CTX-1 and re-equipping with the new CTX phages. Our data suggest that inter-chromosomal recombination between 2 types of CTX phages is possible when a host bacterial cell is infected by multiple CTX phages. Our study also provides molecular insights into population changes in V. cholerae in the absence of significant changes to the genome but by replacement of the CTX prophage that they harbor.

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring.

Science.gov (United States)

Durston, Kirk K; Chiu, David Ky; Wong, Andrew Kc; Li, Gary Cl

2012-07-13

Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Our results

How to make a tree ring: Coupling stem water flow and cambial activity in mature Alpine conifers

Science.gov (United States)

Peters, Richard L.; Frank, David C.; Treydte, Kerstin; Steppe, Kathy; Kahmen, Ansgar; Fonti, Patrick

2017-04-01

Inter-annual tree-ring measurements are used to understand tree-growth responses to climatic variability and reconstruct past climate conditions. In parallel, mechanistic models use experimentally defined plant-atmosphere interactions to explain past growth responses and predict future environmental impact on forest productivity. Yet, substantial inconsistencies within mechanistic model ensembles and mismatches with empirical data indicate that significant progress is still needed to understand the processes occurring at an intra-annual resolution that drive annual growth. However, challenges arise due to i) few datasets describing climatic responses of high-resolution physiological processes over longer time-scales, ii) uncertainties on the main mechanistic process limiting radial stem growth and iii) complex interactions between multiple environmental factors which obscure detection of the main stem growth driver, generating a gap between our understanding of intra- and inter-annual growth mechanisms. We attempt to bridge the gap between inter-annual tree-ring width and sub-daily radial stem-growth and provide a mechanistic perspective on how environmental conditions affect physiological processes that shape tree rings in conifers. We combine sub-hourly sap flow and point dendrometer measurements performed on mature Alpine conifers (Larix decidua) into an individual-based mechanistic tree-growth model to simulate sub-hourly cambial activity. The monitored trees are located along a high elevational transect in the Swiss Alps (Lötschental) to analyse the effect of increasing temperature. The model quantifies internal tree hydraulic pathways that regulate the turgidity within the cambial zone and induce cell enlargement for radial growth. The simulations are validated against intra-annual growth patterns derived from xylogenesis data and anatomical analyses. Our efforts advance the process-based understanding of how climate shapes the annual tree-ring structures

Design analysis of a self-acting spiral-groove ring seal for counter-rotating shafts. [o ring seals

Science.gov (United States)

Dirusso, E.

1983-01-01

A self-acting spiral groove inter-shaft ring seal of nominal 16.33 cm (6.43 in.) diameter for sealing fan bleed air between counter rotating shafts in advanced turbofan engines was analyzed. The analysis focused on the lift force characteristics of the spiral grooves. A NASA Lewis developed computer program for predicting the performance of gas lubricated face seals was used to optimize the spiral groove geometry to produce maximum lift force. Load capacity curves (lift force as function of film thickness) were generated for four advanced turbofan engine operating conditions at relative seal speeds ranging from 17,850 to 29,800 rpm, sealed air pressures from 6 to 42 N/sq cm (9 to 60 psi) absolute and temperatures from 95 to 327 C (203 to 620 F). The relative seal sliding speed range was 152 to 255 m/sec (500 to 836 ft/sec). The analysis showed that the spiral grooves are capable of producing sufficient lift force such that the ring seal will operate in a noncontacting mode over the operating range of typical advanced turbofan engines.

New edge magnetoplasmon for a two-dimensional electron gas in a ring geometry

International Nuclear Information System (INIS)

Proetto, C.R.

1992-09-01

The dynamical response of a classical two-dimensional electron gas confined in a ring geometry under a perpendicular magnetic field is analysed. Within the hydrodynamical approach and in the strong magnetic field limit, a new set of antidot edge magnetoplasmons is obtained, corresponding to density oscillations circulating along the inner boundary of the ring and whose frequency increases with magnetic field. The associated self-induced distribution of densities and currents are presented, together with an analysis of the size dependence of these perimeter waves. (author). 15 refs, 4 figs

In situ study of the impact of inter- and intra-reader variability on region of interest (ROI) analysis in preclinical molecular imaging.

Science.gov (United States)

Habte, Frezghi; Budhiraja, Shradha; Keren, Shay; Doyle, Timothy C; Levin, Craig S; Paik, David S

2013-01-01

We estimated reader-dependent variability of region of interest (ROI) analysis and evaluated its impact on preclinical quantitative molecular imaging. To estimate reader variability, we used five independent image datasets acquired each using microPET and multispectral fluorescence imaging (MSFI). We also selected ten experienced researchers who utilize molecular imaging in the same environment that they typically perform their own studies. Nine investigators blinded to the data type completed the ROI analysis by drawing ROIs manually that delineate the tumor regions to the best of their knowledge and repeated the measurements three times, non-consecutively. Extracted mean intensities of voxels within each ROI are used to compute the coefficient of variation (CV) and characterize the inter- and intra-reader variability. The impact of variability was assessed through random samples iterated from normal distributions for control and experimental groups on hypothesis testing and computing statistical power by varying subject size, measured difference between groups and CV. The results indicate that inter-reader variability was 22.5% for microPET and 72.2% for MSFI. Additionally, mean intra-reader variability was 10.1% for microPET and 26.4% for MSFI. Repeated statistical testing showed that a total variability of CV variability has been observed mainly due to differences in the ROI placement and geometry drawn between readers, which may adversely affect statistical power and erroneously lead to negative study outcomes.

Ordered quantum-ring chains grown on a quantum-dot superlattice template

International Nuclear Information System (INIS)

Wu Jiang; Wang, Zhiming M.; Holmes, Kyland; Marega, Euclydes; Mazur, Yuriy I.; Salamo, Gregory J.

2012-01-01

One-dimensional ordered quantum-ring chains are fabricated on a quantum-dot superlattice template by molecular beam epitaxy. The quantum-dot superlattice template is prepared by stacking multiple quantum-dot layers and quantum-ring chains are formed by partially capping quantum dots. Partially capping InAs quantum dots with a thin layer of GaAs introduces a morphological change from quantum dots to quantum rings. The lateral ordering is introduced by engineering the strain field of a multi-layer InGaAs quantum-dot superlattice.

Gridded Snow Water Equivalent Reconstruction for Utah Using Forest Inventory and Analysis Tree-Ring Data

Directory of Open Access Journals (Sweden)

Daniel Barandiaran

2017-06-01

Full Text Available Snowpack observations in the Intermountain West are sparse and short, making them difficult for use in depicting past variability and extremes. This study presents a reconstruction of April 1 snow water equivalent (SWE for the period of 1850–1989 using increment cores collected by the U.S. Forest Service, Interior West Forest Inventory and Analysis program (FIA. In the state of Utah, SWE was reconstructed for 38 snow course locations using a combination of standardized tree-ring indices derived from both FIA increment cores and publicly available tree-ring chronologies. These individual reconstructions were then interpolated to a 4-km grid using an objective analysis with elevation correction to create an SWE product. The results showed a significant correlation with observed SWE as well as good correspondence to regional tree-ring-based drought reconstructions. Diagnostic analysis showed statewide coherent climate variability on inter-annual and inter-decadal time-scales, with added geographical details that would not be possible using courser pre-instrumental proxy datasets. This SWE reconstruction provides water resource managers and forecasters with better spatial resolution to examine past variability in snowpack, which will be important as future hydroclimatic variability is amplified by climate change.

The structure of molecular liquids. Neutron diffraction and molecular dynamics simulations

International Nuclear Information System (INIS)

Bianchi, L.

2000-05-01

Neutron diffraction (ND) measurements on liquid methanol (CD 3 OD, CD 3 O(H/D), CD 3 OH) under ambient conditions were performed to obtain the distinct (intra- + inter-molecular), G dist (r) and inter-molecular, G inter (r) radial distribution functions (rdfs) for the three samples. The H/D substitution on hydroxyl-hydrogen (Ho) has been used to extract the partial distribution functions, G XHo (r) (X=C, O, and H - a methyl hydrogen) and G XX (r) at both the distinct and inter-molecular levels from the difference techniques of ND. The O-Ho bond length, which has been the subject of controversy in the past, is found purely from the distinct partial distribution function, G XHo (r) to be 0.98 ± 0.01 A. The C-H distance obtained from the distinct G XX (r) partial is 1.08 ± 0.01 A. These distances determined by fitting an intra-molecular model to the total distinct structure functions are 0.961 ± 0.001 A and 1.096 ± 0.001 A, respectively. The inter-molecular G XX (r) function, dominated by contributions from the methyl groups, apart from showing broad oscillations extending up to ∼14 A is featureless, mainly because of cancellation effects from six contributing pairs. The Ho-Ho partial pair distribution function (pdf), g HoHo (r), determined from the second order difference, shows that only one other Ho atom can be found within a mean Ho-Ho separation of 2.36 A. The average position of the O-Ho hydrogen bond determined for the first time purely from experimental inter-molecular G XHo (r) partial distribution function is found to be at 1.75 ± 0.03 A. The experimental structural results at the partial distribution level are compared with those obtained from molecular dynamics (MD) simulations performed in NVE ensemble by using both 3- and 6-site force field models for the first time in this study. The MD simulations with both the models reproduce the ND rdfs rather well. However, discrepancies begin to appear between the simulated and the experimental partial

A COMPREHENSIVE STUDY OF HYDROGEN ADSORBING TO AMORPHOUS WATER ICE: DEFINING ADSORPTION IN CLASSICAL MOLECULAR DYNAMICS

Energy Technology Data Exchange (ETDEWEB)

Dupuy, John L.; Lewis, Steven P.; Stancil, P. C. [Department of Physics and Astronomy and the Center for Simulational Physics, University of Georgia, Athens, GA 30602 (United States)

2016-11-01

Gas–grain and gas–phase reactions dominate the formation of molecules in the interstellar medium (ISM). Gas–grain reactions require a substrate (e.g., a dust or ice grain) on which the reaction is able to occur. The formation of molecular hydrogen (H{sub 2}) in the ISM is the prototypical example of a gas–grain reaction. In these reactions, an atom of hydrogen will strike a surface, stick to it, and diffuse across it. When it encounters another adsorbed hydrogen atom, the two can react to form molecular hydrogen and then be ejected from the surface by the energy released in the reaction. We perform in-depth classical molecular dynamics simulations of hydrogen atoms interacting with an amorphous water-ice surface. This study focuses on the first step in the formation process; the sticking of the hydrogen atom to the substrate. We find that careful attention must be paid in dealing with the ambiguities in defining a sticking event. The technical definition of a sticking event will affect the computed sticking probabilities and coefficients. Here, using our new definition of a sticking event, we report sticking probabilities and sticking coefficients for nine different incident kinetic energies of hydrogen atoms [5–400 K] across seven different temperatures of dust grains [10–70 K]. We find that probabilities and coefficients vary both as a function of grain temperature and incident kinetic energy over the range of 0.99–0.22.

Polyurethane Foams with Pyrimidine Rings

Directory of Open Access Journals (Sweden)

Kania Ewelina

2014-09-01

Full Text Available Oligoetherols based on pyrimidine ring were obtained upon reaction of barbituric acid with glycidol and alkylene carbonates. These oligoetherols were then used to obtain polyurethane foams in the reaction of oligoetherols with isocyanates and water. The protocol of foam synthesis was optimized by the choice of proper kind of oligoetherol and synthetic composition. The thermal resistance was studied by dynamic and static methods with concomitant monitoring of compressive strength. The polyurethane foams have similar physical properties as the classic ones except their enhanced thermal resistance. They stand long-time heating even at 200°C. Moreover thermal exposition of foams results generally in increase of their compressive strength.

Molecular cytogenetic characterization of two Turner syndrome patients with mosaic ring X chromosome.

Science.gov (United States)

Chauhan, Pooja; Jaiswal, Sushil Kumar; Lakhotia, Anjali Rani; Rai, Amit Kumar

2016-09-01

In the present study, we reported two cases of TS with mosaic ring X chromosome showing common clinical characteristics of TS like growth retardation and ovarian dysfunction. The purpose of the present study was to cytogenetically characterize both cases. Whole blood culture and G-banding were performed for karyotyping the cases following standard protocol. Origin of the ring chromosome and degree of mosaicism were further determined by fluorescence in situ hybridization (FISH). Breakpoints and loss of genetic material in formation of different ring X chromosomes r (X) in cases were determined with the help of cytogenetic microarray. Cases 1 and 2 with ring chromosome were cytogenetically characterized as 45, X [114]/46Xr (X) (p22.11q21.32) [116] and 45, X [170]/46, Xr (X) (p22.2q21.33) [92], respectively. Sizes of these ring X chromosomes were found to be ~75 and ~95 Mb in cases 1 and 2, respectively, using visual estimation as part of cytogenetic observation. In both cases, we observed breakpoints on Xq chromosome were within relatively narrow region between Xq21.33 and Xq22.1 compared to regions in previously reported cases associated with ovarian dysgenesis. Our observation agrees with the fact that despite of large heterogeneity, severity of the cases with intact X-inactive specific transcript (XIST) is dependent on degree of mosaicism and extent of Xq deletion having crucial genes involved directly or indirectly in various physiological involving ovarian cyclicity.

Application of quantum-dot multi-wavelength lasers and silicon photonic ring resonators to data-center optical interconnects

Science.gov (United States)

Beckett, Douglas J. S.; Hickey, Ryan; Logan, Dylan F.; Knights, Andrew P.; Chen, Rong; Cao, Bin; Wheeldon, Jeffery F.

2018-02-01

Quantum dot comb sources integrated with silicon photonic ring-resonator filters and modulators enable the realization of optical sub-components and modules for both inter- and intra-data-center applications. Low-noise, multi-wavelength, single-chip, laser sources, PAM4 modulation and direct detection allow a practical, scalable, architecture for applications beyond 400 Gb/s. Multi-wavelength, single-chip light sources are essential for reducing power dissipation, space and cost, while silicon photonic ring resonators offer high-performance with space and power efficiency.

6-Methyl-2-pyridyl N-acetyl-1-thio-β-d-glucosa-minide methanol monosolvate.

Science.gov (United States)

Chen, Bo; Guo, Miao; Jin, Wei-Hua; Wang, Yan-Wei; Liang, Hong-Ze

2010-09-15

In the title compound, C(14)H(20)N(2)O(5)S·CH(4)O, the pyran-ose and pyridine rings are linked through an S atom. The pyran-ose ring has a normal chair conformation. An intra-molecular O-H⋯N hydrogen bond occurs. Inter-molecular O-H⋯O, N-H⋯O, O-H⋯N and weak C-H⋯O hydrogen bonding is present in the crystal structure.

Inter-cellular transport of ran GTPase.

Directory of Open Access Journals (Sweden)

Deepak Khuperkar

Full Text Available Ran, a member of the Ras-GTPase superfamily, has a well-established role in regulating the transport of macromolecules across the nuclear envelope (NE. Ran has also been implicated in mitosis, cell cycle progression, and NE formation. Over-expression of Ran is associated with various cancers, although the molecular mechanism underlying this phenomenon is unclear. Serendipitously, we found that Ran possesses the ability to move from cell-to-cell when transiently expressed in mammalian cells. Moreover, we show that the inter-cellular transport of Ran is GTP-dependent. Importantly, Ran displays a similar distribution pattern in the recipient cells as that in the donor cell and co-localizes with the Ran binding protein Nup358 (also called RanBP2. Interestingly, leptomycin B, an inhibitor of CRM1-mediated export, or siRNA mediated depletion of CRM1, significantly impaired the inter-cellular transport of Ran, suggesting a function for CRM1 in this process. These novel findings indicate a possible role for Ran beyond nucleo-cytoplasmic transport, with potential implications in inter-cellular communication and cancers.

Conformational analysis of six- and twelve-membered ring compounds by molecular dynamics

DEFF Research Database (Denmark)

Christensen, I T; Jørgensen, Flemming Steen

1997-01-01

. A series of methyl-substituted 1,3-dioxanes were investigated at 1000 K, and the number of chair-chair interconversions could be quantitatively correlated to the experimentally determined ring inversion barrier. Similarly, the distribution of sampled minimum-energy conformations correlated with the energy......-derived Boltzmann distribution. The macrocyclic ring system cyclododecane was subjected to an MD simulation at 1000 K and 71 different conformations could be sampled. These conformations were compared with the results of previously reported conformational analyses using stochastic search methods, and the MD method...

Piezoelectric constants for ZnO calculated using classical polarizable core-shell potentials

International Nuclear Information System (INIS)

Dai Shuangxing; Dunn, Martin L; Park, Harold S

2010-01-01

We demonstrate the feasibility of using classical atomistic simulations, i.e. molecular dynamics and molecular statics, to study the piezoelectric properties of ZnO using core-shell interatomic potentials. We accomplish this by reporting the piezoelectric constants for ZnO as calculated using two different classical interatomic core-shell potentials: that originally proposed by Binks and Grimes (1994 Solid State Commun. 89 921-4), and that proposed by Nyberg et al (1996 J. Phys. Chem. 100 9054-63). We demonstrate that the classical core-shell potentials are able to qualitatively reproduce the piezoelectric constants as compared to benchmark ab initio calculations. We further demonstrate that while the presence of the shell is required to capture the electron polarization effects that control the clamped ion part of the piezoelectric constant, the major shortcoming of the classical potentials is a significant underprediction of the clamped ion term as compared to previous ab initio results. However, the present results suggest that overall, these classical core-shell potentials are sufficiently accurate to be utilized for large scale atomistic simulations of the piezoelectric response of ZnO nanostructures.

Interactions between plant RING-H2 and plant-specific NAC (NAM/ATAF1/2/CUC2) proteins: RING-H2 molecular specificity and cellular localization

DEFF Research Database (Denmark)

Greve, Krestine; Bravo Munoz, Tanja La Cour; Jensen, Michael Krogh

2003-01-01

RING miduler, NAC transkriptionsfatorer, abscisinsyre inducerbar, proteinnedbrydning, subcellulær lo......RING miduler, NAC transkriptionsfatorer, abscisinsyre inducerbar, proteinnedbrydning, subcellulær lo...

N-[5-Methyl-2-(2-nitro-phen-yl)-4-oxo-1,3-thia-zolidin-3-yl]pyridine-3-carboxamide monohydrate.

Science.gov (United States)

Akkurt, Mehmet; Celik, Ismail; Demir, Hale; Ozkırımlı, Sumru; Büyükgüngör, Orhan

2011-01-08

In the title compound, C(16)H(14)N(4)O(4)S·H(2)O, the benzene and pyridine rings make a dihedral angle of 85.8 (1)°. Both enanti-omers of the chiral title compound are statistically disordered over the same position in the unit cell. The methyl and carbonyl group attached to the stereogenic center (C(5) of the thia-zolidine ring) were therefore refined with common site-occupation factors of 0.531 (9) and 0.469 (9), respectively, for each stereoisomer. In the crystal, inter-molecular N-H⋯O, O-H⋯O and O-H⋯N hydrogen bonds link the mol-ecules, forming a three-dimensional supra-molecular network. The crystal structure further shows π-π stacking inter-actions [centroid-centroid distance = 3.5063 (13) Å] between the pyridine rings.

Low-emittance Storage Rings

CERN Document Server

Wolski, Andrzej

2014-01-01

The effects of synchrotron radiation on particle motion in storage rings are discussed. In the absence of radiation, particle motion is symplectic, and the beam emittances are conserved. The inclusion of radiation effects in a classical approximation leads to emittance damping: expressions for the damping times are derived. Then, it is shown that quantum radiation effects lead to excitation of the beam emittances. General expressions for the equilibrium longitudinal and horizontal (natural) emittances are derived. The impact of lattice design on the natural emittance is discussed, with particular attention to the special cases of FODO-, achromat- and theoretical-minimum-emittance-style lattices. Finally, the effects of betatron coupling and vertical dispersion (generated by magnet alignment and lattice tuning errors) on the vertical emittance are considered.

Charge transport through molecular rods with reduced pi-conjugation.

Science.gov (United States)

Lörtscher, Emanuel; Elbing, Mark; Tschudy, Meinrad; von Hänisch, Carsten; Weber, Heiko B; Mayor, Marcel; Riel, Heike

2008-10-24

A series of oligophenylene rods of increasing lengths is synthesized to investigate the charge-transport mechanisms. Methyl groups are attached to the phenyl rings to weaken the electronic overlap of the pi-subsystems along the molecular backbones. Out-of-plane rotation of the phenyl rings is confirmed in the solid state by means of X-ray analysis and in solution by using UV/Vis spectroscopy. The influence of the reduced pi-conjugation on the resonant charge transport is studied at the single-molecule level by using the mechanically controllable break-junction technique. Experiments are performed under ultra-high-vacuum conditions at low temperature (50 K). A linear increase of the conductance gap with increasing number of phenyl rings (from 260 meV for one ring to 580 meV for four rings) is revealed. In addition, the absolute conductance of the first resonant peaks does not depend on the length of the molecular wire. Resonant transport through the first molecular orbital is found to be dominated by charge-carrier injection into the molecule, rather than by the intrinsic resistance of the molecular wire length.

Ring Theory

CERN Document Server

Jara, Pascual; Torrecillas, Blas

1988-01-01

The papers in this proceedings volume are selected research papers in different areas of ring theory, including graded rings, differential operator rings, K-theory of noetherian rings, torsion theory, regular rings, cohomology of algebras, local cohomology of noncommutative rings. The book will be important for mathematicians active in research in ring theory.

Finite element analysis of the Girkmann problem using the modern hp-version and the classical h-version

KAUST Repository

Niemi, Antti; Babuška, Ivo M.; Pitkä ranta, Juhani; Demkowicz, Leszek F.

2011-01-01

elasticity theory and (2) by using a dimensionally reduced shell-ring model. In the first approach the problem is solved with a fully automatic hp-adaptive finite element solver whereas the classical h-version of the finite element method is used

Thermodynamics of Small Alkali Metal Halide Cluster Ions: Comparison of Classical Molecular Simulations with Experiment and Quantum Chemistry

Energy Technology Data Exchange (ETDEWEB)

Vlcek, Lukas [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Uhlik, Filip [Charles Univ., Prague (Czech Republic); Moucka, Filip [Purkinje Univ. (Czech Republic); Nezbeda, Ivo [Purkinje Univ. (Czech Republic); Academy of Sciences of the Czech Republic (ASCR), Prague (Czech Republic); Chialvo, Ariel A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2015-12-16

We evaluate the ability of selected classical molecular models to describe the thermodynamic and structural aspects of gas-phase hydration of alkali halide ions and the formation of small water clusters. To understand the effect of many-body interactions (polarization) and charge penetration effects on the accuracy of a force field, we perform Monte Carlo simulations with three rigid water models using different functional forms to account for these effects: (i) point charge non-polarizable SPC/E, (ii) Drude point charge polarizable SWM4- DP, and (iii) Drude Gaussian charge polarizable BK3. Model predictions are compared with experimental Gibbs free energies and enthalpies of ion hydration, and with microscopic structural properties obtained from quantum DFT calculations. We find that all three models provide comparable predictions for pure water clusters and cation hydration, but differ significantly in their description of anion hydration. None of the investigated classical force fields can consistently and quantitatively reproduce the experimental gas phase hydration thermodynamics. The outcome of this study highlights the relation between the functional form that describes the effective intermolecular interactions and the accuracy of the resulting ion hydration properties.

Chemical Reaction Rates from Ring Polymer Molecular Dynamics: Zero Point Energy Conservation in Mu + H2 → MuH + H.

Science.gov (United States)

Pérez de Tudela, Ricardo; Aoiz, F J; Suleimanov, Yury V; Manolopoulos, David E

2012-02-16

A fundamental issue in the field of reaction dynamics is the inclusion of the quantum mechanical (QM) effects such as zero point energy (ZPE) and tunneling in molecular dynamics simulations, and in particular in the calculation of chemical reaction rates. In this work we study the chemical reaction between a muonium atom and a hydrogen molecule. The recently developed ring polymer molecular dynamics (RPMD) technique is used, and the results are compared with those of other methods. For this reaction, the thermal rate coefficients calculated with RPMD are found to be in excellent agreement with the results of an accurate QM calculation. The very minor discrepancies are within the convergence error even at very low temperatures. This exceptionally good agreement can be attributed to the dominant role of ZPE in the reaction, which is accounted for extremely well by RPMD. Tunneling only plays a minor role in the reaction.

Coherent Instabilities of ILC Damping Ring

Energy Technology Data Exchange (ETDEWEB)

Heifets, S.; Stupakov, G.; Bane, K.; /SLAC

2006-09-27

The paper presents the first attempt to estimates the ILC damping ring impedance and compare thresholds of the classical instabilities for several designs initially proposed for the DR. The work was carried out in the spring of 2006. Since then the choice of the DR is narrowed. Nevertheless, the analysis described may be useful for the next iterations of the beam stability. Overall, the conventional instabilities will have little impact on the ring performance provided the careful design of the ring minimizes the impedance below acceptable level indicated above. The only exception is the transverse CB instability. The longitudinal CB is less demanding. However, even the transverse CB instability would have threshold current above nominal provided the aperture in the wigglers is increased from 8 mm to 16 mm. The microwave instability needs more studies. Nevertheless, we should remember that the ILC DR is different from existing high-current machines at least in two respects: absence of the beam-beam tune spread stabilizing beams in colliders, and unusual strict requirements for low emittance. That may cause new problems such as bunch emittance dilution due to high-frequency wakes (BPMs, grooves), etc. Even if such a possibility exists, it probably universal for all machines and ought be addressed in the design of vacuum components rather than have effect on the choice of the machine design.

Nonlinear quantum piston for the controlled generation of vortex rings and soliton trains

KAUST Repository

Pinsker, Florian; Berloff, Natalia G.; Pé rez-Garcí a, Ví ctor M.

2013-01-01

We propose a simple way to generate nonlinear excitations in a controllable way by managing interactions in Bose-Einstein condensates. Under the action of a quantum analog of a classical piston, the condensed atoms are pushed through the trap, generating vortex rings infully three-dimensional condensates or soliton trains in quasi-one-dimensional scenarios. The vortex rings form due to transverse instability of the shock-wave train, enhanced and supported by the energy transfer between waves. We elucidate in what sense the self-interactions within the atom cloud define the properties of the generated vortex rings and soliton trains. Based on the quantum-piston scheme we study the behavior of two-component Bose-Einstein condensates and analyze how the presence of an additional superfluid influences the generation of vortex rings or solitons in the other component, and vice versa. Finally, we show the dynamical emergence of skyrmions within two-component systems in the immiscible regime. © 2013 American Physical Society.

Nonlinear quantum piston for the controlled generation of vortex rings and soliton trains

KAUST Repository

Pinsker, Florian

2013-05-29

We propose a simple way to generate nonlinear excitations in a controllable way by managing interactions in Bose-Einstein condensates. Under the action of a quantum analog of a classical piston, the condensed atoms are pushed through the trap, generating vortex rings infully three-dimensional condensates or soliton trains in quasi-one-dimensional scenarios. The vortex rings form due to transverse instability of the shock-wave train, enhanced and supported by the energy transfer between waves. We elucidate in what sense the self-interactions within the atom cloud define the properties of the generated vortex rings and soliton trains. Based on the quantum-piston scheme we study the behavior of two-component Bose-Einstein condensates and analyze how the presence of an additional superfluid influences the generation of vortex rings or solitons in the other component, and vice versa. Finally, we show the dynamical emergence of skyrmions within two-component systems in the immiscible regime. © 2013 American Physical Society.

Report of the eRHIC Ring-Ring Working Group

Energy Technology Data Exchange (ETDEWEB)

Aschenauer, E. C. [Brookhaven National Lab. (BNL), Upton, NY (United States); Berg, S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Blaskiewicz, M. [Brookhaven National Lab. (BNL), Upton, NY (United States); Brennan, M. [Brookhaven National Lab. (BNL), Upton, NY (United States); Fedotov, A. [Brookhaven National Lab. (BNL), Upton, NY (United States); Fischer, W. [Brookhaven National Lab. (BNL), Upton, NY (United States); Litvinenko, V. [Brookhaven National Lab. (BNL), Upton, NY (United States); Montag, C. [Brookhaven National Lab. (BNL), Upton, NY (United States); Palmer, R. [Brookhaven National Lab. (BNL), Upton, NY (United States); Parker, B. [Brookhaven National Lab. (BNL), Upton, NY (United States); Peggs, S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Ptitsyn, V. [Brookhaven National Lab. (BNL), Upton, NY (United States); Ranjbar, V. [Brookhaven National Lab. (BNL), Upton, NY (United States); Tepikian, S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Trbojevic, D. [Brookhaven National Lab. (BNL), Upton, NY (United States); Willeke, F. [Brookhaven National Lab. (BNL), Upton, NY (United States)

2015-10-13

This report evaluates the ring-ring option for eRHIC as a lower risk alternative to the linac-ring option. The reduced risk goes along with a reduced initial luminosity performance. However, a luminosity upgrade path is kept open. This upgrade path consists of two branches, with the ultimate upgrade being either a ring-ring or a linac-ring scheme. The linac-ring upgrade could be almost identical to the proposed linac-ring scheme, which is based on an ERL in the RHIC tunnel. This linac-ring version has been studied in great detail over the past ten years, and its significant risks are known. On the other hand, no detailed work on an ultimate performance ring-ring scenario has been performed yet, other than the development of a consistent parameter set. Pursuing the ring-ring upgrade path introduces high risks and requires significant design work that is beyond the scope of this report.

