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Sample records for spin molecular cluster

  1. NMR study of spin dynamics in mesoscopic molecular clusters

    Science.gov (United States)

    Borsa, Ferdinando

    1998-03-01

    Recent published and umpublished work regarding the magnetic properties and the spin dynamics of molecules containing rings of 6,8 and 10 spins and of molecules containing clusters of 8 and 12 spins are reviewed. The 1H nuclear spin-lattice relaxation rate (NSLR) and the Muon Spin Resonance relaxation in Mn12 (A.Lascialfari, D.Gatteschi, F.Borsa, A.Shastri, Z.H.Jang and P.Carretta, Phys.Rev. B 1 January 1998) and Fe8 clusters are presented and discussed with regards to the high temperature spin dynamics of the Mn (Fe) magnetic moments and with regards to the low temperature superparamagnetic behavior. 1H and 63Cu NMR results are presented for two "quantum" spin rings : Cu6 and Cu8. The Cu6 is a weakly coupled (J/k=60K) ferromagnetic S=1/2 spin ring while Cu8 is a strongly coupled (J/k greater than 400K) antiferromagnetic S=1/2 spin ring.The dependence of the NSRL from temperature and from applied magnetic field are analyzed in terms of the calculated magnetic energy levels of the magnetic ring. The values of the energy gap between the ground state and the first excited state are extracted from the exponential decrease of the NSLR as the temperature is lowered. The results in the Cu ( S=1/2) "quantum" rings are compared with the results in "quantum" chains and ladders and with the results in "classical" Fe (S=5/2) antiferromagnetic rings : Fe6 and Fe10 (A.Lascialfari, D.Gatteschi, F.Borsa and A.Cornia , Phys.Rev. 55B,14341,1997) ).

  2. Entangled states decoherence in coupled molecular spin clusters

    Science.gov (United States)

    Troiani, Filippo; Szallas, Attila; Bellini, Valerio; Affronte, Marco

    2010-03-01

    Localized electron spins in solid-state systems are widely investigated as potential building blocks of quantum devices and computers. While most efforts in the field have been focused on semiconductor low-dimensional structures, molecular antiferromagnets were recently recognized as alternative implementations of effective few-level spin systems. Heterometallic, Cr-based spin rings behave as effective spin-1/2 systems at low temperature and show long decoherence times [1]; besides, they can be chemically linked and magnetically coupled in a controllable fascion [2]. Here, we theoretically investigate the decoherence of the Bell states in such ring dimers, resulting from hyperfine interactions with nuclear spins. Based on a microscopic description of the molecules [3], we simulate the effect of inhomogeneous broadening, spectral diffusion and electron-nuclear entanglement on the electron-spin coherence, estimating the role of the different nuclei (and of possible chemical substitutions), as well as the effect of simple spin-echo sequences. References: [1] F. Troiani, et al., Phys. Rev. Lett. 94, 207208 (2005). [2] G. A. Timco, S: Carretta, F. Troiani et al., Nature Nanotech. 4, 173 (2009). [3] F. Troiani, V. Bellini, and M. Affronte, Phys. Rev. B 77, 054428 (2008).

  3. Spin dynamics study of magnetic molecular clusters by means of Moessbauer spectroscopy

    International Nuclear Information System (INIS)

    Cianchi, L.; Del Giallo, F.; Spina, G.; Reiff, W.; Caneschi, A.

    2002-01-01

    Spin dynamics of the two magnetic molecular clusters Fe4 and Fe8, with four and eight Fe(III) ions, respectively, was studied by means of Moessbauer spectroscopy. The transition probabilities W's between the spin states of the ground multiplet were obtained from the fitting of the spectra. For the Fe4 cluster we found that, in the range from 1.38 to 77 K, the trend of W's versus the temperature corresponds to an Orbach's process involving an excited state with energy of about 160 K. For the Fe8, which, due to the presence of a low-energy excited state, could not be studied at temperatures greater than 20 K, the trend of W's in the range from 4 to 18 K seems to correspond to a direct process. The correlation functions of the magnetization were then calculated in terms of the W's. They have an exponential trend for the Fe4 cluster, while a small oscillating component is also present for the Fe8 cluster. For the first of the clusters, τ vs T (τ is the decay time of the magnetization) has a trend which, at low temperatures (T 15 K, τ follows the trend of W -1 . For the Fe8, τ follows an Arrhenius law, but with a prefactor which is smaller than the one obtained susceptibility measurements

  4. Inter-cluster coupling effects in high-spin molecular magnets

    International Nuclear Information System (INIS)

    Affronte, M.; Lasjaunias, J.C.; Wernsdorfer, W.; Sessoli, R.; Gatteschi, D.; Heath, S.L.; Fort, A.; Rettori, A.

    2004-01-01

    We report evidences of antiferromagnetic (AF) transition in Fe 19 metheidi, a new molecular nanomagnet with a total spin S=((33)/(2)), among the highest known so far. The temperature (T) dependence of specific heat (C) shows a λ-anomaly at 1.19 K and at the same temperature an anomaly is also observed in the low field (B<0.12 T) magnetization M-vs.-T curves. Since the dipolar interaction between clusters is estimated to be ∼190 mK, the origin of the AF transition is probably due to superexchange

  5. Inter-cluster coupling effects in high-spin molecular magnets

    Energy Technology Data Exchange (ETDEWEB)

    Affronte, M.; Lasjaunias, J.C.; Wernsdorfer, W.; Sessoli, R.; Gatteschi, D.; Heath, S.L.; Fort, A. E-mail: fort@fi.infn.it; Rettori, A

    2004-05-01

    We report evidences of antiferromagnetic (AF) transition in Fe{sub 19}metheidi, a new molecular nanomagnet with a total spin S=((33)/(2)), among the highest known so far. The temperature (T) dependence of specific heat (C) shows a {lambda}-anomaly at 1.19 K and at the same temperature an anomaly is also observed in the low field (B<0.12 T) magnetization M-vs.-T curves. Since the dipolar interaction between clusters is estimated to be {approx}190 mK, the origin of the AF transition is probably due to superexchange.

  6. Cranked cluster wave function for molecular states

    International Nuclear Information System (INIS)

    Horiuchi, Hisashi; Yabana, Kazuhiro; Wada, Takahiro.

    1986-01-01

    Construction of the cranked cluster wave function is discussed by focussing on three problems; the self-consistency between the potential and the density distribution, the properties of the rotational angular frequency which is strongly influenced by the inter-cluster Pauli principle and by the parity projection, and the spin alignment along the rotation axis with the resulting structure-change of the molecular state. (author)

  7. Relay entanglement and clusters of correlated spins

    Science.gov (United States)

    Doronin, S. I.; Zenchuk, A. I.

    2018-06-01

    Considering a spin-1/2 chain, we suppose that the entanglement passes from a given pair of particles to another one, thus establishing the relay transfer of entanglement along the chain. Therefore, we introduce the relay entanglement as a sum of all pairwise entanglements in a spin chain. For more detailed studying the effects of remote pairwise entanglements, we use the partial sums collecting entanglements between the spins separated by up to a certain number of nodes. The problem of entangled cluster formation is considered, and the geometric mean entanglement is introduced as a characteristic of quantum correlations in a cluster. Generally, the lifetime of a cluster decreases with an increase in its size.

  8. Laser ionization of molecular clusters

    International Nuclear Information System (INIS)

    Desai, S.; Feigerle, C.S.

    1995-01-01

    Multiphoton ionization coupled with mass spectrometry was used to investigate molecular cluster distributions. Three examples will be discussed in this presentation. First, in studies of neat nitric oxide clusters, (NO) m , an interesting odd-even intensity alternation was observed and will be discussed in terms of electron-pairing considerations. In a separate study, the binary clusters comprising nitric oxide and methane preferentially form a stoichiometric cluster made up of repeating units of (NO) 2 CH 4 . These presumably represent a particularly strongly bound open-quotes van der Waalsclose quotes subunit. Finally, in similar studies of neat carbon disulfide clusters, (CS 2 ) m , additional photon absorption after the two-photon ionization step stimulates a series of intracluster ion-molecular reactions leading to formation of S m + and (CS) m + polymers, as well as intermediate species such as S m + (CS 2 ). This molecular cluster analogue of open-quotes laser snowclose quotes will be described in detail

  9. Improving the distinguishable cluster results: spin-component scaling

    Science.gov (United States)

    Kats, Daniel

    2018-06-01

    The spin-component scaling is employed in the energy evaluation to improve the distinguishable cluster approach. SCS-DCSD reaction energies reproduce reference values with a root-mean-squared deviation well below 1 kcal/mol, the interaction energies are three to five times more accurate than DCSD, and molecular systems with a large amount of static electron correlation are still described reasonably well. SCS-DCSD represents a pragmatic approach to achieve chemical accuracy with a simple method without triples, which can also be applied to multi-configurational molecular systems.

  10. A molecular spin-photovoltaic device.

    Science.gov (United States)

    Sun, Xiangnan; Vélez, Saül; Atxabal, Ainhoa; Bedoya-Pinto, Amilcar; Parui, Subir; Zhu, Xiangwei; Llopis, Roger; Casanova, Fèlix; Hueso, Luis E

    2017-08-18

    We fabricated a C 60 fullerene-based molecular spin-photovoltaic device that integrates a photovoltaic response with the spin transport across the molecular layer. The photovoltaic response can be modified under the application of a small magnetic field, with a magnetophotovoltage of up to 5% at room temperature. Device functionalities include a magnetic current inverter and the presence of diverging magnetocurrent at certain illumination levels that could be useful for sensing. Completely spin-polarized currents can be created by balancing the external partially spin-polarized injection with the photogenerated carriers. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  11. Microelectromechanical systems integrating molecular spin crossover actuators

    Energy Technology Data Exchange (ETDEWEB)

    Manrique-Juarez, Maria D. [LCC, CNRS and Université de Toulouse, UPS, INP, F-31077 Toulouse (France); LAAS, CNRS and Université de Toulouse, INSA, UPS, F-31077 Toulouse (France); Rat, Sylvain; Salmon, Lionel; Molnár, Gábor; Bousseksou, Azzedine, E-mail: liviu.nicu@laas.fr, E-mail: azzedine.bousseksou@lcc-toulouse.fr [LCC, CNRS and Université de Toulouse, UPS, INP, F-31077 Toulouse (France); Mathieu, Fabrice; Saya, Daisuke; Séguy, Isabelle; Leïchlé, Thierry; Nicu, Liviu, E-mail: liviu.nicu@laas.fr, E-mail: azzedine.bousseksou@lcc-toulouse.fr [LAAS, CNRS and Université de Toulouse, INSA, UPS, F-31077 Toulouse (France)

    2016-08-08

    Silicon MEMS cantilevers coated with a 200 nm thin layer of the molecular spin crossover complex [Fe(H{sub 2}B(pz){sub 2}){sub 2}(phen)] (H{sub 2}B(pz){sub 2} = dihydrobis(pyrazolyl)borate and phen = 1,10-phenantroline) were actuated using an external magnetic field and their resonance frequency was tracked by means of integrated piezoresistive detection. The light-induced spin-state switching of the molecules from the ground low spin to the metastable high spin state at 10 K led to a well-reproducible shift of the cantilever's resonance frequency (Δf{sub r} = −0.52 Hz). Control experiments at different temperatures using coated as well as uncoated devices along with simple calculations support the assignment of this effect to the spin transition. This latter translates into changes in mechanical behavior of the cantilever due to the strong spin-state/lattice coupling. A guideline for the optimization of device parameters is proposed so as to efficiently harness molecular scale movements for large-scale mechanical work, thus paving the road for nanoelectromechanical systems (NEMS) actuators based on molecular materials.

  12. Molecular cluster theory of chemical bonding in actinide oxide

    International Nuclear Information System (INIS)

    Ellis, D.E.; Gubanov, V.A.; Rosen, A.

    1978-01-01

    The electronic structure of actinide monoxides AcO and dioxides AcO 2 , where Ac = Th, U, Np, Pu, Am, Cm and Bk has been studied by molecular cluster methods based on the first-principles one-electron local density theory. Molecular orbitals for nearest neighbor clusters AcO 10- 6 and AcO 12- 8 representative of monoxide and dioxide lattices were obtained using non-relativistic spin-restricted and spin-polarized Hartree-Fock-Slater models for the entire series. Fully relativistic Dirac-Slater calculations were performed for ThO, UO and NpO in order to explore magnitude of spin-orbit splittings and level shifts in valence structure. Self-consistent iterations were carried out for NpO, in which the NpO 6 cluster was embedded in the molecular field of the solid. Finally, a ''moment polarized'' model which combines both spin-polarization and relativistic effects in a consistent fashion was applied to the NpO system. Covalent mixing of oxygen 2p and Ac 5f orbitals was found to increase rapidly across the actinide series; metal s,p,d covalency was found to be nearly constant. Mulliken atomic population analysis of cluster eigenvectors shows that free-ion crystal field models are unreliable, except for the light actinides. X-ray photoelectron line shapes have been calculated and are found to compare rather well with experimental data on the dioxides

  13. Control of entanglement transitions in quantum spin clusters

    Science.gov (United States)

    Irons, Hannah R.; Quintanilla, Jorge; Perring, Toby G.; Amico, Luigi; Aeppli, Gabriel

    2017-12-01

    Quantum spin clusters provide a platform for the experimental study of many-body entanglement. Here we address a simple model of a single-molecule nanomagnet featuring N interacting spins in a transverse field. The field can control an entanglement transition (ET). We calculate the magnetization, low-energy gap, and neutron-scattering cross section and find that the ET has distinct signatures, detectable at temperatures as high as 5% of the interaction strength. The signatures are stronger for smaller clusters.

  14. Computationally inexpensive interpretation of magnetic data for finite spin clusters

    DEFF Research Database (Denmark)

    Thuesen, Christian Aagaard; Weihe, Høgni; Bendix, Jesper

    2010-01-01

    We show that high-temperature expansion of the partition function is a computationally convenient tool to interpretation of magnetic properties of spin clusters wherein the spin centers are interacting via an isotropic Heisenberg exchange operator. High-temperature expansions up to order 12 are u...

  15. Magnetic structure and spin dynamics of the ground state of the molecular cluster Mn12O12 acetate studied by 55Mn NMR

    International Nuclear Information System (INIS)

    Furukawa, Y.; Watanabe, K.; Kumagai, K.; Borsa, F.; Gatteschi, D.

    2001-01-01

    55 Mn nuclear magnetic resonance (NMR) measurements have been carried out in an oriented powder sample of Mn12 acetate at low temperature (1.4--3 K) in order to investigate locally the static and dynamic magnetic properties of the molecule in its high-spin S=10 ground state. We report the observation of three 55 MnNMR lines under zero external magnetic field. From the resonance frequency and the width of the lines we derive the internal hyperfine field and the quadrupole coupling constant at each of the three nonequivalent Mn ion sites. From the field dependence of the spectrum we obtain a direct confirmation of the standard picture, in which spin moments of Mn 4+ ions (S=3/2) of the inner tetrahedron are polarized antiparallel to that of Mn 3+ ions (S=2) of the outer ring with no measurable canting from the easy axis up to an applied field of 6 T. It is found that the splitting of the 55 Mn-NMR lines when a magnetic field is applied at low temperature allows one to monitor the off-equilibrium population of the molecules in the different low lying magnetic states. The measured nuclear spin-lattice relaxation time T 1 strongly depends on temperature and magnetic field. The behavior could be fitted well by considering the local-field fluctuations at the nuclear 55 Mn site due to the thermal reorientation of the total S=10 spin of the molecule. From the fit of the data one can derive the product of the spin-phonon coupling constant times the mean-square value of the fluctuating hyperfine field. The two constants could be estimated separately by making some assumptions. The comparison of the mean-square fluctuation from relaxation with the static hyperfine field from the spectrum suggests that nonuniform terms (q≠0) are important in describing the spin dynamics of the local Mn moments in the ground state

  16. Knitting distributed cluster-state ladders with spin chains

    Energy Technology Data Exchange (ETDEWEB)

    Ronke, R.; D' Amico, I. [Department of Physics, University of York, York YO10 5DD, United Kingdom. (United Kingdom); Spiller, T. P. [School of Physics and Astronomy, E C Stoner Building, University of Leeds, Leeds, LS2 9JT (United Kingdom)

    2011-09-15

    Recently there has been much study on the application of spin chains to quantum state transfer and communication. Here we discuss the utilization of spin chains (set up for perfect quantum state transfer) for the knitting of distributed cluster-state structures, between spin qubits repeatedly injected and extracted at the ends of the chain. The cluster states emerge from the natural evolution of the system across different excitation number sectors. We discuss the decohering effects of errors in the injection and extraction process as well as the effects of fabrication and random errors.

  17. Knitting distributed cluster-state ladders with spin chains

    International Nuclear Information System (INIS)

    Ronke, R.; D'Amico, I.; Spiller, T. P.