Optical properties of helical cylindrical molecular aggregates : the homogeneous limit

NARCIS (Netherlands)

Didraga, C.; Klugkist, J.A.; Knoester, J.

2002-01-01

Using a Frenkel exciton model, we study the optical absorption spectrum and linear and circular dichroism (CD) spectra of cylindrical molecular aggregates. We demonstrate that such aggregates can always be described as a stack of molecular rings with nearest-neighbor rings rotated relative to each

Optical Properties of Helical Cylindrical Molecular Aggregates : The Homogeneous Limit

NARCIS (Netherlands)

Didraga, Cătălin; Klugkist, Joost A.; Knoester, Jasper

2002-01-01

Using a Frenkel exciton model, we study the optical absorption spectrum and linear and circular dichroism (CD) spectra of cylindrical molecular aggregates. We demonstrate that such aggregates can always be described as a stack of molecular rings with nearest-neighbor rings rotated relative to each

Optimal laser control of ultrafast photodissociation of I2- in water: Mixed quantum/classical molecular dynamics simulation

International Nuclear Information System (INIS)

Nishiyama, Yoshikazu; Kato, Tsuyoshi; Ohtsuki, Yukiyoshi; Fujimura, Yuichi

2004-01-01

A linearized optimal control method in combination with mixed quantum/classical molecular dynamics simulation is used for numerically investigating the possibility of controlling photodissociation wave packets of I 2 - in water. Optimal pulses are designed using an ensemble of photodissociation samples, aiming at the creation of localized dissociation wave packets. Numerical results clearly show the effectiveness of the control although the control achievement is reduced with an increase in the internuclear distance associated with a target region. We introduce effective optimal pulses that are designed using a statistically averaged effective dissociation potential, and show that they semiquantitatively reproduce the control achievements calculated by using optimal pulses. The control mechanisms are interpreted from the time- and frequency-resolved spectra of the effective optimal pulses

Classical Wigner method with an effective quantum force: application to reaction rates.

Science.gov (United States)

Poulsen, Jens Aage; Li, Huaqing; Nyman, Gunnar

2009-07-14

We construct an effective "quantum force" to be used in the classical molecular dynamics part of the classical Wigner method when determining correlation functions. The quantum force is obtained by estimating the most important short time separation of the Feynman paths that enter into the expression for the correlation function. The evaluation of the force is then as easy as classical potential energy evaluations. The ideas are tested on three reaction rate problems. The resulting transmission coefficients are in much better agreement with accurate results than transmission coefficients from the ordinary classical Wigner method.

Molecular collision theory

CERN Document Server

Child, M S

2010-01-01

This high-level monograph offers an excellent introduction to the theory required for interpretation of an increasingly sophisticated range of molecular scattering experiments. There are five helpful appendixes dealing with continuum wavefunctions, Green's functions, semi-classical connection formulae, curve-crossing in the momentum representation, and elements of classical mechanics.The contents of this volume have been chosen to emphasize the quantum mechanical and semi-classical nature of collision events, with little attention given to purely classical behavior. The treatment is essentiall

Chiral rings and anomalies in supersymmetric gauge theory

International Nuclear Information System (INIS)

Cachazo, Freddy; Witten, Edward; Seiberg, Nathan; Douglas, Michael R.

2002-01-01

Motivated by recent work of Dijkgraaf and Vafa, we study anomalies and the chiral ring structure in a supersymmetric U(N) gauge theory with an adjoint chiral superfield and an arbitrary superpotential. A certain generalization of the Konishi anomaly leads to an equation which is identical to the loop equation of a bosonic matrix model. This allows us to solve for the expectation values of the chiral operators as functions of a finite number of 'integration constants'. From this, we can derive the Dijkgraaf-Vafa relation of the effective superpotential to a matrix model. Some of our results are applicable to more general theories. For example, we determine the classical relations and quantum deformations of the chiral ring of N=1 super Yang-Mills theory with SU(N) gauge group, showing, as one consequence, that all supersymmetric vacua of this theory have a nonzero chiral condensate. (author)

2,2'-(Carbono-thio-yldisulfanedi-yl)bis-(2-methyl-propanoic acid).

Science.gov (United States)

Moreno-Fuquen, Rodolfo; Grande, Carlos; Advincula, Rigoberto C; Tenorio, Juan C; Ellena, Javier

2013-05-01

The mol-ecular structure of the title compound, C9H14O4S3, exhibits intra-molecular C-H⋯S hydrogen bonds. In the crystal, pairs of O-H⋯O hydrogen bonds lead to the formation of centrosymmetric dimers, which are in turn connected by weak C-H⋯O inter-actions. The combination of these inter-actions generates edge-fused R 2 (2)(8) and R 2 (2)(20) rings running along [211].

Free electron laser on the ACO storage ring

International Nuclear Information System (INIS)

Elleaume, P.

1984-06-01

This dissertation presents the design and characteristics of a Free Electron Laser built on the electron storage ring ACO at Orsay. The weak optical gain available (approximately 0.1% per pass) necessitated the use of an optical klystron instead of an undulator and the use of mirror with extremely high reflectivity. The laser characteristics: spectra, micro and macro-temporal structures, transverse structure and power are presented. They are in very good agreement with a classical theory based on the Lorentz force and Maxwell equations [fr

Quantum interference effect in electron tunneling through a quantum-dot-ring spin valve.

Science.gov (United States)

Ma, Jing-Min; Zhao, Jia; Zhang, Kai-Cheng; Peng, Ya-Jing; Chi, Feng

2011-03-28

Spin-dependent transport through a quantum-dot (QD) ring coupled to ferromagnetic leads with noncollinear magnetizations is studied theoretically. Tunneling current, current spin polarization and tunnel magnetoresistance (TMR) as functions of the bias voltage and the direct coupling strength between the two leads are analyzed by the nonequilibrium Green's function technique. It is shown that the magnitudes of these quantities are sensitive to the relative angle between the leads' magnetic moments and the quantum interference effect originated from the inter-lead coupling. We pay particular attention on the Coulomb blockade regime and find the relative current magnitudes of different magnetization angles can be reversed by tuning the inter-lead coupling strength, resulting in sign change of the TMR. For large enough inter-lead coupling strength, the current spin polarizations for parallel and antiparallel magnetic configurations will approach to unit and zero, respectively.PACS numbers:

Quantum interference effect in electron tunneling through a quantum-dot-ring spin valve

Directory of Open Access Journals (Sweden)

Ma Jing-Min

2011-01-01

Full Text Available Abstract Spin-dependent transport through a quantum-dot (QD ring coupled to ferromagnetic leads with noncollinear magnetizations is studied theoretically. Tunneling current, current spin polarization and tunnel magnetoresistance (TMR as functions of the bias voltage and the direct coupling strength between the two leads are analyzed by the nonequilibrium Green's function technique. It is shown that the magnitudes of these quantities are sensitive to the relative angle between the leads' magnetic moments and the quantum interference effect originated from the inter-lead coupling. We pay particular attention on the Coulomb blockade regime and find the relative current magnitudes of different magnetization angles can be reversed by tuning the inter-lead coupling strength, resulting in sign change of the TMR. For large enough inter-lead coupling strength, the current spin polarizations for parallel and antiparallel magnetic configurations will approach to unit and zero, respectively. PACS numbers:

Effects of different reaction mediums on ring opening polymerization ...

African Journals Online (AJOL)

This work examined the effects of reaction conditions on ring opening ... of this study was to observe molecular weight distribution, conversion rates, and thermal ... M monomer and 0.56 M solvent), 10 mg lipase were used in the experiments.

Dependency of the regio- and stereoselectivity of intramolecular, ring-closing glycosylations upon the ring size

Directory of Open Access Journals (Sweden)

Patrick Claude

2011-12-01

Full Text Available Phenyl 3,4,6-tri-O-benzyl-2-O-(3-carboxypropionyl-1-thio-β-D-galactopyranoside (1 was condensed via its pentafluorophenyl ester 2 with 5-aminopentyl (4a, 4-aminobutyl (4b, 3-aminopropyl (4c and 2-aminoethyl 4,6-O-benzylidene-β-D-glucopyranoside (4d, prepared from the corresponding N-Cbz protected glucosides 3a–d, to give the corresponding 2-[3-(alkylcarbamoylpropionyl] tethered saccharides 5a–d. Intramolecular, ring closing glycosylation of the saccharides with NIS and TMSOTf afforded the tethered β(1→3 linked disaccharides 6a–c, the α(1→3 linked disaccharides 7a–d and the α(1→2 linked disaccharide 8d in ratios depending upon the ring size formed during glycosylation. No β(1→2 linked disaccharides were formed. Molecular modeling of saccharides 6–8 revealed that a strong aromatic stacking interaction between the aromatic parts of the benzyl and benzylidene protecting groups in the galactosyl and glucosyl moieties was mainly responsible for the observed regioselectivity and anomeric selectivity of the ring-closing glycosylation step.

Thermodynamics and Kinetics of Prenucleation Clusters, Classical and Non-Classical Nucleation.

Science.gov (United States)

Zahn, Dirk

2015-07-20

Recent observations of prenucleation species and multi-stage crystal nucleation processes challenge the long-established view on the thermodynamics of crystal formation. Here, we review and generalize extensions to classical nucleation theory. Going beyond the conventional implementation as has been used for more than a century now, nucleation inhibitors, precursor clusters and non-classical nucleation processes are rationalized as well by analogous concepts based on competing interface and bulk energy terms. This is illustrated by recent examples of species formed prior to/instead of crystal nucleation and multi-step nucleation processes. Much of the discussed insights were obtained from molecular simulation using advanced sampling techniques, briefly summarized herein for both nucleation-controlled and diffusion-controlled aggregate formation. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution Non-Commercial NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Status of the Frankfurt low energy electrostatic storage ring (FLSR)

Science.gov (United States)

King, F.; Kruppi, T.; Müller, J.; Dörner, R.; Schmidt, L. Ph H.; Schmidt-Böcking, H.; Stiebing, K. E.

2015-11-01

Frankfurt low-energy storage ring (FLSR) is an electrostatic storage ring for low-energy ions up to q · 80 keV (q being the ion charge state) at Institut für Kernphysik der Goethe-Universität, Frankfurt am Main, Germany. It has especially been designed to provide a basis for experiments on the dynamics of ionic and molecular collisions in complete kinematics, as well as for high precision and time resolved laser spectroscopy. The ring has ‘racetrack’ geometry with a circumference of 14.23 m. It comprises four experimental/diagnostic sections with regions of enhanced ion density (interaction regions). First beam has successfully been stored in FLSR in summer 2013. Since then the performance of the ring has continuously been improved and an electron target for experiments on dissociative recombination has been installed in one of the experimental sections.

WHEELS OF FIRE. IV. STAR FORMATION AND THE NEUTRAL INTERSTELLAR MEDIUM IN THE RING GALAXY AM0644-741

International Nuclear Information System (INIS)

Higdon, James L.; Higdon, Sarah J. U.; Rand, Richard J.

2011-01-01

We combine data from the Australia Telescope National Facility and Swedish ESO Submillimeter Telescope to investigate the neutral interstellar medium (ISM) in AM0644-741, a large and robustly star-forming ring galaxy. The galaxy's ISM is concentrated in the 42 kpc diameter starburst ring, but appears dominated by atomic gas, with a global molecular fraction (f mol ) of only 0.062 ± 0.005. Apart from the starburst peak, the gas ring appears stable against the growth of gravitational instabilities (Q gas = 3-11). Including the stellar component lowers Q overall, but not enough to make Q 2 content. AM0644-741's star formation law is highly peculiar: H I obeys a Schmidt law while H 2 is uncorrelated with star formation rate density. Photodissociation models yield low volume densities in the ring, especially in the starburst quadrant (n ∼ 2 cm -3 ), implying a warm neutral medium dominated ISM. At the same time, the ring's pressure and ambient far-ultraviolet radiation field lead to the expectation of a predominantly molecular ISM. We argue that the ring's high SFE, low f mol and n, and peculiar star formation law follow from the ISM's ∼> 100 Myr confinement time in the starburst ring, which amplifies the destructive effects of embedded massive stars and supernovae. As a result, the ring's molecular ISM becomes dominated by small clouds, causing M H 2 to be significantly underestimated by 12 CO line fluxes: in effect, X CO >> X Gal despite the ring's ≥solar metallicity. The observed H I is primarily a low-density photodissociation product, i.e., a tracer rather than a precursor of massive star formation. Such an 'over-cooked' ISM may be a general characteristic of evolved starburst ring galaxies.

Preparation of Bottlebrush Polymers via a One-Pot Ring-Opening Polymerization (ROP) and Ring-Opening Metathesis Polymerization (ROMP) Grafting-Through Strategy.

Science.gov (United States)

Radzinski, Scott C; Foster, Jeffrey C; Matson, John B

2016-04-01

Bottlebrush polymers are synthesized using a tandem ring-opening polymerization (ROP) and ring-opening metathesis polymerization (ROMP) strategy. For the first time, ROP and ROMP are conducted sequentially in the same pot to yield well-defined bottlebrush polymers with molecular weights in excess of 10(6) Da. The first step of this process involves the synthesis of a polylactide macromonomer (MM) via ROP of d,l-lactide initiated by an alcohol-functionalized norbornene. ROMP grafting-through is then carried out in the same pot to produce the bottlebrush polymer. The applicability of this methodology is evaluated for different MM molecular weights and bottlebrush backbone degrees of polymerization. Size-exclusion chromatographic and (1)H NMR spectroscopic analyses confirm excellent control over both polymerization steps. In addition, bottlebrush polymers are imaged using atomic force microscopy and stain-free transmission electron microscopy on graphene oxide. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Classical and semi-classical treatments of Li3+, Ne10++H(1s) collisions

International Nuclear Information System (INIS)

Errea, L F; Illescas, Clara; Mendez, L; Pons, B; Riera, A; Suarez, J

2004-01-01

We perform molecular close-coupling and impact-parameter classical trajectory Monte Carlo calculations of total and partial cross sections for capture and ionization in collisions of highly charged ions on H(1s). We first consider Li 3+ +H(1s) as a benchmark to ascertain the complementarity of the methods, and then Ne 10+ +H(1s), which has been scarcely studied up to now, and has recently become of interest for fusion plasma research

ASSOCIATIVE RINGS SOLVED AS LIE RINGS

Directory of Open Access Journals (Sweden)

M. B. Smirnov

2011-01-01

Full Text Available The paper has proved that an associative ring which is solvable of a n- class as a Lie ring has a nilpotent ideal of the nilpotent class not more than 3×10n–2  and a corresponding quotient ring satisfies an identity [[x1, x2, [x3, x4

Conformational Effects through Hydrogen Bonding in a Constrained γ-Peptide Template: From Intraresidue Seven-Membered Rings to a Gel-Forming Sheet Structure.

Science.gov (United States)

Awada, Hawraà; Grison, Claire M; Charnay-Pouget, Florence; Baltaze, Jean-Pierre; Brisset, François; Guillot, Régis; Robin, Sylvie; Hachem, Ali; Jaber, Nada; Naoufal, Daoud; Yazbeck, Ogaritte; Aitken, David J

2017-05-05

A series of three short oligomers (di-, tri-, and tetramers) of cis-2-(aminomethyl)cyclobutane carboxylic acid, a γ-amino acid featuring a cyclobutane ring constraint, were prepared, and their conformational behavior was examined spectroscopically and by molecular modeling. In dilute solutions, these peptides showed a number of low-energy conformers, including ribbonlike structures pleated around a rarely observed series of intramolecular seven-membered hydrogen bonds. In more concentrated solutions, these interactions defer to an organized supramolecular assembly, leading to thermoreversible organogel formation notably for the tripeptide, which produced fibrillar xerogels. In the solid state, the dipeptide adopted a fully extended conformation featuring a one-dimensional network of intermolecularly H-bonded molecules stacked in an antiparallel sheet alignment. This work provides unique insight into the interplay between inter- and intramolecular H-bonded conformer topologies for the same peptide template.

Medizinbibliotheken: inter:disziplinär – inter:national –inter:aktiv

Directory of Open Access Journals (Sweden)

Bauer, Bruno

2017-12-01

Full Text Available The focus of the current issue 3/2017 of GMS Medizin – Bibliothek – Information is the annual conference 2017 of the German Medical Libraries Association in Vienna. The motto of the conference was “Medical Libraries: inter:disciplinary – inter:national – inter:active”. The authors in this issue are Bruno Bauer (Austrian Transition to Open Access 2017–2020, Beata Górczynska (Development and structure of Polish veterinary school system and its libraries, Katharina Heldt, Henriette Senst & Jessica Riedel (Salon on the institute’s history: outstanding artifacts. 28.01.2016 to 15.12.2016, Jutta Matrisciano, Martina Semmler-Schmetz & Saskia Rohmer (Advice – From info snack to special menu: Solutions of the MedMA-Bib, Stefan Nortmann (The ‘Ersti-Café’ of the Medical Branch Library Münster, Sandra Rümmele (Toolbox: The new teaching library project of the Central Medical Library of the University Medical Center Hamburg-Eppendorf, Eva Seidlmayer & Christoph Poley (One Health – Transdisciplinarity at ZB MED and Heike Andermann (“Medical Libraries: inter:disciplinary – inter:national – inter:active”. Annual Meeting of the German Medical Library Association (AGMB, September 25 to 27, 2017 in Vienna. Furthermore this focus issue features articles from Stefan Grün & Christoph Poley (Statistical evaluation of semantic entities from metadata and full text on German Medical Science corpora and Iris Reimann (German MLA News; Competition of the German MLA Pioneer projects in medical libraries 2017: Introduction of the winners; Competition of the German MLA (AGMB Pioneer projects in medical libraries 2018 – Announcement.

6-Methyl-2-pyridyl N-acetyl-1-thio-β-d-glucosa­minide methanol monosolvate

Science.gov (United States)

Chen, Bo; Guo, Miao; Jin, Wei-Hua; Wang, Yan-Wei; Liang, Hong-Ze

2010-01-01

In the title compound, C14H20N2O5S·CH4O, the pyran­ose and pyridine rings are linked through an S atom. The pyran­ose ring has a normal chair conformation. An intra­molecular O—H⋯N hydrogen bond occurs. Inter­molecular O—H⋯O, N—H⋯O, O—H⋯N and weak C—H⋯O hydrogen bonding is present in the crystal structure. PMID:21587547

A classical approach in simple nuclear fusion reaction 1H2+1H3 using two-dimension granular molecular dynamics model

International Nuclear Information System (INIS)

Viridi, S.; Kurniadi, R.; Waris, A.; Perkasa, Y. S.

2012-01-01

Molecular dynamics in 2-D accompanied by granular model provides an opportunity to investigate binding between nuclei particles and its properties that arises during collision in a fusion reaction. A fully classical approach is used to observe the influence of initial angle of nucleus orientation to the product yielded by the reaction. As an example, a simplest fusion reaction between 1 H 2 and 1 H 3 is observed. Several products of the fusion reaction have been obtained, even the unreported ones, including temporary 2 He 4 nucleus.

The dynamical role of the central molecular ring within the framework of a seven-component Galaxy model

Science.gov (United States)

Simin, A. A.; Fridman, A. M.; Haud, U. A.

1991-09-01

A Galaxy model in which the surface density of the gas component has a sharp (two orders of magnitude) jump in the region of the outer radius of the molecular ring is constructed on the basis of observational data. This model is used to calculate the contributions of each population to the model curve of Galactic rotation. The value of the dimensionless increment of hydrodynamical instability for the gas component, being much less than 1, coincides with a similar magnitude for the same gas in the gravity field of the entire Galaxy. It is concluded that the unstable gas component of the Galaxy lies near the limit of the hydrodynamical instability, which is in accordance with the Le Chatelier principle. The stellar populations of the Galaxy probably do not affect the generation of the spiral structure in the gaseous component.

Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport.

Science.gov (United States)

Howard, Rebecca J; Carnevale, Vincenzo; Delemotte, Lucie; Hellmich, Ute A; Rothberg, Brad S

2018-04-01

Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.

The role of managers in organizational interventions and non -interventions – at intra and inter- organizational work places

DEFF Research Database (Denmark)

Ipsen, Christine; Nielsen, Karina

), or at the customers’ or clients’ locations (inter-organizational work) (Cropper, Huxham, Ebers, & Ring, 2008; Verburg, Bosch-Sijtsema, & Vartiainen, 2013). According to Fisher and Fisher (2001), time, space, and/or culture constitute the distance between managers and employees. In a systematic review, Crawford et al......Over the years, workplaces and employees have become more dispersed due to organizational changes in large traditional organizations and the development of new business opportunities across the world, such as shifts from production to service- or knowledge- based work environment (Hinds & Kiesler....... (2011) found that only a few studies have investigated the wellbeing of employees who work at clients’ or customers’ offices (inter-organizational work) over a long period of time and how to best manage these employees. In inter-organizations, distance employees are employed by one company (the provider...

Mapping Ring Particle Cooling across Saturn's Rings with Cassini CIRS

Science.gov (United States)

Brooks, Shawn M.; Spilker, L. J.; Edgington, S. G.; Pilorz, S. H.; Deau, E.

2010-10-01

Previous studies have shown that the rings' thermal inertia, a measure of their response to changes in the thermal environment, varies from ring to ring. Thermal inertia can provide insight into the physical structure of Saturn's ring particles and their regoliths. Low thermal inertia and quick temperature responses are suggestive of ring particles that have more porous or fluffy regoliths or that are riddled with cracks. Solid, coherent particles can be expected to have higher thermal inertias (Ferrari et al. 2005). Cassini's Composite Infrared Spectrometer has recorded millions of spectra of Saturn's rings since its arrival at Saturn in 2004 (personal communication, M. Segura). CIRS records far infrared radiation between 10 and 600 cm-1 (16.7 and 1000 µm) at focal plane 1 (FP1), which has a field of view of 3.9 mrad. Thermal emission from Saturn's rings peaks in this wavelength range. FP1 spectra can be used to infer ring temperatures. By tracking how ring temperatures vary, we can determine the thermal inertia of the rings. In this work we focus on CIRS observations of the shadowed portion of Saturn's rings. The thermal budget of the rings is dominated by the solar radiation absorbed by its constituent particles. When ring particles enter Saturn's shadow this source of energy is abruptly cut off. As a result, ring particles cool as they traverse Saturn's shadow. From these shadow observations we can create cooling curves at specific locations across the rings. We will show that the rings' cooling curves and thus their thermal inertia vary not only from ring to ring, but by location within the individual rings. This research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under contract with NASA. Copyright 2010 California Institute of Technology. Government sponsorship acknowledged.

Status of the Frankfurt low energy electrostatic storage ring (FLSR)

International Nuclear Information System (INIS)

King, F; Kruppi, T; Müller, J; Dörner, R; Schmidt, L Ph H; Schmidt-Böcking, H; Stiebing, K E

2015-01-01

Frankfurt low-energy storage ring (FLSR) is an electrostatic storage ring for low-energy ions up to q · 80 keV (q being the ion charge state) at Institut für Kernphysik der Goethe-Universität, Frankfurt am Main, Germany. It has especially been designed to provide a basis for experiments on the dynamics of ionic and molecular collisions in complete kinematics, as well as for high precision and time resolved laser spectroscopy. The ring has ‘racetrack’ geometry with a circumference of 14.23 m. It comprises four experimental/diagnostic sections with regions of enhanced ion density (interaction regions). First beam has successfully been stored in FLSR in summer 2013. Since then the performance of the ring has continuously been improved and an electron target for experiments on dissociative recombination has been installed in one of the experimental sections. (paper)

Numerical Simulations of Saturn's B Ring: Granular Friction as a Mediator between Self-gravity Wakes and Viscous Overstability

Energy Technology Data Exchange (ETDEWEB)

Ballouz, Ronald-Louis; Richardson, Derek C. [Department of Astronomy, University of Maryland, College Park, MD 20742-2421 (United States); Morishima, Ryuji [University of California, Los Angeles, Institute of Geophysics and Planetary Physics, Los Angeles, CA (United States)

2017-04-01

We study the B ring’s complex optical depth structure. The source of this structure may be the complex dynamics of the Keplerian shear and the self-gravity of the ring particles. The outcome of these dynamic effects depends sensitively on the collisional and physical properties of the particles. Two mechanisms can emerge that dominate the macroscopic physical structure of the ring: self-gravity wakes and viscous overstability. Here we study the interplay between these two mechanisms by using our recently developed particle collision method that allows us to better model the inter-particle contact physics. We find that for a constant ring surface density and particle internal density, particles with rough surfaces tend to produce axisymmetric ring features associated with the viscous overstability, while particles with smoother surfaces produce self-gravity wakes.

Supported Catalysts Useful in Ring-Closing Metathesis, Cross Metathesis, and Ring-Opening Metathesis Polymerization

Directory of Open Access Journals (Sweden)

Jakkrit Suriboot

2016-04-01

Full Text Available Ruthenium and molybdenum catalysts are widely used in synthesis of both small molecules and macromolecules. While major developments have led to new increasingly active catalysts that have high functional group compatibility and stereoselectivity, catalyst/product separation, catalyst recycling, and/or catalyst residue/product separation remain an issue in some applications of these catalysts. This review highlights some of the history of efforts to address these problems, first discussing the problem in the context of reactions like ring-closing metathesis and cross metathesis catalysis used in the synthesis of low molecular weight compounds. It then discusses in more detail progress in dealing with these issues in ring opening metathesis polymerization chemistry. Such approaches depend on a biphasic solid/liquid or liquid separation and can use either always biphasic or sometimes biphasic systems and approaches to this problem using insoluble inorganic supports, insoluble crosslinked polymeric organic supports, soluble polymeric supports, ionic liquids and fluorous phases are discussed.

Inter-annual to multi-decadal variability in prairie water resources over the past millennium

International Nuclear Information System (INIS)

Sauchyn, D.

2008-01-01

In the Prairie Provinces, declining levels have been recently recorded for various rivers and lakes, and further reductions are projected. These trends reflect human impact in terms of increasing water consumption and possibly anthropogenic climate change. From the coupling of hydrological models and climate change scenarios, researchers have projected lower future summer flows as global warming brings shorter warmer winters and longer and generally drier summers to western Canada. However, the detection and interpretation of trends from gauge records and model outputs are constrained by the relatively short perspective of decades and the uncertainties associated with projecting climate change and its impacts on hydrological regimes. A longer perspective on inter-annual to multi-decadal variability in water resources is available from moisture-sensitive tree-ring chronologies. We have established a dense network of low elevation chronologies spanning the headwaters of the Saskatchewan, Missouri, Churchill and Mackenzie River basins. Standardized tree-ring width for a large sample of trees and sites is a strong regional signal of annual and seasonal hydroclimate, and an especially good proxy of low water levels. Proxy streamflow records, up to 800 years in length, show quasi-periodic variability at inter-annual to multi-decadal scales that correspond to the tempo of sea-surface temperature anomalies. The industrial sponsors of our research, Manitoba Hydro and EPCOR, anticipate the use of our tree-ring reconstructions for informing forecasts of future water supplies and planning adaptation to climate change. Engineers from these companies, and more than 50 other water managers and planners from the Prairie Provinces, attended a workshop in March 2008 to explore potential applications of paleo-hydrological records to water resource management. (author)

Use of a ring chromosome and pulsed-field gels to study recombinational repair

International Nuclear Information System (INIS)

Game, J.C.; Arabi, S.; Mortimer, R.K.

1989-01-01

In wild type yeast, it is known that x-ray induced DNA double-strand breaks (dsb) are repaired, leading to recovery of high molecular-weight molecules on gradients or pulsed-field gels. There is genetic evidence that some or all of this repair occurs via recombinational mechanisms involving sister-chromatid exchange (SCE) and (in diploids) inter-homologue recombination. However, this evidence is indirect and qualitative. The authors of this paper are attempting to use pulsed-field gels to detect and measure recombinational repair at the physical level in yeast strains with a circular homologue of Chr. III. The authors have previously used such strains to study meiotic recombination. The authors have shown that double-size circular molecules can be detected in log-phase haploid yeast cells carrying a ring chromosome, when such cells are exposed to x-rays and allowed time for subsequent repair. Large circular molecules will not enter our pulsed-field gels, but treatment of the DNA samples with radiation prior to running the gels will linearize a fraction of such molecules with a single dsb. Such linearized molecules will run as a band whose position indicates the size of the original unbroken circles

Molecular Connectivity Predefines Polypharmacology: Aliphatic Rings, Chirality, and sp3 Centers Enhance Target Selectivity

Directory of Open Access Journals (Sweden)

Stefania Monteleone

2017-08-01

Full Text Available Dark chemical matter compounds are small molecules that have been recently identified as highly potent and selective hits. For this reason, they constitute a promising class of possible candidates in the process of drug discovery and raise the interest of the scientific community. To this purpose, Wassermann et al. (2015 have described the application of 2D descriptors to characterize dark chemical matter. However, their definition was based on the number of reported positive assays rather than the number of known targets. As there might be multiple assays for one single target, the number of assays does not fully describe target selectivity. Here, we propose an alternative classification of active molecules that is based on the number of known targets. We cluster molecules in four classes: black, gray, and white compounds are active on one, two to four, and more than four targets respectively, whilst inactive compounds are found to be inactive in the considered assays. In this study, black and inactive compounds are found to have not only higher solubility, but also a higher number of chiral centers, sp3 carbon atoms and aliphatic rings. On the contrary, white compounds contain a higher number of double bonds and fused aromatic rings. Therefore, the design of a screening compound library should consider these molecular properties in order to achieve target selectivity or polypharmacology. Furthermore, analysis of four main target classes (GPCRs, kinases, proteases, and ion channels shows that GPCR ligands are more selective than the other classes, as the number of black compounds is higher in this target superfamily. On the other side, ligands that hit kinases, proteases, and ion channels bind to GPCRs more likely than to other target classes. Consequently, depending on the target protein family, appropriate screening libraries can be designed in order to minimize the likelihood of unwanted side effects early in the drug discovery process

Mechanochemical Ring-Opening Polymerization of Lactide: Liquid-Assisted Grinding for the Green Synthesis of Poly(lactic acid) with High Molecular Weight.

Science.gov (United States)

Ohn, Nuri; Shin, Jihoon; Kim, Sung Sik; Kim, Jeung Gon

2017-09-22

Mechanochemical polymerization of lactide is carried out by using ball milling. Mechanical energy from collisions between the balls and the vessel efficiently promotes an organic-base-mediated metal- and solvent-free solid-state polymerization. Investigation of the parameters of the ball-milling synthesis revealed that the degree of lactide ring-opening polymerization could be modulated by the ball-milling time, vibration frequency, mass of the ball media, and liquid-assisted grinding. Liquid-assisted grinding was found to be an especially important factor for achieving a high degree of mechanochemical polymerization. Although polymer-chain scission from the strong collision energy prevented mechanical-force-driven high-molecular-weight polymer synthesis, the addition of only a small amount of liquid enabled sufficient energy dissipation and poly(lactic acid) was thereby obtained with a molecular weight of over 1×10 5  g mol -1 . © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atomic cranks and levers control sugar ring conformations

International Nuclear Information System (INIS)

Zhang Qingmin; Lee, Gwangrog; Marszalek, Piotr E

2005-01-01

In this paper we review the conformational analysis of sugar rings placed under tension during mechanical manipulations of single polysaccharide molecules with the atomic force microscope and during steered molecular dynamics simulations. We examine the role of various chemical bonds and linkages between sugar rings in inhibiting or promoting their conformational transitions by means of external forces. Small differences in the orientation of one chemical bond on the sugar ring can produce significantly different mechanical properties at the polymer level as exemplified by two polysaccharides: cellulose, composed of β-1→4-linked D-glucose, and amylose, composed of α-1→4-linked D-glucose. In contrast to β-glucose rings, which are mechanically stable and produce simple entropic elasticity of the chain, α-glucose rings flip under tension from their chair to a boat-like structure and these transitions produce deviations of amylose elasticity from the freely jointed chain model. We also examine the deformation of two mechanically complementary 1→6-linked polysaccharides: pustulan, a β-1→6-linked glucan, and dextran, a α-1→6-linked glucan. Forced rotations about the C 5 -C 6 bonds govern the elasticity of pustulan, and complex conformational transitions that involve simultaneous C 5 -C 6 rotations and chair-boat transitions govern the elasticity of dextran. Finally, we discuss the likelihood of various conformational transitions in sugar rings in biological settings and speculate on their significance

Inter-individual cognitive variability in children with Asperger’s syndrome

Directory of Open Access Journals (Sweden)

Maria Luz Gonzalez-Gadea

2014-07-01

Full Text Available Multiple studies have tried to establish the distinctive profile of individuals with Asperger’s syndrome (AS. However, recent reports suggest that adults with AS feature heterogeneous cognitive profiles. The present study explores inter-individual variability in children with AS through group comparison and multiple case series analysis. All participants completed an extended battery including measures of fluid and crystallized intelligence, executive functions, theory of mind, and classical neuropsychological tests. Significant group differences were found in theory of mind and other domains related to global information processing. However, the AS group showed high inter-individual variability (both sub- and supra-normal performance on most cognitive tasks. Furthermore, high fluid intelligence correlated with less general cognitive impairment, high cognitive flexibility, and speed motor processing. In light of these findings, we propose that children with AS are characterized by a distinct, uneven pattern of cognitive strengths and weaknesses.

Atomic collision experiments at the border line between classical and quantum mechanics

International Nuclear Information System (INIS)

Aquilanti, V.

1984-01-01

In order to understand atomic and molecular interactions, one has to learn how to live with the wave-particle duality, considering classical nuclei and quantum electrons. A better way, illustrated by reference to experiments, is by quasiclassical (or semi-classical) mechanics, governing a world with a quasi-zero Planck's constant. One thus explains optical analogs (shadows, rainbows, glories) as interference effects in atomic collisions. Reference is also made to Wheeler's 'black bird' on the inversion problem from spectroscopy and scattering to molecular structure. The paper concludes outlining a journey in the hyperspace to escape from Einstein's torus and to find interferences and resonances in three body scattering and reactions. (Auth.)

Crosslinking of SAVY-4000 O-rings as a Function of Aging Conditions

Energy Technology Data Exchange (ETDEWEB)

Van Buskirk, Caleb Griffith [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-09-08

SAVY-4000 containers were developed as a part of DOE M 441.1-1 to protect workers who handle stored nuclear material from exposure due to loss of containment.1 The SAVY-4000 is comprised of three parts: a lid, a container, and a cross-linked fluoropolymer O-ring. Degradation of the O-ring during use could limit the lifetime of the SAVY-4000. In order to quantify the chemical changes of the Oring over time, the molecular weight between crosslinks was determined as a function of aging conditions using a swelling technique. Because the O-ring is a cross-linked polymer, it will absorb solvent into its matrix without dissolving. The relative amount of solvent uptake can be related to the degree of crosslinking using an equation developed by Paul Flory and John Rehner Jr3. This method was used to analyze O-ring samples aged under thermal and ionizing-radiation conditions. It was found that at the harsher thermal gaining conditions in absence of ionizing-radiation the average molecular weight between crosslinks decreased, indicating a rise in crosslinks, which may be attributable to advanced aging with no ionizing radiation present. Inversely, in the presence of ionizing radiation it was found that material has a higher level of cross-linking with age. This information could be used to help predict the lifetime of the O-rings in SAVY-4000 containers under service conditions.

A ring polymer molecular dynamics study of the isotopologues of the H + H2 reaction.

Science.gov (United States)

Suleimanov, Yury V; de Tudela, Ricardo Pérez; Jambrina, Pablo G; Castillo, Jesús F; Sáez-Rábanos, Vicente; Manolopoulos, David E; Aoiz, F Javier

2013-03-14

The inclusion of Quantum Mechanical (QM) effects such as zero point energy (ZPE) and tunneling in simulations of chemical reactions, especially in the case of light atom transfer, is an important problem in computational chemistry. In this respect, the hydrogen exchange reaction and its isotopic variants constitute an excellent benchmark for the assessment of approximate QM methods. In particular, the recently developed ring polymer molecular dynamics (RPMD) technique has been demonstrated to give very good results for bimolecular chemical reactions in the gas phase. In this work, we have performed a detailed RPMD study of the H + H(2) reaction and its isotopologues Mu + H(2), D + H(2) and Heμ + H(2), at temperatures ranging from 200 to 1000 K. Thermal rate coefficients and kinetic isotope effects have been computed and compared with exact QM calculations as well as with quasiclassical trajectories and experiment. The agreement with the QM results is good for the heaviest isotopologues, with errors ranging from 15% to 45%, and excellent for Mu + H(2), with errors below 15%. We have seen that RPMD is able to capture the ZPE effect very accurately, a desirable feature of any method based on molecular dynamics. We have also verified Richardson and Althorpe's prediction [J. O. Richardson and S. C. Althorpe, J. Chem. Phys., 2009, 131, 214106] that RPMD will overestimate thermal rates for asymmetric reactions and underestimate them for symmetric reactions in the deep tunneling regime. The ZPE effect along the reaction coordinate must be taken into account when assigning the reaction symmetry in the multidimensional case.

Ehlers-Danlos syndrome, classical type.

Science.gov (United States)

Bowen, Jessica M; Sobey, Glenda J; Burrows, Nigel P; Colombi, Marina; Lavallee, Mark E; Malfait, Fransiska; Francomano, Clair A

2017-03-01

Classical EDS is a heritable disorder of connective tissue. Patients are affected with joint hypermobility, skin hyperextensibilty, and skin fragility leading to atrophic scarring and significant bruising. These clinical features suggest consideration of the diagnosis which then needs to be confirmed, preferably by genetic testing. The most recent criteria for the diagnosis of EDS were devised in Villefranche in 1997. [Beighton et al. (1998); Am J Med Genet 77:31-37]. The aims set out in the Villefranche Criteria were: to enable diagnostic uniformity for clinical and research purposes, to understand the natural history of each subtype of EDS, to inform management and genetic counselling, and to identify potential areas of research. The authors recognized that the criteria would need updating, but viewed the Villefranche nosology as a good starting point. Since 1997, there have been major advances in the molecular understanding of classical EDS. Previous question marks over genetic heterogeneity have been largely surpassed by evidence that abnormalities in type V collagen are the cause. Advances in molecular testing have made it possible to identify the causative mutation in the majority of patients. This has aided the further clarification of this diagnosis. The aim of this literature review is to summarize the current knowledge and highlight areas for future research. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Robustness of cluster synchronous patterns in small-world networks with inter-cluster co-competition balance

International Nuclear Information System (INIS)

Zhang, Jianbao; Ma, Zhongjun; Chen, Guanrong

2014-01-01

All edges in the classical Watts and Strogatz's small-world network model are unweighted and cooperative (positive). By introducing competitive (negative) inter-cluster edges and assigning edge weights to mimic more realistic networks, this paper develops a modified model which possesses co-competitive weighted couplings and cluster structures while maintaining the common small-world network properties of small average shortest path lengths and large clustering coefficients. Based on theoretical analysis, it is proved that the new model with inter-cluster co-competition balance has an important dynamical property of robust cluster synchronous pattern formation. More precisely, clusters will neither merge nor split regardless of adding or deleting nodes and edges, under the condition of inter-cluster co-competition balance. Numerical simulations demonstrate the robustness of the model against the increase of the coupling strength and several topological variations

Robustness of cluster synchronous patterns in small-world networks with inter-cluster co-competition balance

Science.gov (United States)

Zhang, Jianbao; Ma, Zhongjun; Chen, Guanrong

2014-06-01

All edges in the classical Watts and Strogatz's small-world network model are unweighted and cooperative (positive). By introducing competitive (negative) inter-cluster edges and assigning edge weights to mimic more realistic networks, this paper develops a modified model which possesses co-competitive weighted couplings and cluster structures while maintaining the common small-world network properties of small average shortest path lengths and large clustering coefficients. Based on theoretical analysis, it is proved that the new model with inter-cluster co-competition balance has an important dynamical property of robust cluster synchronous pattern formation. More precisely, clusters will neither merge nor split regardless of adding or deleting nodes and edges, under the condition of inter-cluster co-competition balance. Numerical simulations demonstrate the robustness of the model against the increase of the coupling strength and several topological variations.

Robustness of cluster synchronous patterns in small-world networks with inter-cluster co-competition balance

Energy Technology Data Exchange (ETDEWEB)

Zhang, Jianbao [School of Science, Hangzhou Dianzi University, Hangzhou 310018 (China); Ma, Zhongjun, E-mail: mzj1234402@163.com [School of Mathematics and Computing Science, Guilin University of Electronic Technology, Guilin 541004 (China); Chen, Guanrong [Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong (China)

2014-06-15

All edges in the classical Watts and Strogatz's small-world network model are unweighted and cooperative (positive). By introducing competitive (negative) inter-cluster edges and assigning edge weights to mimic more realistic networks, this paper develops a modified model which possesses co-competitive weighted couplings and cluster structures while maintaining the common small-world network properties of small average shortest path lengths and large clustering coefficients. Based on theoretical analysis, it is proved that the new model with inter-cluster co-competition balance has an important dynamical property of robust cluster synchronous pattern formation. More precisely, clusters will neither merge nor split regardless of adding or deleting nodes and edges, under the condition of inter-cluster co-competition balance. Numerical simulations demonstrate the robustness of the model against the increase of the coupling strength and several topological variations.

Self-organized formation of GaSb/GaAs quantum rings.

Science.gov (United States)

Timm, R; Eisele, H; Lenz, A; Ivanova, L; Balakrishnan, G; Huffaker, D L; Dähne, M

2008-12-19

Ring-shaped GaSb/GaAs quantum dots, grown by molecular beam epitaxy, were studied using cross-sectional scanning tunneling microscopy. These quantum rings have an outer shape of a truncated pyramid with baselengths around 15 nm and heights of about 2 nm but are characterized by a clear central opening extending over about 40% of the outer baselength. They form spontaneously during the growth and subsequent continuous capping of GaSb/GaAs quantum dots due to the large strain and substantial As-for-Sb exchange reactions leading to strong Sb segregation.

Quantum computation with classical light: Implementation of the Deutsch–Jozsa algorithm

International Nuclear Information System (INIS)

Perez-Garcia, Benjamin; McLaren, Melanie; Goyal, Sandeep K.; Hernandez-Aranda, Raul I.; Forbes, Andrew; Konrad, Thomas

2016-01-01

Highlights: • An implementation of the Deutsch–Jozsa algorithm using classical optics is proposed. • Constant and certain balanced functions can be encoded and distinguished efficiently. • The encoding and the detection process does not require to access single path qubits. • While the scheme might be scalable in principle, it might not be in practice. • We suggest a generalisation of the Deutsch–Jozsa algorithm and its implementation. - Abstract: We propose an optical implementation of the Deutsch–Jozsa Algorithm using classical light in a binary decision-tree scheme. Our approach uses a ring cavity and linear optical devices in order to efficiently query the oracle functional values. In addition, we take advantage of the intrinsic Fourier transforming properties of a lens to read out whether the function given by the oracle is balanced or constant.

Quantum computation with classical light: Implementation of the Deutsch–Jozsa algorithm

Energy Technology Data Exchange (ETDEWEB)

Perez-Garcia, Benjamin [Photonics and Mathematical Optics Group, Tecnológico de Monterrey, Monterrey 64849 (Mexico); University of the Witwatersrand, Private Bag 3, Johannesburg 2050 (South Africa); School of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X54001, Durban 4000 (South Africa); McLaren, Melanie [University of the Witwatersrand, Private Bag 3, Johannesburg 2050 (South Africa); Goyal, Sandeep K. [School of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X54001, Durban 4000 (South Africa); Institute of Quantum Science and Technology, University of Calgary, Alberta T2N 1N4 (Canada); Hernandez-Aranda, Raul I. [Photonics and Mathematical Optics Group, Tecnológico de Monterrey, Monterrey 64849 (Mexico); Forbes, Andrew [University of the Witwatersrand, Private Bag 3, Johannesburg 2050 (South Africa); Konrad, Thomas, E-mail: konradt@ukzn.ac.za [School of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X54001, Durban 4000 (South Africa); National Institute of Theoretical Physics, Durban Node, Private Bag X54001, Durban 4000 (South Africa)

2016-05-20

Highlights: • An implementation of the Deutsch–Jozsa algorithm using classical optics is proposed. • Constant and certain balanced functions can be encoded and distinguished efficiently. • The encoding and the detection process does not require to access single path qubits. • While the scheme might be scalable in principle, it might not be in practice. • We suggest a generalisation of the Deutsch–Jozsa algorithm and its implementation. - Abstract: We propose an optical implementation of the Deutsch–Jozsa Algorithm using classical light in a binary decision-tree scheme. Our approach uses a ring cavity and linear optical devices in order to efficiently query the oracle functional values. In addition, we take advantage of the intrinsic Fourier transforming properties of a lens to read out whether the function given by the oracle is balanced or constant.

Pseudo-random Aloha for inter-frame soft combining in RFID systems

DEFF Research Database (Denmark)

Castiglione, Paolo; Ricciato, Fabio; Popovski, Petar

2013-01-01

In this work we consider a recently proposed variant of the classical Framed Slotted-ALOHA where slot selection is based on a pseudo-random function of the message to be transmitted and of the frame index. We couple this feature with convolutional encoding, that allows to perform Inter-frame Soft...... cancellation (instead of combining). Numerical simulation results show that the ISoC scheme brings a noticeable throughput gain over traditional schemes in a dense RFID scenario with multiple concurrent Tag transmissions....

Oxygen transport properties estimation by classical trajectory–direct simulation Monte Carlo

Energy Technology Data Exchange (ETDEWEB)

Bruno, Domenico, E-mail: domenico.bruno@cnr.it [Istituto di Metodologie Inorganiche e dei Plasmi, Consiglio Nazionale delle Ricerche– Via G. Amendola 122, 70125 Bari (Italy); Frezzotti, Aldo, E-mail: aldo.frezzotti@polimi.it; Ghiroldi, Gian Pietro, E-mail: gpghiro@gmail.com [Dipartimento di Scienze e Tecnologie Aerospaziali, Politecnico di Milano–Via La Masa 34, 20156 Milano (Italy)

2015-05-15

Coupling direct simulation Monte Carlo (DSMC) simulations with classical trajectory calculations is a powerful tool to improve predictive capabilities of computational dilute gas dynamics. The considerable increase in computational effort outlined in early applications of the method can be compensated by running simulations on massively parallel computers. In particular, Graphics Processing Unit acceleration has been found quite effective in reducing computing time of classical trajectory (CT)-DSMC simulations. The aim of the present work is to study dilute molecular oxygen flows by modeling binary collisions, in the rigid rotor approximation, through an accurate Potential Energy Surface (PES), obtained by molecular beams scattering. The PES accuracy is assessed by calculating molecular oxygen transport properties by different equilibrium and non-equilibrium CT-DSMC based simulations that provide close values of the transport properties. Comparisons with available experimental data are presented and discussed in the temperature range 300–900 K, where vibrational degrees of freedom are expected to play a limited (but not always negligible) role.

Post-use assay of vaginal rings (VRs) as a potential measure of clinical trial adherence.

Science.gov (United States)

Spence, Patrick; Nel, Annalene; van Niekerk, Neliëtte; Derrick, Tiffany; Wilder, Susan; Devlin, Bríd

2016-06-05

Adherence measurement for microbicide use within the clinical trial setting remains a challenge for the HIV prevention field. This paper describes an assay method used for determining residual dapivirine levels in post-use vaginal rings from clinical trials conducted with the Dapivirine Vaginal Matrix Ring-004 developed by the International Partnership for Microbicides to prevent male to female HIV transmission. Post-use assay results from three Ring-004 clinical trials showed that of the 25mg drug load, approximately 4mg of dapivirine is released from the matrix ring over a 28-day use period. Data obtained by both in vitro and in vivo studies indicate that dapivirine is released according to a diffusion mechanism, as determined by conformance of both data sets to the Higuchi equation. This, coupled with the low variability associated with batch production over two manufacturing sites and 20 batches of material, provides evidence that post-use ring analysis can contribute to the assessment of adherence to ring use. Limitations of this method include the potential of intra-participant and inter-participant variability and uncertainty associated with measuring the low amount of dapivirine actually released relative to the drug load. Therefore, residual drug levels should not serve as the only direct measurement for microbicide adherence in vaginal ring clinical trials but should preferably be used as part of a multi-pronged approach towards understanding and assessing adherence to vaginal ring use. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Mixed quantum-classical simulations of the vibrational relaxation of photolyzed carbon monoxide in a hemoprotein

Energy Technology Data Exchange (ETDEWEB)

Schubert, Alexander, E-mail: schubert@irsamc.ups-tlse.fr; Meier, Christoph [Laboratoire Collisions Agrégats et Réactivité, IRSAMC, UMR CNRS 5589, Université Paul Sabatier, 31062 Toulouse (France); Falvo, Cyril [Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay (France)

2016-08-07

We present mixed quantum-classical simulations on relaxation and dephasing of vibrationally excited carbon monoxide within a protein environment. The methodology is based on a vibrational surface hopping approach treating the vibrational states of CO quantum mechanically, while all remaining degrees of freedom are described by means of classical molecular dynamics. The CO vibrational states form the “surfaces” for the classical trajectories of protein and solvent atoms. In return, environmentally induced non-adiabatic couplings between these states cause transitions describing the vibrational relaxation from first principles. The molecular dynamics simulation yields a detailed atomistic picture of the energy relaxation pathways, taking the molecular structure and dynamics of the protein and its solvent fully into account. Using the ultrafast photolysis of CO in the hemoprotein FixL as an example, we study the relaxation of vibrationally excited CO and evaluate the role of each of the FixL residues forming the heme pocket.

A quantum-classical simulation of a multi-surface multi-mode ...

Indian Academy of Sciences (India)

Multi surface multi mode quantum dynamics; parallelized quantum classical approach; TDDVR method. 1. ... cal simulation on molecular system is a great cha- llenge for ..... on a multiple core cluster with shared memory using. OpenMP based ...

Hybrid organic-inorganic rotaxanes and molecular shuttles.

Science.gov (United States)

Lee, Chin-Fa; Leigh, David A; Pritchard, Robin G; Schultz, David; Teat, Simon J; Timco, Grigore A; Winpenny, Richard E P

2009-03-19

The tetravalency of carbon and its ability to form covalent bonds with itself and other elements enables large organic molecules with complex structures, functions and dynamics to be constructed. The varied electronic configurations and bonding patterns of inorganic elements, on the other hand, can impart diverse electronic, magnetic, catalytic and other useful properties to molecular-level structures. Some hybrid organic-inorganic materials that combine features of both chemistries have been developed, most notably metal-organic frameworks, dense and extended organic-inorganic frameworks and coordination polymers. Metal ions have also been incorporated into molecules that contain interlocked subunits, such as rotaxanes and catenanes, and structures in which many inorganic clusters encircle polymer chains have been described. Here we report the synthesis of a series of discrete rotaxane molecules in which inorganic and organic structural units are linked together mechanically at the molecular level. Structural units (dialkyammonium groups) in dumb-bell-shaped organic molecules template the assembly of essentially inorganic 'rings' about 'axles' to form rotaxanes consisting of various numbers of rings and axles. One of the rotaxanes behaves as a 'molecular shuttle': the ring moves between two binding sites on the axle in a large-amplitude motion typical of some synthetic molecular machine systems. The architecture of the rotaxanes ensures that the electronic, magnetic and paramagnetic characteristics of the inorganic rings-properties that could make them suitable as qubits for quantum computers-can influence, and potentially be influenced by, the organic portion of the molecule.

Black rings

International Nuclear Information System (INIS)

Emparan, Roberto; Reall, Harvey S

2006-01-01

A black ring is a five-dimensional black hole with an event horizon of topology S 1 x S 2 . We provide an introduction to the description of black rings in general relativity and string theory. Novel aspects of the presentation include a new approach to constructing black ring coordinates and a critical review of black ring microscopics. (topical review)

First description of multivalent ring structures in eutherian mammalian meiosis: new chromosomal characterization of Cormura brevirostris (Emballonuridae, Chiroptera).

Science.gov (United States)

de Araújo, Ramon Everton Ferreira; Nagamachi, Cleusa Yoshiko; da Costa, Marlyson Jeremias Rodrigues; Noronha, Renata Coelho Rodrigues; Rodrigues, Luís Reginaldo Ribeiro; Pieczarka, Julio César

2016-08-01

Twelve specimens of the bat Cormura brevirostris (Emballonuridae: Chiroptera) were collected from four localities in the Brazilian Amazon region and analyzed by classical and molecular cytogenetics. The diploid number and autosomal fundamental number were as previously reported (2n = 22 and FNa = 40, respectively). Fluorescence in situ hybridization using rDNA probes and silver nitrate technique demonstrated the presence of two NOR sites and the presence of internal telomeric sequences at pericentromeric regions of all chromosomes with exception of Y. Based on meiotic studies and chromosome banding we suggest that the sex chromosome pair of C. brevirostris was equivocally identified as it appears in the literature. Meiotic analysis demonstrated that at diplotene-diakinesis the cells had a ring conformation involving four chromosome pairs. This suggests the occurrence of multiple reciprocal translocations among these chromosomes, which is a very rare phenomenon in vertebrates, and has never been described in Eutheria.

Three dimensional atom probe imaging of GaAsSb quantum rings.

Science.gov (United States)

Beltrán, A M; Marquis, E A; Taboada, A G; Ripalda, J M; García, J M; Molina, S I

2011-07-01

Unambiguous evidence of ring-shaped self-assembled GaSb nanostructures grown by molecular beam epitaxy is presented on the basis of atom-probe tomography reconstructions and dark field transmission electron microscopy imaging. The GaAs capping process causes a strong segregation of Sb out of the center of GaSb quantum dots, leading to the self-assembled GaAs(x)Sb(1-x) quantum rings of 20-30 nm in diameter with x ∼ 0.33. Copyright © 2011 Elsevier B.V. All rights reserved.

Rovibrational dynamics of the RbCs molecule in static electric fields. Classical study

Energy Technology Data Exchange (ETDEWEB)

Arnaiz, Pedro F.; Iñarrea, Manuel [Área de Física, Universidad de la Rioja, E-26006 Logroño (Spain); Salas, J. Pablo, E-mail: josepablo.salas@unirioja.es [Área de Física, Universidad de la Rioja, E-26006 Logroño (Spain)

2012-04-02

We study the classical dynamics of the RbCs molecule in the presence of a static electric field. Under the Born–Oppenheimer approximation, we perform a rovibrational investigation which includes the interaction of the field with the molecular polarizability. The stability of the equilibrium points and the phase space structure of the system are explored in detail. We find that, for strong electric fields or for energies close to the dissociation threshold, the molecular polarizability causes relevant effects on the system dynamics. -- Highlights: ► We study the classical rovibrational dynamics of the alkali polar dimer RbCs. ► In the model we consider the interaction of the field with the molecular polarizability. ► The potential energy surface is studied depending on the electric field strength. ► Using surfaces of section we study the phase space structure. ► We find that the molecular polarizability causes relevant effects on the system dynamics.

Rovibrational dynamics of the RbCs molecule in static electric fields. Classical study

International Nuclear Information System (INIS)

Arnaiz, Pedro F.; Iñarrea, Manuel; Salas, J. Pablo

2012-01-01

We study the classical dynamics of the RbCs molecule in the presence of a static electric field. Under the Born–Oppenheimer approximation, we perform a rovibrational investigation which includes the interaction of the field with the molecular polarizability. The stability of the equilibrium points and the phase space structure of the system are explored in detail. We find that, for strong electric fields or for energies close to the dissociation threshold, the molecular polarizability causes relevant effects on the system dynamics. -- Highlights: ► We study the classical rovibrational dynamics of the alkali polar dimer RbCs. ► In the model we consider the interaction of the field with the molecular polarizability. ► The potential energy surface is studied depending on the electric field strength. ► Using surfaces of section we study the phase space structure. ► We find that the molecular polarizability causes relevant effects on the system dynamics.

Classically exact surface diffusion constants at arbitrary temperature

International Nuclear Information System (INIS)

Voter, A.F.; Cohen, J.M.

1989-01-01

An expression is presented for computing the classical diffusion constant of a point defect (e.g., an adatom) in an infinite lattice of binding sites at arbitrary temperature. The transition state theory diffusion constant is simply multiplied by a dynamical correction factor that is computed from short-time classical trajectories initiated at the site boundaries. The time scale limitations of direct molecular dynamics are thus avoided in the low- and middle-temperature regimes. The expression results from taking the time derivative of the particle mean-square displacement in the lattice-discretized coordinate system. Applications are presented for surface diffusion on fcc(100) and fcc(111) Lennard-Jones crystal faces

Classical dynamics of triatomic system: energized harmonic molecules

International Nuclear Information System (INIS)

Parr, C.A.; Kuppermann, A.; Porter, R.N.