    2011-01-01

    Recently there has been much study on the application of spin chains to quantum state transfer and communication. Here we discuss the utilization of spin chains (set up for perfect quantum state transfer) for the knitting of distributed cluster-state structures, between spin qubits repeatedly injected and extracted at the ends of the chain. The cluster states emerge from the natural evolution of the system across different excitation number sectors. We discuss the decohering effects of errors in the injection and extraction process as well as the effects of fabrication and random errors.

  18. Higher-spin cluster algorithms: the Heisenberg spin and U(1) quantum link models

    Energy Technology Data Exchange (ETDEWEB)

    Chudnovsky, V

    2000-03-01

    I discuss here how the highly-efficient spin-1/2 cluster algorithm for the Heisenberg antiferromagnet may be extended to higher-dimensional representations; some numerical results are provided. The same extensions can be used for the U(1) flux cluster algorithm, but have not yielded signals of the desired Coulomb phase of the system.

  19. Higher-spin cluster algorithms: the Heisenberg spin and U(1) quantum link models

    International Nuclear Information System (INIS)

    Chudnovsky, V.

    2000-01-01

    I discuss here how the highly-efficient spin-1/2 cluster algorithm for the Heisenberg antiferromagnet may be extended to higher-dimensional representations; some numerical results are provided. The same extensions can be used for the U(1) flux cluster algorithm, but have not yielded signals of the desired Coulomb phase of the system

  20. NMR studies of selective population inversion and spin clustering

    International Nuclear Information System (INIS)

    Baum, J.S.

    1986-02-01

    This work describes the development and application of selective excitation techniques in Nuclear Magnetic Resonance. Composite pulses and multiple-quantum methods are used to accomplish various goals, such as broadband and narrowband excitation in liquids, and collective excitation of groups of spins in solids. These methods are applied to a variety of problems, including non-invasive spatial localization, spin cluster size characterization in disordered solids and solid state NMR imaging

  1. Spin-diffusions and diffusive molecular dynamics

    Science.gov (United States)

    Farmer, Brittan; Luskin, Mitchell; Plecháč, Petr; Simpson, Gideon

    2017-12-01

    Metastable configurations in condensed matter typically fluctuate about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of classical molecular dynamics (MD) methods and has spurned the development of a host of approximate algorithms. One recently proposed method is diffusive MD which aims at integrating a system of ordinary differential equations describing the likelihood of occupancy by one of two species, in the case of a binary alloy, while quasistatically evolving the locations of the atoms. While diffusive MD has shown itself to be efficient and provide agreement with observations, it is fundamentally a model, with unclear connections to classical MD. In this work, we formulate a spin-diffusion stochastic process and show how it can be connected to diffusive MD. The spin-diffusion model couples a classical overdamped Langevin equation to a kinetic Monte Carlo model for exchange amongst the species of a binary alloy. Under suitable assumptions and approximations, spin-diffusion can be shown to lead to diffusive MD type models. The key assumptions and approximations include a well-defined time scale separation, a choice of spin-exchange rates, a low temperature approximation, and a mean field type approximation. We derive several models from different assumptions and show their relationship to diffusive MD. Differences and similarities amongst the models are explored in a simple test problem.

  2. 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.

  3. Spin tunneling in magnetic molecules: Quantitative estimates for Fe8 clusters

    Science.gov (United States)

    Galetti, D.; Silva, Evandro C.

    2007-12-01

    Spin tunneling in the particular case of the magnetic molecular cluster octanuclear iron(III), Fe8, is treated by an effective Hamiltonian that allows for an angle-based description of the process. The presence of an external magnetic field along the easy axis is also taken into account in this description. Analytic expressions for the energy levels and barriers are obtained from a harmonic approximation of the potential function which give results in good agreement with the experimental results. The energy splittings due to spin tunneling is treated in an adapted WKB approach and it is shown that the present description can give results to a reliable degree of accuracy.

  4. The molecular spin filter constructed from 1D organic chain

    International Nuclear Information System (INIS)

    Chen, Wei; Xu, Ning; Wang, Baolin; Bian, Baoan

    2014-01-01

    We proposed a molecular spin filter, which is constructed from the 1D metallic organic chain (Fe n+1 (C 6 H 4 ) n ). The spin-polarized transport properties of the molecular spin filter are explored by combining density functional theory with nonequilibrium Green's function formalism. Theoretical results reveal that Fe n+1 (C 6 H 4 ) n molecular chain exhibits robust spin filtering effect, and only the spin-down electrons can transmit through the molecular chain. At the given bias voltage window [−1 eV,1 eV], the calculated spin filter efficiency is close to 100% in the case of n≥3. We find that the effect of spin polarization origin from both Fe n+1 and (C 6 H 4 ) n . In addition, negative difference resistance behavior appears in Fe n+1 (C 6 H 4 ) n molecular chain. The results can help us understand the spin transport properties of organic molecular chain. - Highlights: • Theoretical results reveal that Fe n+1 (C 6 H 4 ) n molecular chain exhibits robust spin filtering effect. • The effect of spin polarization origin from both of Fe n+1 and (C 6 H 4 ) n . • Negative difference resistance behavior appears in Fe n+1 (C 6 H 4 ) n molecular chain

  5. Molecular clusters of the main group elements

    CERN Document Server

    Driess, Matthias

    2008-01-01

    ""To summarize, Molecular Clusters of the Main Group Elements is certainly not a popular science book, nor is it a textbook; it is a very good, up-to-date collection of articles for the specialist. Als Fazit bleibt: Molecular Clusters of the Main Group Elements ist sicher kein populissenschaftliches Werk, auch kein Lehrbuch, aber eine gelungene, hoch aktuelle Zusammenstellung fen interessierten Fachmann."" -Michael Ruck, TU Dresden, Angewandte Chemie, 2004 - 116/36 + International Edition 2004 - 43/36

  6. Cluster algorithms with empahsis on quantum spin systems

    International Nuclear Information System (INIS)

    Gubernatis, J.E.; Kawashima, Naoki

    1995-01-01

    The purpose of this lecture is to discuss in detail the generalized approach of Kawashima and Gubernatis for the construction of cluster algorithms. We first present a brief refresher on the Monte Carlo method, describe the Swendsen-Wang algorithm, show how this algorithm follows from the Fortuin-Kastelyn transformation, and re=interpret this transformation in a form which is the basis of the generalized approach. We then derive the essential equations of the generalized approach. This derivation is remarkably simple if done from the viewpoint of probability theory, and the essential assumptions will be clearly stated. These assumptions are implicit in all useful cluster algorithms of which we are aware. They lead to a quite different perspective on cluster algorithms than found in the seminal works and in Ising model applications. Next, we illustrate how the generalized approach leads to a cluster algorithm for world-line quantum Monte Carlo simulations of Heisenberg models with S = 1/2. More succinctly, we also discuss the generalization of the Fortuin- Kasetelyn transformation to higher spin models and illustrate the essential steps for a S = 1 Heisenberg model. Finally, we summarize how to go beyond S = 1 to a general spin, XYZ model

  7. Spin chain simulations with a meron cluster algorithm

    International Nuclear Information System (INIS)

    Boyer, T.; Bietenholz, W.; Deutsches Elektronen-Synchrotron; Wuilloud, J.; Geneve Univ.

    2007-01-01

    We apply a meron cluster algorithm to the XY spin chain, which describes a quantum rotor. This is a multi-cluster simulation supplemented by an improved estimator, which deals with objects of half-integer topological charge. This method is powerful enough to provide precise results for the model with a θ-term - it is therefore one of the rare examples, where a system with a complex action can be solved numerically. In particular we measure the correlation length, as well as the topological and magnetic susceptibility. We discuss the algorithmic efficiency in view of the critical slowing down. Due to the excellent performance that we observe, it is strongly motivated to work on new applications of meron cluster algorithms in higher dimensions. (orig.)

  8. Spin polarized electron tunneling and magnetoresistance in molecular junctions.

    Science.gov (United States)

    Szulczewski, Greg

    2012-01-01

    This chapter reviews tunneling of spin-polarized electrons through molecules positioned between ferromagnetic electrodes, which gives rise to tunneling magnetoresistance. Such measurements yield important insight into the factors governing spin-polarized electron injection into organic semiconductors, thereby offering the possibility to manipulate the quantum-mechanical spin degrees of freedom for charge carriers in optical/electrical devices. In the first section of the chapter a brief description of the Jullière model of spin-dependent electron tunneling is reviewed. Next, a brief description of device fabrication and characterization is presented. The bulk of the review highlights experimental studies on spin-polarized electron tunneling and magnetoresistance in molecular junctions. In addition, some experiments describing spin-polarized scanning tunneling microscopy/spectroscopy on single molecules are mentioned. Finally, some general conclusions and prospectus on the impact of spin-polarized tunneling in molecular junctions are offered.

  9. Advances in molecular vibrations and collision dynamics molecular clusters

    CERN Document Server

    Bacic, Zatko

    1998-01-01

    This volume focuses on molecular clusters, bound by van der Waals interactions and hydrogen bonds. Twelve chapters review a wide range of recent theoretical and experimental advances in the areas of cluster vibrations, spectroscopy, and reaction dynamics. The authors are leading experts, who have made significant contributions to these topics.The first chapter describes exciting results and new insights in the solvent effects on the short-time photo fragmentation dynamics of small molecules, obtained by combining heteroclusters with femtosecond laser excitation. The second is on theoretical work on effects of single solvent (argon) atom on the photodissociation dynamics of the solute H2O molecule. The next two chapters cover experimental and theoretical aspects of the energetics and vibrations of small clusters. Chapter 5 describes diffusion quantum Monte Carlo calculations and non additive three-body potential terms in molecular clusters. The next six chapters deal with hydrogen-bonded clusters, refle...

  10. Solid state {sup 1}H spin-lattice relaxation and isolated-molecule and cluster electronic structure calculations in organic molecular solids: The relationship between structure and methyl group and t-butyl group rotation

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xianlong, E-mail: WangXianlong@uestc.edu.cn, E-mail: pbeckman@brynmawr.edu [Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, 4 North Jianshe Rd., 2nd Section, Chengdu 610054 (China); Mallory, Frank B. [Department of Chemistry, Bryn Mawr College, 101 North Merion Ave., Bryn Mawr, Pennsylvania 19010-2899 (United States); Mallory, Clelia W. [Department of Chemistry, Bryn Mawr College, 101 North Merion Ave., Bryn Mawr, Pennsylvania 19010-2899 (United States); Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323 (United States); Odhner, Hosanna R.; Beckmann, Peter A., E-mail: WangXianlong@uestc.edu.cn, E-mail: pbeckman@brynmawr.edu [Department of Physics, Bryn Mawr College, 101 North Merion Ave., Bryn Mawr, Pennsylvania 19010-2899 (United States)

    2014-05-21

    We report ab initio density functional theory electronic structure calculations of rotational barriers for t-butyl groups and their constituent methyl groups both in the isolated molecules and in central molecules in clusters built from the X-ray structure in four t-butyl aromatic compounds. The X-ray structures have been reported previously. We also report and interpret the temperature dependence of the solid state {sup 1}H nuclear magnetic resonance spin-lattice relaxation rate at 8.50, 22.5, and 53.0 MHz in one of the four compounds. Such experiments for the other three have been reported previously. We compare the computed barriers for methyl group and t-butyl group rotation in a central target molecule in the cluster with the activation energies determined from fitting the {sup 1}H NMR spin-lattice relaxation data. We formulate a dynamical model for the superposition of t-butyl group rotation and the rotation of the t-butyl group's constituent methyl groups. The four compounds are 2,7-di-t-butylpyrene, 1,4-di-t-butylbenzene, 2,6-di-t-butylnaphthalene, and 3-t-butylchrysene. We comment on the unusual ground state orientation of the t-butyl groups in the crystal of the pyrene and we comment on the unusually high rotational barrier of these t-butyl groups.

  11. Young star clusters in nearby molecular clouds

    Science.gov (United States)

    Getman, K. V.; Kuhn, M. A.; Feigelson, E. D.; Broos, P. S.; Bate, M. R.; Garmire, G. P.

    2018-06-01

    The SFiNCs (Star Formation in Nearby Clouds) project is an X-ray/infrared study of the young stellar populations in 22 star-forming regions with distances ≲ 1 kpc designed to extend our earlier MYStIX (Massive Young Star-Forming Complex Study in Infrared and X-ray) survey of more distant clusters. Our central goal is to give empirical constraints on cluster formation mechanisms. Using parametric mixture models applied homogeneously to the catalogue of SFiNCs young stars, we identify 52 SFiNCs clusters and 19 unclustered stellar structures. The procedure gives cluster properties including location, population, morphology, association with molecular clouds, absorption, age (AgeJX), and infrared spectral energy distribution (SED) slope. Absorption, SED slope, and AgeJX are age indicators. SFiNCs clusters are examined individually, and collectively with MYStIX clusters, to give the following results. (1) SFiNCs is dominated by smaller, younger, and more heavily obscured clusters than MYStIX. (2) SFiNCs cloud-associated clusters have the high ellipticities aligned with their host molecular filaments indicating morphology inherited from their parental clouds. (3) The effect of cluster expansion is evident from the radius-age, radius-absorption, and radius-SED correlations. Core radii increase dramatically from ˜0.08 to ˜0.9 pc over the age range 1-3.5 Myr. Inferred gas removal time-scales are longer than 1 Myr. (4) Rich, spatially distributed stellar populations are present in SFiNCs clouds representing early generations of star formation. An appendix compares the performance of the mixture models and non-parametric minimum spanning tree to identify clusters. This work is a foundation for future SFiNCs/MYStIX studies including disc longevity, age gradients, and dynamical modelling.

  12. Interfacial spin cluster effects in exchange bias systems

    Energy Technology Data Exchange (ETDEWEB)

    Carpenter, R., E-mail: rc548@york.ac.uk; Vallejo-Fernandez, G.; O' Grady, K. [Department of Physics, The University of York, York YO10 5DD (United Kingdom)

    2014-05-07

    In this work, the effect of exchange bias on the hysteresis loop of CoFe is observed. The evolution of the coercivities and the shift of the hysteresis loop during the annealing process has been measured for films deposited on NiCr and Cu seed layers. Through comparison of the as deposited and field annealed loops, it is clear that for an exchange biased material, the two coercivities are due to different reversal processes. This behaviour is attributed to spin clusters at the ferromagnet/antiferromagnet interface, which behave in a similar manner to a fine particle system.

  13. Spin nutation effects in molecular nanomagnet–superconductor tunnel junctions

    International Nuclear Information System (INIS)

    Abouie, J; Abdollahipour, B; Rostami, A A

    2013-01-01

    We study the spin nutation effects of a molecular nanomagnet on the Josephson current through a superconductor|molecular nanomagnet|superconductor tunnel junction. We explicitly demonstrate that, due to the spin nutation of the molecular nanomagnet, two oscillatory terms emerge in the ac Josephson current in addition to the conventional ac Josephson current. Some resonances occur in the junction due to the interactions of the transported quasiparticles with the bias voltage and molecular nanomagnet spin dynamics. Their appearance indicates that the energy exchanged during these interactions is in the range of the superconducting energy gap. We also show that the spin nutation is able to convert the ac Josephson current to a dc current, which is interesting for applications. (paper)

  14. Shapiro like steps reveals molecular nanomagnets’ spin dynamics

    International Nuclear Information System (INIS)

    Abdollahipour, Babak; Abouie, Jahanfar; Ebrahimi, Navid

    2015-01-01

    We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields

  15. Tuning the effective spin-orbit coupling in molecular semiconductors

    KAUST Repository

    Schott, Sam

    2017-05-11

    The control of spins and spin to charge conversion in organics requires understanding the molecular spin-orbit coupling (SOC), and a means to tune its strength. However, quantifying SOC strengths indirectly through spin relaxation effects has proven difficult due to competing relaxation mechanisms. Here we present a systematic study of the g-tensor shift in molecular semiconductors and link it directly to the SOC strength in a series of high-mobility molecular semiconductors with strong potential for future devices. The results demonstrate a rich variability of the molecular g-shifts with the effective SOC, depending on subtle aspects of molecular composition and structure. We correlate the above g-shifts to spin-lattice relaxation times over four orders of magnitude, from 200 to 0.15 μs, for isolated molecules in solution and relate our findings for isolated molecules in solution to the spin relaxation mechanisms that are likely to be relevant in solid state systems.