1976-01-01

The dynamical assumptions underlying the Slater and RRK classical-mechanical theories of unimolecular reaction rates are investigated. The predictions of these theories for several nonlinear, triatomic, harmonically-bonded molecular models are compared with the results obtained from the integration of the classical equations of motion. The accuracy of the small-vibration and weak-coupling assumptions are found to break down at energies above about one quarter of a bond dissociation energy. Nonetheless, the small-vibration approximation predicts reaction frequencies in good agreement with the exact results for the models. The effects of rotation on intramolecular energy exchange are examined and found to be significant

Influencing factors on the size uniformity of self-assembled SiGe quantum rings grown by molecular beam epitaxy.

Science.gov (United States)

Cui, J; Lv, Y; Yang, X J; Fan, Y L; Zhong, Z; Jiang, Z M

2011-03-25

The size uniformity of self-assembled SiGe quantum rings, which are formed by capping SiGe quantum dots with a thin Si layer, is found to be greatly influenced by the growth temperature and the areal density of SiGe quantum dots. Higher growth temperature benefits the size uniformity of quantum dots, but results in low Ge concentration as well as asymmetric Ge distribution in the dots, which induces the subsequently formed quantum rings to be asymmetric in shape or even broken somewhere in the ridge of rings. Low growth temperature degrades the size uniformity of quantum dots, and thus that of quantum rings. A high areal density results in the expansion and coalescence of neighboring quantum dots to form a chain, rather than quantum rings. Uniform quantum rings with a size dispersion of 4.6% and an areal density of 7.8×10(8) cm(-2) are obtained at the optimized growth temperature of 640°C.

An update of the classical Bokhman’s dualistic model of endometrial cancer

Directory of Open Access Journals (Sweden)

Miłosz Wilczyński

2016-07-01

Full Text Available According to the classical dualistic model introduced by Bokhman in 1983, endometrial cancer (EC is divided into two basic types. The prototypical histological type for type I and type II of EC is endometrioid carcinoma and serous carcinoma, respectively. The traditional classification is based on clinical, endocrine and histopathological features, however, it sometimes does not reflect the full heterogeneity of EC. New molecular evidence, supported by clinical diversity of the cancer, indicates that the classical dualistic model is valid only to some extent. The review updates a mutational diversity of EC, introducing a new molecular classification of the tumour in regard to data presented by The Cancer Genome Atlas Research Network (TGCA.

Volumetric real-time imaging using a CMUT ring array.

Science.gov (United States)

Choe, Jung Woo; Oralkan, Ömer; Nikoozadeh, Amin; Gencel, Mustafa; Stephens, Douglas N; O'Donnell, Matthew; Sahn, David J; Khuri-Yakub, Butrus T

2012-06-01

A ring array provides a very suitable geometry for forward-looking volumetric intracardiac and intravascular ultrasound imaging. We fabricated an annular 64-element capacitive micromachined ultrasonic transducer (CMUT) array featuring a 10-MHz operating frequency and a 1.27-mm outer radius. A custom software suite was developed to run on a PC-based imaging system for real-time imaging using this device. This paper presents simulated and experimental imaging results for the described CMUT ring array. Three different imaging methods--flash, classic phased array (CPA), and synthetic phased array (SPA)--were used in the study. For SPA imaging, two techniques to improve the image quality--Hadamard coding and aperture weighting--were also applied. The results show that SPA with Hadamard coding and aperture weighting is a good option for ring-array imaging. Compared with CPA, it achieves better image resolution and comparable signal-to-noise ratio at a much faster image acquisition rate. Using this method, a fast frame rate of up to 463 volumes per second is achievable if limited only by the ultrasound time of flight; with the described system we reconstructed three cross-sectional images in real-time at 10 frames per second, which was limited by the computation time in synthetic beamforming.

Hard x-ray measurements of the hot-electron rings in EBT-S

International Nuclear Information System (INIS)

Hillis, D.L.

1982-06-01

A thorough understanding of the hot electron rings in ELMO Bumpy Torus-Scale (EBT-S) is essential to the bumpy torus concept of plasma production, since the rings provide bulk plasma stability. The hot electrons are produced via electron cyclotron resonant heating using a 28-GHz cw gyrotron, which has operated up to power levels of 200 kW. The parameters of the energetic electron rings are studied via hard x-ray measurement techniques and with diamagnetic pickup coils. The hard x-ray measurements have used collimated NaI(Tl) detectors to determine the electron temperature T/sub e/ and electron density n/sub e/ for the hot electron annulus. Typical values of T/sub e/ are 400 to 500 keV and of n/sub e/ 2 to 5 x 10 11 cm -3 . The total stored energy of a single energetic electron ring as measured by diamagnetic pickup loops approaches approx. 40 J and is in good agreement with that deduced from hard x-ray measurements. By combining the experimental measurements from hard x-rays and the diamagnetic loops, an estimate can be obtained for the volume of a single hot electron ring. The ring volume is determined to be approx. 2.2 litres, and this volume remains approximately constant over the T-mode operating regime. Finally, the power in the electrons scattered out of the ring is measured indirectly by measuring the x-ray radiation produced when those electrons strike the chamber walls. The variation of this radiation with increasing microwave power levels is found to be consistent with classical scattering estimates

Variation in GMC Association Properties across the Bars, Spiral Arms, Inter-arms, and Circumnuclear Region of M100 (NGC 4321) Extracted from ALMA Observations

Energy Technology Data Exchange (ETDEWEB)

Pan, Hsi-An [Academia Sinica, Institute of Astronomy and Astrophysics (ASIAA), P.O. Box 23-141, Taipei 10617, Taiwan (China); Kuno, Nario, E-mail: hapan@asiaa.sinica.edu.tw [Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 350-8577 (Japan)

2017-04-20

We study the physical properties of giant molecular cloud associations (GMAs) in M100 (NGC 4321) using the ALMA Science Verification feathered (12 m+ACA) data in {sup 12}CO (1–0). To examine the environmental dependence of their properties, GMAs are classified based on their locations in various environments as circumnuclear ring (CNR), bar, spiral, and inter-arm GMAs. The CNR GMAs are massive and compact, while the inter-arm GMAs are diffuse, with low surface density. GMA mass and size are strongly correlated, as suggested by Larson. However, the diverse power-law index of the relation implies that the GMA properties are not uniform among the environments. The CNR and bar GMAs show higher velocity dispersion than those in other environments. We find little evidence for a correlation between GMA velocity dispersion and size, which indicates that the GMAs are in diverse dynamical states. Indeed, the virial parameter of the GMAs spans nearly two orders of magnitude. Only the spiral GMAs are generally self-gravitating. Star formation activity decreases in order over the CNR, spiral, bar, and inter-arm GMAs. The diverse GMA and star formation properties in different environments lead to variations in the Kennicutt–Schmidt relation. A combination of multiple mechanisms or gas phase change is necessary to explain the observed slopes. Comparisons of GMA properties acquired with the use of the 12 m array observations with those from the feathered data are also presented. The results show that the missing flux and extended emission cannot be neglected for the study of environmental dependence.

TDDFT-MD Study on Dynamics in Photoinduced Ring Opening of Benzene

Science.gov (United States)

Tateyama, Yoshitaka; Miyamoto, Yoshiyuki; Oyama, Norihisa; Ohno, Takahisa

2004-03-01

Coupled dynamics of ions and electrons in the excited states of molecular and solid benzene is investigated on the femtosecond scale by the efficient simulation scheme recently developed for the time-dependent density functional theory. Within the π arrow π excitations, any out-of-plane motion of ions is not induced in the molecular system basically. In the solid, however, we found that large swing of the C-H bonds and subsequent twist of the carbon ring takes place, leading to sp^3-like bonding of carbon ions. This swing-to-twist motion presents a plausible mechanism underlying the photoinduced ring opening in solid benzene experimentally observed under pressure. This research is partially supported by ACT-JST, and also by FSIS and Special Coordination Funds of Ministry of Education, Culture, Sports, Science and Technology of Japanese Government.

Forward modeling of tree-ring data: a case study with a global network

Science.gov (United States)

Breitenmoser, P. D.; Frank, D.; Brönnimann, S.

2012-04-01

Information derived from tree-rings is one of the most powerful tools presently available for studying past climatic variability as well as identifying fundamental relationships between tree-growth and climate. Climate reconstructions are typically performed by extending linear relationships, established during the overlapping period of instrumental and climate proxy archives into the past. Such analyses, however, are limited by methodological assumptions, including stationarity and linearity of the climate-proxy relationship. We investigate climate and tree-ring data using the Vaganov-Shashkin-Lite (VS-Lite) forward model of tree-ring width formation to examine the relations among actual tree growth and climate (as inferred from the simulated chronologies) to reconstruct past climate variability. The VS-lite model has been shown to produce skill comparable to that achieved using classical dendrochronological statistical modeling techniques when applied on simulations of a network of North American tree-ring chronologies. Although the detailed mechanistic processes such as photosynthesis, storage, or cell processes are not modeled directly, the net effect of the dominating nonlinear climatic controls on tree-growth are implemented into the model by the principle of limiting factors and threshold growth response functions. The VS-lite model requires as inputs only latitude, monthly mean temperature and monthly accumulated precipitation. Hence, this simple, process-based model enables ring-width simulation at any location where monthly climate records exist. In this study, we analyse the growth response of simulated tree-rings to monthly climate conditions obtained from the 20th century reanalysis project back to 1871. These simulated tree-ring chronologies are compared to the climate-driven variability in worldwide observed tree-ring chronologies from the International Tree Ring Database. Results point toward the suitability of the relationship among actual tree

The cryogenic storage ring CSR

Science.gov (United States)

von Hahn, R.; Becker, A.; Berg, F.; Blaum, K.; Breitenfeldt, C.; Fadil, H.; Fellenberger, F.; Froese, M.; George, S.; Göck, J.; Grieser, M.; Grussie, F.; Guerin, E. A.; Heber, O.; Herwig, P.; Karthein, J.; Krantz, C.; Kreckel, H.; Lange, M.; Laux, F.; Lohmann, S.; Menk, S.; Meyer, C.; Mishra, P. M.; Novotný, O.; O'Connor, A. P.; Orlov, D. A.; Rappaport, M. L.; Repnow, R.; Saurabh, S.; Schippers, S.; Schröter, C. D.; Schwalm, D.; Schweikhard, L.; Sieber, T.; Shornikov, A.; Spruck, K.; Sunil Kumar, S.; Ullrich, J.; Urbain, X.; Vogel, S.; Wilhelm, P.; Wolf, A.; Zajfman, D.

2016-06-01

An electrostatic cryogenic storage ring, CSR, for beams of anions and cations with up to 300 keV kinetic energy per unit charge has been designed, constructed, and put into operation. With a circumference of 35 m, the ion-beam vacuum chambers and all beam optics are in a cryostat and cooled by a closed-cycle liquid helium system. At temperatures as low as (5.5 ± 1) K inside the ring, storage time constants of several minutes up to almost an hour were observed for atomic and molecular, anion and cation beams at an energy of 60 keV. The ion-beam intensity, energy-dependent closed-orbit shifts (dispersion), and the focusing properties of the machine were studied by a system of capacitive pickups. The Schottky-noise spectrum of the stored ions revealed a broadening of the momentum distribution on a time scale of 1000 s. Photodetachment of stored anions was used in the beam lifetime measurements. The detachment rate by anion collisions with residual-gas molecules was found to be extremely low. A residual-gas density below 140 cm-3 is derived, equivalent to a room-temperature pressure below 10-14 mbar. Fast atomic, molecular, and cluster ion beams stored for long periods of time in a cryogenic environment will allow experiments on collision- and radiation-induced fragmentation processes of ions in known internal quantum states with merged and crossed photon and particle beams.

The cryogenic storage ring CSR.

Science.gov (United States)

von Hahn, R; Becker, A; Berg, F; Blaum, K; Breitenfeldt, C; Fadil, H; Fellenberger, F; Froese, M; George, S; Göck, J; Grieser, M; Grussie, F; Guerin, E A; Heber, O; Herwig, P; Karthein, J; Krantz, C; Kreckel, H; Lange, M; Laux, F; Lohmann, S; Menk, S; Meyer, C; Mishra, P M; Novotný, O; O'Connor, A P; Orlov, D A; Rappaport, M L; Repnow, R; Saurabh, S; Schippers, S; Schröter, C D; Schwalm, D; Schweikhard, L; Sieber, T; Shornikov, A; Spruck, K; Sunil Kumar, S; Ullrich, J; Urbain, X; Vogel, S; Wilhelm, P; Wolf, A; Zajfman, D

2016-06-01

An electrostatic cryogenic storage ring, CSR, for beams of anions and cations with up to 300 keV kinetic energy per unit charge has been designed, constructed, and put into operation. With a circumference of 35 m, the ion-beam vacuum chambers and all beam optics are in a cryostat and cooled by a closed-cycle liquid helium system. At temperatures as low as (5.5 ± 1) K inside the ring, storage time constants of several minutes up to almost an hour were observed for atomic and molecular, anion and cation beams at an energy of 60 keV. The ion-beam intensity, energy-dependent closed-orbit shifts (dispersion), and the focusing properties of the machine were studied by a system of capacitive pickups. The Schottky-noise spectrum of the stored ions revealed a broadening of the momentum distribution on a time scale of 1000 s. Photodetachment of stored anions was used in the beam lifetime measurements. The detachment rate by anion collisions with residual-gas molecules was found to be extremely low. A residual-gas density below 140 cm(-3) is derived, equivalent to a room-temperature pressure below 10(-14) mbar. Fast atomic, molecular, and cluster ion beams stored for long periods of time in a cryogenic environment will allow experiments on collision- and radiation-induced fragmentation processes of ions in known internal quantum states with merged and crossed photon and particle beams.

The cryogenic storage ring CSR

Energy Technology Data Exchange (ETDEWEB)

Hahn, R. von; Becker, A.; Berg, F.; Blaum, K.; Fadil, H.; Fellenberger, F.; Froese, M.; George, S.; Göck, J.; Grieser, M.; Grussie, F.; Guerin, E. A.; Herwig, P.; Karthein, J.; Krantz, C.; Kreckel, H.; Lange, M.; Laux, F.; Lohmann, S.; Menk, S. [Max-Planck-Institut für Kernphysik, 69117 Heidelberg (Germany); and others

2016-06-15

An electrostatic cryogenic storage ring, CSR, for beams of anions and cations with up to 300 keV kinetic energy per unit charge has been designed, constructed, and put into operation. With a circumference of 35 m, the ion-beam vacuum chambers and all beam optics are in a cryostat and cooled by a closed-cycle liquid helium system. At temperatures as low as (5.5 ± 1) K inside the ring, storage time constants of several minutes up to almost an hour were observed for atomic and molecular, anion and cation beams at an energy of 60 keV. The ion-beam intensity, energy-dependent closed-orbit shifts (dispersion), and the focusing properties of the machine were studied by a system of capacitive pickups. The Schottky-noise spectrum of the stored ions revealed a broadening of the momentum distribution on a time scale of 1000 s. Photodetachment of stored anions was used in the beam lifetime measurements. The detachment rate by anion collisions with residual-gas molecules was found to be extremely low. A residual-gas density below 140 cm{sup −3} is derived, equivalent to a room-temperature pressure below 10{sup −14} mbar. Fast atomic, molecular, and cluster ion beams stored for long periods of time in a cryogenic environment will allow experiments on collision- and radiation-induced fragmentation processes of ions in known internal quantum states with merged and crossed photon and particle beams.

Modeling of lipase catalyzed ring-opening polymerization of epsilon-caprolactone.

Science.gov (United States)

Sivalingam, G; Madras, Giridhar

2004-01-01

Enzymatic ring-opening polymerization of epsilon-caprolactone by various lipases was investigated in toluene at various temperatures. The determination of molecular weight and structural identification was carried out with gel permeation chromatography and proton NMR, respectively. Among the various lipases employed, an immobilized lipase from Candida antartica B (Novozym 435) showed the highest catalytic activity. The polymerization of epsilon-caprolactone by Novozym 435 showed an optimal temperature of 65 degrees C and an optimum toluene content of 50/50 v/v of toluene and epsilon-caprolactone. As lipases can degrade polyesters, a maximum in the molecular weight with time was obtained due to the competition of ring opening polymerization and degradation by specific chain end scission. The optimum temperature, toluene content, and the variation of molecular weight with time are consistent with earlier observations. A comprehensive model based on continuous distribution kinetics was developed to model these phenomena. The model accounts for simultaneous polymerization, degradation and enzyme deactivation and provides a technique to determine the rate coefficients for these processes. The dependence of these rate coefficients with temperature and monomer concentration is also discussed.

Exact classical scaling formalism for nonreactive processes

International Nuclear Information System (INIS)

DePristo, A.E.

1981-01-01

A general nonreactive collision system is considered with internal molecular variables (p, r) and/or (I, theta) of arbitrary dimensions and relative translational variables (P, R) of three or less dimensions. We derive an exact classical scaling formalism which relates the collisional change in any function of molecular variables directly to the initial values of these variables. The collision dynamics is then described by an explicit function of the initial point in the internal molecular phase space, for a fixed point in the relative translational phase space. In other words, the systematic variation of the internal molecular properties (e.g., actions and average internal kinetic energies) is given as a function of the initial internal action-angle variables. A simple three term approximation to the exact formalism is derived, the natural variables of which are the internal action I and internal linear momenta p. For the final average internal kinetic energies T, the result is T-T/sup( 0 ) = α+βp/sup( 0 )+γI/sup( 0 ), where the superscripted ''0'' indicates the initial value. The parameters α, β, and γ in this scaling theory are directly related to the moments of the change in average internal kinetic energy. Utilizing a very limited number of input moments generated from classical trajectory calculations, the scaling can be used to predict the entire distribution of final internal variables as a function of initial internal actions and linear momenta. Initial examples for atom--collinear harmonic oscillator collision systems are presented in detail, with the scaling predictions (e.g., moments and quasiclassical histogram transition probabilities) being generally very good to excellent quantitatively

Variations in Ring Particle Cooling across Saturn's Rings with Cassini CIRS

Science.gov (United States)

Brooks, S. M.; Spilker, L. J.; Pilorz, S.; Edgington, S. G.; Déau, E.; Altobelli, N.

2010-12-01

Cassini's Composite Infrared Spectrometer has recorded over two million of spectra of Saturn's rings in the far infrared since arriving at Saturn in 2004. CIRS records far infrared radiation between 10 and 600 cm-1 ( 16.7 and 1000 μ {m} ) at focal plane 1 (FP1), which has a field of view of 3.9 mrad. Thermal emission from Saturn’s rings peaks in this wavelength range. Ring temperatures can be inferred from FP1 data. By tracking how ring temperatures vary, we can determine the thermal inertia of the rings. Previous studies have shown that the rings' thermal inertia, a measure of their response to changes in the thermal environment, varies from ring to ring. Thermal inertia can provide insight into the physical structure of Saturn's ring particles and their regoliths. Low thermal inertia and rapidly changing temperatures are suggestive of ring particles that have more porous or fluffy regoliths or that are riddled with cracks. Solid particles can be expected to have higher thermal inertias. Ferrari et al. (2005) fit thermal inertia values of 5218 {Jm)-2 {K}-1 {s}-1/2 to their B ring data and 6412 {Jm)-2 {K}-1 {s}-1/2 to their C ring data. In this work we focus on CIRS observations of the shadowed portion of Saturn's rings. The rings’ thermal budget is dominated by its absorption of solar radiation. As a result, ring particles abruptly cool as they traverse Saturn's shadow. From these shadow observations we can create cooling curves at specific locations across the rings. We will show that the rings' cooling curves and thus their thermal inertia vary not only from ring to ring, but by location within the individual rings. This research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under contract with NASA. Copyright 2010 California Institute of Technology. Government sponsorship acknowledged.

The c-Ring of the F1FO-ATP Synthase: Facts and Perspectives.

Science.gov (United States)

Nesci, Salvatore; Trombetti, Fabiana; Ventrella, Vittoria; Pagliarani, Alessandra

2016-04-01

The F1FO-ATP synthase is the only enzyme in nature endowed with bi-functional catalytic mechanism of synthesis and hydrolysis of ATP. The enzyme functions, not only confined to energy transduction, are tied to three intrinsic features of the annular arrangement of c subunits which constitutes the so-called c-ring, the core of the membrane-embedded FO domain: (i) the c-ring constitution is linked to the number of ions (H(+) or Na(+)) channeled across the membrane during the dissipation of the transmembrane electrochemical gradient, which in turn determines the species-specific bioenergetic cost of ATP, the "molecular currency unit" of energy transfer in all living beings; (ii) the c-ring is increasingly involved in the mitochondrial permeability transition, an event linked to cell death and to most mitochondrial dysfunctions; (iii) the c subunit species-specific amino acid sequence and susceptibility to post-translational modifications can address antibacterial drug design according to the model of enzyme inhibitors which target the c subunits. Therefore, the simple c-ring structure not only allows the F1FO-ATP synthase to perform the two opposite tasks of molecular machine of cell life and death, but it also amplifies the enzyme's potential role as a drug target.

Molecular dynamics study of the coordination sphere of trivalent lanthanum in a highly concentrated LiCl aqueous solution: A combined classical and ab initio approach

International Nuclear Information System (INIS)

Vuilleumier, R.; Petit, L.; Maldivi, P.; Adamo, C.

2008-01-01

The first coordination sphere of trivalent lanthanum in a highly concentrated (14 M) lithium chloride solution is studied with a combination of classical molecular dynamics and density functional theory based first principle molecular dynamics. This method enables us to obtain a solvation shell of La 3+ containing 2 chloride ions and 6 water molecules. After refinement using first principle molecular dynamics, the resulting cation-water and cation-anion distances are in very good agreement with experiment. The 2 Cl - and the 6 water molecules arrange in a square anti-prism around La 3+ . Exchange of water molecules was also observed in the first-principle simulation, with an intermediate structure comprising 7 water molecules stable for 2.5 ps. Finally, evaluation of dipole moments using maximally localized Wannier functions shows a substantial polarization of the chloride anions and the water molecules in the first solvation shell of trivalent lanthanum. (authors)

A comparison of wood density between classical Cremonese and modern violins.

Directory of Open Access Journals (Sweden)

Berend C Stoel

Full Text Available Classical violins created by Cremonese masters, such as Antonio Stradivari and Giuseppe Guarneri Del Gesu, have become the benchmark to which the sound of all violins are compared in terms of their abilities of expressiveness and projection. By general consensus, no luthier since that time has been able to replicate the sound quality of these classical instruments. The vibration and sound radiation characteristics of a violin are determined by an instrument's geometry and the material properties of the wood. New test methods allow the non-destructive examination of one of the key material properties, the wood density, at the growth ring level of detail. The densities of five classical and eight modern violins were compared, using computed tomography and specially developed image-processing software. No significant differences were found between the median densities of the modern and the antique violins, however the density difference between wood grains of early and late growth was significantly smaller in the classical Cremonese violins compared with modern violins, in both the top (Spruce and back (Maple plates (p = 0.028 and 0.008, respectively. The mean density differential (SE of the top plates of the modern and classical violins was 274 (26.6 and 183 (11.7 gram/liter. For the back plates, the values were 128 (2.6 and 115 (2.0 gram/liter. These differences in density differentials may reflect similar changes in stiffness distributions, which could directly impact vibrational efficacy or indirectly modify sound radiation via altered damping characteristics. Either of these mechanisms may help explain the acoustical differences between the classical and modern violins.

Molecular modeling studies of interactions between sodium polyacrylate polymer and calcite surface

Energy Technology Data Exchange (ETDEWEB)

Ylikantola, A. [University of Jyväskylä, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 (Finland); Linnanto, J., E-mail: juha.m.linnanto@gmail.com [University of Jyväskylä, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 (Finland); University of Tartu, Institute of Physics, Riia 142, EE-51014 Tartu (Estonia); Knuutinen, J.; Oravilahti, A. [University of Jyväskylä, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 (Finland); Toivakka, M. [Åbo Akademi University, Laboratory of Paper Coating and Converting and Center for Functional Materials, FI-20500 Turku/Åbo (Finland)

2013-07-01

The interactions between calcite pigment and sodium polyacrylate dispersing agent, widely used in papermaking as paper coating components, were investigated using classical force field and quantum chemical approaches. The objective was to understand interactions between the calcite surface and sodium polyacrylate polymer at 300 K using molecular dynamics simulations. A quantum mechanical ab initio Hartree–Fock method was also used to obtain detailed information about the sodium polyacrylate polymer structure. The effect of water molecules (moisture) on the interactions was also examined. Calculations showed that molecular weight, branching and the orientation of sodium polyacrylate polymers influence the interactions between the calcite surface and the polymer. The force field applied, and also water molecules, were found to have an impact on all systems studied. Ab initio Hartree–Fock calculations indicated that there are two types of coordination between sodium atoms and carboxylate groups of the sodium polyacrylate polymer, inter- and intra-carboxylate group coordination. In addition, ab initio Hartree–Fock calculations of the structure of the sodium polyacrylate polymer produced important information regarding interactions between the polymers and carboxylated styrene-butadiene latex particles.

INSIGHTS INTO THE MECHANICS OF CYTOKINETIC RING ASSEMBLY USING 3D MODELING.

Science.gov (United States)

Bidone, Tamara Carla; Tang, Haosu; Vavylonis, Dimitrios

During fission yeast cytokinesis, actin filaments nucleated by cortical formin Cdc12 are captured by myosin motors bound to a band of cortical nodes. The myosin motors exert forces that pull nodes together into a contractile ring. Cross-linking interactions help align actin filaments and nodes into a single bundle. Mutations in the myosin motor domain and changes in the concentration of cross-linkers alpha-actinin and fimbrin alter the morphology of the condensing network, leading to clumps, rings or extended meshworks. How the contractile tension developing during ring formation depends on the interplay between network morphology, myosin motor activity, cross-linking and actin filament turnover remains to be elucidated. We addressed this question using a 3D computational model in which semiflexible actin filaments (represented as beads connected by springs) grow from formins, can be captured by myosin in neighboring nodes, and get cross-linked with one another through an attractive interaction. We identify regimes of tension generation between connected nodes under a wide set of conditions regarding myosin dynamics and strength of cross-linking between actin filaments. We find conditions that maximize circumferential tension, correlate them with network morphology and propose experiments to test these predictions. This work addresses "Morphogenesis of soft and living matter" using computational modeling to simulate cytokinetic ring assembly from the key molecular mechanisms of viscoelastic cross-linked actin networks that include active molecular motors.

Multicolor Graphic Picture With Original Ring Raster Element

Directory of Open Access Journals (Sweden)

Jana Ziljak Vujic

2006-12-01

Full Text Available This paper deals with graphics and color rastering using new raster forms as well as raster combinations in vector anda pixel graphics, with combining both graphics in the same document. The unwanted increase or decrease of color coverage depends most of all on the fringe volume length bordering the raster element. The idea of this research work is to find a form alters in the least extent the raster element fringe volume in respect to its increase or decrease. The innovation in this research work is not only in the fact that the raster element's volume is altered in the minimal degree, but also that it does not change at all with the covering capacity increase or decrease. The solution led in the direction of creating such a raster element that has at least two independent shells where one increases in size together with the raster element increase, and the other one decreases when the raster element size increases. We have named this raster form as the ring form due to its similarity with a classical smooth ring.

Polymers Containing 1, 3, 4-Oxadiazole Rings for Advanced Materials

Directory of Open Access Journals (Sweden)

Mariana-Dana Damaceanu

2011-10-01

Full Text Available This paper presents the synthesis, properties and potential applications of new polymers containing 1, 3, 4-oxadiazole rings, tacking into account the requirements of the modern technologies. Two classes of polymers containing oxadiazole rings were approached: polyamides and polyimides. All the polymers were characterized with respect to the identification of their chemical structure, solubility, molecular weights, film forming ability, thermal, dielectric and optical properties, and the behaviour of polyoxadiazole films upon irradiation with pulsed KrF laser. All the properties were discussed in correlation with their chemical structure and compared with those of related polymers.

4-Chloro­selanyl-3,5-diethyl-1H-pyrazol-2-ium chloride

Science.gov (United States)

Seredyuk, Maksym; Znovjyak, Kateryna O.; Sliva, Tetyana Yu.; Haukka, Matti; Fritsky, Igor O.

2011-01-01

In the cation of the title compound, C7H12ClN2Se+·Cl−, the ethyl­ene groups and the Se–Cl fragment adopt a cis configuration with a C—Se—Cl angle of 96.09 (6)°. In the crystal, inter­molecular N—H⋯Cl hydrogen bonds link two cations and two chlorine anions into centrosymmetric clusters. π–π inter­actions between the pyrazole rings [centroid–centroid distance of 3.530 (2) Å] link these clusters into columns along [001] with short inter­molecular Se⋯Cl− contacts of 2.995 (1) Å. PMID:22220089

THREE-DIMENSIONAL DUST MAPPING REVEALS THAT ORION FORMS PART OF A LARGE RING OF DUST

International Nuclear Information System (INIS)

Schlafly, E. F.; Rix, H.-W.; Martin, N. F.; Green, G.; Finkbeiner, D. P.; Burgett, W. S.; Chambers, K. C.; Kaiser, N.; Morgan, J. S.; Tonry, J. L.; Wainscoat, R. J.; Waters, C.; Draper, P. W.; Metcalfe, N.; Price, P. A.

2015-01-01

The Orion Molecular Complex is the nearest site of ongoing high-mass star formation, making it one of the most extensively studied molecular complexes in the Galaxy. We have developed a new technique for mapping the three-dimensional distribution of dust in the Galaxy using Pan-STARRS1 photometry. We isolate the dust at the distance to Orion using this technique, revealing a large (100 pc, 14° diameter), previously unrecognized ring of dust, which we term the ''Orion dust ring''. The ring includes Orion A and B, and is not coincident with current Hα features. The circular morphology suggests formation as an ancient bubble in the interstellar medium, though we have not been able to conclusively identify the source of the bubble. This hint at the history of Orion may have important consequences for models of high-mass star formation and triggered star formation

Alternative loop rings

CERN Document Server

Goodaire, EG; Polcino Milies, C

1996-01-01

For the past ten years, alternative loop rings have intrigued mathematicians from a wide cross-section of modern algebra. As a consequence, the theory of alternative loop rings has grown tremendously. One of the main developments is the complete characterization of loops which have an alternative but not associative, loop ring. Furthermore, there is a very close relationship between the algebraic structures of loop rings and of group rings over 2-groups. Another major topic of research is the study of the unit loop of the integral loop ring. Here the interaction between loop rings and group ri

Primitivity and weak distributivity in near rings and matrix near rings

International Nuclear Information System (INIS)

Abbasi, S.J.

1993-08-01

This paper shows the structure of matrix near ring constructed over a weakly distributive and primative near ring. It is proved that a weakly distributive primitive near ring is a ring and the matrix near rings constructed over it is also a bag. (author). 14 refs

Perturbing the ground ring of 2D string theory

CERN Document Server

Barbón, José L F

1992-01-01

We use free field techniques in D=2 string theory to calculate the perturbation of the special state algebras when the cosmologi- cal constant is turned on. In particular, we find that the "ground cone" preserved by the ring structure is promoted to a three dimen- sional hyperboloid as conjectured by Witten. On the other hand, the perturbed (1,1) a three dimensional hyperboloid as conjectured by Witten. On the other hand, the perturbed (1,1) current algebra of moduli deformations is computed completely, and no simple geometrical inter- pretation is found. We also quote some facts concerning the Liouville/matrix model dictio- nary in this class of theories.

Rediscovery by Whole Genome Sequencing: Classical Mutations and Genome Polymorphisms in Neurospora crassa

Energy Technology Data Exchange (ETDEWEB)

McCluskey, Kevin; Wiest, Aric E.; Grigoriev, Igor V.; Lipzen, Anna; Martin, Joel; Schackwitz, Wendy; Baker, Scott E.

2011-06-02

Classical forward genetics has been foundational to modern biology, and has been the paradigm for characterizing the role of genes in shaping phenotypes for decades. In recent years, reverse genetics has been used to identify the functions of genes, via the intentional introduction of variation and subsequent evaluation in physiological, molecular, and even population contexts. These approaches are complementary and whole genome analysis serves as a bridge between the two. We report in this article the whole genome sequencing of eighteen classical mutant strains of Neurospora crassa and the putative identification of the mutations associated with corresponding mutant phenotypes. Although some strains carry multiple unique nonsynonymous, nonsense, or frameshift mutations, the combined power of limiting the scope of the search based on genetic markers and of using a comparative analysis among the eighteen genomes provides strong support for the association between mutation and phenotype. For ten of the mutants, the mutant phenotype is recapitulated in classical or gene deletion mutants in Neurospora or other filamentous fungi. From thirteen to 137 nonsense mutations are present in each strain and indel sizes are shown to be highly skewed in gene coding sequence. Significant additional genetic variation was found in the eighteen mutant strains, and this variability defines multiple alleles of many genes. These alleles may be useful in further genetic and molecular analysis of known and yet-to-be-discovered functions and they invite new interpretations of molecular and genetic interactions in classical mutant strains.

Controlled switching of single-molecule junctions by mechanical motion of a phenyl ring

Directory of Open Access Journals (Sweden)

Yuya Kitaguchi

2015-10-01

Full Text Available Mechanical methods for single-molecule control have potential for wide application in nanodevices and machines. Here we demonstrate the operation of a single-molecule switch made functional by the motion of a phenyl ring, analogous to the lever in a conventional toggle switch. The switch can be actuated by dual triggers, either by a voltage pulse or by displacement of the electrode, and electronic manipulation of the ring by chemical substitution enables rational control of the on-state conductance. Owing to its simple mechanics, structural robustness, and chemical accessibility, we propose that phenyl rings are promising components in mechanical molecular devices.

Classics in Chemical Neuroscience: Haloperidol.

Science.gov (United States)

Tyler, Marshall W; Zaldivar-Diez, Josefa; Haggarty, Stephen J

2017-03-15

The discovery of haloperidol catalyzed a breakthrough in our understanding of the biochemical basis of schizophrenia, improved the treatment of psychosis, and facilitated deinstitutionalization. In doing so, it solidified the role for chemical neuroscience as a means to elucidate the molecular underpinnings of complex neuropsychiatric disorders. In this Review, we will cover aspects of haloperidol's synthesis, manufacturing, metabolism, pharmacology, approved and off-label indications, and adverse effects. We will also convey the fascinating history of this classic molecule and the influence that it has had on the evolution of neuropsychopharmacology and neuroscience.

Interaction of ring dark solitons with ring impurities in Bose-Einstein condensates

International Nuclear Information System (INIS)

Xue Jukui

2005-01-01

The interaction of ring dark solitons/vortexes with the ring-shaped repulsive and attractive impurities in two-dimensional Bose-Einstein condensates is investigated numerically. Very rich interaction phenomena are obtained, i.e., not only the interaction between the ring soliton and the impurity, but also the interaction between vortexes and the impurity. The interaction characters, i.e., snaking of ring soliton, quasitrapping or reflection of ring soliton and vortexes by the impurity, strongly depend on initial ring soliton velocity, impurity strength, initial position of ring soliton and impurity. The numerical results also reveal that ring dark solitons/vortexes can be trapped and dragged by an adiabatically moving attractive ring impurity

Classical analog for electronic degrees of freedom in nonadiabatic collision processes

International Nuclear Information System (INIS)

Meyer, H.; Miller, W.H.

1979-01-01

It is shown how a formally exact classical analog can be defined for a finite dimensional (in Hilbert space) quantum mechanical system. This approach is then used to obtain a classical model for the electronic degrees of freedom in a molecular collision system, and the combination of this with the usual classical description of the heavy particle (i.e., nuclear) motion provides a completely classical model for the electronic and heavy particle degrees of freedom. The resulting equations of motion are shown to be equivalent to describing the electronic degrees of freedom by the time-dependent Schroedinger equation, the time dependence arising from the classical motion of the nuclei, the trajectory of which is determined by the quantum mechanical average (i.e., Ehrenfest) force on the nuclei. Quantizing the system via classical S-matrix theory is shown to provide a dynamically consistent description of nonadiabatic collision processes; i.e., different electronic transitions have different heavy particle trajectories and, for example, the total energy of the electronic and heavy particle degrees of freedom is conserved. Application of this classical model for the electronic degrees of freedom (plus classical S-matrix theory) to the two-state model problem shows that the approach provides a good description of the electronic dynamics

FY 1991 Report on the results of the research and development of silicon-based high-molecular-weight materials; 1991 nendo keisokei kobunshi zairyo no kenkyu kaihatsu seika hokokusho

Energy Technology Data Exchange (ETDEWEB)

NONE

1992-03-01

The research and development project has been started to establish the basic technologies for molecular designs, synthesis, material production and evaluation of silicon-based high-molecular-weight materials expected to exhibit excellent characteristics, e.g., electro-optical functions, resistance to heat, flame retardance and mechanical properties. The efforts in FY 1991, the first year for the 10-year project, are mainly directed to the surveys on the R and D trends, both domestic and foreign, to clarify the relationship between the structures and functions/properties. The R and D projects followed include the technologies for synthesizing (1) electroconductive silicon-based high-molecular-weight materials, (2) novel silicon-based high-molecular-weight materials capable of drawing circuits, (3) novel, light-emitting silicon-based high-molecular-weight materials and (4) silicon-based opto-electric conversion materials for the electro-optical functional high-molecular-weight materials; and (1) synthesis of high-molecular-weight structural materials of sea island structure, (2) technologies for forming inter-penetrating type structures (IPN), (3) development of composite structural materials of organometallic complex and silicon-based high-molecular-weight material, and (4) development of silicon-based high-molecular-weight materials of ring structure for the high-molecular-weight structural materials. (NEDO)

Theoretical modeling of electronic transport in molecular devices

Science.gov (United States)

Piccinin, Simone

In this thesis a novel approach for simulating electronic transport in nanoscale structures is introduced. We consider an open quantum system (the electrons of structure) accelerated by an external electromotive force and dissipating energy through inelastic scattering with a heat bath (phonons) acting on the electrons. This method can be regarded as a quantum-mechanical extension of the semi-classical Boltzmann transport equation. We use periodic boundary conditions and employ Density Functional Theory to recast the many-particle problem in an effective single-particle mean-field problem. By explicitly treating the dissipation in the electrodes, the behavior of the potential is an outcome of our method, at variance with the scattering approaches based on the Landauer formalism. We study the self-consistent steady-state solution, analyzing the out-of-equilibrium electron distribution, the electrical characteristics, the behavior of the self-consistent potential and the density of states of the system. We apply the method to the study of electronic transport in several molecular devices, consisting of small organic molecules or atomic wires sandwiched between gold surfaces. For gold wires we recover the experimental evidence that transport in short wires is ballistic, independent of the length of the wire and with conductance of one quantum. In benzene-1,4-dithiol we find that the delocalization of the frontier orbitals of the molecule is responsible for the high value of conductance and that, by inserting methylene groups to decouple the sulfur atoms from the carbon ring, the current is reduced, in agreement with the experimental measurements. We study the effect a geometrical distortion in a molecular device, namely the relative rotation of the carbon rings in a biphenyl-4,4'-dithiol molecule. We find that the reduced coupling between pi orbitals of the rings induced by the rotation leads to a reduction of the conductance and that this behavior is captured by a

Engineering Circular Gliding of Actin Filaments Along Myosin-Patterned DNA Nanotube Rings To Study Long-Term Actin-Myosin Behaviors.

Science.gov (United States)

Hariadi, Rizal F; Appukutty, Abhinav J; Sivaramakrishnan, Sivaraj

2016-09-27

Nature has evolved molecular motors that are critical in cellular processes occurring over broad time scales, ranging from seconds to years. Despite the importance of the long-term behavior of molecular machines, topics such as enzymatic lifetime are underexplored due to the lack of a suitable approach for monitoring motor activity over long time periods. Here, we developed an "O"-shaped Myosin Empowered Gliding Assay (OMEGA) that utilizes engineered micron-scale DNA nanotube rings with precise arrangements of myosin VI to trap gliding actin filaments. This circular gliding assay platform allows the same individual actin filament to glide over the same myosin ensemble (50-1000 motors per ring) multiple times. First, we systematically characterized the formation of DNA nanotubes rings with 4, 6, 8, and 10 helix circumferences. Individual actin filaments glide along the nanotube rings with high processivity for up to 12.8 revolutions or 11 min in run time. We then show actin gliding speed is robust to variation in motor number and independent of ring curvature within our sample space (ring diameter of 0.5-4 μm). As a model application of OMEGA, we then analyze motor-based mechanical influence on "stop-and-go" gliding behavior of actin filaments, revealing that the stop-to-go transition probability is dependent on motor flexibility. Our circular gliding assay may provide a closed-loop platform for monitoring long-term behavior of broad classes of molecular motors and enable characterization of motor robustness and long time scale nanomechanical processes.

Millennium-scale crossdating and inter-annual climate sensitivities of standing California redwoods.

Science.gov (United States)

Carroll, Allyson L; Sillett, Stephen C; Kramer, Russell D

2014-01-01

Extremely decay-resistant wood and fire-resistant bark allow California's redwoods to accumulate millennia of annual growth rings that can be useful in biological research. Whereas tree rings of Sequoiadendron giganteum (SEGI) helped formalize the study of dendrochronology and the principle of crossdating, those of Sequoia sempervirens (SESE) have proven much more difficult to decipher, greatly limiting dendroclimatic and other investigations of this species. We overcame these problems by climbing standing trees and coring trunks at multiple heights in 14 old-growth forest locations across California. Overall, we sampled 1,466 series with 483,712 annual rings from 120 trees and were able to crossdate 83% of SESE compared to 99% of SEGI rings. Standard and residual tree-ring chronologies spanning up to 1,685 years for SESE and 1,538 years for SEGI were created for each location to evaluate crossdating and to examine correlations between annual growth and climate. We used monthly values of temperature, precipitation, and drought severity as well as summer cloudiness to quantify potential drivers of inter-annual growth variation over century-long time series at each location. SESE chronologies exhibited a latitudinal gradient of climate sensitivities, contrasting cooler northern rainforests and warmer, drier southern forests. Radial growth increased with decreasing summer cloudiness in northern rainforests and a central SESE location. The strongest dendroclimatic relationship occurred in our southernmost SESE location, where radial growth correlated negatively with dry summer conditions and exhibited responses to historic fires. SEGI chronologies showed negative correlations with June temperature and positive correlations with previous October precipitation. More work is needed to understand quantitative relationships between SEGI radial growth and moisture availability, particularly snowmelt. Tree-ring chronologies developed here for both redwood species have

Millennium-scale crossdating and inter-annual climate sensitivities of standing California redwoods.

Directory of Open Access Journals (Sweden)

Allyson L Carroll

Full Text Available Extremely decay-resistant wood and fire-resistant bark allow California's redwoods to accumulate millennia of annual growth rings that can be useful in biological research. Whereas tree rings of Sequoiadendron giganteum (SEGI helped formalize the study of dendrochronology and the principle of crossdating, those of Sequoia sempervirens (SESE have proven much more difficult to decipher, greatly limiting dendroclimatic and other investigations of this species. We overcame these problems by climbing standing trees and coring trunks at multiple heights in 14 old-growth forest locations across California. Overall, we sampled 1,466 series with 483,712 annual rings from 120 trees and were able to crossdate 83% of SESE compared to 99% of SEGI rings. Standard and residual tree-ring chronologies spanning up to 1,685 years for SESE and 1,538 years for SEGI were created for each location to evaluate crossdating and to examine correlations between annual growth and climate. We used monthly values of temperature, precipitation, and drought severity as well as summer cloudiness to quantify potential drivers of inter-annual growth variation over century-long time series at each location. SESE chronologies exhibited a latitudinal gradient of climate sensitivities, contrasting cooler northern rainforests and warmer, drier southern forests. Radial growth increased with decreasing summer cloudiness in northern rainforests and a central SESE location. The strongest dendroclimatic relationship occurred in our southernmost SESE location, where radial growth correlated negatively with dry summer conditions and exhibited responses to historic fires. SEGI chronologies showed negative correlations with June temperature and positive correlations with previous October precipitation. More work is needed to understand quantitative relationships between SEGI radial growth and moisture availability, particularly snowmelt. Tree-ring chronologies developed here for both redwood

Figures of equilibrium inside a gravitating ring and the limiting oblateness of elliptical galaxies

Science.gov (United States)

Kondratyev, B. P.; Trubitsyna, N. G.; Kireeva, E. N.

2016-05-01

A new class of figures of equilibrium for a rotating gravitating fluid located inside a gravitating ring or torus is studied. These figures form a family of sequences of generalized oblate spheroids, in which there is for any value of the tidal parameter α in the interval 0 ≤ 0 ≤slant α /{π Gρ } ≤slant 0.1867 ≤ 0.1867 a sequence of spheroids with oblatenesses emin ( α) ≤ e ≤ e max ( α). A series of classicalMaclaurin spheroids from a sphere to a flat disk is obtained for α = 0. At intermediate values 0 isolated non-rotating galaxy is unstable, and it cannot be supported purely by anisotropy of the stellar velocity dispersion. A ring of dark matter can stabilize a weakly rotating galaxy, supplementing standard dynamical models for such stellar systems. In order for a galaxy to acquire appreciable oblateness, the mass of the ring must be an order of magnitude higher than the mass of the galaxy itself, consistent with the ratios of the masses of dark and baryonic matter in the Universe. The influence of massive external rings could shed light on the existence of galaxies with the critical oblateness E7.

Study of the time evolution of correlation functions of the transverse Ising chain with ring frustration by perturbative theory

Science.gov (United States)

Zheng, Zhen-Yu; Li, Peng

2018-04-01

We consider the time evolution of two-point correlation function in the transverse-field Ising chain (TFIC) with ring frustration. The time-evolution procedure we investigated is equivalent to a quench process in which the system is initially prepared in a classical kink state and evolves according to the time-dependent Schrödinger equation. Within a framework of perturbative theory (PT) in the strong kink phase, the evolution of the correlation function is disclosed to demonstrate a qualitatively new behavior in contrast to the traditional case without ring frustration.

248 nm photolysis of CH2Br2 by using cavity ring-down absorption spectroscopy: Br2 molecular elimination at room temperature.

Science.gov (United States)

Wei, Pei-Ying; Chang, Yuan-Ping; Lee, Wei-Bin; Hu, Zhengfa; Huang, Hong-Yi; Lin, King-Chuen; Chen, K T; Chang, A H H

2006-10-07

Following photodissociation of CH2Br2 at 248 nm, Br2 molecular elimination is detected by using a tunable laser beam, as crossed perpendicular to the photolyzing laser beam in a ring-down cell, probing the Br2 fragment in the B 3Piou+ -X 1Sigmag+ transition. The nascent vibrational population is obtained, yielding a population ratio of Br2(v = 1)Br2(v = 0) to be 0.7 +/- 0.2. The quantum yield for the Br2 elimination reaction is determined to be 0.2 +/- 0.1. Nevertheless, when CH2Br2 is prepared in a supersonic molecular beam under cold temperature, photofragmentation gives no Br2 detectable in a time-of-flight mass spectrometer. With the aid of ab initio potential energy calculations, a plausible pathway is proposed. Upon excitation to the 1B1 or 3B1 state, C-Br bond elongation may change the molecular symmetry of Cs and enhance the resultant 1 1,3A'-X 1A' (or 1 1,3B1-X 1A1 as C2v is used) coupling to facilitate the process of internal conversion, followed by asynchronous concerted photodissociation. Temperature dependence measurements lend support to the proposed pathway.

Recent Advances and Perspectives on Nonadiabatic Mixed Quantum-Classical Dynamics.

Science.gov (United States)

Crespo-Otero, Rachel; Barbatti, Mario

2018-05-16

Nonadiabatic mixed quantum-classical (NA-MQC) dynamics methods form a class of computational theoretical approaches in quantum chemistry tailored to investigate the time evolution of nonadiabatic phenomena in molecules and supramolecular assemblies. NA-MQC is characterized by a partition of the molecular system into two subsystems: one to be treated quantum mechanically (usually but not restricted to electrons) and another to be dealt with classically (nuclei). The two subsystems are connected through nonadiabatic couplings terms to enforce self-consistency. A local approximation underlies the classical subsystem, implying that direct dynamics can be simulated, without needing precomputed potential energy surfaces. The NA-MQC split allows reducing computational costs, enabling the treatment of realistic molecular systems in diverse fields. Starting from the three most well-established methods-mean-field Ehrenfest, trajectory surface hopping, and multiple spawning-this review focuses on the NA-MQC dynamics methods and programs developed in the last 10 years. It stresses the relations between approaches and their domains of application. The electronic structure methods most commonly used together with NA-MQC dynamics are reviewed as well. The accuracy and precision of NA-MQC simulations are critically discussed, and general guidelines to choose an adequate method for each application are delivered.

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

Science.gov (United States)

Lemkul, Justin A; MacKerell, Alexander D

2017-05-09

Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus yielding the forces governing its dynamics, using classical physics rather than more expensive quantum mechanical calculations that are computationally intractable for large systems. Most force fields used to simulate biomolecular systems use fixed atomic partial charges, neglecting the influence of electronic polarization, instead making use of a mean-field approximation that may not be transferable across environments. Recent hardware and software developments make polarizable simulations feasible, and to this end, polarizable force fields represent the next generation of molecular dynamics simulation technology. In this work, we describe the refinement of a polarizable force field for DNA based on the classical Drude oscillator model by targeting quantum mechanical interaction energies and conformational energy profiles of model compounds necessary to build a complete DNA force field. The parametrization strategy employed in the present work seeks to correct weak base stacking in A- and B-DNA and the unwinding of Z-DNA observed in the previous version of the force field, called Drude-2013. Refinement of base nonbonded terms and reparametrization of dihedral terms in the glycosidic linkage, deoxyribofuranose rings, and important backbone torsions resulted in improved agreement with quantum mechanical potential energy surfaces. Notably, we expand on previous efforts by explicitly including Z-DNA conformational energetics in the refinement.

Robust Adaptive Synchronization of Ring Configured Uncertain Chaotic FitzHugh–Nagumo Neurons under Direction-Dependent Coupling

Directory of Open Access Journals (Sweden)

Muhammad Iqbal

2018-02-01

Full Text Available This paper exploits the dynamical modeling, behavior analysis, and synchronization of a network of four different FitzHugh–Nagumo (FHN neurons with unknown parameters linked in a ring configuration under direction-dependent coupling. The main purpose is to investigate a robust adaptive control law for the synchronization of uncertain and perturbed neurons, communicating in a medium of bidirectional coupling. The neurons are assumed to be different and interconnected in a ring structure. The strength of the gap junctions is taken to be different for each link in the network, owing to the inter-neuronal coupling medium properties. Robust adaptive control mechanism based on Lyapunov stability analysis is employed and theoretical criteria are derived to realize the synchronization of the network of four FHN neurons in a ring form with unknown parameters under direction-dependent coupling and disturbances. The proposed scheme for synchronization of dissimilar neurons, under external electrical stimuli, coupled in a ring communication topology, having all parameters unknown, and subject to directional coupling medium and perturbations, is addressed for the first time as per our knowledge. To demonstrate the efficacy of the proposed strategy, simulation results are provided.

Robust Adaptive Synchronization of Ring Configured Uncertain Chaotic FitzHugh–Nagumo Neurons under Direction-Dependent Coupling

Science.gov (United States)

Iqbal, Muhammad; Rehan, Muhammad; Hong, Keum-Shik

2018-01-01

This paper exploits the dynamical modeling, behavior analysis, and synchronization of a network of four different FitzHugh–Nagumo (FHN) neurons with unknown parameters linked in a ring configuration under direction-dependent coupling. The main purpose is to investigate a robust adaptive control law for the synchronization of uncertain and perturbed neurons, communicating in a medium of bidirectional coupling. The neurons are assumed to be different and interconnected in a ring structure. The strength of the gap junctions is taken to be different for each link in the network, owing to the inter-neuronal coupling medium properties. Robust adaptive control mechanism based on Lyapunov stability analysis is employed and theoretical criteria are derived to realize the synchronization of the network of four FHN neurons in a ring form with unknown parameters under direction-dependent coupling and disturbances. The proposed scheme for synchronization of dissimilar neurons, under external electrical stimuli, coupled in a ring communication topology, having all parameters unknown, and subject to directional coupling medium and perturbations, is addressed for the first time as per our knowledge. To demonstrate the efficacy of the proposed strategy, simulation results are provided. PMID:29535622

Polarization effects in molecular mechanical force fields

Energy Technology Data Exchange (ETDEWEB)

Cieplak, Piotr [Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92120 (United States); Dupradeau, Francois-Yves [UMR CNRS 6219-Faculte de Pharmacie, Universite de Picardie Jules Verne, 1 rue des Louvels, F-80037 Amiens (France); Duan, Yong [Genome Center and Department of Applied Science, University of California, Davis, One Shields Avenue, Davis, CA 95616 (United States); Wang Junmei, E-mail: pcieplak@burnham.or [Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Boulevard, ND9.136, Dallas, TX 75390-9050 (United States)

2009-08-19

The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component-polarization energy-and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations. (topical review)

Finite element analysis of the Girkmann problem using the modern hp-version and the classical h-version

KAUST Repository

Niemi, Antti

2011-06-03

We perform finite element analysis of the so called Girkmann problem in structural mechanics. The problem involves an axially symmetric spherical shell stiffened with a foot ring and is approached (1) by using the axisymmetric formulation of linear elasticity theory and (2) by using a dimensionally reduced shell-ring model. In the first approach the problem is solved with a fully automatic hp-adaptive finite element solver whereas the classical h-version of the finite element method is used in the second approach. We study the convergence behaviour of the different numerical models and show that accurate stress resultants can be obtained with both models by using effective post-processing formulas. © Springer-Verlag London Limited 2011.

Self-assembled formation and transformation of In/CdZnTe(110) nano-rings into camel-humps

International Nuclear Information System (INIS)

Cohen-Taguri, G.; Ruzin, A.; Goldfarb, I.

2012-01-01

We used in situ scanning tunneling microscopy to monitor in real time the formation of nano-rings at the molecular beam epitaxially grown In/CdZnTe(110) surface, and Auger electron spectroscopy to explore the corresponding compositional changes. In-diffusion of In and segregation of Cd to the surface in course of annealing lead to a formation of elliptically distorted nano-rings, elongated along the fast [110] diffusion direction. Exacerbated diffusion anisotropy in the liquid state, at temperatures above the melting point of In, further distorts the nano-rings into a camel-hump shape.

G345.45+1.50: an expanding ring-like structure with massive star formation

Science.gov (United States)

López-Calderón, Cristian; Bronfman, Leonardo; Nyman, Lars-Åke; Garay, Guido; de Gregorio-Monsalvo, Itziar; Bergman, Per

2016-11-01

Context. Ring-like structures in the interstellar medium (ISM) are commonly associated with high-mass stars. Kinematic studies of large structures in giant molecular clouds (GMCs) toward these ring-like structures may help us to understand how massive stars form. Aims: The origin and properties of the ring-like structure G345.45+1.50 is investigated through observations of the 13CO(3-2) line. The aim of the observations is to determine the kinematics in the region and to compare physical characteristics estimated from gas emission with those previously determined using dust continuum emission. This area in the sky is well suited for studies like this because the ring is located 1.5° above the Galactic plane at 1.8 kpc from the Sun, thus molecular structures are rarely superposed on our line of sight, which minimizes confusion effects that might hinder identifying of individual molecular condensations. Methods: The 13CO(3-2) line was mapped toward the whole ring using the Atacama Pathfinder Experiment (APEX) telescope. The observations cover 17' × 20' in the sky with a spatial resolution of 0.2 pc and an rms of 1 K at a spectral resolution of 0.1 km s-1. Results: The ring is found to be expanding with a velocity of 1.0 km s-1, containing a total mass of 6.9 × 103M⊙, which agrees well with that determined using 1.2 mm dust continuum emission. An expansion timescale of 3 × 106 yr and a total energy of 7 × 1046 erg are estimated. The origin of the ring might have been a supernova explosion, since a 35.5 cm source, J165920-400424, is located at the center of the ring without an infrared counterpart. The ring is fragmented, and 104 clumps were identified with diameters of between 0.3 and 1.6 pc, masses of between 2.3 and 7.5 × 102M⊙, and densities of between 102 and 104 cm-3. At least 18% of the clumps are forming stars, as is shown in infrared images. Assuming that the clumps can be modeled as Bonnor-Ebert spheres, 13 clumps are collapsing, and the rest of

Mean-field density functional theory of a nanoconfined classical, three-dimensional Heisenberg fluid. I. The role of molecular anchoring

Science.gov (United States)

Cattes, Stefanie M.; Gubbins, Keith E.; Schoen, Martin

2016-05-01

In this work, we employ classical density functional theory (DFT) to investigate for the first time equilibrium properties of a Heisenberg fluid confined to nanoscopic slit pores of variable width. Within DFT pair correlations are treated at modified mean-field level. We consider three types of walls: hard ones, where the fluid-wall potential becomes infinite upon molecular contact but vanishes otherwise, and hard walls with superimposed short-range attraction with and without explicit orientation dependence. To model the distance dependence of the attractions, we employ a Yukawa potential. The orientation dependence is realized through anchoring of molecules at the substrates, i.e., an energetic discrimination of specific molecular orientations. If the walls are hard or attractive without specific anchoring, the results are "quasi-bulk"-like in that they can be linked to a confinement-induced reduction of the bulk mean field. In these cases, the precise nature of the walls is completely irrelevant at coexistence. Only for specific anchoring nontrivial features arise, because then the fluid-wall interaction potential affects the orientation distribution function in a nontrivial way and thus appears explicitly in the Euler-Lagrange equations to be solved for minima of the grand potential of coexisting phases.