  16. Tuning the effective spin-orbit coupling in molecular semiconductors

    KAUST Repository

    Schott, Sam; McNellis, Erik R.; Nielsen, Christian B.; Chen, Hung-Yang; Watanabe, Shun; Tanaka, Hisaaki; McCulloch, Iain; Takimiya, Kazuo; Sinova, Jairo; Sirringhaus, Henning

    2017-01-01

    The control of spins and spin to charge conversion in organics requires understanding the molecular spin-orbit coupling (SOC), and a means to tune its strength. However, quantifying SOC strengths indirectly through spin relaxation effects has proven difficult due to competing relaxation mechanisms. Here we present a systematic study of the g-tensor shift in molecular semiconductors and link it directly to the SOC strength in a series of high-mobility molecular semiconductors with strong potential for future devices. The results demonstrate a rich variability of the molecular g-shifts with the effective SOC, depending on subtle aspects of molecular composition and structure. We correlate the above g-shifts to spin-lattice relaxation times over four orders of magnitude, from 200 to 0.15 μs, for isolated molecules in solution and relate our findings for isolated molecules in solution to the spin relaxation mechanisms that are likely to be relevant in solid state systems.

  17. Magnetism of iron, cobalt and nickel clusters studied in molecular beams

    International Nuclear Information System (INIS)

    Billas, I.

    1995-01-01

    The magnetic properties of iron, cobalt and nickel clusters in a molecular beam have been studied in a magnetic Stern-Gerlach deflection experiment. The molecular beam apparatus consists of a laser vaporization cluster source with high intensity and stability and a high-resolution time-of-flight mass spectrometer for the deflection measurements. Several novel experimental features have been developed in this work, like a nozzle which can be heated up to 1000 K and a chopper to measure the dwell times of the clusters in the source and their corresponding velocities. These new developments have allowed the measurement and the control of the temperature of the free clusters. The Stern-Gerlach deflection experiments have been performed on Fe, Co and Ni clusters in the mass range from 20 to 700 atoms. All clusters show single-sided deflection toward increasing field. This observation indicates that a spin relaxation process occurs within the isolated clusters. The participation of both the cluster rotational and vibrational degrees of freedom to the spin relaxation has been experimentally demonstrated. The cluster magnetization has been determined as a function of applied magnetic field B and as a function of dwell times of the clusters in the source before the supersonic expansion into vacuum. Superparamagnetic behavior has been observed when the cluster rotational speed is much larger than the Larmor frequency of the cluster magnetic moment μ in the field B. In particular, for μB<< kT, the cluster magnetization depends on B/T. For lower rotational speeds, reduced values of the magnetization have been observed. The magnetic moments of the superparamagnetic Fe, Co and Ni clusters have been measured as a) a function of cluster size N at low temperature and b) as a function of cluster temperature T for various size ranges. (author) figs., tabs., refs

  18. Properties of liquid clusters in large-scale molecular dynamics nucleation simulations

    International Nuclear Information System (INIS)

    Angélil, Raymond; Diemand, Jürg; Tanaka, Kyoko K.; Tanaka, Hidekazu

    2014-01-01

    We have performed large-scale Lennard-Jones molecular dynamics simulations of homogeneous vapor-to-liquid nucleation, with 10 9 atoms. This large number allows us to resolve extremely low nucleation rates, and also provides excellent statistics for cluster properties over a wide range of cluster sizes. The nucleation rates, cluster growth rates, and size distributions are presented in Diemand et al. [J. Chem. Phys. 139, 74309 (2013)], while this paper analyses the properties of the clusters. We explore the cluster temperatures, density profiles, potential energies, and shapes. A thorough understanding of the properties of the clusters is crucial to the formulation of nucleation models. Significant latent heat is retained by stable clusters, by as much as ΔkT = 0.1ε for clusters with size i = 100. We find that the clusters deviate remarkably from spherical—with ellipsoidal axis ratios for critical cluster sizes typically within b/c = 0.7 ± 0.05 and a/c = 0.5 ± 0.05. We examine cluster spin angular momentum, and find that it plays a negligible role in the cluster dynamics. The interfaces of large, stable clusters are thinner than planar equilibrium interfaces by 10%−30%. At the critical cluster size, the cluster central densities are between 5% and 30% lower than the bulk liquid expectations. These lower densities imply larger-than-expected surface areas, which increase the energy cost to form a surface, which lowers nucleation rates

  19. Observation of the Distribution of Molecular Spin States by Resonant Quantum Tunneling of the Magnetization

    Science.gov (United States)

    Wernsdorfer, W.; Ohm, T.; Sangregorio, C.; Sessoli, R.; Mailly, D.; Paulsen, C.

    1999-05-01

    Below 360 mK, Fe8 magnetic molecular clusters are in the pure quantum relaxation regime and we show that the predicted ``square-root time'' relaxation is obeyed, allowing us to develop a new method for watching the evolution of the distribution of molecular spin states in the sample. We measure as a function of applied field H the statistical distribution P\\(ξH\\) of magnetic energy bias ξH acting on the molecules. Tunneling initially causes rapid transitions of molecules, thereby ``digging a hole'' in P\\(ξH\\) (around the resonant condition ξH = 0). For small initial magnetization values, the hole width shows an intrinsic broadening which may be due to nuclear spins.

  20. A cluster-bethe-lattice approach to spin-waves in dilute ferromagnets

    International Nuclear Information System (INIS)

    Salzberg, J.B.; Silva, C.E.T.G. da; Falicov, L.M.

    1975-01-01

    The spin-wave spectra of a dilute ferromagnet within the cluster-bethe-lattice approximation is studied. Short range order effects for the alloy are included. A study of finite size clusters connected at their edges to Bethe lattices of the same coordination number allows one to determine:(i) the stability condition for the magnetic system; (ii) the continuum spin-wave local density of states and (iii) the existence of localized states below and above the continuum states

  1. Molecular spinning by a chiral train of short laser pulses

    Science.gov (United States)

    Floß, Johannes; Averbukh, Ilya Sh.

    2012-12-01

    We provide a detailed theoretical analysis of molecular rotational excitation by a chiral pulse train, a sequence of linearly polarized pulses with the polarization direction rotating from pulse to pulse by a controllable angle. Molecular rotation with a preferential rotational sense (clockwise or counterclockwise) can be excited by this scheme. We show that the directionality of the rotation is caused by quantum interference of different excitation pathways. The chiral pulse train is capable of selective excitation of molecular isotopologs and nuclear spin isomers in a mixture. We demonstrate this using 14N2 and 15N2 as examples for isotopologs and para- and ortho-nitrogen as examples for nuclear-spin isomers.

  2. Characterization of the isolated [Co3Ni (EtOH )] + cluster by IR spectroscopy and spin-dynamics calculations

    Science.gov (United States)

    Dutta, D.; Becherer, M.; Bellaire, D.; Dietrich, F.; Gerhards, M.; Lefkidis, G.; Hübner, W.

    2018-06-01

    We experimentally and theoretically study the geometry, as well as the electronic and vibrational properties, of the heterotetranuclear magnetic cluster [Co3Ni (EtOH )] +, which is prepared in the gas phase with molecular beam expansion. We characterize the cluster and identify possible isomers through the comparison of experimentally observed infrared spectra with state-of-the-art quantum chemistry calculations, more specifically by focusing on the OH stretching frequency. Furthermore, we suggest ultrafast, laser-induced, local spin-flip scenarios on every Co atom, and report a cooperative effect, in which the spin density is localized on one Co atom, gets transiently transferred to another, and then bounces back pointing in the opposite direction. Finally, we predict a tolerance of the suggested scenarios with respect to the laser detuning of about 20 meV, which lies within an experimentally applicable range. Our joint investigation is an additional step toward the implementation of laser-controlled nanospintronic devices.

  3. An approach to spin-resolved molecular gas microscopy

    Science.gov (United States)

    Covey, Jacob P.; De Marco, Luigi; Acevedo, Óscar L.; Rey, Ana Maria; Ye, Jun

    2018-04-01

    Ultracold polar molecules are an ideal platform for studying many-body physics with long-range dipolar interactions. Experiments in this field have progressed enormously, and several groups are pursuing advanced apparatus for manipulation of molecules with electric fields as well as single-atom-resolved in situ detection. Such detection has become ubiquitous for atoms in optical lattices and tweezer arrays, but has yet to be demonstrated for ultracold polar molecules. Here we present a proposal for the implementation of site-resolved microscopy for polar molecules, and specifically discuss a technique for spin-resolved molecular detection. We use numerical simulation of spin dynamics of lattice-confined polar molecules to show how such a scheme would be of utility in a spin-diffusion experiment.

  4. Spin models for the single molecular magnet Mn12-AC

    Science.gov (United States)

    Al-Saqer, Mohamad A.

    2005-11-01

    The single molecular magnet (SMM) Mn12-AC attracted the attention of scientists since the discovery of its magnetic hystereses which are accompanied by sudden jumps in magnetic moments at low temperature. Unlike conventional bulk magnets, hysteresis in SMMs is of molecular origin. This qualifies them as candidates for next generation of high density storage media where a molecule which is at most few nanometers in size can be used to store a bit of information. However, the jumps in these hystereses, due to spin tunneling, can lead to undesired loss of information. Mn12-AC molecule contains twelve magnetic ions antiferromagnetically coupled by exchanges leading to S = 10 ground state manifold. The magnetic ions are surrounded by ligands which isolate them magnetically from neighboring molecules. The lowest state of S = 9 manifold is believed to lie at about 40 K above the ground state. Therefore, at low temperatures, the molecule is considered as a single uncoupled moment of spin S = 10. Such model has been used widely to understand phenomena exhibited by the molecule at low temperatures including the tunneling of its spin, while a little attention has been paid for the multi-spin nature of the molecule. Using the 8-spin model, we demonstrate that in order to understand the phenomena of tunneling, a full spin description of the molecule is required. We utilized a calculation scheme where a fraction of energy levels are used in the calculations and the influence of levels having higher energy is neglected. From the dependence of tunnel splittings on the number of states include, we conclude that models based on restricting the number of energy levels (single-spin and 8-spin models) lead to unreliable results of tunnel splitting calculations. To attack the full 12-spin model, we employed the Davidson algorithm to calculated lowest energy levels produced by exchange interactions and single ion anisotropies. The model reproduces the anisotropy properties at low

  5. Photoelectron Spectroscopy and Density Functional Theory Studies of Iron Sulfur (FeS)m- (m = 2-8) Cluster Anions: Coexisting Multiple Spin States.

    Science.gov (United States)

    Yin, Shi; Bernstein, Elliot R

    2017-10-05

    Iron sulfur cluster anions (FeS) m - (m = 2-8) are studied by photoelectron spectroscopy (PES) at 3.492 eV (355 nm) and 4.661 eV (266 nm) photon energies, and by density functional theory (DFT) calculations. The most probable structures and ground state spin multiplicities for (FeS) m - (m = 2-8) clusters are tentatively assigned through a comparison of their theoretical and experiment first vertical detachment energy (VDE) values. Many spin states lie within 0.5 eV of the ground spin state for the larger (FeS) m - (m ≥ 4) clusters. Theoretical VDEs of these low lying spin states are in good agreement with the experimental VDE values. Therefore, multiple spin states of each of these iron sulfur cluster anions probably coexist under the current experimental conditions. Such available multiple spin states must be considered when evaluating the properties and behavior of these iron sulfur clusters in real chemical and biological systems. The experimental first VDEs of (FeS) m - (m = 1-8) clusters are observed to change with the cluster size (number m). The first VDE trends noted can be related to the different properties of the highest singly occupied molecular orbitals (NBO, HSOMOs) of each cluster anion. The changing nature of the NBO/HSOMO of these (FeS) m - (m = 1-8) clusters from a p orbital on S, to a d orbital on Fe, and to an Fe-Fe bonding orbital is probably responsible for the observed increasing trend for their first VDEs with respect to m.

  6. Molecular clusters of 3D and lower magnetic dimensionality

    International Nuclear Information System (INIS)

    Papaefthymiou, G.C

    1991-01-01

    Controlled polymerization of iron leads to the synthesis of molecular clusters of ever-increasing size, tending to extended structures. Polymerization of oxo-bridged octahedrally coordinated iron leads to clusters with 3D magnetic interactions between iron ions, while sulfide- and selenide-bridged tetrahedrally coordinated iron ions produce clusters of lower magnetic dimensionality. In this paper the magnetic properties of the resulting large molecular clusters with N ≥ 17 (where N = the number of iron ions in the cluster) are investigated for the presence of collective magnetic correlations associated with the solid state

  7. Experimental and theoretical investigation of the magnetization dynamics of an artificial square spin ice cluster

    Energy Technology Data Exchange (ETDEWEB)

    Pohlit, Merlin, E-mail: pohlit@physik.uni-frankfurt.de; Porrati, Fabrizio; Huth, Michael; Müller, Jens [Institute of Physics, Goethe-University Frankfurt, Frankfurt/Main (Germany); Stockem, Irina; Schröder, Christian [Bielefeld Institute for Applied Materials Research, FH Bielefeld-University of Applied Sciences, Bielefeld (Germany)

    2016-10-14

    We study the magnetization dynamics of a spin ice cluster which is a building block of an artificial square spin ice fabricated by focused electron-beam-induced deposition both experimentally and theoretically. The spin ice cluster is composed of twelve interacting Co nanoislands grown directly on top of a high-resolution micro-Hall sensor. By employing micromagnetic simulations and a macrospin model, we calculate the magnetization and the experimentally investigated stray field emanating from a single nanoisland. The parameters determined from a comparison with the experimental hysteresis loop are used to derive an effective single-dipole macrospin model that allows us to investigate the dynamics of the spin ice cluster. Our model reproduces the experimentally observed non-deterministic sequences in the magnetization curves as well as the distinct temperature dependence of the hysteresis loop.

  8. A molecular quantum spin network controlled by a single qubit.

    Science.gov (United States)

    Schlipf, Lukas; Oeckinghaus, Thomas; Xu, Kebiao; Dasari, Durga Bhaktavatsala Rao; Zappe, Andrea; de Oliveira, Felipe Fávaro; Kern, Bastian; Azarkh, Mykhailo; Drescher, Malte; Ternes, Markus; Kern, Klaus; Wrachtrup, Jörg; Finkler, Amit

    2017-08-01

    Scalable quantum technologies require an unprecedented combination of precision and complexity for designing stable structures of well-controllable quantum systems on the nanoscale. It is a challenging task to find a suitable elementary building block, of which a quantum network can be comprised in a scalable way. We present the working principle of such a basic unit, engineered using molecular chemistry, whose collective control and readout are executed using a nitrogen vacancy (NV) center in diamond. The basic unit we investigate is a synthetic polyproline with electron spins localized on attached molecular side groups separated by a few nanometers. We demonstrate the collective readout and coherent manipulation of very few (≤ 6) of these S = 1/2 electronic spin systems and access their direct dipolar coupling tensor. Our results show that it is feasible to use spin-labeled peptides as a resource for a molecular qubit-based network, while at the same time providing simple optical readout of single quantum states through NV magnetometry. This work lays the foundation for building arbitrary quantum networks using well-established chemistry methods, which has many applications ranging from mapping distances in single molecules to quantum information processing.

  9. 2012 Gordon Research Conference On Molecular And Ionic Clusters

    International Nuclear Information System (INIS)

    McCoy, Anne

    2012-01-01

    The Gordon Research Conference on 'Molecular and Ionic Clusters' focuses on clusters, which are the initial molecular species found in gases when condensation begins to occur. Condensation can take place solely from molecules interacting with each other, mostly at low temperatures, or when molecules condense around charged particles (electrons, protons, metal cations, molecular ions), producing ion molecule clusters. These clusters provide models for solvation, allow a pristine look at geometric as well as electronic structures of molecular complexes or matter in general, their interaction with radiation, their reactivity, their thermodynamic properties and, in particular, the related dynamics. This conference focuses on new ways to make clusters composed of different kinds of molecules, new experimental techniques to investigate the properties of the clusters and new theoretical methods with which to calculate the structures, dynamical motions and energetics of the clusters. Some of the main experimental methods employed include molecular beams, mass spectrometry, laser spectroscopy (from infrared to XUV; in the frequency as well as the time domain) and photoelectron spectroscopy. Techniques include laser absorption spectroscopy, laser induced fluorescence, resonance enhanced photoionization, mass-selected photodissociation, photofragment imaging, ZEKE photoelectron spectroscopy, etc. From the theoretical side, this conference highlights work on potential surfaces and measurable properties of the clusters. The close ties between experiment, theory and computation have been a hallmark of the Gordon Research Conference on Molecular and Ionic Clusters. In the 2012 meeting, we plan to have sessions that will focus on topics including: (1) The use of cluster studies to probe fundamental phenomena; (2) Finite size effects on structure and thermodynamics; (3) Intermolecular forces and cooperative effects; (4) Molecular clusters as models for solvation; and (5) Studies of

  10. Single reference Coupled Cluster treatment of nearly degenerate problems: Cohesive energy of antiferromagnetic lattices of spin 1 centers

    International Nuclear Information System (INIS)

    Malrieu, Jean-Paul

    2012-01-01

    Lattices of antiferromagnetically coupled spins, ruled by Heisenberg Hamiltonians, are intrinsically highly degenerate systems. The present work tries to estimate the ground state energy of regular bipartite spin lattices of S = 1 sites from a single reference Coupled Cluster expansion starting from a Néel function, taken as reference. The simultaneous changes of spin momentum on adjacent sites play the role of the double excitations in molecular electronic problems. Propagation of the spin changes plays the same role as the triple excitations. The treatment takes care of the deviation of multiple excitation energies from additivity. Specific difficulties appear for 1D chains, which are not due to a near degeneracy between the reference and the vectors which directly interact with it but to the complexity of the processes which lead to the low energy configurations where a consistent reversed-Néel domain is created inside the Néel starting spin wave. Despite these difficulties a reasonable value of the cohesive energy is obtained.