Si-Imidazole-HSO4 Functionalized Magnetic Fe3O4 Nanoparticles as an Efficient and Reusable Catalyst for the Regioselective Ring Opening of Epoxides in Water

Directory of Open Access Journals (Sweden)

Eshagh Rezaee Nezhad

2016-01-01

Full Text Available An efficient and simple method for the preparation of Si-Imidazole-HSO4 functionalized magnetic Fe3O4 nanoparticles (Si-Im-HSO4 MNPs and used as an efficient and reusable magnetic catalysts for the regioselective ring opening of epoxides under green conditions in water. This catalyst was used for the ring opening of epoxide corresponding to the thiocyanohydrins and azidohydrines. Compared to the classical ring opening of epoxides, this new method consistently has the advantage of excellent yields, short reaction times, and methodological simplicity.

Fluctuation Solution Theory Properties from Molecular Simulation

DEFF Research Database (Denmark)

Abildskov, Jens; Wedberg, R.; O’Connell, John P.

2013-01-01

The thermodynamic properties obtained in the Fluctuation Solution Theory are based on spatial integrals of molecular TCFs between component pairs in the mixture. Molecular simulation, via either MD or MC calculations, can yield these correlation functions for model inter- and intramolecular...

Autoamplification of molecular chirality through the induction of supramolecular chirality

NARCIS (Netherlands)

van Dijken, Derk Jan; Beierle, John M.; Stuart, Marc C. A.; Szymanski, Wiktor; Browne, Wesley R.; Feringa, Ben L.

2014-01-01

The novel concept for the autoamplification of molecular chirality, wherein the amplification proceeds through the induction of supramolecular chirality, is presented. A solution of prochiral, ring-open diarylethenes is doped with a small amount of their chiral, ring-closed counterpart. The

FLSR - The Frankfurt low energy storage ring

International Nuclear Information System (INIS)

Stiebing, K.E.; Alexandrov, V.; Doerner, R.; Enz, S.; Kazarinov, N.Yu.; Kruppi, T.; Schempp, A.; Schmidt Boecking, H.; Voelp, M.; Ziel, P.; Dworak, M.; Dilfer, W.

2010-01-01

An electrostatic storage ring for low-energy ions with a design energy of 50 keV is presently being set up at the Institut fuer Kernphysik der Johann Wolfgang Goethe-Universitaet Frankfurt am Main, Germany (IKF). This new device will provide a basis for new experiments on the dynamics of ionic and molecular collisions, as well as for high precision and time resolved laser spectroscopy. In this article, the design parameters of this instrument are reported.

Construction of classical and non-classical coherent photon states

International Nuclear Information System (INIS)

Honegger, Reinhard; Rieckers, Alfred

2001-01-01

It is well known that the diagonal matrix elements of all-order coherent states for the quantized electromagnetic field have to constitute a Poisson distribution with respect to the photon number. The present work gives first the summary of a constructive scheme, developed previously, which determines in terms of an auxiliary Hilbert space all possible off-diagonal elements for the all-order coherent density operators in Fock space and which identifies all extremal coherent states. In terms of this formalism it is then demonstrated that each pure classical coherent state is a uniformly phase locked (quantum) coherent superposition of number states. In a mixed classical coherent state the exponential of the locked phase is shown to be replaced by a rather arbitrary unitary operator in the auxiliary Hilbert space. On the other hand classes for density operators--and for their normally ordered characteristic functions--of non-classical coherent states are obtained, especially by rather weak perturbations of classical coherent states. These illustrate various forms of breaking the classical uniform phase locking and exhibit rather peculiar properties, such as asymmetric fluctuations for the quadrature phase operators. Several criteria for non-classicality are put forward and applied to the elaborated non-classical coherent states, providing counterexamples against too simple arguments for classicality. It is concluded that classicality is only a stable concept for coherent states with macroscopic intensity

White Ring; White ring

Energy Technology Data Exchange (ETDEWEB)

Aoki, H.; Yuzawa, H. [Nikken Sekkei Ltd., Osaka (Japan)

1998-01-05

White Ring is a citizen`s gymnasium used for figure skating and short track speed skating games of 18th Winter Olympic Games in 1998. White Ring is composed of a main-arena and a sub-arena. For the main-arena with an area 41mtimes66m, an ice link can be made by disengaging the potable floor and by flowing brine in the bridged polystyrene pipes embedded in the concrete floor. Due to the fortunate groundwater in this site, well water is used for the outside air treatment energy in 63% during heating and in 35% during cooling. Ammonia is used as a cooling medium for refrigerating facility. For the heating of audience area in the large space, heat load from the outside is reduced by enhancing the heat insulation performance of the roof of arena. The audience seats are locally heated using heaters. For the White Ring, high quality environment is realized for games through various functions of the large-scale roof of the large space. Success of the big event was expected. 15 figs., 4 tabs.

Token Ring Project

Directory of Open Access Journals (Sweden)

Adela Ionescu

2007-01-01

Full Text Available Ring topology is a simple configuration used to connect processes that communicate among themselves. A number of network standards such as token ring, token bus, and FDDI are based on the ring connectivity. This article will develop an implementation of a ring of processes that communicate among themselves via pipe links. The processes are nodes in the ring. Each process reads from its standard input and writes in its standard output. N-1 process redirects the its standard output to a standard input of the process through a pipe. When the ring-structure is designed, the project can be extended to simulate networks or to implement algorithms for mutual exclusion

A simple program to measure and analyse tree rings using Excel, R and SigmaScan

Science.gov (United States)

Hietz, Peter

2011-01-01

I present a new software that links a program for image analysis (SigmaScan), one for spreadsheets (Excel) and one for statistical analysis (R) for applications of tree-ring analysis. The first macro measures ring width marked by the user on scanned images, stores raw and detrended data in Excel and calculates the distance to the pith and inter-series correlations. A second macro measures darkness along a defined path to identify latewood–earlywood transition in conifers, and a third shows the potential for automatic detection of boundaries. Written in Visual Basic for Applications, the code makes use of the advantages of existing programs and is consequently very economic and relatively simple to adjust to the requirements of specific projects or to expand making use of already available code. PMID:26109835

A simple program to measure and analyse tree rings using Excel, R and SigmaScan.

Science.gov (United States)

Hietz, Peter

I present a new software that links a program for image analysis (SigmaScan), one for spreadsheets (Excel) and one for statistical analysis (R) for applications of tree-ring analysis. The first macro measures ring width marked by the user on scanned images, stores raw and detrended data in Excel and calculates the distance to the pith and inter-series correlations. A second macro measures darkness along a defined path to identify latewood-earlywood transition in conifers, and a third shows the potential for automatic detection of boundaries. Written in Visual Basic for Applications, the code makes use of the advantages of existing programs and is consequently very economic and relatively simple to adjust to the requirements of specific projects or to expand making use of already available code.

Semi-algebraic function rings and reflectors of partially ordered rings

CERN Document Server

Schwartz, Niels

1999-01-01

The book lays algebraic foundations for real geometry through a systematic investigation of partially ordered rings of semi-algebraic functions. Real spectra serve as primary geometric objects, the maps between them are determined by rings of functions associated with the spectra. The many different possible choices for these rings of functions are studied via reflections of partially ordered rings. Readers should feel comfortable using basic algebraic and categorical concepts. As motivational background some familiarity with real geometry will be helpful. The book aims at researchers and graduate students with an interest in real algebra and geometry, ordered algebraic structures, topology and rings of continuous functions.

B13+ : a photodriven molecular Wankel engine.

Science.gov (United States)

Zhang, Jin; Sergeeva, Alina P; Sparta, Manuel; Alexandrova, Anastassia N

2012-08-20

Revved-up rotary: A molecular Wankel motor, the dual-ring structure B(13)(+), is driven by circularly-polarized infrared electromagnetic radiation. Calculations show that this illumination leads to a guided unidirectional rotation of the outer ring, which is achieved with rotational frequency of the order of 300 GHz. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simulating the spread of classical swine fever virus between a hypothetical wild-boar population and domestic pig herds in Denmark

DEFF Research Database (Denmark)

Boklund, Anette; Goldbach, Stine G.; Uttenthal, Åse

2008-01-01

of CSFV between the hypothetical wild-boar population and the domestic population. Furthermore, the economic impact is assessed taking the perspective of the Danish national budget and the Danish pig industry. We used InterSpreadPlus to model the differential classical swine fever (CSF) risk due to wild......Denmark has no free-range wild-boar population. However, Danish wildlife organizations have suggested that wild boar should be reintroduced into the wild to broaden national biodiversity. Danish pig farmers fear that this would lead to a higher risk of introduction of classical swine fever virus...

Rotating ring-ring electrode theory and experiment

NARCIS (Netherlands)

Kuiken, H.K.; Bakkers, E.P.A.M.; Ligthart, H.; Kellyb, J.J.

2000-01-01

A model is presented for the rotating ring-ring electrode. Although the electrode is defined by four characteristic lengths, it is shown that the collection efficiency depends on only two dimensionless parameters. A simple relationship between these and the corresponding parameters for the rotating

Emergency vaccination for classical swine fever will not be cost-effective for countries with a large export

DEFF Research Database (Denmark)

Boklund, Anette; Toft, Nils; Alban, Lis

2009-01-01

the epidemiological and economic consequences of such control strategies under Danish conditions with respect to herd demographics and geography as well as to investigate the effect of extra biosecurity on farms. We used InterSpread Plus to model the effect of nine different control strategies: the minimum measures......,H.M., Smak,J.A., Pluimers,F.H., 1999. The classical swine fever epidemic 1997-1998 in The Netherlands: descriptive epidemiology, Prev.Vet.Med., 42, 157-184. Fritzemeier,J., Teuffert,J., Greiser,Wilke,I, Staubach,Ch, Schlüter,H., Moennig,V., 2000. Epidemiology of classical swine fever in Germany in the 1990s......, Vet.Microbiol. 77, 29-41. MacKinnon, J.D., 2001. Some clinical and epidemiological aspects of the outbreak of Classical Swine Fe-ver in East Anglia in 2000, State Vet.J,, 11, 2-7....

Size filtering effect in vertical stacks of In(Ga)As/GaAs self-assembled quantum rings

International Nuclear Information System (INIS)

Ouerghui, W.; Melliti, A.; Maaref, M.A.; Martinez-Pastor, J.; Gomis, J.; Granados, D.; Garcia, J.M.

2006-01-01

We present a systematic study of closely In(Ga)As/InAs quantum rings (QRs) grown by molecular beam epitaxy (MBE). Photoluminescence (PL) experiments show a strong filtering effect in the ring being stacked and simultaneous linewidth narrowing for the appropriate layer thickness (thinner thickness). If the spacer thickness is further reduced, a strong coupling between the nanostructures is produced and the signal shifts to low energy

Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution.

Science.gov (United States)

Liu, Peng; Wang, Qiong; Niu, Meixing; Wang, Dunyou

2017-08-10

Combining multi-level quantum mechanics theories and molecular mechanics with an explicit water model, we investigated the ring opening process of guanine damage by hydroxyl radical in aqueous solution. The detailed, atomic-level ring-opening mechanism along the reaction pathway was revealed in aqueous solution at the CCSD(T)/MM levels of theory. The potentials of mean force in aqueous solution were calculated at both the DFT/MM and CCSD(T)/MM levels of the theory. Our study found that the aqueous solution has a significant effect on this reaction in solution. In particular, by comparing the geometries of the stationary points between in gas phase and in aqueous solution, we found that the aqueous solution has a tremendous impact on the torsion angles much more than on the bond lengths and bending angles. Our calculated free-energy barrier height 31.6 kcal/mol at the CCSD(T)/MM level of theory agrees well with the one obtained based on gas-phase reaction profile and free energies of solvation. In addition, the reaction path in gas phase was also mapped using multi-level quantum mechanics theories, which shows a reaction barrier at 19.2 kcal/mol at the CCSD(T) level of theory, agreeing very well with a recent ab initio calculation result at 20.8 kcal/mol.

Introducing Catastrophe-QSAR. Application on Modeling Molecular Mechanisms of Pyridinone Derivative-Type HIV Non-Nucleoside Reverse Transcriptase Inhibitors

Directory of Open Access Journals (Sweden)

Marius Lazea

2011-12-01

Full Text Available The classical method of quantitative structure-activity relationships (QSAR is enriched using non-linear models, as Thom’s polynomials allow either uni- or bi-variate structural parameters. In this context, catastrophe QSAR algorithms are applied to the anti-HIV-1 activity of pyridinone derivatives. This requires calculation of the so-called relative statistical power and of its minimum principle in various QSAR models. A new index, known as a statistical relative power, is constructed as an Euclidian measure for the combined ratio of the Pearson correlation to algebraic correlation, with normalized t-Student and the Fisher tests. First and second order inter-model paths are considered for mono-variate catastrophes, whereas for bi-variate catastrophes the direct minimum path is provided, allowing the QSAR models to be tested for predictive purposes. At this stage, the max-to-min hierarchies of the tested models allow the interaction mechanism to be identified using structural parameter succession and the typical catastrophes involved. Minimized differences between these catastrophe models in the common structurally influential domains that span both the trial and tested compounds identify the “optimal molecular structural domains” and the molecules with the best output with respect to the modeled activity, which in this case is human immunodeficiency virus type 1 HIV-1 inhibition. The best molecules are characterized by hydrophobic interactions with the HIV-1 p66 subunit protein, and they concur with those identified in other 3D-QSAR analyses. Moreover, the importance of aromatic ring stacking interactions for increasing the binding affinity of the inhibitor-reverse transcriptase ligand-substrate complex is highlighted.

(E)-Methyl 3-(3,4-dimeth-oxy-phen-yl)-2-[(1,3-dioxoisoindolin-2-yl)meth-yl]acrylate.

Science.gov (United States)

Kannan, D; Bakthadoss, M; Lakshmanan, D; Murugavel, S

2012-04-01

In the title compound, C(21)H(19)NO(6), the isoindole ring system is essentially planar [maximum deviation = 0.019 (2) Å for the N atom] and is oriented at a dihedral angle of 51.3 (1)° with respect to the benzene ring. The two meth-oxy groups are almost coplanar with the attached benzene ring [C-O-C-C = 3.7 (4) and 4.3 (4)°]. The mol-ecular conformation is stabilized by an intra-molecular C-H⋯O hydrogen bond, which generates an S(9) ring motif. In the crystal, mol-ecules are linked through bifurcated C-H⋯(O,O) hydrogen bonds having R(1) (2)(5) ring motifs, forming chains along the b-axis direction. The crystal packing is further stabilzed by π-π inter-actions [centriod-centroid distance = 3.463 (1) Å].

Spectral shapes of Ar-broadened HCl lines in the fundamental band by classical molecular dynamics simulations and comparison with experiments

Energy Technology Data Exchange (ETDEWEB)

Tran, H., E-mail: ha.tran@lisa.u-pec.fr [Laboratoire Interuniversitaire des Systèmes Atmosphériques, UMR CNRS 7583, Université Paris Est Créteil, Université Paris Diderot, Institut Pierre-Simon Laplace, 94010 Créteil Cedex (France); Domenech, J.-L. [Instituto de Estructura de la Materia, Consejo Superior de Investigaciones Cientificas, (IEM-CSIC), Serrano 123, 28006 Madrid (Spain)

2014-08-14

Spectral shapes of isolated lines of HCl perturbed by Ar are investigated for the first time using classical molecular dynamics simulations (CMDS). Using reliable intermolecular potentials taken from the literature, these CMDS provide the time evolution of the auto-correlation function of the dipole moment, whose Fourier-Laplace transform leads to the absorption spectrum. In order to test these calculations, room temperature spectra of various lines in the fundamental band of HCl diluted in Ar are measured, in a large pressure range, with a difference-frequency laser spectrometer. Comparisons between measured and calculated spectra show that the CMDS are able to predict the large Dicke narrowing effect on the shape of HCl lines and to satisfactorily reproduce the shapes of HCl spectra at different pressures and for various rotational quantum numbers.

Plant molecular farming: Opportunities and challenges

Directory of Open Access Journals (Sweden)

Valkova Rumyana

2013-01-01

Full Text Available The modern human life is impossible without products derived from the classical, contemporary biotechnology. However, large scale production of biotechnology wares opens a discussion about the economic impact, waste management, biosafety, and bioethical issues. Plant molecular farming offers a relatively inexpensive option for yielding of many valuable products and demonstrates number of advantages over the classical technologies, but also brings the question of further development perspectives, hazard identification and risk assessment. This review is focused on those two questions: opportunities offered and challenges faced by modern plant molecular farming systems.

Kayser-Fleischer Rings

Science.gov (United States)

... Support Contacts Lab Tracker/Copper Calculator Stories Programs & Research ... About Everything you need to know about Wilson Disease Kayser-Fleischer Rings Definition Kayser-Fleischer Ring: Clinical sign. Brownish-yellow ring visible around the corneo- ...

Communication: Proper treatment of classically forbidden electronic transitions significantly improves detailed balance in surface hopping

Energy Technology Data Exchange (ETDEWEB)

Sifain, Andrew E. [Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089-0485 (United States); Wang, Linjun [Department of Chemistry, Zhejiang University, Hangzhou 310027 (China); Prezhdo, Oleg V. [Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089-0485 (United States); Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062 (United States)

2016-06-07

Surface hopping is the most popular method for nonadiabatic molecular dynamics. Many have reported that it does not rigorously attain detailed balance at thermal equilibrium, but does so approximately. We show that convergence to the Boltzmann populations is significantly improved when the nuclear velocity is reversed after a classically forbidden hop. The proposed prescription significantly reduces the total number of classically forbidden hops encountered along a trajectory, suggesting that some randomization in nuclear velocity is needed when classically forbidden hops constitute a large fraction of attempted hops. Our results are verified computationally using two- and three-level quantum subsystems, coupled to a classical bath undergoing Langevin dynamics.

FLSR - The Frankfurt low energy storage ring

Science.gov (United States)

Stiebing, K. E.; Alexandrov, V.; Dörner, R.; Enz, S.; Kazarinov, N. Yu.; Kruppi, T.; Schempp, A.; Schmidt Böcking, H.; Völp, M.; Ziel, P.; Dworak, M.; Dilfer, W.

2010-02-01

An electrostatic storage ring for low-energy ions with a design energy of 50 keV is presently being set up at the Institut für Kernphysik der Johann Wolfgang Goethe-Universität Frankfurt am Main, Germany (IKF). This new device will provide a basis for new experiments on the dynamics of ionic and molecular collisions, as well as for high precision and time resolved laser spectroscopy. In this article, the design parameters of this instrument are reported.

Synthesis and studies on structural, optical and nonlinear optical properties of novel organic inter-molecular compounds: 4-chloro-3-nitroaniline-3-hydroxy benzaldehyde and urea-4-dimethylaminopyridine

Science.gov (United States)

Pandey, Priyanka; Rai, R. N.

2018-05-01

Two novel organic inter-molecular compounds (IMCs), (3-(4-chloro-3-nitrophenylimino) methyl) phenol) (CNMP) and urea ̶ 4-dimethylaminopyridine complex (UDMAP), have been synthesized by solid state reaction. These two IMCs were identified by phase diagram study of CNA-HB and U-DMAP systems. The single crystals of newly obtained IMCs were grown by slow solvent evaporation technique at room temperature. Both the IMCs were further studied for their thermal, spectral, single crystal XRD for their atomic packing in molecule, crystallinity, optical and nonlinear optical behaviour. In both the cases, melting point of inter-molecular compounds was found to be higher than that of their parent components, CNMP was found to be thermally stable up to 158 °C while UDMAP was stable up to 144 °C, which indicate their extra stability than their parents. The single crystal XRD studies confirmed that CNMP has crystallized in orthorhombic unit cell with non-centrosymmetric space group P212121 while UDMAP has crystallized in monoclinic unit cell with centrosymmetric space group C2/c. The absorption spectrum of CNMP was found to be in between the absorption of parents, while broadening of peak and red shift was observed in UDMAP as compared to the parents. Second order nonlinear optical property of CNMP and UDMAP was studied using Kurtz Perry powder technique and intense green light emission was observed with CNMP on excitation with 1064 nm of Nd:YAG laser while no emission was observed with UDMAP.

Breathing and Singing: Objective Characterization of Breathing Patterns in Classical Singers.

Science.gov (United States)

Salomoni, Sauro; van den Hoorn, Wolbert; Hodges, Paul

2016-01-01

Singing involves distinct respiratory kinematics (i.e. movements of rib cage and abdomen) to quiet breathing because of different demands on the respiratory system. Professional classical singers often advocate for the advantages of an active control of the abdomen on singing performance. This is presumed to prevent shortening of the diaphragm, elevate the rib cage, and thus promote efficient generation of subglottal pressure during phonation. However, few studies have investigated these patterns quantitatively and inter-subject variability has hindered the identification of stereotypical patterns of respiratory kinematics. Here, seven professional classical singers and four untrained individuals were assessed during quiet breathing, and when singing both a standard song and a piece of choice. Several parameters were extracted from respiratory kinematics and airflow, and principal component analysis was used to identify typical patterns of respiratory kinematics. No group differences were observed during quiet breathing. During singing, both groups adapted to rhythmical constraints with decreased time of inspiration and increased peak airflow. In contrast to untrained individuals, classical singers used greater percentage of abdominal contribution to lung volume during singing and greater asynchrony between movements of rib cage and abdomen. Classical singers substantially altered the coordination of rib cage and abdomen during singing from that used for quiet breathing. Despite variations between participants, principal component analysis revealed consistent pre-phonatory inward movements of the abdominal wall during singing. This contrasted with untrained individuals, who demonstrated synchronous respiratory movements during all tasks. The inward abdominal movements observed in classical singers elevates intra-abdominal pressure and may increase the length and the pressure-generating capacity of rib cage expiratory muscles for potential improvements in voice

Planetary Rings

Science.gov (United States)

Nicholson, P. D.

2001-11-01

A revolution in the studies in planetary rings studies occurred in the period 1977--1981, with the serendipitous discovery of the narrow, dark rings of Uranus, the first Voyager images of the tenuous jovian ring system, and the many spectacular images returned during the twin Voyager flybys of Saturn. In subsequent years, ground-based stellar occultations, HST observations, and the Voyager flybys of Uranus (1986) and Neptune (1989), as well as a handful of Galileo images, provided much additional information. Along with the completely unsuspected wealth of detail these observations revealed came an unwelcome problem: are the rings ancient or are we privileged to live at a special time in history? The answer to this still-vexing question may lie in the complex gravitational interactions recent studies have revealed between the rings and their retinues of attendant satellites. Among the four known ring systems, we see elegant examples of Lindblad and corotation resonances (first invoked in the context of galactic disks), electromagnetic resonances, spiral density waves and bending waves, narrow ringlets which exhibit internal modes due to collective instabilities, sharp-edged gaps maintained via tidal torques from embedded moonlets, and tenuous dust belts created by meteoroid impact onto parent bodies. Perhaps most puzzling is Saturn's multi-stranded, clumpy F ring, which continues to defy a simple explanation 20 years after it was first glimpsed in grainy images taken by Pioneer 11. Voyager and HST images reveal a complex, probably chaotic, dynamical interaction between unseen parent bodies within this ring and its two shepherd satellites, Pandora and Prometheus. The work described here reflects contributions by Joe Burns, Jeff Cuzzi, Luke Dones, Dick French, Peter Goldreich, Colleen McGhee, Carolyn Porco, Mark Showalter, and Bruno Sicardy, as well as those of the author. This research has been supported by NASA's Planetary Geology and Geophysics program and the

Classical and semiclassical treatments of highly charged ions + H(1s) collisions

International Nuclear Information System (INIS)

Errea, L.F.; Illescas, C.; Mendez, L.; Pons, B.; Riera, A.; Suarez, J.

2005-01-01

We present impact-parameter classical trajectory Monte-Carlo and molecular close-coupling calculations for total and partial cross sections for Ne 10+ , Ar 18 + H(1s) collisions, which have recently became of interest in fusion plasma research

Molecular Dynamics Simulation of the Structure and Properties of Lithium Phosphate Glasses

Energy Technology Data Exchange (ETDEWEB)

Liang, J-J; Cygan, R.T.; Alam, T.M.

1999-07-09

A new forcefield model was developed for the computer simulation of phosphate materials that have many important applications in the electronics and biomedical industries. The model provides a fundamental basis for the evaluation of phosphate glass structure and thermodynamics. Molecular dynamics simulations of a series of lithium phosphate glass compositions were performed using the forcefield model. A high concentration of three-membered rings (P{sub 3}O{sub 3}) occurs in the glass of intermediate composition (0.2 Li{sub 2}O {center_dot} 0.8P{sub 2}O{sub 5}) that corresponds to the minimum in the glass transition temperature curve for the compositional series. Molecular orbital calculations of various phosphate ring clusters indicate an increasing stabilization of the phosphate ring structure going from two- to four-membered rings.

1-[1-(4-Chloro-phen-yl)ethyl-idene]carbono-hydrazide.

Science.gov (United States)

Du, Lingyun; Du, Lei; Wang, Shuhao

2009-08-12

The mol-ecular skeleton of the title mol-ecule, C(9)H(11)ClN(4)O, is essentially planar, the dihedral angle between the ring and the and N/N/C plane being 6.7 (3)°. In the crystal, inter-molecular N-H⋯O and N-H⋯N hydrogen bonds link the mol-ecules into ribbons propagated along [010].

Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors

Science.gov (United States)

Korobenko, Aleksey; Milner, Alexander; Hepburn, John; Milner, Valery

2015-05-01

Using the technique of an optical centrifuge, we excite diatomic molecules to ultrafast synchronous rotation. Femtosecond velocity-map imaging allows us to visualize and study the coherent dynamics of molecular superrotors under field free conditions and in external magnetic field. We demonstrate that when the created rotational wave packet is narrow, its free evolution is nondispersing and follows the motion of a classically rotating dumbbell or a hand of the smallest natural stopwatch. For wider rotational distributions, we observe the breakdown of classical rotation, when a dumbbell shape changes to that of a ``quantum cogwheel'' - a molecular state simultaneously aligned along multiple direction. Our measurements in external magnetic field reveal other peculiar aspects of the rich dynamics of molecular superrotors. The rotation of a non-magnetic molecule interacts with the applied field only weakly, giving rise to slow precession of the molecular angular momentum around the field direction. In contrast, the electronic spin of a paramagnetic superrotor mediates this interaction, causing the initial disk-like angular distribution to split into several spatial components, each precessing with its own frequency determined by the spin projection.

Comparing the results of lattice and off-lattice simulations for the melt of nonconcatenated rings

International Nuclear Information System (INIS)

Halverson, Jonathan D; Kremer, Kurt; Grosberg, Alexander Y

2013-01-01

To study the conformational properties of unknotted and nonconcatenated ring polymers in the melt, we present a detailed qualitative and quantitative comparison of simulation data obtained by molecular dynamics simulation using an off-lattice bead-spring model and by Monte Carlo simulation using a lattice model. We observe excellent, and sometimes even unexpectedly good, agreement between the off-lattice and lattice results for many quantities measured including the gyration radii of the ring polymers, gyration radii of their subchains, contact probabilities, surface characteristics, number of contacts between subchains, and the static structure factors of the rings and their subchains. These results are, in part, put in contrast to Moore curves, and the open, linear polymer counterparts. While our analysis is extensive, our understanding of the ring melt conformations is still rather preliminary. (paper)

Preparation for electron ring - plasma ring merging experiments in RECE-MERGE

International Nuclear Information System (INIS)

Taggart, D.; Sekiguchi, A.; Fleischmann, H.H.

1986-01-01

The formation of a mixed-CT using relativistic electron rings and gun-produced plasma rings by MERGE-ing them axially is simulated. This process is similar to the axial stacking of relativistic electron rings in RECE-Christa. The results of their first plasm production experiment are reported here. After study of the gun-produced plasma's properties is completed, the gun will be mounted at the downstream end of the vacuum tank and the source of relativistic electron rings will be at the upstream end. The two rings, formed at opposite ends of the tank, will be translated axially and merged

Classical two-slit interference effects in double photoionization of molecular hydrogen at high energies

Energy Technology Data Exchange (ETDEWEB)

Horner, Daniel A.; Miyabe, Shungo; Rescigno, Thomas N; McCurdy, C. William; Morales, Felipe; Martin, Fernando

2008-07-06

Recent experiments on double photoionization of H$_2$ with photon energies between 160 and 240 eV have revealed body-frame angular distributions that suggest classical two-slit interference effects may be present when one electron carries most of the available energy and the second electron is not observed. We report precise quantum mechanical calculations that reproduce the experimental findings. They reveal that the interpretation in terms of classical diffraction is only appropriate atsubstantially higher photon energies. At the energies considered in the experiment we offer an alternative explanation based on the mixing of two non-diffractive contributions by circularly polarized light.

Simple improvements to classical bubble nucleation models.