  11. Single reference Coupled Cluster treatment of nearly degenerate problems: Cohesive energy of antiferromagnetic lattices of spin 1 centers

    Science.gov (United States)

    Malrieu, Jean-Paul

    2012-06-01

    Lattices of antiferromagnetically coupled spins, ruled by Heisenberg Hamiltonians, are intrinsically highly degenerate systems. The present work tries to estimate the ground state energy of regular bipartite spin lattices of S = 1 sites from a single reference Coupled Cluster expansion starting from a Néel function, taken as reference. The simultaneous changes of spin momentum on adjacent sites play the role of the double excitations in molecular electronic problems. Propagation of the spin changes plays the same role as the triple excitations. The treatment takes care of the deviation of multiple excitation energies from additivity. Specific difficulties appear for 1D chains, which are not due to a near degeneracy between the reference and the vectors which directly interact with it but to the complexity of the processes which lead to the low energy configurations where a consistent reversed-Néel domain is created inside the Néel starting spin wave. Despite these difficulties a reasonable value of the cohesive energy is obtained.

  12. Evolution of ferromagnetic interactions from cluster spin glass state in Co–Ga alloy

    Energy Technology Data Exchange (ETDEWEB)

    Mohammad Yasin, Sk. [Department of Physics, Indian Institute of Technology Madras, Chennai 600036 (India); Saha, Ritwik [Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Mumbai 400005 (India); Srinivas, V., E-mail: veeturi@iitm.ac.in [Department of Physics, Indian Institute of Technology Madras, Chennai 600036 (India); Kasiviswanathan, S. [Department of Physics, Indian Institute of Technology Madras, Chennai 600036 (India); Nigam, A.K. [Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Mumbai 400005 (India)

    2016-11-15

    Low temperature magnetic properties of binary Co{sub x}Ga{sub 100−x} (x=54–57) alloy have been investigated. Analysis of frequency dependence of ac susceptibility provided a conclusive evidence for the existence of cluster spin glass like behavior with the freezing temperature ~8, 14 K for x=54, 55.5 respectively. The parameters for conventional ‘slowing down’ of the spin dynamics have been extracted from the acs data, which confirm the presence of glassy phase. The magnitude of Mydosh parameter obtained from the fits is larger than that reported for typical canonical spin glasses and smaller than those for non-interacting ideal superparamagnetic systems but comparable to those of known cluster-glass systems. Memory phenomena using specific cooling protocols also support the spin-glass features in Co{sub 55.5}Ga{sub 44.5} composition. Further the development of ferromagnetic clusters from the cluster spin glass state has been observed in x=57 composition. - Highlights: • Temperature dependence of DC and AC susceptibility (acs) analysis has been carried out on Co{sub x}Ga{sub 1−x,} (x=54–57). • M–H data above transition suggests presence of spin clusters. • A detailed analysis of acs data suggests a cluster glass behavior as oppose to SPM state for x=54 and 55.5. • Memory phenomena using specific cooling protocols also support the spin-glass features in Co{sub 55.5}Ga{sub 44.5} composition. • Development of ferromagnetic like behavior for x≥57 has been suggested from DC and AC magnetization data.

  13. EPR spin probe and spin label studies of some low molecular and polymer micelles

    Science.gov (United States)

    Wasserman, A. M.; Kasaikin, V. A.; Timofeev, V. P.

    1998-12-01

    The rotational mobility of spin probes of different shape and size in low molecular and polymer micelles has been studied. Several probes having nitroxide fragment localized either in the vicinity of micelle interface or in the hydrocarbon core have been used. Upon increasing the number of carbon atoms in hydrocarbon chain of detergent from 7 to 13 (sodium alkyl sulfate micelles) or from 12 to 16 (alkyltrimethylammonium bromide micelles) the rotational mobility of spin probes is decreased by the factor 1.5-2.0. The spin probe rotational mobility in polymer micelles (the complexes of alkyltrimethylammonium bromides and polymethacrylic or polyacrylic acids) is less than mobility in free micelles of the same surfactants. The study of EPR-spectra of spin labeled polymethacrylic acid (PMA) indicated that formation of water soluble complexes of polymer and alkyltrimethylammonium bromides in alkaline solutions (pH 9) does not affect the polymer segmental mobility. On the other hand, the polymer complexes formation in slightly acidic water solution (pH 6) breaks down the compact PMA conformation, thus increasing the polymer segmental mobility. Possible structures of polymer micelles are discussed.

  14. Spin polarized tunnelling investigation of nanometre Co clusters by means of a Ni bulk tip

    International Nuclear Information System (INIS)

    Rastei, M V; Bucher, J P

    2006-01-01

    A massive Ni tip is used in spin polarized scanning tunnelling microscopy (SP STM) to explore the magnetization state of nanometre Co clusters, self-organized on the Au(111) surface. Constant current STM images taken at 4.6 K show a bimodal distribution of the cluster heights, accounting for the spin polarization of the STM junction. The spin polarization of the tunnel junction as a function of the bias voltage is found to depend on the local density of states of the sample examined. Changing the vacuum barrier parameters by bringing the tip closer to the surface leads to a reduction in the tunnelling magnetoresistance that may be attributed to spin flip effects. (letter to the editor)

  15. Molecular dynamics simulations of cluster fission and fusion processes

    DEFF Research Database (Denmark)

    Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia

    2004-01-01

    Results of molecular dynamics simulations of fission reactions Na_10^2+ --> Na_7^+ +Na_3^+ and Na_18^2+ --> 2Na_9^+ are presented. The dependence of the fission barriers on the isomer structure of the parent cluster is analyzed. It is demonstrated that the energy necessary for removing homothetic...... separation of the daughter fragments begins and/or forming a "neck" between the separating fragments. A novel algorithm for modeling the cluster growth process is described. This approach is based on dynamic search for the most stable cluster isomers and allows one to find the optimized cluster geometries...... groups of atoms from the parent cluster is largely independent of the isomer form of the parent cluster. The importance of rearrangement of the cluster structure during the fission process is elucidated. This rearrangement may include transition to another isomer state of the parent cluster before actual...

  16. A numerical study of spin-dependent organization of alkali-metal atomic clusters using density-functional method

    International Nuclear Information System (INIS)

    Liu Xuan; Ito, Haruhiko; Torikai, Eiko

    2012-01-01

    We calculate the different geometric isomers of spin clusters composed of a small number of alkali-metal atoms using the UB3LYP density-functional method. The electron density distribution of clusters changes according to the value of total spin. Steric structures as well as planar structures arise when the number of atoms increases. The lowest spin state is the most stable and Li n , Na n , K n , Rb n , and Cs n with n = 2–8 can be formed in higher spin states. In the highest spin state, the preparation of clusters depends on the kind and the number of constituent atoms. The interaction energy between alkali-metal atoms and rare-gas atoms is smaller than the binding energy of spin clusters. Consequently, it is possible to self-organize the alkali-metal-atom clusters on a non-wetting substrate coated with rare-gas atoms.

  17. Spin magnetic moments from single atoms to small Cr clusters

    Energy Technology Data Exchange (ETDEWEB)

    Boeglin, C.; Decker, R.; Bulou, H.; Scheurer, F.; Chado, I. [IPCMS-GSI - UMR 7504, 67037 Strasbourg Cedex (France); Ohresser, P. [LURE, 91405 Orsay (France); Dhesi, S.S. [ESRF, BP 220, 38043 Grenoble Cedex (France); Present permanent address: Diamond Light Source, Chilton, Didcot OX11 0QX (United Kingdom); Gaudry, E. [LMCP, 4, place Jussieu, 75252 Paris (France); Lazarovits, B. [CCMS, T.U. Vienna, Gumpendorfstr. 1a, 1060 Wien (Austria)

    2005-07-01

    Morphology studies at the first stages of the growth of Cr/Au(111) are reported and compared to the magnetic properties of the nanostructures. We analyze by Scanning Tunneling Microscopy and Low Energy Electron Diffraction the Cr clusters growth between 200 K and 300 K. In the early stages of the growth the morphology of the clusters shows monoatomic high islands located at the kinks of the herringbone reconstructed Au(111) surface. By X-ray Magnetic Circular Dichroism performed on the Cr L{sub 2,3} edges it is shown that the temperature dependent morphology strongly influences the magnetic properties of the Cr clusters. We show that in the sub-monolayer regime Cr clusters are antiferromagnetic and paramagnetic when the size reaches the atomic limit. (copyright 2005 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  18. Molecular transport network security using multi-wavelength optical spins.

    Science.gov (United States)

    Tunsiri, Surachai; Thammawongsa, Nopparat; Mitatha, Somsak; Yupapin, Preecha P

    2016-01-01

    Multi-wavelength generation system using an optical spin within the modified add-drop optical filter known as a PANDA ring resonator for molecular transport network security is proposed. By using the dark-bright soliton pair control, the optical capsules can be constructed and applied to securely transport the trapped molecules within the network. The advantage is that the dark and bright soliton pair (components) can securely propagate for long distance without electromagnetic interference. In operation, the optical intensity from PANDA ring resonator is fed into gold nano-antenna, where the surface plasmon oscillation between soliton pair and metallic waveguide is established.

  19. Electrically Tunable g Factors in Quantum Dot Molecular Spin States

    Science.gov (United States)

    Doty, M. F.; Scheibner, M.; Ponomarev, I. V.; Stinaff, E. A.; Bracker, A. S.; Korenev, V. L.; Reinecke, T. L.; Gammon, D.

    2006-11-01

    We present a magnetophotoluminescence study of individual vertically stacked InAs/GaAs quantum dot pairs separated by thin tunnel barriers. As an applied electric field tunes the relative energies of the two dots, we observe a strong resonant increase or decrease in the g factors of different spin states that have molecular wave functions distributed over both quantum dots. We propose a phenomenological model for the change in g factor based on resonant changes in the amplitude of the wave function in the barrier due to the formation of bonding and antibonding orbitals.

  20. Phase separation, clustering, and fractal characteristics in glass: A magic-angle-spinning NMR spin-lattice relaxation study

    Science.gov (United States)

    Sen, S.; Stebbins, J. F.

    1994-07-01

    A comparative study of the 29Si spin-lattice relaxation behavior (induced by trace amounts of paramagnetic dopants in the glass) in phase-separated Li2Si4O9 and monophasic Li2Si2O5 and Na2Si2O5 glasses has been made in order to understand the nature of clustering and the resulting intermediate-range ordering. Optically clear tetrasilicate and disilicate glasses were prepared with 500 to 2000 ppm of Gd2O3, a paramagnetic dopant. The constituent structural units (Q3 and Q4 species) in all tetrasilicate glasses show strong differential relaxation following a power-law behavior. This is due to preferential partitioning of Gd3+ into the lower silica (Q3-rich) regions of these glasses, indicating the presence of Q species clusters too small to produce optical opalescence (a few nm to perhaps tens of nm). Preliminary results on 6Li spin-lattice relaxation in these glasses support this hypothesis. Differential relaxation becomes more pronounced on annealing due to growth of such clusters. No such differential relaxation was observed in the monophase disilicate glasses. For spin-lattice relaxation induced by direct dipolar coupling to paramagnetic ions, the recovery of magnetization is proportional to time as M(t)~tα where α is a function of the dimensionality D of mass distribution of the constituent Q species around the Gd3+ paramagnetic centers in the glass. For tetrasilicate glasses D~=2.62+/-0.22 and the system behaves as a mass fractal up to a length scale of 2 to 3 nm. D is thus equal to, within error, the theoretical value of 2.6 for an infinite percolation cluster of one type of Q species in another. For disilicate glasses, D~=3.06+/-0.18 which indicates a three-dimensional (and thus nonfractal) mass distribution of the constituent Q species over the same length scale.

  1. Tuning spin transport properties and molecular magnetoresistance through contact geometry

    Science.gov (United States)

    Ulman, Kanchan; Narasimhan, Shobhana; Delin, Anna

    2014-01-01

    Molecular spintronics seeks to unite the advantages of using organic molecules as nanoelectronic components, with the benefits of using spin as an additional degree of freedom. For technological applications, an important quantity is the molecular magnetoresistance. In this work, we show that this parameter is very sensitive to the contact geometry. To demonstrate this, we perform ab initio calculations, combining the non-equilibrium Green's function method with density functional theory, on a dithienylethene molecule placed between spin-polarized nickel leads of varying geometries. We find that, in general, the magnetoresistance is significantly higher when the contact is made to sharp tips than to flat surfaces. Interestingly, this holds true for both resonant and tunneling conduction regimes, i.e., when the molecule is in its "closed" and "open" conformations, respectively. We find that changing the lead geometry can increase the magnetoresistance by up to a factor of ˜5. We also introduce a simple model that, despite requiring minimal computational time, can recapture our ab initio results for the behavior of magnetoresistance as a function of bias voltage. This model requires as its input only the density of states on the anchoring atoms, at zero bias voltage. We also find that the non-resonant conductance in the open conformation of the molecule is significantly impacted by the lead geometry. As a result, the ratio of the current in the closed and open conformations can also be tuned by varying the geometry of the leads, and increased by ˜400%.

  2. Tuning spin transport properties and molecular magnetoresistance through contact geometry

    International Nuclear Information System (INIS)

    Ulman, Kanchan; Narasimhan, Shobhana; Delin, Anna

    2014-01-01

    Molecular spintronics seeks to unite the advantages of using organic molecules as nanoelectronic components, with the benefits of using spin as an additional degree of freedom. For technological applications, an important quantity is the molecular magnetoresistance. In this work, we show that this parameter is very sensitive to the contact geometry. To demonstrate this, we perform ab initio calculations, combining the non-equilibrium Green's function method with density functional theory, on a dithienylethene molecule placed between spin-polarized nickel leads of varying geometries. We find that, in general, the magnetoresistance is significantly higher when the contact is made to sharp tips than to flat surfaces. Interestingly, this holds true for both resonant and tunneling conduction regimes, i.e., when the molecule is in its “closed” and “open” conformations, respectively. We find that changing the lead geometry can increase the magnetoresistance by up to a factor of ∼5. We also introduce a simple model that, despite requiring minimal computational time, can recapture our ab initio results for the behavior of magnetoresistance as a function of bias voltage. This model requires as its input only the density of states on the anchoring atoms, at zero bias voltage. We also find that the non-resonant conductance in the open conformation of the molecule is significantly impacted by the lead geometry. As a result, the ratio of the current in the closed and open conformations can also be tuned by varying the geometry of the leads, and increased by ∼400%

  3. Tuning spin transport properties and molecular magnetoresistance through contact geometry.

    Science.gov (United States)

    Ulman, Kanchan; Narasimhan, Shobhana; Delin, Anna

    2014-01-28

    Molecular spintronics seeks to unite the advantages of using organic molecules as nanoelectronic components, with the benefits of using spin as an additional degree of freedom. For technological applications, an important quantity is the molecular magnetoresistance. In this work, we show that this parameter is very sensitive to the contact geometry. To demonstrate this, we perform ab initio calculations, combining the non-equilibrium Green's function method with density functional theory, on a dithienylethene molecule placed between spin-polarized nickel leads of varying geometries. We find that, in general, the magnetoresistance is significantly higher when the contact is made to sharp tips than to flat surfaces. Interestingly, this holds true for both resonant and tunneling conduction regimes, i.e., when the molecule is in its "closed" and "open" conformations, respectively. We find that changing the lead geometry can increase the magnetoresistance by up to a factor of ∼5. We also introduce a simple model that, despite requiring minimal computational time, can recapture our ab initio results for the behavior of magnetoresistance as a function of bias voltage. This model requires as its input only the density of states on the anchoring atoms, at zero bias voltage. We also find that the non-resonant conductance in the open conformation of the molecule is significantly impacted by the lead geometry. As a result, the ratio of the current in the closed and open conformations can also be tuned by varying the geometry of the leads, and increased by ∼400%.

  4. Spin flipping in ring-coupled-cluster-doubles theory

    DEFF Research Database (Denmark)

    Klopper, Wim; M. Teale, Andrew; Coriani, Sonia

    2011-01-01

    We report a critical analysis and comparison of a variety of random-phase-approximation (RPA) based approaches to determine the electronic ground-state energy. Interrelations between RPA variants are examined by numerical examples with particular attention paid to the role of spin......-flipped excitations and the behaviour of the adiabatic-connection integrands where appropriate. In general, it is found that RPA variants that include Hartree–Fock exchange contributions are unsuitable as generally applicable methods for the determination of correlation energies. Of the remaining methods only...... the direct RPA and RPA with second-order screened exchange are recommended for general use....

  5. Pleiades cluster. IV. The visit of a molecular CO cloud

    International Nuclear Information System (INIS)

    Breger, M.

    1987-01-01

    The location, size, and mass of the CO molecular cloud seen in the direction of the Pleiades cluster is determined from a study of the polarization and reddening of cluster members and nonmembers. Arguments are presented against both a foreground and background location of the molecular cloud, so that the cloud should be presently situated inside the cluster. Stellar reddening determinations with the appropriate value of R = 3.3 for the region, as well as star counts, lead to a determination of a total extinction of A(V) in the range of 1.0-1.6 mag for the central region of the CO cloud. The extinction determinations for cluster members and background stars indicate a mass of 20 solar masses for the CO cloud visiting the Pleiades cluster. 20 references

  6. Radiative width of molecular-cluster states

    International Nuclear Information System (INIS)

    Alhassid, Y.; Gai, M.; Bertsch, G.F.

    1982-01-01

    Molecular states are characterized by enhanced electromagnetic deexcitations of many different multipolarities. The expected enhancement of E1, E2, and E3 transitions is examined by deriving molecular sum rules for radiative deexcitation widths and via a dimensionality approach. The enhancement of the E1 transitions is the most striking

  7. A Kondo cluster-glass model for spin glass Cerium alloys

    International Nuclear Information System (INIS)

    Zimmer, F M; Magalhaes, S G; Coqblin, B

    2011-01-01

    There are clear indications that the presence of disorder in Ce alloys, such as Ce(Ni,Cu) or Ce(Pd,Rh), is responsible for the existence of a cluster spin glass state which changes continuously into inhomogeneous ferromagnetism at low temperatures. We present a study of the competition between magnetism and Kondo effect in a cluster-glass model composed by a random inter-cluster interaction term and an intra-cluster one, which contains an intra-site Kondo interaction J k and an inter-site ferromagnetic one J 0 . The random interaction is given by the van Hemmen type of randomness which allows to solve the problem without the use of the replica method. The inter-cluster term is solved within the cluster mean-field theory and the remaining intra-cluster interactions can be treated by exact diagonalization. Results show the behavior of the cluster glass order parameter and the Kondo correlation function for several sizes of the clusters, J k , J 0 and values of the ferromagnetic inter-cluster average interaction I 0 . Particularly, for small J k , the magnetic solution is strongly dependent on I 0 and J 0 and a Kondo cluster-glass or a mixed phase can be obtained, while, for large J k , the Kondo effect is still dominant, both in good agreement with experiment in Ce(Ni,Cu) or Ce(Pd,Rh) alloys.

  8. Quantum model of a solid-state spin qubit: Ni cluster on a silicon surface by the generalized spin Hamiltonian and X-ray absorption spectroscopy investigations

    Science.gov (United States)

    Farberovich, Oleg V.; Mazalova, Victoria L.; Soldatov, Alexander V.

    2015-11-01

    We present here the quantum model of a Ni solid-state electron spin qubit on a silicon surface with the use of a density-functional scheme for the calculation of the exchange integrals in the non-collinear spin configurations in the generalized spin Hamiltonian (GSH) with the anisotropic exchange coupling parameters linking the nickel ions with a silicon substrate. In this model the interaction of a spin qubit with substrate is considered in GSH at the calculation of exchange integrals Jij of the nanosystem Ni7-Si in the one-electron approach taking into account chemical bonds of all Si-atoms of a substrate (environment) with atoms of the Ni7-cluster. The energy pattern was found from the effective GSH Hamiltonian acting in the restricted spin space of the Ni ions by the application of the irreducible tensor operators (ITO) technique. In this paper we offer the model of the quantum solid-state N-spin qubit based on the studying of the spin structure and the spin-dynamics simulations of the 3d-metal Ni clusters on the silicon surface. The solution of the problem of the entanglement between spin states in the N-spin systems is becoming more interesting when considering clusters or molecules with a spectral gap in their density of states. For quantifying the distribution of the entanglement between the individual spin eigenvalues (modes) in the spin structure of the N-spin system we use the density of entanglement (DOE). In this study we have developed and used the advanced high-precision numerical techniques to accurately assess the details of the decoherence process governing the dynamics of the N-spin qubits interacting with a silicon surface. We have studied the Rabi oscillations to evaluate the N-spin qubits system as a function of the time and the magnetic field. We have observed the stabilized Rabi oscillations and have stabilized the quantum dynamical qubit state and Rabi driving after a fixed time (0.327 μs). The comparison of the energy pattern with the

  9. Development of New Open-Shell Perturbation and Coupled-Cluster Theories Based on Symmetric Spin Orbitals

    Science.gov (United States)

    Lee, Timothy J.; Arnold, James O. (Technical Monitor)

    1994-01-01

    A new spin orbital basis is employed in the development of efficient open-shell coupled-cluster and perturbation theories that are based on a restricted Hartree-Fock (RHF) reference function. The spin orbital basis differs from the standard one in the spin functions that are associated with the singly occupied spatial orbital. The occupied orbital (in the spin orbital basis) is assigned the delta(+) = 1/square root of 2(alpha+Beta) spin function while the unoccupied orbital is assigned the delta(-) = 1/square root of 2(alpha-Beta) spin function. The doubly occupied and unoccupied orbitals (in the reference function) are assigned the standard alpha and Beta spin functions. The coupled-cluster and perturbation theory wave functions based on this set of "symmetric spin orbitals" exhibit much more symmetry than those based on the standard spin orbital basis. This, together with interacting space arguments, leads to a dramatic reduction in the computational cost for both coupled-cluster and perturbation theory. Additionally, perturbation theory based on "symmetric spin orbitals" obeys Brillouin's theorem provided that spin and spatial excitations are both considered. Other properties of the coupled-cluster and perturbation theory wave functions and models will be discussed.

  10. Validating clustering of molecular dynamics simulations using polymer models

    Directory of Open Access Journals (Sweden)

    Phillips Joshua L

    2011-11-01

    Full Text Available Abstract Background Molecular dynamics (MD simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our

  11. Luminescent properties of fluorophosphate glasses with lead chalcogenides molecular clusters

    International Nuclear Information System (INIS)

    Kolobkova, E.V.; Kukushkin, D.S.; Nikonorov, N.V.; Shakhverdov, T.A.; Sidorov, A.I.; Vasiliev, V.N.

    2015-01-01

    Fluorophosphate glasses containing lead, selenium, and sulfur exhibit an intense luminescence in the 400–620 nm spectral region when excited by the 240–420 nm radiation. This luminescence is due to the presence of (PbSe) n and/or (PbS) n molecular clusters in the glasses, which appear in the as-prepared glasses before quantum dots formation. The thermal treatment at temperatures less than the glass transition temperature results in the red-shift of the luminescence bands and in an increase in the luminescence intensity. Heating the thermally treated glass samples leads to the reversible thermal quenching of the luminescence. - Highlights: • Fluorophosphate glasses with Pb, Se, and S ions contain (PbSe) n or (PbS) n molecular clusters. • (PbSe) n and (PbS) n molecular clusters possess luminescence in the visible with UV excitation. • Heating the glass leads to the reversible thermal quenching of the luminescence

  12. Molecular Polarizability of Sc and C (Fullerene and Graphite Clusters

    Directory of Open Access Journals (Sweden)

    Francisco Torrens

    2001-05-01

    Full Text Available A method (POLAR for the calculation of the molecular polarizability is presented. It uses the interacting induced dipoles polarization model. As an example, the method is applied to Scn and Cn (fullerene and one-shell graphite model clusters. On varying the number of atoms, the clusters show numbers indicative of particularly polarizable structures. The are compared with reference calculations (PAPID. In general, the Scn calculated (POLAR and Cn computed (POLAR and PAPID are less polarizable than what is inferred from the bulk. However, the Scn calculated (PAPID are more polarizable than what is inferred. Moreover, previous theoretical work yielded the same trend for Sin, Gen and GanAsm small clusters. The high polarizability of the Scn clusters (PAPID is attributed to arise from dangling bonds at the surface of the cluster.

  13. Post-Newtonian Dynamics in Dense Star Clusters: Highly Eccentric, Highly Spinning, and Repeated Binary Black Hole Mergers.

    Science.gov (United States)

    Rodriguez, Carl L; Amaro-Seoane, Pau; Chatterjee, Sourav; Rasio, Frederic A

    2018-04-13

    We present models of realistic globular clusters with post-Newtonian dynamics for black holes. By modeling the relativistic accelerations and gravitational-wave emission in isolated binaries and during three- and four-body encounters, we find that nearly half of all binary black hole mergers occur inside the cluster, with about 10% of those mergers entering the LIGO/Virgo band with eccentricities greater than 0.1. In-cluster mergers lead to the birth of a second generation of black holes with larger masses and high spins, which, depending on the black hole natal spins, can sometimes be retained in the cluster and merge again. As a result, globular clusters can produce merging binaries with detectable spins regardless of the birth spins of black holes formed from massive stars. These second-generation black holes would also populate any upper mass gap created by pair-instability supernovae.

  14. Post-Newtonian Dynamics in Dense Star Clusters: Highly Eccentric, Highly Spinning, and Repeated Binary Black Hole Mergers

    Science.gov (United States)

    Rodriguez, Carl L.; Amaro-Seoane, Pau; Chatterjee, Sourav; Rasio, Frederic A.

    2018-04-01

    We present models of realistic globular clusters with post-Newtonian dynamics for black holes. By modeling the relativistic accelerations and gravitational-wave emission in isolated binaries and during three- and four-body encounters, we find that nearly half of all binary black hole mergers occur inside the cluster, with about 10% of those mergers entering the LIGO/Virgo band with eccentricities greater than 0.1. In-cluster mergers lead to the birth of a second generation of black holes with larger masses and high spins, which, depending on the black hole natal spins, can sometimes be retained in the cluster and merge again. As a result, globular clusters can produce merging binaries with detectable spins regardless of the birth spins of black holes formed from massive stars. These second-generation black holes would also populate any upper mass gap created by pair-instability supernovae.

  15. The effect of electrodes on 11 acene molecular spin valve: Semi-empirical study

    Science.gov (United States)

    Aadhityan, A.; Preferencial Kala, C.; John Thiruvadigal, D.

    2017-10-01

    A new revolution in electronics is molecular spintronics, with the contemporary evolution of the two novel disciplines of spintronics and molecular electronics. The key point is the creation of molecular spin valve which consists of a diamagnetic molecule in between two magnetic leads. In this paper, non-equilibrium Green's function (NEGF) combined with Extended Huckel Theory (EHT); a semi-empirical approach is used to analyse the electron transport characteristics of 11 acene molecular spin valve. We examine the spin-dependence transport on 11 acene molecular junction with various semi-infinite electrodes as Iron, Cobalt and Nickel. To analyse the spin-dependence transport properties the left and right electrodes are joined to the central region in parallel and anti-parallel configurations. We computed spin polarised device density of states, projected device density of states of carbon and the electrode element, and transmission of these devices. The results demonstrate that the effect of electrodes modifying the spin-dependence behaviours of these systems in a controlled way. In Parallel and anti-parallel configuration the separation of spin up and spin down is lager in the case of iron electrode than nickel and cobalt electrodes. It shows that iron is the best electrode for 11 acene spin valve device. Our theoretical results are reasonably impressive and trigger our motivation for comprehending the transport properties of these molecular-sized contacts.

  16. Thermodynamics of small clusters of atoms: A molecular dynamics simulation

    DEFF Research Database (Denmark)

    Damgaard Kristensen, W.; Jensen, E. J.; Cotterill, Rodney M J

    1974-01-01

    The thermodynamic properties of clusters containing 55, 135, and 429 atoms have been calculated using the molecular dynamics method. Structural and vibrational properties of the clusters were examined at different temperatures in both the solid and the liquid phase. The nature of the melting...... transition was investigated, and a number of properties, such as melting temperature, latent heat of melting, and premelting phenomena, were found to vary with cluster size. These properties were also found to depend on the structure of the solid phase. In this phase the configuration of lowest free energy...

  17. Percolation approach for atomic and molecular cluster formation

    International Nuclear Information System (INIS)

    Knospe, O.; Seifert, G.

    1987-12-01

    We apply a percolation approach for the theoretical analysis of mass spectra of molecular microclusters obtained by adiabatic expansion technique. The evolution of the shape of the experimental size distributions as function of stagnation pressure and stagnation temperature are theoretically reproduced by varying the percolation parameter. Remaining discrepancies between theory and experiment are discussed. In addition, the even-odd alternation as well as the 'magic' shell structure within metallic, secondary ion mass spectra are investigated by introducing statistical weights for the cluster formation probabilities. Shell correction energies of atomic clusters as function of cluster-size are deduced from the experimental data. (orig.)

  18. Hydration dynamics in water clusters via quantum molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Turi, László, E-mail: turi@chem.elte.hu [Department of Physical Chemistry, Eötvös Loránd University, Budapest 112, P. O. Box 32, H-1518 (Hungary)

    2014-05-28

    We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of

  19. Magnetic cluster mean-field description of spin glasses in amorphous La-Gd-Au alloys

    International Nuclear Information System (INIS)

    Poon, S.J.; Durand, J.

    1978-03-01

    Bulk magnetic properties of splat-cooled amorphous alloys of composition La/sub 80-x/Gd/sub x/Au 20 (0 less than or equal to x less than or equal to 80) were studied. Zero-field susceptibility, high-field magnetization (up to 75 kOe) and saturated remanence were measured between 1.8 and 290 0 K. Data were analyzed using a cluster mean-field approximation for the spin-glass and mictomagnetic alloys (x less than or equal to 56). Mean-field theories can account for the experimental freezing-temperatures of dilute spin-glasses in which the Ruderman-Kittel-Kasuya-Yosida interaction is dominant. For the dilute alloys, the role of amorphousness on the magnetic interactions is discussed. By extending the mean-field approximation, the concentrated spin-glasses are represented by rigid ferromagnetic clusters as individual spin-entities interacting via random forces. Scaling laws for the magnetization M and saturation remanent magnetization M/sub rs/ are obtained and presented graphically for the x less than or equal to 32 alloys in which M/x = g(H/x*, T/x), M/sub rs/(T)/x = M/sub rs/(0)/x/ exp (-α*T/x/sup p/) where x* is the concentration of clusters, α* is a constant, and p is the freezing-temperature exponent given by T/sub M/ infinity x/sup p/. It is found that p = 1 and 1.3 for the regions 4 less than or equal to x less than or equal to 40 respectively. An attempt is also made to account for the freezing temperatures of concentrated spin glasses. The strength of the interaction among clusters is determined from high-field magnetization measurements using the Larkin-Smith method modified for clusters. It is shown that for the x < 24 alloys, the size of the clusters can be correlated to the structural short-range order in the amorphous state. More concentrated alloys are marked by the emergence of cluster percolation

  20. Coulomb explosion of large penetrating molecular clusters

    International Nuclear Information System (INIS)

    Wegner, H.E.; Thieberger, P.

    1981-01-01

    The main purpose of these Coulomb explosion measurements is to determine what kind of structure these and other complex molecules may have and also to determine what other special phenomena may come into play as these complex molecules pass through matter. Although the first preliminary measurements involving the Coulomb explosion of these molecules was reported at this workshop last year, the results are briefly summarized before going on to the more recent measurements obtained with a completely new kind of detector system. This new image intensifier detector system, coupled with a microcomputer, has proven to be a valuable tool in the study of the Coulomb explosion of complex molecules that penetrate matter. In the future, with some additional improvements in the system, and much better statistics for most of the molecules studied to date, it is expected that much new information will be gained about the structure of many kinds of complex molecular ions including the special effects that may be encountered when these fast molecular ions penetrate matter

  1. Phase diagram and quench dynamics of the cluster-XY spin chain.

    Science.gov (United States)

    Montes, Sebastián; Hamma, Alioscia

    2012-08-01

    We study the complete phase space and the quench dynamics of an exactly solvable spin chain, the cluster-XY model. In this chain, the cluster term and the XY couplings compete to give a rich phase diagram. The phase diagram is studied by means of the quantum geometric tensor. We study the time evolution of the system after a critical quantum quench using the Loschmidt echo. The structure of the revivals after critical quantum quenches presents a nontrivial behavior depending on the phase of the initial state and the critical point.