Science.gov (United States)

Tanaka, Kyoko K; Tanaka, Hidekazu; Angélil, Raymond; Diemand, Jürg

2015-08-01

We revisit classical nucleation theory (CNT) for the homogeneous bubble nucleation rate and improve the classical formula using a correct prefactor in the nucleation rate. Most of the previous theoretical studies have used the constant prefactor determined by the bubble growth due to the evaporation process from the bubble surface. However, the growth of bubbles is also regulated by the thermal conduction, the viscosity, and the inertia of liquid motion. These effects can decrease the prefactor significantly, especially when the liquid pressure is much smaller than the equilibrium one. The deviation in the nucleation rate between the improved formula and the CNT can be as large as several orders of magnitude. Our improved, accurate prefactor and recent advances in molecular dynamics simulations and laboratory experiments for argon bubble nucleation enable us to precisely constrain the free energy barrier for bubble nucleation. Assuming the correction to the CNT free energy is of the functional form suggested by Tolman, the precise evaluations of the free energy barriers suggest the Tolman length is ≃0.3σ independently of the temperature for argon bubble nucleation, where σ is the unit length of the Lennard-Jones potential. With this Tolman correction and our prefactor one gets accurate bubble nucleation rate predictions in the parameter range probed by current experiments and molecular dynamics simulations.

Morphometric, molecular and histopathologic description of hepatic infection by Orthosplanchnus arcticus (Trematoda: Digenea: Brachycladiidae) in ringed seals (Pusa hispida) from Northwest Greenland

DEFF Research Database (Denmark)

Andersen-Ranberg, Emilie; Lehnert, Kristina; Leifsson, Páll S.

2018-01-01

For the first time in > 30 years of routine sampling under the Arctic Monitoring and Assessment Program, a parasite was found in the liver of ringed seals (Phoca hispida) collected near Qaanaaq (Thule), Northwest Greenland, in 2008 and 2014. Concerns regarding changes to parasite occurrence......, possibly related to climate change and bioaccumulation of immunomodulating anthropogenic pollutants, spurred further investigations into parasite characterization, and implications for wildlife health and seal hunters. Microscopic, molecular, and morphometric analyses are presented herein. Of 40 seals, 6...... (15%) were infected, and 5 of 6 of these seals had severe infections. The parasite was identified morphologically as Orthosplanchnus arcticus Odhner, 1905 (Trematoda; Digenea: Brachycladiidae). Macro- and microscopic pathologic study indicated mild-to-severe biliary hyperplasia associated, stasis...

Growth ring analysis of Euxylophora paraensis through x-ray microdensitometry

Directory of Open Access Journals (Sweden)

Eva Santos de Andrade

Full Text Available ABSTRACT: Euxylophora paraensis Huber - Rutaceae, popularly known as yellow heart, is a species with a low-density population that has suffered intense exploitation in recent decades. This has led to its inclusion in the IBAMA list of endangered species. This study aimed to evaluate the existence of growth rings and their annuity in five trees of Euxylophora paraensis through the x-ray microdensitometry technique, as well as to compare them using the classical method. Application feasibility of this technique can be deepened through future, broader dendroecological studies, which may better elucidate the understanding of the species population dynamics and promote more sustainable uses. Wood disks were collected from the base of five 29-year-old trees from a planting site in the Curua-Una Experimental Station, located in Prainha, Pará State, Brazil. Samples were polished and sanded for the x-ray microdensitometric analysis. Values of minimum, average, and maximum density (0.581, 0.84, and 1.077gcm-3, respectively were obtained. There was a significant difference in density between the studied trees. Growth rings boundaries, through densitometric pith-bark profile are demarcated by fibrous zones, with density variation between the early wood and late wood. This study concludes that the growth rings of the studied species are distinct and annual, validating the technique used.

Rapid learning dynamics in individual honeybees during classical conditioning.

Science.gov (United States)

Pamir, Evren; Szyszka, Paul; Scheiner, Ricarda; Nawrot, Martin P

2014-01-01

Associative learning in insects has been studied extensively by a multitude of classical conditioning protocols. However, so far little emphasis has been put on the dynamics of learning in individuals. The honeybee is a well-established animal model for learning and memory. We here studied associative learning as expressed in individual behavior based on a large collection of data on olfactory classical conditioning (25 datasets, 3298 animals). We show that the group-averaged learning curve and memory retention score confound three attributes of individual learning: the ability or inability to learn a given task, the generally fast acquisition of a conditioned response (CR) in learners, and the high stability of the CR during consecutive training and memory retention trials. We reassessed the prevailing view that more training results in better memory performance and found that 24 h memory retention can be indistinguishable after single-trial and multiple-trial conditioning in individuals. We explain how inter-individual differences in learning can be accommodated within the Rescorla-Wagner theory of associative learning. In both data-analysis and modeling we demonstrate how the conflict between population-level and single-animal perspectives on learning and memory can be disentangled.

Rapid learning dynamics in individual honeybees during classical conditioning

Directory of Open Access Journals (Sweden)

Evren ePamir

2014-09-01

Full Text Available Associative learning in insects has been studied extensively by a multitude of classical conditioning protocols. However, so far little emphasis has been put on the dynamics of learning in individuals. The honeybee is a well-established animal model for learning and memory. We here studied associative learning as expressed in individual behavior based on a large collection of data on olfactory classical conditioning (25 datasets, 3,298 animals. We show that the group-averaged learning curve and memory retention score confound three attributes of individual learning: the ability or inability to learn a given task, the generally fast acquisition of a conditioned response in learners, and the high stability of the conditioned response during consecutive training and memory retention trials. We reassessed the prevailing view that more training results in better memory performance and found that 24h memory retention can be indistinguishable after single-trial and multiple-trial conditioning in individuals. We explain how inter-individual differences in learning can be accommodated within the Rescorla-Wagner theory of associative learning. In both data-analysis and modeling we demonstrate how the conflict between population-level and single-animal perspectives on learning and memory can be disentangled.

Role of four-membered rings in C32 fullerene stability and mechanisms of generalized Stone-Wales transformation: a density functional theory investigation.

Science.gov (United States)

Wang, Weiwei; Dang, Jingshuang; Zhao, Xiang

2011-08-28

Density functional theory (DFT) methods have been applied to study C(32) fullerenes built from four-, five-, and six-membered rings. The relative energies of pure C(32) fullerenes have been evaluated to locate three most stable structures, 32:D(4d) with two squares, 1:D(3) without square and 5:C(s) with one square. Structural analysis reveals that there is a rearrangement pathway between the lowest energy classical isomer 1:D(3) and the lowest energy non-classical isomer 32:D(4d), and 5:C(s) behaves just as an intermediate between them. The kinetic processes of generalized Stone-Wales transformation (GSWT) with four-membered rings have been explored and two distinct reaction mechanisms are determined by all the transition states and intrinsic reaction coordinates with PBE1PBE/6-31G(d) approach for the first time. One mechanism is the concerted reaction with a rotating dimer closed to the cage surface and another is the stepwise reaction with a carbene-like sp(3) structure, whereas the latter is sorted into two paths based on four-membered ring vanishing before or after the formation of the carbene-like structure. It is indicated that there is no absolute preference for any mechanism, which depends on the adaptability of different reactants on the diverse mechanisms. Furthermore, it's found that the interconversion process with the participation of squares is more reactive than the rearrangement between C(60)_I(h) and C(60)_C(2v), implying some potential importance of non-classical small fullerenes in the fullerene isomerization.

Structure of layered C[sub 60] on Si(100) surface studied by ab initio and classical molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Kawazoe, Yoshiyuki (Inst. for Materials Research, Tohoku Univ., Sendai (Japan)); Maruyama, Yutaka (Inst. for Materials Research, Tohoku Univ., Sendai (Japan)); Rafii-Tabar, H. (Inst. for Materials Research, Tohoku Univ., Sendai (Japan)); Ikeda, Makoto (Inst. for Materials Research, Tohoku Univ., Sendai (Japan)); Kamiyama, Hiroshi (Inst. for Materials Research, Tohoku Univ., Sendai (Japan)); Ohno, Kaoru (Inst. for Materials Research, Tohoku Univ., Sendai (Japan))

1993-04-19

The recent scanning tunnelling microscopy (STM) observations by Hashizume et al. concerning C[sub 60] buckeyballs deposited on an Si(100) surface revealed self-aligned c(4 x 4) and c(4 x 3) structures. Specific stripes on the buckeyballs in the STM images are also reported and this result proves that the buckeyballs on the Si surface are standing still, showing them to be pseudoatoms. A mixed-basis, all-electron calculation with the Car-Parinnello formalism has been introduced and performed to obtain a detailed understanding of the electronic states and dynamics of a single buckeyball. Based on the knowledge concerning a single buckeyball, a band structure calculation using the same formalism has been carried out and the experimental results have been explained clearly. A classical molecular dynamics simulation has also been performed to obtain the dynamics of the buckeyball motion on the Si surface. (orig.)

Statistical analysis of hydrological response in urbanising catchments based on adaptive sampling using inter-amount times

Science.gov (United States)

ten Veldhuis, Marie-Claire; Schleiss, Marc

2017-04-01

Urban catchments are typically characterised by a more flashy nature of the hydrological response compared to natural catchments. Predicting flow changes associated with urbanisation is not straightforward, as they are influenced by interactions between impervious cover, basin size, drainage connectivity and stormwater management infrastructure. In this study, we present an alternative approach to statistical analysis of hydrological response variability and basin flashiness, based on the distribution of inter-amount times. We analyse inter-amount time distributions of high-resolution streamflow time series for 17 (semi-)urbanised basins in North Carolina, USA, ranging from 13 to 238 km2 in size. We show that in the inter-amount-time framework, sampling frequency is tuned to the local variability of the flow pattern, resulting in a different representation and weighting of high and low flow periods in the statistical distribution. This leads to important differences in the way the distribution quantiles, mean, coefficient of variation and skewness vary across scales and results in lower mean intermittency and improved scaling. Moreover, we show that inter-amount-time distributions can be used to detect regulation effects on flow patterns, identify critical sampling scales and characterise flashiness of hydrological response. The possibility to use both the classical approach and the inter-amount-time framework to identify minimum observable scales and analyse flow data opens up interesting areas for future research.

Optical spectroscopy and system–bath interactions in molecular aggregates with full configuration interaction Frenkel exciton model

Energy Technology Data Exchange (ETDEWEB)

Seibt, Joachim; Sláma, Vladislav; Mančal, Tomáš, E-mail: mancal@karlov.mff.cuni.cz

2016-12-20

Highlights: • Standard Frenkel exciton model is extended to include inter-band coupling. • It is formally linked with configuration interaction method of quantum chemistry. • Spectral shifts due to inter-band coupling are found in molecular aggregates. • Effects of peak amplitude redistribution in two-dimensional spectra are found. - Abstract: Standard application of the Frenkel exciton model neglects resonance coupling between collective molecular aggregate states with different number of excitations. These inter-band coupling terms are, however, of the same magnitude as the intra-band coupling between singly excited states. We systematically derive the Frenkel exciton model from quantum chemical considerations, and identify it as a variant of the configuration interaction method. We discuss all non-negligible couplings between collective aggregate states, and provide compact formulae for their calculation. We calculate absorption spectra of molecular aggregate of carotenoids and identify significant band shifts as a result of inter-band coupling. The presence of inter-band coupling terms requires renormalization of the system–bath coupling with respect to standard formulation, but renormalization effects are found to be weak. We present detailed discussion of molecular dimer and calculate its time-resolved two-dimensional Fourier transformed spectra to find weak but noticeable effects of peak amplitude redistribution due to inter-band coupling.

Molecular dynamics study of the RNA ring nanostructure: a phenomenon of self-stabilization

International Nuclear Information System (INIS)

Paliy, Maxim; Melnik, Roderick; Shapiro, Bruce A

2009-01-01

We study mechanical and thermodynamic properties of RNA nanostructures focusing on a hexagonal nanoring discussed in Yingling and Shapiro (2007 Nano Lett. 7 2328). We are concerned with the following main issues: (i) the stability of the nanoring versus temperature; (ii) the effect of the environment (solvent, counterions) on its stability; (iii) conformations and dynamics under external force. The process of evaporation of the ions from the ring upon temperature drop has been found, demonstrating a surprising feature—the uptake of ions by the nanoring increases with the temperature. The connection of this behavior to the dielectric constant of water, hydration and structural changes in the nanoring is discussed. Several properties of the nanoring, such as elastic and transport coefficients, have been determined. A measure of the tensile elasticity of the ring against its uniform 2D in-plane compression has been given, as K eff ≤ 0.01 GPa, which is a much lower value compared to typical values found for soft matter other than RNA

Low temperature magnetic properties and spin dynamics in single crystals of Cr{sub 8}Zn antiferromagnetic molecular rings

Energy Technology Data Exchange (ETDEWEB)

Adelnia, Fatemeh [Dipartimento di Fisica, Università degli Studi di Milano and INSTM, I-20133 Milano (Italy); Dipartimento di Fisica, Università degli Studi di Pavia and INSTM, I-27100 Pavia (Italy); Chiesa, Alessandro; Bordignon, Sara; Carretta, Stefano [Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Parma, I-43124 Parma (Italy); Ghirri, Alberto; Candini, Andrea [CNR Institute Nanosciences S3, I- 41125 Modena (Italy); Cervetti, Christian [Dipartimento di Scienze Fisiche, Informatiche, Matematiche, Università di Modena e Reggio Emilia, I-41125 Modena (Italy); Evangelisti, Marco [CNR Institute Nanosciences S3, I- 41125 Modena (Italy); Dipartimento di Scienze Fisiche, Informatiche, Matematiche, Università di Modena e Reggio Emilia, I-41125 Modena (Italy); Instituto de Ciencia de Materiales de Aragón and Departamento de Física de la Materia Condensada, CSIC-Universidad de Zaragoza, 50009 Zaragoza (Spain); Affronte, Marco [CNR Institute Nanosciences S3, I- 41125 Modena (Italy); Dipartimento di Scienze Fisiche, Informatiche, Matematiche, Università di Modena e Reggio Emilia, I-41125 Modena (Italy); Sheikin, Ilya [Grenoble High Magnetic Field Laboratory, CNRS-LNCMI, 25, B.P. 166, 38042 Grenoble Cedex 9 (France); Winpenny, Richard; Timco, Grigore [The Lewis Magnetism Laboratory, The University of Manchester, M13 9PL Manchester (United Kingdom); Borsa, Ferdinando [Dipartimento di Fisica, Università degli Studi di Pavia and INSTM, I-27100 Pavia (Italy); and others

2015-12-28

A detailed experimental investigation of the effects giving rise to the magnetic energy level structure in the vicinity of the level crossing (LC) at low temperature is reported for the open antiferromagnetic molecular ring Cr{sub 8}Zn. The study is conducted by means of thermodynamic techniques (torque magnetometry, magnetization and specific heat measurements) and microscopic techniques (nuclear magnetic resonance line width, nuclear spin lattice, and spin-spin relaxation measurements). The experimental results are shown to be in excellent agreement with theoretical calculations based on a minimal spin model Hamiltonian, which includes a Dzyaloshinskii-Moriya interaction. The first ground state level crossing at μ{sub 0}H{sub c1} = 2.15 T is found to be an almost true LC while the second LC at μ{sub 0}H{sub c2} = 6.95 T has an anti-crossing gap of Δ{sub 12} = 0.19 K. In addition, both NMR and specific heat measurements show the presence of a level anti-crossing between excited states at μ{sub 0}H = 4.5 T as predicted by the theory. In all cases, the fit of the experimental data is improved by introducing a distribution of the isotropic exchange couplings (J), i.e., using a J strain model. The peaks at the first and second LCs in the nuclear spin-lattice relaxation rate are dominated by inelastic scattering and a value of Γ ∼ 10{sup 10} rad/s is inferred for the life time broadening of the excited state of the open ring, due to spin phonon interaction. A loss of NMR signal (wipe-out effect) is observed for the first time at LC and is explained by the enhancement of the spin-spin relaxation rate due to the inelastic scattering.

Friction in Carborane-Based Molecular Rotors Driven by Gas Flow or Electric Field: Classical Molecular Dynamics

Czech Academy of Sciences Publication Activity Database

Prokop, Alexandr; Vacek, Jaroslav; Michl, Josef

2012-01-01

Roč. 6, č. 3 (2012), s. 1901-1914 ISSN 1936-0851 R&D Projects: GA ČR GA203/09/1802; GA MŠk ME09020 Institutional research plan: CEZ:AV0Z40550506 Keywords : molecular rotors * molecular dynamics * potential energy barriers * friction * intramolecular vibrational redistribution Subject RIV: CC - Organic Chemistry Impact factor: 12.062, year: 2012

Connotation and category of functional-molecular imaging

International Nuclear Information System (INIS)

Li Tianran; Tian Jiahe

2007-01-01

Function and molecular lmaging represent medical imaging' s direction. The review article introduce function and molecular's concept and category and its characteristic. Comparing with traditionary classics radiology, function and molecular imaging have many features, such as micro-mount and specificity and quantitative. There are many technology about function and molecular imaging. Function and molecular imaging is important ingredient of modern medical and play a considerable role. (authors)

Ring faults and ring dikes around the Orientale basin on the Moon.

Science.gov (United States)

Andrews-Hanna, Jeffrey C; Head, James W; Johnson, Brandon; Keane, James T; Kiefer, Walter S; McGovern, Patrick J; Neumann, Gregory A; Wieczorek, Mark A; Zuber, Maria T

2018-08-01

The Orientale basin is the youngest and best-preserved multiring impact basin on the Moon, having experienced only modest modification by subsequent impacts and volcanism. Orientale is often treated as the type example of a multiring basin, with three prominent rings outside of the inner depression: the Inner Rook Montes, the Outer Rook Montes, and the Cordillera. Here we use gravity data from NASA's Gravity Recovery and Interior Laboratory (GRAIL) mission to reveal the subsurface structure of Orientale and its ring system. Gradients of the gravity data reveal a continuous ring dike intruded into the Outer Rook along the plane of the fault associated with the ring scarp. The volume of this ring dike is ~18 times greater than the volume of all extrusive mare deposits associated with the basin. The gravity gradient signature of the Cordillera ring indicates an offset along the fault across a shallow density interface, interpreted to be the base of the low-density ejecta blanket. Both gravity gradients and crustal thickness models indicate that the edge of the central cavity is shifted inward relative to the equivalent Inner Rook ring at the surface. Models of the deep basin structure show inflections along the crust-mantle interface at both the Outer Rook and Cordillera rings, indicating that the basin ring faults extend from the surface to at least the base of the crust. Fault dips range from 13-22° for the Cordillera fault in the northeastern quadrant, to 90° for the Outer Rook in the northwestern quadrant. The fault dips for both outer rings are lowest in the northeast, possibly due to the effects of either the direction of projectile motion or regional gradients in pre-impact crustal thickness. Similar ring dikes and ring faults are observed around the majority of lunar basins.

Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

Science.gov (United States)

Leng, Yongsheng; Krstić, Predrag S.; Wells, Jack C.; Cummings, Peter T.; Dean, David J.

2005-06-01

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as ˜100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

A Molecular Dynamics Study of Lunasin | Singh | South African ...

African Journals Online (AJOL)

A Molecular Dynamics Study of Lunasin. ... profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. ... Keywords: Lunasin, molecular dynamics, amber, CLASICO, α-helix, β-turn, PTRAJ, RGD, RMSD ...

Saturn's Rings Edge-on

Science.gov (United States)

1995-01-01

In one of nature's most dramatic examples of 'now-you see-them, now-you-don't', NASA's Hubble Space Telescope captured Saturn on May 22, 1995 as the planet's magnificent ring system turned edge-on. This ring-plane crossing occurs approximately every 15 years when the Earth passes through Saturn's ring plane.For comparison, the top picture was taken by Hubble on December 1, 1994 and shows the rings in a more familiar configuration for Earth observers.The bottom picture was taken shortly before the ring plane crossing. The rings do not disappear completely because the edge of the rings reflects sunlight. The dark band across the middle of Saturn is the shadow of the rings cast on the planet (the Sun is almost 3 degrees above the ring plane.) The bright stripe directly above the ring shadow is caused by sunlight reflected off the rings onto Saturn's atmosphere. Two of Saturn's icy moons are visible as tiny starlike objects in or near the ring plane. They are, from left to right, Tethys (slightly above the ring plane) and Dione.This observation will be used to determine the time of ring-plane crossing and the thickness of the main rings and to search for as yet undiscovered satellites. Knowledge of the exact time of ring-plane crossing will lead to an improved determination of the rate at which Saturn 'wobbles' about its axis (polar precession).Both pictures were taken with Hubble's Wide Field Planetary Camera 2. The top image was taken in visible light. Saturn's disk appears different in the bottom image because a narrowband filter (which only lets through light that is not absorbed by methane gas in Saturn's atmosphere) was used to reduce the bright glare of the planet. Though Saturn is approximately 900 million miles away, Hubble can see details as small as 450 miles across.The Wide Field/Planetary Camera 2 was developed by the Jet Propulsion Laboratory and managed by the Goddard Spaced Flight Center for NASA's Office of Space Science.This image and other images and

The Rotating Ring-Ring Electrode. Theory and Experiment

NARCIS (Netherlands)

Kuiken, H.K.; Bakkers, E.P.A.M.; Ligthart, H.; Kelly, J.J.

2000-01-01

A model is presented for the rotating ring-ring electrode. Although the electrode is defined by four characteristic lengths, it is shown that the collection efficiency depends on only two dimensionless parameters. A simple relationship between these and the corresponding parameters for the rotating

Crystal structure of 4-meth-oxy-N-(piperidine-1-carbono-thio-yl)benzamide.

Science.gov (United States)

Suhud, Khairi; Hasbullah, Siti Aishah; Ahmad, Musa; Heng, Lee Yook; Kassim, Mohammad B

2017-10-01

In the title compound, C 14 H 18 N 2 O 2 S, the piperidine ring has a chair conformation. Its mean plane is twisted with respect to the 4-meth-oxy-benzoyl ring, with a dihedral angle of 63.0 (3)°. The central N-C(=S)-N(H)-C(=O) bridge is twisted with an N-C-N-C torsion angle of 74.8 (6)°. In the crystal, mol-ecules are linked by N-H⋯O and C-H⋯O hydrogen bonds, forming chains along the c -axis direction. Adjacent chains are linked by C-H⋯π inter-actions, forming layers parallel to the ac plane. The layers are linked by offset π-π inter-actions [inter-centroid distance = 3.927 (3) Å], forming a supra-molecular three-dimensional structure.

SEEING THROUGH THE RING: NEAR-INFRARED PHOTOMETRY OF V582 MON (KH 15D)

Energy Technology Data Exchange (ETDEWEB)

Arulanantham, Nicole A.; Herbst, William [Astronomy Department, Wesleyan University, Middletown, CT 06459 (United States); Cody, Ann Marie [NASA Ames Research Center, Moffett Field, CA 94035 (United States); Stauffer, John R.; Rebull, Luisa M. [Spitzer Science Center, California Institute of Technology, Pasadena, CA 91125 (United States); Agol, Eric; Windemuth, Diana [Department of Astronomy, University of Washington, Seattle, WA 98195-1580 (United States); Marengo, Massimo [Department of Physics and Astronomy, Iowa State University, Ames, IA 50011 (United States); Winn, Joshua N. [Department of Physics and Kavli Institute for Astrophysics and Space Research, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Hamilton, Catrina M. [Physics and Astronomy Department, Dickinson College, Carlisle, PA 17013 (United States); Mundt, Reinhard [Max Planck Institute for Astronomy, D-69117 Heidelberg (Germany); Johns-Krull, Christopher M. [Department of Physics and Astronomy, Rice University, Houston, TX 77005 (United States); Gutermuth, Robert A. [Department of Astronomy, University of Massachusetts, Amherst, MA 01002 (United States)

2016-04-15

We examine the light and color evolution of the T Tauri binary KH 15D through photometry obtained at wavelengths between 0.55 and 8.0 μm. The data were collected with A Novel Dual Imaging CAMera (ANDICAM) on the 1.3 m SMARTS telescope at Cerro-Tololo Inter-American Observatory and with InfraRed Array Camera on the Spitzer Space Telescope. We show that the system’s circumbinary ring, which acts as a screen that covers and uncovers different portions of the binary orbit as the ring precesses, has reached an orientation where the brighter component (star B) fully or nearly fully emerges during each orbital cycle. The fainter component (star A) remains fully occulted by the screen at all phases. The leading and trailing edges of the screen move across the sky at the same rate of ∼15 m s{sup −1}, consistent with expectation for a ring with a radius and width of ∼4 au and a precession period of ∼6500 years. Light and color variations continue to indicate that the screen is sharp edged and opaque at VRIJH wavelengths. However, we find an increasing transparency of the ring edge at 2.2, 3.6, and 4.5 μm. Reddening seen at the beginning of the eclipse that occurred during the CSI 2264 campaign particularly suggests selective extinction by a population of large dust grains. Meanwhile, the gradual bluing observed while star B is setting is indicative of forward scattering effects at the edge of the ring. The spectral energy distribution of the system at its bright phase shows no evidence of infrared excess emission that can be attributed to radiation from the ring or other dust component out to 8 μm.

Inter-laboratory agreement on embryo classification and clinical decision: Conventional morphological assessment vs. time lapse.

Science.gov (United States)

Martínez-Granados, Luis; Serrano, María; González-Utor, Antonio; Ortíz, Nereyda; Badajoz, Vicente; Olaya, Enrique; Prados, Nicolás; Boada, Montse; Castilla, Jose A

2017-01-01

The aim of this study is to determine inter-laboratory variability on embryo assessment using time-lapse platform and conventional morphological assessment. This study compares the data obtained from a pilot study of external quality control (EQC) of time lapse, performed in 2014, with the classical EQC of the Spanish Society for the Study of Reproductive Biology (ASEBIR) performed in 2013 and 2014. In total, 24 laboratories (8 using EmbryoScope™, 15 using Primo Vision™ and one with both platforms) took part in the pilot study. The clinics that used EmbryoScope™ analysed 31 embryos and those using Primo Vision™ analysed 35. The classical EQC was implemented by 39 clinics, based on an analysis of 25 embryos per year. Both groups were required to evaluate various qualitative morphological variables (cell fragmentation, the presence of vacuoles, blastomere asymmetry and multinucleation), to classify the embryos in accordance with ASEBIR criteria and to stipulate the clinical decision taken. In the EQC time-lapse pilot study, the groups were asked to determine, as well as the above characteristics, the embryo development times, the number, opposition and size of pronuclei, the direct division of 1 into 3 cells and/or of 3 into 5 cells and false divisions. The degree of agreement was determined by calculating the intra-class correlation coefficients and the coefficient of variation for the quantitative variables and the Gwet index for the qualitative variables. For both EmbryoScope™ and Primo Vision™, two periods of greater inter-laboratory variability were observed in the times of embryo development events. One peak of variability was recorded among the laboratories addressing the first embryo events (extrusion of the second polar body and the appearance of pronuclei); the second peak took place between the times corresponding to the 8-cell and morula stages. In most of the qualitative variables analysed regarding embryo development, there was almost

Inter-laboratory agreement on embryo classification and clinical decision: Conventional morphological assessment vs. time lapse.

Directory of Open Access Journals (Sweden)

Luis Martínez-Granados

Full Text Available The aim of this study is to determine inter-laboratory variability on embryo assessment using time-lapse platform and conventional morphological assessment. This study compares the data obtained from a pilot study of external quality control (EQC of time lapse, performed in 2014, with the classical EQC of the Spanish Society for the Study of Reproductive Biology (ASEBIR performed in 2013 and 2014. In total, 24 laboratories (8 using EmbryoScope™, 15 using Primo Vision™ and one with both platforms took part in the pilot study. The clinics that used EmbryoScope™ analysed 31 embryos and those using Primo Vision™ analysed 35. The classical EQC was implemented by 39 clinics, based on an analysis of 25 embryos per year. Both groups were required to evaluate various qualitative morphological variables (cell fragmentation, the presence of vacuoles, blastomere asymmetry and multinucleation, to classify the embryos in accordance with ASEBIR criteria and to stipulate the clinical decision taken. In the EQC time-lapse pilot study, the groups were asked to determine, as well as the above characteristics, the embryo development times, the number, opposition and size of pronuclei, the direct division of 1 into 3 cells and/or of 3 into 5 cells and false divisions. The degree of agreement was determined by calculating the intra-class correlation coefficients and the coefficient of variation for the quantitative variables and the Gwet index for the qualitative variables. For both EmbryoScope™ and Primo Vision™, two periods of greater inter-laboratory variability were observed in the times of embryo development events. One peak of variability was recorded among the laboratories addressing the first embryo events (extrusion of the second polar body and the appearance of pronuclei; the second peak took place between the times corresponding to the 8-cell and morula stages. In most of the qualitative variables analysed regarding embryo development, there

Insights into the Reaction Mechanism of Aromatic Ring Cleavage by Homogentisate Dioxygenase: A Quantum Mechanical/Molecular Mechanical Study.