  2. Electromagnetic spin–orbit interaction and giant spin-Hall effect in dielectric particle clusters

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yineng [Department of Physics, Beijing Normal University, Beijing 100875 (China); Zhang, Xiangdong, E-mail: zhangxd@bit.edu.cn [School of Physics and Beijing Key Laboratory of Nanophotonics and Ultrafine Optoelectronic Systems, Beijing Institute of Technology, 100081, Beijing (China)

    2013-12-09

    We report a phenomenon that electromagnetic spin–orbit interactions can be tailored by dielectric nanoparticles, and self-similar giant spin-Hall effect has been observed in the dielectric particle cluster. The near-field phase singularities and phase vorticity in the longitudinal component of scattered field can also be controlled by such a dielectric structure. The origin of phenomena is believed to be due to the collective resonance excitation in the dielectric particle cluster. It is expected to find applications in optics information processing and designing new nanophotonic devices.

  3. Tunable Quantum Spin Liquidity in Mo3O13 Cluster Mott Insulators

    Science.gov (United States)

    Akbari-Sharbaf, Arash; Ziat, Djamel; Verrier, Aime; Quilliam, Jeffrey A.; Sinclair, Ryan; Zhou, Haidong D.; Sun, Xuefeng F.

    A study of a tunable quantum spin liquid (QSL) phase in the compound Li2In1- x ScxMo3O8 (x = 0.2, 0.4, 0.6, 0.8, 1) will be presented. Crystal structure of these compounds can be viewed as Mo ions arranged on an asymmetric Kagome lattice (KL), with two different Mo-Mo bond lengths, separated by nonmagnetic layers composed of Li, In, and Sc ions. Using X-ray diffraction spectroscopy, muon spin relaxation spectroscopy, bulk magnetic susceptibility and specific heat measurements we show that by changing the composition of the nonmagnetic layers we can drive the system from an ordered antiferromagnetic state to a quantum spin liquid state. The mechanism responsible for the tunability of the magnetic phase in this class of materials may be associated with the degree of asymmetry of the KL controlled by the composition of the nonmagnetic layers. For high degree of asymmetry the constraint on the electronic distribution leads to a configuration of Mo3O8 clusters with net spin-1/2 per cluster arrange on a triangular lattice and long range antiferromagnetic order. For low degree of asymmetry the electronic distribution leads to a magnetic phase with QSL character. We acknowledge support from NSERC and CFREF.

  4. Metal cluster fission: jellium model and Molecular dynamics simulations

    DEFF Research Database (Denmark)

    Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia

    2004-01-01

    Fission of doubly charged sodium clusters is studied using the open-shell two-center deformed jellium model approximation and it ab initio molecular dynamic approach accounting for all electrons in the system. Results of calculations of fission reactions Na_10^2+ --> Na_7^+ + Na_3^+ and Na_18...

  5. Spin dynamics in a molecular ferrimagnetic ring, [Mn(hfac)2NITPh]6

    International Nuclear Information System (INIS)

    Itou, T.; Funahashi, S.; Oyamada, A.; Maegawa, S.; Fujita, K.; Amezawa, K.; Yamaguchi, R.

    2007-01-01

    We studied the spin dynamics of a ferrimagnetic ring [Mn(hfac) 2 NITPh] 6 with an S=12 ground state by means of H-NMR1 experiments under several fields. The spin-lattice relaxation rate increases monotonically with increasing temperature. This monotonous behavior is not reproduced by the calculation based on the lifetimes of eigenstates caused by the spin-phonon interaction. The relaxation rate is possibly caused by the dispersion resulting from the interaction between the clusters, which is far smaller than the interaction in the cluster but comparable to the nuclear Zeeman energy

  6. Picosecond multiphoton ionization of atomic and molecular clusters

    International Nuclear Information System (INIS)

    Miller, J.C.; Smith, D.B.

    1990-01-01

    High peak-power picosecond laser pulses have been used for the first time to effect nonresonant or resonant multiphoton ionization (MPI) of clusters generated in a supersonic nozzle expansion. The resulting ions are subsequently detected and characterized by time-of-flight mass spectroscopy. Specifically, we present results involving MPI of clusters of xenon and nitric oxide. Previous MPI studies of many molecular clusters using nanosecond lasers have not been successful in observing the parent ion, presumably due to fast dissociation channels. It is proposed that the present technique is a new and rather general ionization source for cluster studies which is complementary to electron impact but may, in addition, provide unique spectroscopic or dynamical information. 23 refs., 5 figs

  7. Field-induced cluster spin glass and inverse symmetry breaking enhanced by frustration

    Science.gov (United States)

    Schmidt, M.; Zimmer, F. M.; Magalhaes, S. G.

    2018-03-01

    We consider a cluster disordered model to study the interplay between short- and long-range interactions in geometrically frustrated spin systems under an external magnetic field (h). In our approach, the intercluster long-range disorder (J) is analytically treated to get an effective cluster model that is computed exactly. The clusters follow a checkerboard lattice with first-neighbor (J1) and second-neighbor (J2) interactions. We find a reentrant transition from the cluster spin-glass (CSG) state to a paramagnetic (PM) phase as the temperature decreases for a certain range of h. This inverse symmetry breaking (ISB) appears as a consequence of both quenched disorder with frustration and h, that introduce a CSG state with higher entropy than the polarized PM phase. The competitive scenario introduced by antiferromagnetic (AF) short-range interactions increases the CSG state entropy, leading to continuous ISB transitions and enhancing the ISB regions, mainly in the geometrically frustrated case (J1 =J2). Remarkably, when strong AF intracluster couplings are present, field-induced CSG phases can be found. These CSG regions are strongly related to the magnetization plateaus observed in this cluster disordered system. In fact, it is found that each field-induced magnetization jump brings a CSG region. We notice that geometrical frustration, as well as cluster size, play an important role in the magnetization plateaus and, therefore, are also relevant in the field-induced glassy states. Our findings suggest that competing interactions support ISB and field-induced CSG phases in disordered cluster systems under an external magnetic field.

  8. The threshold bootstrap clustering: a new approach to find families or transmission clusters within molecular quasispecies.

    Directory of Open Access Journals (Sweden)

    Mattia C F Prosperi

    2010-10-01

    Full Text Available Phylogenetic methods produce hierarchies of molecular species, inferring knowledge about taxonomy and evolution. However, there is not yet a consensus methodology that provides a crisp partition of taxa, desirable when considering the problem of intra/inter-patient quasispecies classification or infection transmission event identification. We introduce the threshold bootstrap clustering (TBC, a new methodology for partitioning molecular sequences, that does not require a phylogenetic tree estimation.The TBC is an incremental partition algorithm, inspired by the stochastic Chinese restaurant process, and takes advantage of resampling techniques and models of sequence evolution. TBC uses as input a multiple alignment of molecular sequences and its output is a crisp partition of the taxa into an automatically determined number of clusters. By varying initial conditions, the algorithm can produce different partitions. We describe a procedure that selects a prime partition among a set of candidate ones and calculates a measure of cluster reliability. TBC was successfully tested for the identification of type-1 human immunodeficiency and hepatitis C virus subtypes, and compared with previously established methodologies. It was also evaluated in the problem of HIV-1 intra-patient quasispecies clustering, and for transmission cluster identification, using a set of sequences from patients with known transmission event histories.TBC has been shown to be effective for the subtyping of HIV and HCV, and for identifying intra-patient quasispecies. To some extent, the algorithm was able also to infer clusters corresponding to events of infection transmission. The computational complexity of TBC is quadratic in the number of taxa, lower than other established methods; in addition, TBC has been enhanced with a measure of cluster reliability. The TBC can be useful to characterise molecular quasipecies in a broad context.

  9. The threshold bootstrap clustering: a new approach to find families or transmission clusters within molecular quasispecies.

    Science.gov (United States)

    Prosperi, Mattia C F; De Luca, Andrea; Di Giambenedetto, Simona; Bracciale, Laura; Fabbiani, Massimiliano; Cauda, Roberto; Salemi, Marco

    2010-10-25

    Phylogenetic methods produce hierarchies of molecular species, inferring knowledge about taxonomy and evolution. However, there is not yet a consensus methodology that provides a crisp partition of taxa, desirable when considering the problem of intra/inter-patient quasispecies classification or infection transmission event identification. We introduce the threshold bootstrap clustering (TBC), a new methodology for partitioning molecular sequences, that does not require a phylogenetic tree estimation. The TBC is an incremental partition algorithm, inspired by the stochastic Chinese restaurant process, and takes advantage of resampling techniques and models of sequence evolution. TBC uses as input a multiple alignment of molecular sequences and its output is a crisp partition of the taxa into an automatically determined number of clusters. By varying initial conditions, the algorithm can produce different partitions. We describe a procedure that selects a prime partition among a set of candidate ones and calculates a measure of cluster reliability. TBC was successfully tested for the identification of type-1 human immunodeficiency and hepatitis C virus subtypes, and compared with previously established methodologies. It was also evaluated in the problem of HIV-1 intra-patient quasispecies clustering, and for transmission cluster identification, using a set of sequences from patients with known transmission event histories. TBC has been shown to be effective for the subtyping of HIV and HCV, and for identifying intra-patient quasispecies. To some extent, the algorithm was able also to infer clusters corresponding to events of infection transmission. The computational complexity of TBC is quadratic in the number of taxa, lower than other established methods; in addition, TBC has been enhanced with a measure of cluster reliability. The TBC can be useful to characterise molecular quasipecies in a broad context.

  10. Quantum model of a solid-state spin qubit: Ni cluster on a silicon surface by the generalized spin Hamiltonian and X-ray absorption spectroscopy investigations

    Energy Technology Data Exchange (ETDEWEB)

    Farberovich, Oleg V. [School of Physics and Astronomy, Beverly and Raymond Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978 (Israel); Research Center for Nanoscale Structure of Matter, Southern Federal University, Zorge 5, 344090 Rostov-on-Don (Russian Federation); Voronezh State University, Voronezh 394000 (Russian Federation); Mazalova, Victoria L., E-mail: mazalova@sfedu.ru [Research Center for Nanoscale Structure of Matter, Southern Federal University, Zorge 5, 344090 Rostov-on-Don (Russian Federation); Soldatov, Alexander V. [Research Center for Nanoscale Structure of Matter, Southern Federal University, Zorge 5, 344090 Rostov-on-Don (Russian Federation)

    2015-11-15

    We present here the quantum model of a Ni solid-state electron spin qubit on a silicon surface with the use of a density-functional scheme for the calculation of the exchange integrals in the non-collinear spin configurations in the generalized spin Hamiltonian (GSH) with the anisotropic exchange coupling parameters linking the nickel ions with a silicon substrate. In this model the interaction of a spin qubit with substrate is considered in GSH at the calculation of exchange integrals J{sub ij} of the nanosystem Ni{sub 7}–Si in the one-electron approach taking into account chemical bonds of all Si-atoms of a substrate (environment) with atoms of the Ni{sub 7}-cluster. The energy pattern was found from the effective GSH Hamiltonian acting in the restricted spin space of the Ni ions by the application of the irreducible tensor operators (ITO) technique. In this paper we offer the model of the quantum solid-state N-spin qubit based on the studying of the spin structure and the spin-dynamics simulations of the 3d-metal Ni clusters on the silicon surface. The solution of the problem of the entanglement between spin states in the N-spin systems is becoming more interesting when considering clusters or molecules with a spectral gap in their density of states. For quantifying the distribution of the entanglement between the individual spin eigenvalues (modes) in the spin structure of the N-spin system we use the density of entanglement (DOE). In this study we have developed and used the advanced high-precision numerical techniques to accurately assess the details of the decoherence process governing the dynamics of the N-spin qubits interacting with a silicon surface. We have studied the Rabi oscillations to evaluate the N-spin qubits system as a function of the time and the magnetic field. We have observed the stabilized Rabi oscillations and have stabilized the quantum dynamical qubit state and Rabi driving after a fixed time (0.327 μs). The comparison of the energy

  11. Quantum model of a solid-state spin qubit: Ni cluster on a silicon surface by the generalized spin Hamiltonian and X-ray absorption spectroscopy investigations

    International Nuclear Information System (INIS)

    Farberovich, Oleg V.; Mazalova, Victoria L.; Soldatov, Alexander V.

    2015-01-01

    We present here the quantum model of a Ni solid-state electron spin qubit on a silicon surface with the use of a density-functional scheme for the calculation of the exchange integrals in the non-collinear spin configurations in the generalized spin Hamiltonian (GSH) with the anisotropic exchange coupling parameters linking the nickel ions with a silicon substrate. In this model the interaction of a spin qubit with substrate is considered in GSH at the calculation of exchange integrals J ij of the nanosystem Ni 7 –Si in the one-electron approach taking into account chemical bonds of all Si-atoms of a substrate (environment) with atoms of the Ni 7 -cluster. The energy pattern was found from the effective GSH Hamiltonian acting in the restricted spin space of the Ni ions by the application of the irreducible tensor operators (ITO) technique. In this paper we offer the model of the quantum solid-state N-spin qubit based on the studying of the spin structure and the spin-dynamics simulations of the 3d-metal Ni clusters on the silicon surface. The solution of the problem of the entanglement between spin states in the N-spin systems is becoming more interesting when considering clusters or molecules with a spectral gap in their density of states. For quantifying the distribution of the entanglement between the individual spin eigenvalues (modes) in the spin structure of the N-spin system we use the density of entanglement (DOE). In this study we have developed and used the advanced high-precision numerical techniques to accurately assess the details of the decoherence process governing the dynamics of the N-spin qubits interacting with a silicon surface. We have studied the Rabi oscillations to evaluate the N-spin qubits system as a function of the time and the magnetic field. We have observed the stabilized Rabi oscillations and have stabilized the quantum dynamical qubit state and Rabi driving after a fixed time (0.327 μs). The comparison of the energy pattern with

  12. Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

    Directory of Open Access Journals (Sweden)

    Renata De Paris

    2015-01-01

    Full Text Available Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.

  13. Generalized extended Navier-Stokes theory: Multiscale spin relaxation in molecular fluids

    DEFF Research Database (Denmark)

    Hansen, Jesper Schmidt

    2013-01-01

    This paper studies the relaxation of the molecular spin angular velocity in the framework of generalized extended Navier-Stokes theory. Using molecular dynamics simulations, it is shown that for uncharged diatomic molecules the relaxation time decreases with increasing molecular moment of inertia...

  14. A numerical study of spin-dependent organization of alkali-metal atomic clusters using density-functional method

    Energy Technology Data Exchange (ETDEWEB)

    Liu Xuan, E-mail: liu.x.ad@m.titech.ac.jp; Ito, Haruhiko [Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology (Japan); Torikai, Eiko [Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi (Japan)

    2012-08-15

    We calculate the different geometric isomers of spin clusters composed of a small number of alkali-metal atoms using the UB3LYP density-functional method. The electron density distribution of clusters changes according to the value of total spin. Steric structures as well as planar structures arise when the number of atoms increases. The lowest spin state is the most stable and Li{sub n}, Na{sub n}, K{sub n}, Rb{sub n}, and Cs{sub n} with n = 2-8 can be formed in higher spin states. In the highest spin state, the preparation of clusters depends on the kind and the number of constituent atoms. The interaction energy between alkali-metal atoms and rare-gas atoms is smaller than the binding energy of spin clusters. Consequently, it is possible to self-organize the alkali-metal-atom clusters on a non-wetting substrate coated with rare-gas atoms.

  15. Accommodating error analysis in comparison and clustering of molecular fingerprints.

    Science.gov (United States)

    Salamon, H; Segal, M R; Ponce de Leon, A; Small, P M

    1998-01-01

    Molecular epidemiologic studies of infectious diseases rely on pathogen genotype comparisons, which usually yield patterns comprising sets of DNA fragments (DNA fingerprints). We use a highly developed genotyping system, IS6110-based restriction fragment length polymorphism analysis of Mycobacterium tuberculosis, to develop a computational method that automates comparison of large numbers of fingerprints. Because error in fragment length measurements is proportional to fragment length and is positively correlated for fragments within a lane, an align-and-count method that compensates for relative scaling of lanes reliably counts matching fragments between lanes. Results of a two-step method we developed to cluster identical fingerprints agree closely with 5 years of computer-assisted visual matching among 1,335 M. tuberculosis fingerprints. Fully documented and validated methods of automated comparison and clustering will greatly expand the scope of molecular epidemiology.

  16. Cluster Mean-Field Approach to the Steady-State Phase Diagram of Dissipative Spin Systems

    Directory of Open Access Journals (Sweden)

    Jiasen Jin

    2016-07-01

    Full Text Available We show that short-range correlations have a dramatic impact on the steady-state phase diagram of quantum driven-dissipative systems. This effect, never observed in equilibrium, follows from the fact that ordering in the steady state is of dynamical origin, and is established only at very long times, whereas in thermodynamic equilibrium it arises from the properties of the (free energy. To this end, by combining the cluster methods extensively used in equilibrium phase transitions to quantum trajectories and tensor-network techniques, we extend them to nonequilibrium phase transitions in dissipative many-body systems. We analyze in detail a model of spin-1/2 on a lattice interacting through an XYZ Hamiltonian, each of them coupled to an independent environment that induces incoherent spin flips. In the steady-state phase diagram derived from our cluster approach, the location of the phase boundaries and even its topology radically change, introducing reentrance of the paramagnetic phase as compared to the single-site mean field where correlations are neglected. Furthermore, a stability analysis of the cluster mean field indicates a susceptibility towards a possible incommensurate ordering, not present if short-range correlations are ignored.

  17. Electronic readout of a single nuclear spin using a molecular spin transistor

    Science.gov (United States)

    Vincent, R.; Klyastskaya, S.; Ruben, M.; Wernsdorfer, W.; Balestro, F.

    2012-02-01

    Quantum control of individual spins in condensed matter devices is an emerging field with a wide range of applications ranging from nanospintronics to quantum computing [1,2]. The electron, with its spin and orbital degrees of freedom, is conventionally used as carrier of the quantum information in the devices proposed so far. However, electrons exhibit a strong coupling to the environment leading to reduced relaxation and coherence times. Indeed quantum coherence and stable entanglement of electron spins are extremely difficult to achieve. We propose a new approach using the nuclear spin of an individual metal atom embedded in a single-molecule magnet (SMM). In order to perform the readout of the nuclear spin, the quantum tunneling of the magnetization (QTM) of the magnetic moment of the SMM in a transitor-like set-up is electronically detected. Long spin lifetimes of an individual nuclear spin were observed and the relaxation characteristics were studied. The manipulation of the nuclear spin state of individual atoms embedded in magnetic molecules opens a completely new world, where quantum logic may be integrated.[4pt] [1] L. Bogani, W. Wernsdorfer, Nature Mat. 7, 179 (2008).[0pt] [2] M. Urdampilleta, S. Klyatskaya, J.P. Cleuziou, M. Ruben, W. Wernsdorfer, Nature Mat. 10, 502 (2011).

  18. Equation-of-motion coupled cluster method for high spin double electron attachment calculations

    Energy Technology Data Exchange (ETDEWEB)

    Musiał, Monika, E-mail: musial@ich.us.edu.pl; Lupa, Łukasz; Kucharski, Stanisław A. [Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice (Poland)

    2014-03-21

    The new formulation of the equation-of-motion (EOM) coupled cluster (CC) approach applicable to the calculations of the double electron attachment (DEA) states for the high spin components is proposed. The new EOM equations are derived for the high spin triplet and quintet states. In both cases the new equations are easier to solve but the substantial simplification is observed in the case of quintets. Out of 21 diagrammatic terms contributing to the standard DEA-EOM-CCSDT equations for the R{sub 2} and R{sub 3} amplitudes only four terms survive contributing to the R{sub 3} part. The implemented method has been applied to the calculations of the excited states (singlets, triplets, and quintets) energies of the carbon and silicon atoms and potential energy curves for selected states of the Na{sub 2} (triplets) and B{sub 2} (quintets) molecules.

  19. Molecular Clusters: Nanoscale Building Blocks for Solid-State Materials.

    Science.gov (United States)

    Pinkard, Andrew; Champsaur, Anouck M; Roy, Xavier

    2018-04-17

    The programmed assembly of nanoscale building blocks into multicomponent hierarchical structures is a powerful strategy for the bottom-up construction of functional materials. To develop this concept, our team has explored the use of molecular clusters as superatomic building blocks to fabricate new classes of materials. The library of molecular clusters is rich with exciting properties, including diverse functionalization, redox activity, and magnetic ordering, so the resulting cluster-assembled solids, which we term superatomic crystals (SACs), hold the promise of high tunability, atomic precision, and robust architectures among a diverse range of other material properties. Molecular clusters have only seldom been used as precursors for functional materials. Our team has been at the forefront of new developments in this exciting research area, and this Account focuses on our progress toward designing materials from cluster-based precursors. In particular, this Account discusses (1) the design and synthesis of molecular cluster superatomic building blocks, (2) their self-assembly into SACs, and (3) their resulting collective properties. The set of molecular clusters discussed herein is diverse, with different cluster cores and ligand arrangements to create an impressive array of solids. The cluster cores include octahedral M 6 E 8 and cubane M 4 E 4 (M = metal; E = chalcogen), which are typically passivated by a shell of supporting ligands, a feature upon which we have expanded upon by designing and synthesizing more exotic ligands that can be used to direct solid-state assembly. Building from this library, we have designed whole families of binary SACs where the building blocks are held together through electrostatic, covalent, or van der Waals interactions. Using single-crystal X-ray diffraction (SCXRD) to determine the atomic structure, a remarkable range of compositional variability is accessible. We can also use this technique, in tandem with vibrational

  20. Spinning Gland Transcriptomics from Two Main Clades of Spiders (Order: Araneae) - Insights on Their Molecular, Anatomical and Behavioral Evolution

    Science.gov (United States)

    Prosdocimi, Francisco; Bittencourt, Daniela; da Silva, Felipe Rodrigues; Kirst, Matias; Motta, Paulo C.; Rech, Elibio L.

    2011-01-01

    Characterized by distinctive evolutionary adaptations, spiders provide a comprehensive system for evolutionary and developmental studies of anatomical organs, including silk and venom production. Here we performed cDNA sequencing using massively parallel sequencers (454 GS-FLX Titanium) to generate ∼80,000 reads from the spinning gland of Actinopus spp. (infraorder: Mygalomorphae) and Gasteracantha cancriformis (infraorder: Araneomorphae, Orbiculariae clade). Actinopus spp. retains primitive characteristics on web usage and presents a single undifferentiated spinning gland while the orbiculariae spiders have seven differentiated spinning glands and complex patterns of web usage. MIRA, Celera Assembler and CAP3 software were used to cluster NGS reads for each spider. CAP3 unigenes passed through a pipeline for automatic annotation, classification by biological function, and comparative transcriptomics. Genes related to spider silks were manually curated and analyzed. Although a single spidroin gene family was found in Actinopus spp., a vast repertoire of specialized spider silk proteins was encountered in orbiculariae. Astacin-like metalloproteases (meprin subfamily) were shown to be some of the most sampled unigenes and duplicated gene families in G. cancriformis since its evolutionary split from mygalomorphs. Our results confirm that the evolution of the molecular repertoire of silk proteins was accompanied by the (i) anatomical differentiation of spinning glands and (ii) behavioral complexification in the web usage. Finally, a phylogenetic tree was constructed to cluster most of the known spidroins in gene clades. This is the first large-scale, multi-organism transcriptome for spider spinning glands and a first step into a broad understanding of spider web systems biology and evolution. PMID:21738742

  1. Spinning gland transcriptomics from two main clades of spiders (order: Araneae--insights on their molecular, anatomical and behavioral evolution.

    Directory of Open Access Journals (Sweden)

    Francisco Prosdocimi

    Full Text Available Characterized by distinctive evolutionary adaptations, spiders provide a comprehensive system for evolutionary and developmental studies of anatomical organs, including silk and venom production. Here we performed cDNA sequencing using massively parallel sequencers (454 GS-FLX Titanium to generate ∼80,000 reads from the spinning gland of Actinopus spp. (infraorder: Mygalomorphae and Gasteracantha cancriformis (infraorder: Araneomorphae, Orbiculariae clade. Actinopus spp. retains primitive characteristics on web usage and presents a single undifferentiated spinning gland while the orbiculariae spiders have seven differentiated spinning glands and complex patterns of web usage. MIRA, Celera Assembler and CAP3 software were used to cluster NGS reads for each spider. CAP3 unigenes passed through a pipeline for automatic annotation, classification by biological function, and comparative transcriptomics. Genes related to spider silks were manually curated and analyzed. Although a single spidroin gene family was found in Actinopus spp., a vast repertoire of specialized spider silk proteins was encountered in orbiculariae. Astacin-like metalloproteases (meprin subfamily were shown to be some of the most sampled unigenes and duplicated gene families in G. cancriformis since its evolutionary split from mygalomorphs. Our results confirm that the evolution of the molecular repertoire of silk proteins was accompanied by the (i anatomical differentiation of spinning glands and (ii behavioral complexification in the web usage. Finally, a phylogenetic tree was constructed to cluster most of the known spidroins in gene clades. This is the first large-scale, multi-organism transcriptome for spider spinning glands and a first step into a broad understanding of spider web systems biology and evolution.

  2. Spin-filtering and giant magnetoresistance effects in polyacetylene-based molecular devices

    Science.gov (United States)

    Chen, Tong; Yan, Shenlang; Xu, Liang; Liu, Desheng; Li, Quan; Wang, Lingling; Long, Mengqiu

    2017-07-01

    Using the non-equilibrium Green's function formalism in combination with density functional theory, we performed ab initio calculations of spin-dependent electron transport in molecular devices consisting of a polyacetylene (CnHn+1) chain vertically attached to a carbon chain sandwiched between two semi-infinite zigzag-edged graphene nanoribbon electrodes. Spin-charge transport in the device could be modulated to different magnetic configurations by an external magnetic field. The results showed that single spin conduction could be obtained. Specifically, the proposed CnHn+1 devices exhibited several interesting effects, including (dual) spin filtering, spin negative differential resistance, odd-even oscillation, and magnetoresistance (MR). Marked spin polarization with a filtering efficiency of up to 100% over a large bias range was found, and the highest MR ratio for the CnHn+1 junctions reached 4.6 × 104. In addition, the physical mechanisms for these phenomena were also revealed.

  3. GOLD CLUSTER LABELS AND RELATED TECHNOLOGIES IN MOLECULAR MORPHOLOGY.

    Energy Technology Data Exchange (ETDEWEB)

    HAINFELD,J.F.; POWELL,R.D.

    2004-02-04

    Although intensely colored, even the largest colloidal gold particles are not, on their own, sufficiently colored for routine use as a light microscopy stain: only with very abundant antigens or with specialized illumination methods can bound gold be seen. Colloidal gold probes were developed primarily as markers for electron microscopy, for which their very high electron density and selectivity for narrow size distributions when prepared in different ways rendered them highly suited. The widespread use of gold labeling for light microscopy was made possible by the introduction of autometallographic enhancement methods. In these processes, the bound gold particles are exposed to a solution containing metal ions and a reducing agent; they catalyze the reduction of the ions, resulting in the deposition of additional metal selectively onto the particles. On the molecular level, the gold particles are enlarged up to 30-100 nm in diameter; on the macroscale level, this results in the formation of a dark stain in regions containing bound gold particles, greatly increasing visibility and contrast. The applications of colloidal gold have been described elsewhere in this chapter, we will focus on the use of covalently linked cluster complexes of gold and other metals. A gold cluster complex is a discrete molecular coordination compound comprising a central core, or ''cluster'' of electron-dense metal atoms, ligated by a shell of small organic molecules (ligands), which are linked to the metal atoms on the surface of the core. This structure gives clusters several important advantages as labels. The capping of the metal surface by ligands prevents non-specific binding to cell and tissue components, which can occur with colloidal gold. Cluster compounds are more stable and may be used under a wider range of conditions. Unlike colloidal gold, clusters do not require additional macromolecules such as bovine serum albumin or polyethylene glycol for

  4. Exploring molecular and spin interactions of Tellurium adatom in reduced graphene oxide

    Energy Technology Data Exchange (ETDEWEB)

    Alegaonkar, Ashwini [Department of Chemistry, Savitribai Phule Pune University (Formerly University of Pune), Ganeshkhind, Pune, 411 007, MS (India); Alegaonkar, Prashant [Department of Applied Physics, Defence Institute of Advance Technology, Girinagar, Pune, 411 025, MS (India); Pardeshi, Satish, E-mail: skpar@chem.unipune.ac.in [Department of Chemistry, Savitribai Phule Pune University (Formerly University of Pune), Ganeshkhind, Pune, 411 007, MS (India)

    2017-07-01

    The transport of spin information fundamentally requires favourable molecular architecture and tunable spin moments to make the medium pertinent for spintronic. We report on achieving coherent molecular-spin parameters for rGO due to Tellurium (Te) adatom. Initially, GO prepared using graphite, was modified into rGO by in situ incorporation of 1 (w/w)% of Te. Both the systems were subjected to ESCA, FTIR, Raman dispersion, ESR spectroscopy, and electron microscopy. Analysis revealed that, Te substantially reacted with epoxides, carbonyl, and carboxylate groups that improved C-to-O ratio by twice. However, the spin splitting character, between Te and C, seems to be quenched. Moreover, Te altered the dynamical force constant between C-C and C=C that generated the mechanical stress within rGO network. The layer conjugation, nature of folding, symmetry, and electronic states of the edges were also affected by precipitation and entrapment of Te. The calculated dynamic molecular Raman and ESR spin parameters indicated that, Te acted as a bridging element for long range spin transport. This is particularly due to, the p-orbital moments of Te contributing, vectorially, to spin relaxation process operative at broken inversion symmetry sites. Our study suggests that, facile addition of Te in rGO is useful to achieve favourable spintronic properties. - Highlights: • Spin interactions and molecular dynamics modification due to Tellurium adatom in rGO. • Molecular level manipulation of Tellurium adatom for favourable spintronic properties. • Bychocov-Rashaba coupling are the operative channels in rGO. • Extrinsic coupling component get added vectorially by Tellurium. • Te-rGO is a viable medium for molecular spintronics.

  5. Formation and partial melting of two types of spin-cluster glass behavior in vanadate spinel

    International Nuclear Information System (INIS)

    Huang Yuanjie; Pi Li; Tan Shun; Zhang Yuheng; Yang Zhaorong

    2012-01-01

    We report the doping effect on the various properties of spinels Co 1-x Zn x V 2 O 4 (0 ≤ x ≤ 0.2). For the parent compounds, the rise in magnetization, the valley in thermal conductance, the transition from the ferromagnetic arrangement to non-collinear alignment indicated by the specific heat for the V sublattice, especially the frequency dependence of AC susceptibility around T 1 = 59 K, verify the occurrence of the transition at T 1 besides the ferrimagnetic transition at T C . The ferrimagnetic transition at T C induces the spin-cluster glass behavior and the transition at T 1 yields the new spin-cluster glass (NSCG) behavior. As the Zn 2+ -doped content increases, the above phenomena are gradually weakening to vanishing, but the glassy behavior at T C still exists for all samples. Through the fourth-order perturbation theory, we discuss the reasons for the gradual vanishing of the transition at T 1 . (paper)

  6. Molecular dynamics simulation of gold cluster growth during sputter deposition

    Energy Technology Data Exchange (ETDEWEB)

    Abraham, J. W., E-mail: abraham@theo-physik.uni-kiel.de; Bonitz, M., E-mail: bonitz@theo-physik.uni-kiel.de [Institut für Theoretische Physik und Astrophysik, Christian-Albrechts-Universität zu Kiel, Leibnizstraße 15, D-24098 Kiel (Germany); Strunskus, T.; Faupel, F. [Institut für Materialwissenschaft, Lehrstuhl für Materialverbunde, Christian-Albrechts-Universität zu Kiel, Kaiserstraße 2, D-24143 Kiel (Germany)

    2016-05-14

    We present a molecular dynamics simulation scheme that we apply to study the time evolution of the self-organized growth process of metal cluster assemblies formed by sputter-deposited gold atoms on a planar surface. The simulation model incorporates the characteristics of the plasma-assisted deposition process and allows for an investigation over a wide range of deposition parameters. It is used to obtain data for the cluster properties which can directly be compared with recently published experimental data for gold on polystyrene [M. Schwartzkopf et al., ACS Appl. Mater. Interfaces 7, 13547 (2015)]. While good agreement is found between the two, the simulations additionally provide valuable time-dependent real-space data of the surface morphology, some of whose details are hidden in the reciprocal-space scattering images that were used for the experimental analysis.

  7. Quantum Interference in the Longitudinal Oscillations of the Total Spin of a Dimeric Molecular Nanomagnet

    Science.gov (United States)

    Ramsey, Christopher; Del Barco, Enrique; Hill, Stephen; Shah, Sonali; Beedle, Christopher; Hendrickson, David

    2008-03-01

    The synthetic flexibility of molecular magnets allows one to systematically produce samples with desirable properties such as those with entangled spin states for implementation in quantum logic gates. Here we report direct evidence of quantum oscillations of the total spin length of a dimeric molecular nanomagnet through the observation of quantum interference associated with tunneling trajectories between states having different spin quantum numbers. As we outline, this is a consequence of the unique characteristics of a molecular Mn12 wheel which behaves as a (weak) ferromagnetic exchange-coupled molecular dimer: each half of the molecule acts as a single-molecule magnet (SMM), while the weak coupling between the two halves gives rise to an additional internal spin degree of freedom within the molecule, namely that its total spin may fluctuate. This extra degree of freedom accounts for several magnetization tunneling resonances that cannot be explained within the usual giant spin approximation. More importantly, the observation of quantum interference provides unambiguous evidence for the quantum mechanical superposition involving entangled states of both halves of the wheel.