Science.gov (United States)

Qi, Yue; Lu, Jiarui; Lai, Wenzhen

2016-05-26

To elucidate the reaction mechanism of the ring cleavage of homogentisate by homogentisate dioxygenase, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out by using two systems in different protonation states of the substrate C2 hydroxyl group. When the substrate C2 hydroxyl group is ionized (the ionized pathway), the superoxo attack on the substrate is the rate-limiting step in the catalytic cycle, with a barrier of 15.9 kcal/mol. Glu396 was found to play an important role in stabilizing the bridge species and its O-O cleavage product by donating a proton via a hydrogen-bonded water molecule. When the substrate C2 hydroxyl group is not ionized (the nonionized pathway), the O-O bond cleavage of the bridge species is the rate-limiting step, with a barrier of 15.3 kcal/mol. The QM/MM-optimized geometries for the dioxygen and alkylperoxo complexes using the nonionized model (for the C2 hydroxyl group) are in agreement with the experimental crystal structures, suggesting that the C2 hydroxyl group is more likely to be nonionized.

Mixed quantum-classical equilibrium in global flux surface hopping

International Nuclear Information System (INIS)

Sifain, Andrew E.; Wang, Linjun; Prezhdo, Oleg V.

2015-01-01

Global flux surface hopping (GFSH) generalizes fewest switches surface hopping (FSSH)—one of the most popular approaches to nonadiabatic molecular dynamics—for processes exhibiting superexchange. We show that GFSH satisfies detailed balance and leads to thermodynamic equilibrium with accuracy similar to FSSH. This feature is particularly important when studying electron-vibrational relaxation and phonon-assisted transport. By studying the dynamics in a three-level quantum system coupled to a classical atom in contact with a classical bath, we demonstrate that both FSSH and GFSH achieve the Boltzmann state populations. Thermal equilibrium is attained significantly faster with GFSH, since it accurately represents the superexchange process. GFSH converges closer to the Boltzmann averages than FSSH and exhibits significantly smaller statistical errors

Cryptosporidium meleagridis in an Indian ring-necked parrot (Psittacula krameri).

Science.gov (United States)

Morgan, U M; Xiao, L; Limor, J; Gelis, S; Raidal, S R; Fayer, R; Lal, A; Elliot, A; Thompson, R C

2000-03-01

To perform a morphological and genetic characterisation of a Cryptosporidium infection in an Indian ring-necked parrot (Psittacula krameri) and to compare this with C meleagridis from a turkey. Tissue and intestinal sections from an Indian ring-necked parrot were examined microscopically for Cryptosporidium. The organism was also purified from the crop and intestine, the DNA extracted and a portion of the 18S rDNA gene amplified, sequenced and compared with sequence and biological information obtained for C meleagridis from a turkey as well as sequence information for other species of Cryptosporidium. Morphological examination of tissue sections from an Indian ring-necked parrot revealed large numbers of Cryptosporidium oocysts attached to the apical border of enterocytes lining the intestinal tract. Purified Cryptosporidium oocysts measured about 5.1 x 4.5 microns, which conformed morphologically to C meleagridis. The sequence obtained from this isolate was identical to sequence information obtained from a C meleagridis isolate from a turkey. Cryptosporidium meleagridis was detected in an Indian ring-necked parrot using morphological and molecular methods. This is the first time that this species of Cryptosporidium has been reported in a non-galliform host and extends the known host range of C meleagridis.

Explicitly-correlated ring-coupled-cluster-doubles theory: Including exchange for computations on closed-shell systems

Energy Technology Data Exchange (ETDEWEB)

Hehn, Anna-Sophia; Holzer, Christof; Klopper, Wim, E-mail: klopper@kit.edu

2016-11-10

Highlights: • Ring-coupled-cluster-doubles approach now implemented with exchange terms. • Ring-coupled-cluster-doubles approach now implemented with F12 functions. • Szabo–Ostlund scheme (SO2) implemented for use in SAPT. • Fast convergence to the limit of a complete basis. • Implementation in the TURBOMOLE program system. - Abstract: Random-phase-approximation (RPA) methods have proven to be powerful tools in electronic-structure theory, being non-empirical, computationally efficient and broadly applicable to a variety of molecular systems including small-gap systems, transition-metal compounds and dispersion-dominated complexes. Applications are however hindered due to the slow basis-set convergence of the electron-correlation energy with the one-electron basis. As a remedy, we present approximate explicitly-correlated RPA approaches based on the ring-coupled-cluster-doubles formulation including exchange contributions. Test calculations demonstrate that the basis-set convergence of correlation energies is drastically accelerated through the explicitly-correlated approach, reaching 99% of the basis-set limit with triple-zeta basis sets. When implemented in close analogy to early work by Szabo and Ostlund [36], the new explicitly-correlated ring-coupled-cluster-doubles approach including exchange has the perspective to become a valuable tool in the framework of symmetry-adapted perturbation theory (SAPT) for the computation of dispersion energies of molecular complexes of weakly interacting closed-shell systems.

Wear Analysis of Top Piston Ring to Reduce Top Ring Reversal Bore Wear

Directory of Open Access Journals (Sweden)

P. Ilanthirayan

2017-12-01

Full Text Available The piston rings are the most important part in engine which controls the lubricating oil consumption and blowby of the gases. The lubricating film of oil is provided to seal of gases towards crankcase and also to give smooth friction free translatory motion between rings and liner. Of the three rings present top ring is more crucial as it does the main work of restricting gases downwards the crankcase. Boundary lubrication is present at the Top dead centre (TDC and Bottom dead centre (BDC of the liner surface. In addition to this, top ring is exposed to high temperature gases which makes the oil present near the top ring to get evaporated and decreasing its viscosity, making metal-metal contact most of the time. Due to this at TDC, excess wear happens on the liner which is termed as Top ring reversal bore wear. The wear rate depends upon many parameters such as lubrication condition, viscosity index, contact type, normal forces acting on ring, geometry of ring face, surface roughness, material property. The present work explores the wear depth for different geometries of barrel ring using Finite Element model with the help of Archard wear law and the same is validated through experimentation. The study reveals that Asymmetric barrel rings have less contact pressure which in turn reduces the wear at Top dead centre.

Combined quantum chemical density functional theory and spectroscopic Raman and UV-vis-NIR study of oligothienoacenes with five and seven rings.

Science.gov (United States)

Osuna, Reyes Malavé; Zhang, Xinnan; Matzger, Adam Jay; Hernandez, Víctor; López Navarrete, Juan Teodomiro

2006-04-20

In this article, we report the characterization of novel oligothienoacenes with five and seven fused thiophene rings, materials with potential applications in organic electronics. In contrast to usual alpha-linked oligothiophenes, these fused oligothiophenes have a larger band gap than most semiconductors currently used in the fabrication of organic field-effect transistors (OFETs) and therefore they are expected to be more stable in air. The synthesis of these fused-ring oligomers was motivated by the notion that a more rigid and planar structure should reduce defects (such as torsion about single bonds between alpha-linked units or S-syn defects) and thus improve conjugation for better charge-carrier mobility. The conjugational properties of these two molecular materials have been investigated by means of FT-Raman spectroscopy, revealing that conjugation still increases in passing from the five-ring oligomer to that with seven-rings. DFT and TDDFT quantum chemical calculations have been performed, at the B3LYP/6-31G level, to assess information regarding the minimum-energy molecular structure, topologies, and absolute energies of the frontier molecular orbitals (MOs.) around the gap, vibrational normal modes related to the main Raman features, and vertical one-electron excitations giving rise to the main optical absorptions.

Asymmetric ring structure of Vps4 required for ESCRT-III disassembly

Science.gov (United States)

Caillat, Christophe; Macheboeuf, Pauline; Wu, Yuanfei; McCarthy, Andrew A.; Boeri-Erba, Elisabetta; Effantin, Gregory; Göttlinger, Heinrich G.; Weissenhorn, Winfried; Renesto, Patricia

2015-12-01

The vacuolar protein sorting 4 AAA-ATPase (Vps4) recycles endosomal sorting complexes required for transport (ESCRT-III) polymers from cellular membranes. Here we present a 3.6-Å X-ray structure of ring-shaped Vps4 from Metallosphera sedula (MsVps4), seen as an asymmetric pseudohexamer. Conserved key interface residues are shown to be important for MsVps4 assembly, ATPase activity in vitro, ESCRT-III disassembly in vitro and HIV-1 budding. ADP binding leads to conformational changes within the protomer, which might propagate within the ring structure. All ATP-binding sites are accessible and the pseudohexamer binds six ATP with micromolar affinity in vitro. In contrast, ADP occupies one high-affinity and five low-affinity binding sites in vitro, consistent with conformational asymmetry induced on ATP hydrolysis. The structure represents a snapshot of an assembled Vps4 conformation and provides insight into the molecular motions the ring structure undergoes in a concerted action to couple ATP hydrolysis to ESCRT-III substrate disassembly.

Vortex rings

CERN Document Server

Akhmetov, D G

2009-01-01

This text on vortex rings covers their theoretical foundation, systematic investigations, and practical applications such as the extinction of fires at gushing oil wells. It pays special attention to the formation and motion of turbulent vortex rings.

An extended two-lane car-following model accounting for inter-vehicle communication

Science.gov (United States)

Ou, Hui; Tang, Tie-Qiao

2018-04-01

In this paper, we develop a novel car-following model with inter-vehicle communication to explore each vehicle's movement in a two-lane traffic system when an incident occurs on a lane. The numerical results show that the proposed model can perfectly describe each vehicle's motion when an incident occurs, i.e., no collision occurs while the classical full velocity difference (FVD) model produces collision on each lane, which shows the proposed model is more reasonable. The above results can help drivers to reasonably adjust their driving behaviors when an incident occurs in a two-lane traffic system.

Influence of N-Oxide Introduction on the Stability of Nitrogen-Rich Heteroaromatic Rings: A Quantum Chemical Study.

Science.gov (United States)

Yuan, Jia; Long, Xinping; Zhang, Chaoyang

2016-12-01

N-Oxidization is an important strategy for enhancing the density and energy of energetic materials. Nevertheless, the influence of N + -O - introduction on molecular stability remains relatively unknown. Thus, the present work comprehensively studied 102 basic N-rich ring structures, including azoles, furazans, and azines, as well as their N-oxides by quantum chemical calculations. The introduction of N + -O - weakens molecular stability in most cases because the process elongates chemical bonds, decreases ring aromaticity, narrows the gaps between the highest occupied and lowest unoccupied molecular orbitals, and increases the photochemical reactivity. Besides, the easy H transfer to the neighboring O atom, which forms a N-OH isomer in azoles, renders the stabilization by N-oxide introduction ineffective. However, N-oxide introduction can enhance the molecular stability of 1,2,3,4-tetrazine-1,3-dioxide and tetrazino-tetrazine 1,3,6,8-tetraoxide by promoting σ-π separation and relieving lone-pair repulsion. Moreover, the alternate arrangement of positive and negative charges is another factor stabilizing the 1,2,3,4-tetrazine ring by 1,3-dioxidation. Finally, we assess the accessibility of N-oxidized azoles and azines by regarding N 2 O and H 2 O 2 as oxidizers. We find that all the oxidations were exothermic, thermodynamically spontaneous, and kinetically feasible. After an overall evaluation, we propose 19 N-oxides as basic structures for high-energy materials with considerable stability.

Quantum Transport Through Tunable Molecular Diodes

KAUST Repository

Obodo, Tobechukwu Joshua

2017-07-31

Employing self-interaction corrected density functional theory combined with the non-equilibrium Green\\'s function method, we study the quantum transport through molecules with different numbers of phenyl (donor) and pyrimidinyl (acceptor) rings in order to evaluate the effects of the molecular composition on the transport properties. Excellent agreement with the results of recent experiments addressing the rectification behavior of molecular junctions is obtained, which demonstrates the potential of quantum transport simulations for designing high performance junctions by tuning the molecular specifications.

Three dimensional atom probe imaging of GaAsSb quantum rings

International Nuclear Information System (INIS)

Beltran, A.M.; Marquis, E.A.; Taboada, A.G.; Ripalda, J.M.; Garcia, J.M.; Molina, S.I.

2011-01-01

Unambiguous evidence of ring-shaped self-assembled GaSb nanostructures grown by molecular beam epitaxy is presented on the basis of atom-probe tomography reconstructions and dark field transmission electron microscopy imaging. The GaAs capping process causes a strong segregation of Sb out of the center of GaSb quantum dots, leading to the self-assembled GaAs x Sb 1-x quantum rings of 20-30 nm in diameter with x∼0.33. -- Highlights: → Atom-probe tomography resolves QR morphology of GaSb self-assembled GaSb buried nanostructures. → From atom-probe tomography compositional distribution has been obtained. → Strong segregation and morphological changes are observed with respect to uncapped QR.

Lectures on a theory of computation and complexity over the reals (or an arbitrary ring)

International Nuclear Information System (INIS)

Blum, L.

1990-01-01

These lectures will discuss a new theory of computation and complexity which attempts to integrate key ideas from the classical theory in a setting more amenable to problems defined over continuous domains. The approach taken here is both algebraic and concrete; the underlying space is an arbitrary ring (or field) and the basic operations are polynominal (or rational) maps and tests. This approach yields results in the continuous setting analogous to the pivotal classical results of undecidability and NP-completeness over the integers, yet reflecting the special mathematical character of the underlying space. The goal of these lectures is to highlight key aspects of the new theory as well as to give exposition, in this setting, of classical ideas and results. Indeed, since this new theory is more mathematical, perhaps less dependent on logic than the classical theory, a number of key results have more straightforward and transparent proofs in this setting. One of our themes will be the comparison of results over the integers with results over the reals and complex numbers. Contrasting one theory with the other will help illuminate each, and give deeper understanding to such basic concepts as decidability, definability, computability, and complexity. 53 refs

Ensemble simulations with discrete classical dynamics

DEFF Research Database (Denmark)

Toxværd, Søren

2013-01-01

For discrete classical Molecular dynamics (MD) obtained by the "Verlet" algorithm (VA) with the time increment $h$ there exist a shadow Hamiltonian $\\tilde{H}$ with energy $\\tilde{E}(h)$, for which the discrete particle positions lie on the analytic trajectories for $\\tilde{H}$. $\\tilde......{E}(h)$ is employed to determine the relation with the corresponding energy, $E$ for the analytic dynamics with $h=0$ and the zero-order estimate $E_0(h)$ of the energy for discrete dynamics, appearing in the literature for MD with VA. We derive a corresponding time reversible VA algorithm for canonical dynamics...

Polarization Insensitivity in Double-Split Ring and Triple-Split Ring Terahertz Resonators

International Nuclear Information System (INIS)

Wu Qian-Nan; Lan Feng; Tang Xiao-Pin; Yang Zi-Qiang

2015-01-01

A modified double-split ring resonator and a modified triple-split ring resonator, which offer polarization-insensitive performance, are investigated, designed and fabricated. By displacing the two gaps of the conventional double-split ring resonator away from the center, the second resonant frequency for the 0° polarized wave and the resonant frequency for the 90° polarized wave become increasingly close to each other until they are finally identical. Theoretical and experimental results show that the modified double-split ring resonator and the modified triple-split ring resonator are insensitive to different polarized waves and show strong resonant frequency dips near 433 and 444 GHz, respectively. The results of this work suggest new opportunities for the investigation and design of polarization-dependent terahertz devices based on split ring resonators. (paper)

Somatotopic Map and Inter- and Intra-Digit Distance in Brodmann Area 2 by Pressure Stimulation

Science.gov (United States)

Choi, Mi-Hyun; Kim, Sung-Phil; Kim, Hyung-Sik; Gim, Seon-Young; Kim, Woo-Ram; Mun, Kyung-Ryul; Lim, Dae-Woon; Lee, Bongsoo; Chung, Soon-Cheol

2016-01-01

The somatotopic representation of the tactile stimulation on the finger in the brain is an essential part of understanding the human somatosensory system as well as rehabilitation and other clinical therapies. Many studies have used vibrotactile stimulations and reported finger somatotopic representations in the Brodmann area 3 (BA 3). On the contrary, few studies investigated finger somatotopic representation using pressure stimulations. Therefore, the present study aimed to find a comprehensive somatotopic representation (somatotopic map and inter- and intra-digit distance) within BA 2 of humans that could describe tactile stimulations on different joints across the fingers by applying pressure stimulation to three joints-the first (p1), second (p2), and third (p3) joints-of four fingers (index, middle, ring, and little finger). Significant differences were observed in the inter-digit distance between the first joints (p1) of the index and little fingers, and between the third joints (p3) of the index and little fingers. In addition, a significant difference was observed in the intra-digit distance between p1 and p3 of the little finger. This study suggests that a somatotopic map and inter- and intra-digit distance could be found in BA 2 in response to pressure stimulation on finger joints. PMID:27452859

Classic-Ada(TM)

Science.gov (United States)

Valley, Lois

1989-01-01

The SPS product, Classic-Ada, is a software tool that supports object-oriented Ada programming with powerful inheritance and dynamic binding. Object Oriented Design (OOD) is an easy, natural development paradigm, but it is not supported by Ada. Following the DOD Ada mandate, SPS developed Classic-Ada to provide a tool which supports OOD and implements code in Ada. It consists of a design language, a code generator and a toolset. As a design language, Classic-Ada supports the object-oriented principles of information hiding, data abstraction, dynamic binding, and inheritance. It also supports natural reuse and incremental development through inheritance, code factoring, and Ada, Classic-Ada, dynamic binding and static binding in the same program. Only nine new constructs were added to Ada to provide object-oriented design capabilities. The Classic-Ada code generator translates user application code into fully compliant, ready-to-run, standard Ada. The Classic-Ada toolset is fully supported by SPS and consists of an object generator, a builder, a dictionary manager, and a reporter. Demonstrations of Classic-Ada and the Classic-Ada Browser were given at the workshop.

Determination of thermo-physical properties of (Th,Ce)O2 MOX using classical molecular dynamics simulations

International Nuclear Information System (INIS)

Ghosh, P.S.; Arya, A.; Dey, G.K.; Somayajulu, P.S.

2015-01-01

This paper calculates lattice thermal expansion (LTE) and thermal conductivity (TC) of Th 1-x Ce x O 2 (x=0.0, 0.0625 and 0.125) MOX using classical molecular dynamic simulations. The potential parameters of Coulomb-Buckingham function for Th-O, Ce-O and O-O were determined by fitting experimentally available LTE data for pure ThO 2 and CeO 2 . The calculated linear thermal expansion coefficients in the temperature range 300-1500K for ThO 2 , CeO 2 , Th 93.75 Ce 6.25 O 2 and Th 87.5 Ce 12.5 O 2 are 10.61, 13.08, 10.78 and 10.93x10 -6 K -1 , respectively. The MD calculated LTE values of ThO 2 and (Th,Ce)O 2 MOX are slightly higher than the experimentally determined values. The MD calculated TC values of ThO 2 and (Th,Ce)O 2 MOX in the high temperature range (600 to 1200 K) our results accords very well with the experimental measurements and at the low temperature range (300-500 K) our results are slightly different from some experimental results as the difference comes from our presumption that the dominant mechanism for phonon scattering is the Umklapp process. (author)

Natural occupation numbers in two-electron quantum rings.

Science.gov (United States)

Tognetti, Vincent; Loos, Pierre-François

2016-02-07

Natural orbitals (NOs) are central constituents for evaluating correlation energies through efficient approximations. Here, we report the closed-form expression of the NOs of two-electron quantum rings, which are prototypical finite-extension systems and new starting points for the development of exchange-correlation functionals in density functional theory. We also show that the natural occupation numbers for these two-electron paradigms are in general non-vanishing and follow the same power law decay as atomic and molecular two-electron systems.

Natural occupation numbers in two-electron quantum rings

Energy Technology Data Exchange (ETDEWEB)

Tognetti, Vincent, E-mail: vincent.tognetti@univ-rouen.fr [Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére, 76821 Mont Saint Aignan, Cedex (France); Loos, Pierre-François [Research School of Chemistry, Australian National University, Canberra ACT 2601 (Australia)

2016-02-07

Natural orbitals (NOs) are central constituents for evaluating correlation energies through efficient approximations. Here, we report the closed-form expression of the NOs of two-electron quantum rings, which are prototypical finite-extension systems and new starting points for the development of exchange-correlation functionals in density functional theory. We also show that the natural occupation numbers for these two-electron paradigms are in general non-vanishing and follow the same power law decay as atomic and molecular two-electron systems.

Ion association in concentrated NaCl brines from ambient to supercritical conditions: results from classical molecular dynamics simulations

Directory of Open Access Journals (Sweden)

Collings Matthew D

2002-11-01

Full Text Available Highly concentrated NaCl brines are important geothermal fluids; chloride complexation of metals in such brines increases the solubility of minerals and plays a fundamental role in the genesis of hydrothermal ore deposits. There is experimental evidence that the molecular nature of the NaCl–water system changes over the pressure–temperature range of the Earth's crust. A transition of concentrated NaCl–H2O brines to a "hydrous molten salt" at high P and T has been argued to stabilize an aqueous fluid phase in the deep crust. In this work, we have done molecular dynamic simulations using classical potentials to determine the nature of concentrated (0.5–16 m NaCl–water mixtures under ambient (25°C, 1 bar, hydrothermal (325°C, 1 kbar and deep crustal (625°C, 15 kbar conditions. We used the well-established SPCE model for water together with the Smith and Dang Lennard-Jones potentials for the ions (J. Chem. Phys., 1994, 100, 3757. With increasing temperature at 1 kbar, the dielectric constant of water decreases to give extensive ion-association and the formation of polyatomic (NanClmn-m clusters in addition to simple NaCl ion pairs. Large polyatomic (NanClmn-m clusters resemble what would be expected in a hydrous NaCl melt in which water and NaCl were completely miscible. Although ion association decreases with pressure, temperatures of 625°C are not enough to overcome pressures of 15 kbar; consequently, there is still enhanced Na–Cl association in brines under deep crustal conditions.

RINGED ACCRETION DISKS: EQUILIBRIUM CONFIGURATIONS

Energy Technology Data Exchange (ETDEWEB)

Pugliese, D.; Stuchlík, Z., E-mail: d.pugliese.physics@gmail.com, E-mail: zdenek.stuchlik@physics.cz [Institute of Physics and Research Centre of Theoretical Physics and Astrophysics, Faculty of Philosophy and Science, Silesian University in Opava, Bezručovo náměstí 13, CZ-74601 Opava (Czech Republic)

2015-12-15

We investigate a model of a ringed accretion disk, made up by several rings rotating around a supermassive Kerr black hole attractor. Each toroid of the ringed disk is governed by the general relativity hydrodynamic Boyer condition of equilibrium configurations of rotating perfect fluids. Properties of the tori can then be determined by an appropriately defined effective potential reflecting the background Kerr geometry and the centrifugal effects. The ringed disks could be created in various regimes during the evolution of matter configurations around supermassive black holes. Therefore, both corotating and counterrotating rings have to be considered as being a constituent of the ringed disk. We provide constraints on the model parameters for the existence and stability of various ringed configurations and discuss occurrence of accretion onto the Kerr black hole and possible launching of jets from the ringed disk. We demonstrate that various ringed disks can be characterized by a maximum number of rings. We present also a perturbation analysis based on evolution of the oscillating components of the ringed disk. The dynamics of the unstable phases of the ringed disk evolution seems to be promising in relation to high-energy phenomena demonstrated in active galactic nuclei.

Stirling engine piston ring

Science.gov (United States)

Howarth, Roy B.

1983-01-01

A piston ring design for a Stirling engine wherein the contact pressure between the piston and the cylinder is maintained at a uniform level, independent of engine conditions through a balancing of the pressure exerted upon the ring's surface and thereby allowing the contact pressure on the ring to be predetermined through the use of a preloaded expander ring.

How does the blue-ringed octopus (Hapalochlaena lunulata) flash its blue rings?

Science.gov (United States)

Mäthger, Lydia M; Bell, George R R; Kuzirian, Alan M; Allen, Justine J; Hanlon, Roger T

2012-11-01

The blue-ringed octopus (Hapalochlaena lunulata), one of the world's most venomous animals, has long captivated and endangered a large audience: children playing at the beach, divers turning over rocks, and biologists researching neurotoxins. These small animals spend much of their time in hiding, showing effective camouflage patterns. When disturbed, the octopus will flash around 60 iridescent blue rings and, when strongly harassed, bite and deliver a neurotoxin that can kill a human. Here, we describe the flashing mechanism and optical properties of these rings. The rings contain physiologically inert multilayer reflectors, arranged to reflect blue-green light in a broad viewing direction. Dark pigmented chromatophores are found beneath and around each ring to enhance contrast. No chromatophores are above the ring; this is unusual for cephalopods, which typically use chromatophores to cover or spectrally modify iridescence. The fast flashes are achieved using muscles under direct neural control. The ring is hidden by contraction of muscles above the iridophores; relaxation of these muscles and contraction of muscles outside the ring expose the iridescence. This mechanism of producing iridescent signals has not previously been reported in cephalopods and we suggest that it is an exceptionally effective way to create a fast and conspicuous warning display.

Pooled versus separate measurements of tree-ring stable isotopes

Energy Technology Data Exchange (ETDEWEB)

Dorado Linan, Isabel, E-mail: isabel@gfz-potsdam.de [Universitat de Barcelona, Departament d' Ecologia, Diagonal 645, 08028, Barcelona (Spain); German Centre for Geosciences, Climate Dynamics and Landscape Evolution, Dendro Laboratory, Telegrafenberg, 14473, Potsdam (Germany); Gutierrez, Emilia, E-mail: emgutierrez@ub.edu [Universitat de Barcelona, Departament d' Ecologia, Diagonal 645, 08028, Barcelona (Spain); Helle, Gerhard, E-mail: ghelle@gfz-potsdam.de [German Centre for Geosciences, Climate Dynamics and Landscape Evolution, Dendro Laboratory, Telegrafenberg, 14473, Potsdam (Germany); Heinrich, Ingo, E-mail: heinrich@gfz-potsdam.de [German Centre for Geosciences, Climate Dynamics and Landscape Evolution, Dendro Laboratory, Telegrafenberg, 14473, Potsdam (Germany); Andreu-Hayles, Laia, E-mail: laiandreu@ub.edu [Universitat de Barcelona, Departament d' Ecologia, Diagonal 645, 08028, Barcelona (Spain); Tree-Ring Laboratory, Lamont-Doherty Earth Observatory of Columbia University, Palisades NY (United States); Planells, Octavi, E-mail: leocarpus@hotmail.com [Universitat de Barcelona, Departament d' Ecologia, Diagonal 645, 08028, Barcelona (Spain); Leuenberger, Markus, E-mail: leuenberger@climate.unibe.ch [Climate and Environmental Physics, Physics Institute, University of Bern, Sidlerstrasse 5, 3012 Bern (Switzerland); Oeschger Centre of Climate Change Research, University of Bern, Zaehringerstrasse 25, 3012 Bern (Switzerland); Buerger, Carmen, E-mail: buerger@gfz-potsdam.de [German Centre for Geosciences, Climate Dynamics and Landscape Evolution, Dendro Laboratory, Telegrafenberg, 14473, Potsdam (Germany); Schleser, Gerhard, E-mail: schleser@gfz-potsdam.de [German Centre for Geosciences, Climate Dynamics and Landscape Evolution, Dendro Laboratory, Telegrafenberg, 14473, Potsdam (Germany)

2011-05-01

{delta}{sup 13}C and {delta}{sup 18}O of tree rings contain time integrated information about the environmental conditions weighted by seasonal growth dynamics and are well established as sources of palaeoclimatic and ecophysiological data. Annually resolved isotope chronologies are frequently produced by pooling dated growth rings from several trees prior to the isotopic analyses. This procedure has the advantage of saving time and resources, but precludes from defining the isotopic error or statistical uncertainty related to the inter-tree variability. Up to now only a few studies have compared isotope series from pooled tree rings with isotopic measurements from individual trees. We tested whether or not the {delta}{sup 13}C and the {delta}{sup 18}O chronologies derived from pooled and from individual tree rings display significant differences at two locations from the Iberian Peninsula to assess advantages and constraints of both methodologies. The comparisons along the period 1900-2003 reveal a good agreement between pooled chronologies and the two mean master series which were created by averaging raw individual values (Mean) or by generating a mass calibrated mean (MassC). In most of the cases, pooled chronologies show high synchronicity with averaged individual samples at interannual scale but some differences also show up especially when comparing {delta}{sup 18}O decadal to multi-decadal variations. Moreover, differences in the first order autocorrelation among individuals may be obscured by pooling strategies. The lack of replication of pooled chronologies prevents detection of a bias due to a higher mass contribution of one sample but uncertainties associated with the analytical process itself, as sample inhomogeneity, seems to account for the observed differences. - Research Highlights: {yields} Pooled {delta}{sup 13}C and {delta}{sup 18}O chronologies are expected to be similar to the mean. {yields} Empirical pooled chronologies {delta}{sup 13}C and