  8. Communication: electron transfer mediated decay enabled by spin-orbit interaction in small krypton/xenon clusters.

    Science.gov (United States)

    Zobel, J Patrick; Kryzhevoi, Nikolai V; Pernpointner, Markus

    2014-04-28

    In this work we study the influence of relativistic effects, in particular spin-orbit coupling, on electronic decay processes in KrXe2 clusters of various geometries. For the first time it is shown that inclusion of spin-orbit coupling has decisive influence on the accessibility of a specific decay pathway in these clusters. The radiationless relaxation process is initiated by a Kr 4s ionization followed by an electron transfer from xenon to krypton and a final second ionization of the system. We demonstrate the existence of competing electronic decay pathways depending in a subtle way on the geometry and level of theory. For our calculations a fully relativistic framework was employed where omission of spin-orbit coupling leads to closing of two decay pathways. These findings stress the relevance of an adequate relativistic description for clusters with heavy elements and their fragmentation dynamics.

  9. Coupled-cluster treatment of molecular strong-field ionization

    Science.gov (United States)

    Jagau, Thomas-C.

    2018-05-01

    Ionization rates and Stark shifts of H2, CO, O2, H2O, and CH4 in static electric fields have been computed with coupled-cluster methods in a basis set of atom-centered Gaussian functions with a complex-scaled exponent. Consideration of electron correlation is found to be of great importance even for a qualitatively correct description of the dependence of ionization rates and Stark shifts on the strength and orientation of the external field. The analysis of the second moments of the molecular charge distribution suggests a simple criterion for distinguishing tunnel and barrier suppression ionization in polyatomic molecules.

  10. Hydration of Atmospheric Molecular Clusters: Systematic Configurational Sampling.

    Science.gov (United States)

    Kildgaard, Jens; Mikkelsen, Kurt V; Bilde, Merete; Elm, Jonas

    2018-05-09

    We present a new systematic configurational sampling algorithm for investigating the potential energy surface of hydrated atmospheric molecular clusters. The algo- rithm is based on creating a Fibonacci sphere around each atom in the cluster and adding water molecules to each point in 9 different orientations. To allow the sam- pling of water molecules to existing hydrogen bonds, the cluster is displaced along the hydrogen bond and a water molecule is placed in between in three different ori- entations. Generated redundant structures are eliminated based on minimizing the root mean square distance (RMSD) of different conformers. Initially, the clusters are sampled using the semiempirical PM6 method and subsequently using density func- tional theory (M06-2X and ωB97X-D) with the 6-31++G(d,p) basis set. Applying the developed algorithm we study the hydration of sulfuric acid with up to 15 water molecules. We find that the additions of the first four water molecules "saturate" the sulfuric acid molecule and are more thermodynamically favourable than the addition of water molecule 5-15. Using the large generated set of conformers, we assess the performance of approximate methods (ωB97X-D, M06-2X, PW91 and PW6B95-D3) in calculating the binding energies and assigning the global minimum conformation compared to high level CCSD(T)-F12a/VDZ-F12 reference calculations. The tested DFT functionals systematically overestimates the binding energies compared to cou- pled cluster calculations, and we find that this deficiency can be corrected by a simple scaling factor.

  11. Heisenberg coupling constant predicted for molecular magnets with pairwise spin-contamination correction

    Energy Technology Data Exchange (ETDEWEB)

    Masunov, Artëm E., E-mail: amasunov@ucf.edu [NanoScience Technology Center, Department of Chemistry, and Department of Physics, University of Central Florida, Orlando, FL 32826 (United States); Photochemistry Center RAS, ul. Novatorov 7a, Moscow 119421 (Russian Federation); Gangopadhyay, Shruba [Department of Physics, University of California, Davis, CA 95616 (United States); IBM Almaden Research Center, 650 Harry Road, San Jose, CA 95120 (United States)

    2015-12-15

    New method to eliminate the spin-contamination in broken symmetry density functional theory (BS DFT) calculations is introduced. Unlike conventional spin-purification correction, this method is based on canonical Natural Orbitals (NO) for each high/low spin coupled electron pair. We derive an expression to extract the energy of the pure singlet state given in terms of energy of BS DFT solution, the occupation number of the bonding NO, and the energy of the higher spin state built on these bonding and antibonding NOs (not self-consistent Kohn–Sham orbitals of the high spin state). Compared to the other spin-contamination correction schemes, spin-correction is applied to each correlated electron pair individually. We investigate two binuclear Mn(IV) molecular magnets using this pairwise correction. While one of the molecules is described by magnetic orbitals strongly localized on the metal centers, and spin gap is accurately predicted by Noodleman and Yamaguchi schemes, for the other one the gap is predicted poorly by these schemes due to strong delocalization of the magnetic orbitals onto the ligands. We show our new correction to yield more accurate results in both cases. - Highlights: • Magnetic orbitails obtained for high and low spin states are not related. • Spin-purification correction becomes inaccurate for delocalized magnetic orbitals. • We use the natural orbitals of the broken symmetry state to build high spin state. • This new correction is made separately for each electron pair. • Our spin-purification correction is more accurate for delocalised magnetic orbitals.

  12. Clustering the Orion B giant molecular cloud based on its molecular emission.

    Science.gov (United States)

    Bron, Emeric; Daudon, Chloé; Pety, Jérôme; Levrier, François; Gerin, Maryvonne; Gratier, Pierre; Orkisz, Jan H; Guzman, Viviana; Bardeau, Sébastien; Goicoechea, Javier R; Liszt, Harvey; Öberg, Karin; Peretto, Nicolas; Sievers, Albrecht; Tremblin, Pascal

    2018-02-01

    Previous attempts at segmenting molecular line maps of molecular clouds have focused on using position-position-velocity data cubes of a single molecular line to separate the spatial components of the cloud. In contrast, wide field spectral imaging over a large spectral bandwidth in the (sub)mm domain now allows one to combine multiple molecular tracers to understand the different physical and chemical phases that constitute giant molecular clouds (GMCs). We aim at using multiple tracers (sensitive to different physical processes and conditions) to segment a molecular cloud into physically/chemically similar regions (rather than spatially connected components), thus disentangling the different physical/chemical phases present in the cloud. We use a machine learning clustering method, namely the Meanshift algorithm, to cluster pixels with similar molecular emission, ignoring spatial information. Clusters are defined around each maximum of the multidimensional Probability Density Function (PDF) of the line integrated intensities. Simple radiative transfer models were used to interpret the astrophysical information uncovered by the clustering analysis. A clustering analysis based only on the J = 1 - 0 lines of three isotopologues of CO proves suffcient to reveal distinct density/column density regimes ( n H ~ 100 cm -3 , ~ 500 cm -3 , and > 1000 cm -3 ), closely related to the usual definitions of diffuse, translucent and high-column-density regions. Adding two UV-sensitive tracers, the J = 1 - 0 line of HCO + and the N = 1 - 0 line of CN, allows us to distinguish two clearly distinct chemical regimes, characteristic of UV-illuminated and UV-shielded gas. The UV-illuminated regime shows overbright HCO + and CN emission, which we relate to a photochemical enrichment effect. We also find a tail of high CN/HCO + intensity ratio in UV-illuminated regions. Finer distinctions in density classes ( n H ~ 7 × 10 3 cm -3 ~ 4 × 10 4 cm -3 ) for the densest regions are also

  13. Study of CP(N-1) theta-vacua by cluster simulation of SU(N) quantum spin ladders.

    Science.gov (United States)

    Beard, B B; Pepe, M; Riederer, S; Wiese, U-J

    2005-01-14

    D-theory provides an alternative lattice regularization of the 2D CP(N-1) quantum field theory in which continuous classical fields emerge from the dimensional reduction of discrete SU(N) quantum spins. Spin ladders consisting of n transversely coupled spin chains lead to a CP(N-1) model with a vacuum angle theta=npi. In D-theory no sign problem arises and an efficient cluster algorithm is used to investigate theta-vacuum effects. At theta=pi there is a first order phase transition with spontaneous breaking of charge conjugation symmetry for CP(N-1) models with N>2.

  14. Structure and dynamics of molecular clusters. 2. Melting and freezing of CCl4 clusters

    International Nuclear Information System (INIS)

    Bartell, L.S.; Chen, Jian

    1992-01-01

    Phase transitions of a 225-molecule cluster of carbon tetrachloride have been studied by a molecular dynamics simulation. A five-site model potential function was developed to reproduce the density and heat of vaporization of the bulk liquid. Computations began with orientationally disordered molecules distributed in fcc lattice sites of a nearly spherical cluster. The cluster was heated from a low temperature to 200 K in 10-deg steps of 50 ps each and then cooled to 10 K. Translational and rotational transitions were monitored by following several indicators including the translational and rotational diffusion and rotational entropies of individual molecules. Melting began at the surface and propagated inward as the temperature increased. Solidification of the molten cluster proceeded from the center to the surface. At the high cooling rate of the simulation, however, molecules were unable to organize into a crystalline array and solidified into a glassy structure instead. Except for spatial order, the indicators of degree of liquefaction exhibited almost the same temperature dependence in the crystsl → liquid as in the liquid → glass transition, a behavior that could be rationalized on the basis of Lindemann's theory of melting. Results were compared with predictions of an illustrative model due to Reiss, Mirabel, and Whetten. Qualitatively, the model included all of the features of the simulation. Quantitatively, the model grossly underestimated the range over which the melting transition took place. 40 refs., 10 figs., 1 tab

  15. 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.

  16. 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

  17. Magnetic Switching of a Single Molecular Magnet due to Spin-Polarized Current

    OpenAIRE

    Misiorny, Maciej; Barnas, Józef

    2006-01-01

    Magnetic switching of a single molecular magnet (SMM) due to spin-polarized current flowing between ferromagnetic metallic electrodes is investigated theoretically. Magnetic moments of the electrodes are assumed to be collinear and parallel to the magnetic easy axis of the molecule. Electrons tunneling through a barrier between magnetic leads are coupled to the SMM via exchange interaction. The current flowing through the system as well as the spin relaxation times of the SMM are calculated f...

  18. Pumping $ac$ Josephson current in the Single Molecular Magnets by spin nutation

    OpenAIRE

    Abdollahipour, B.; Abouie, J.; Rostami, A. A.

    2012-01-01

    We demonstrate that an {\\it ac} Josephson current is pumped through the Single Molecular Magnets (SMM) by the spin nutation. The spin nutation is generated by applying a time dependent magnetic field to the SMM. We obtain the flowing charge current through the junction by working in the tunneling limit and employing Green's function technique. At the resonance conditions some discontinuities and divergencies are appeared in the normal and Josephson currents, respectively. Such discontinuities...

  19. [OsF6]x−: Molecular Models for Spin-Orbit Entangled Phenomena

    DEFF Research Database (Denmark)

    Pedersen, Kasper Steen; Woodruff, Daniel N.; Singh, Saurabh Kumar

    2017-01-01

    Heavy 5d elements, like osmium, feature strong spin-orbit interactions which are at the origin of exotic physical behaviors. Revealing the full potential of, for example, novel osmium oxide materials (“osmates”) is however contingent upon a detailed understanding of the local single-ion propertie...... state was elucidated; mirroring the osmium electronic structure in osmates. The realization of such molecular model systems provides a unique chemical playground to engineer materials exhibiting spin-orbit entangled phenomena....

  20. Tuning magnetoresistance in molybdenum disulphide and graphene using a molecular spin transition.

    Science.gov (United States)

    Datta, Subhadeep; Cai, Yongqing; Yudhistira, Indra; Zeng, Zebing; Zhang, Yong-Wei; Zhang, Han; Adam, Shaffique; Wu, Jishan; Loh, Kian Ping

    2017-09-22

    Coupling spins of molecular magnets to two-dimensional (2D) materials provides a framework to manipulate the magneto-conductance of 2D materials. However, with most molecules, the spin coupling is usually weak and devices fabricated from these require operation at low temperatures, which prevents practical applications. Here, we demonstrate field-effect transistors based on the coupling of a magnetic molecule quinoidal dithienyl perylenequinodimethane (QDTP) to 2D materials. Uniquely, QDTP switches from a spin-singlet state at low temperature to a spin-triplet state above 370 K, and the spin transition can be electrically transduced by both graphene and molybdenum disulphide. Graphene-QDTP shows hole-doping and a large positive magnetoresistance ( ~ 50%), while molybdenum disulphide-QDTP demonstrates electron-doping and a switch to large negative magnetoresistance ( ~ 100%) above the magnetic transition. Our work shows the promise of spin detection at high temperature by coupling 2D materials and molecular magnets.Engineering a coupling between magnetic molecules and conducting materials at room temperature could help the development of spintronic devices. Loh et al. show that the spin state of QDTP molecules deposited on graphene and MoS 2 couples to their electronic structure, affecting magnetotransport.

  1. Molecular dynamics simulations of nucleation and phase transitions in molecular clusters of hexafluorides

    International Nuclear Information System (INIS)

    Xu, S.

    1993-01-01

    Molecular dynamics simulations of nucleation and phase transitions in TeF 6 and SeF 6 clusters containing 100-350 molecules were carried out. Simulations successfully reproduced the crystalline structures observed in electron diffraction studies of large clusters (containing about 10 4 molecules) of the same materials. When the clusters were cooled, they spontaneously underwent the same bcc the monoclinic phase transition in simulations as in experiment, despite the million-fold difference in the time scales involved. Other transitions observed included melting and freezing. Several new techniques based on molecular translation and orientation were introduced to identify different condensed phases, to study nucleation and phase transitions, and to define characteristic temperatures of transitions. The solid-state transition temperatures decreased with cluster size in the same way as did the melting temperature, in that the depression of transition temperature was inversely proportional to the cluster radius. Rotational melting temperatures, as inferred from the rotational diffusion of molecules, coincided with those of the solid-state transition. Nucleation in liquid-solid and bcc-monoclinic transitions started in the interior of clusters on cooling, and at the surface on heating. Transition temperatures on cooling were always lower than those on heating due to the barriers to nucleation. Linear growth rates of nuclei in freezing were an order of magnitude lower than those in the bcc-monoclinic transition. Revealing evidence about the molecular behavior associated with phase changes was found. Simulations showed the formation of the actual transition complexes along the transition pathway, i.e., the critical nuclei of the new phase. These nuclei, consisting of a few dozen molecules, were distinguishable in the midst of the surrounding matter

  2. Magnetoresistance effect of heat generation in a single-molecular spin-valve

    International Nuclear Information System (INIS)

    Jiang, Feng; Yan, Yonghong; Wang, Shikuan; Yan, Yijing

    2016-01-01

    Based on non-equilibrium Green's functions' theory and small polaron transformation's technology, we study the heat generation by current through a single-molecular spin-valve. Numerical results indicate that the variation of spin polarization degree can change heat generation effectively, the spin-valve effect happens not only in electrical current but also in heat generation when Coulomb repulsion in quantum dot is smaller than phonon frequency and interestingly, when Coulomb repulsion is larger than phonon frequency, the inverse spin-valve effect appears by sweeping gate voltage and is enlarged with bias increasing. The inverse spin-valve effect will induce the unique heat magnetoresistance effect, which can be modulated from heat-resistance to heat-gain by gate voltage easily. - Highlights: • Spin-valve effect of heat generation happens when Coulomb repulsion in quantum dot is less than phonon frequency. • When Coulomb repulsion is larger than phonon frequency, inverse spin-valve effect appears and is enlarged with bias increasing. • The variation of spin polarization degree can change heat generation effectively. • The heat magnetoresistance can be modulated from heat-resistance to heat-gain by gate voltage easily.

  3. Fen (n=1–6) clusters chemisorbed on vacancy defects in graphene: Stability, spin-dipole moment, and magnetic anisotropy

    KAUST Repository

    Haldar, Soumyajyoti

    2014-05-09

    In this work, we have studied the chemical and magnetic interactions of Fen (n=1–6) clusters with vacancy defects (monovacancy to correlated vacancies with six missing C atoms) in a graphene sheet by ab initio density functional calculations combined with Hubbard U corrections for correlated Fe-d electrons. It is found that the vacancy formation energies are lowered in the presence of Fe, indicating an easier destruction of the graphene sheet. Due to strong chemical interactions between Fe clusters and vacancies, a complex distribution of magnetic moments appear on the distorted Fe clusters which results in reduced averaged magnetic moments compared to the free clusters. In addition to that, we have calculated spin-dipole moments and magnetic anisotropy energies. The calculated spin-dipole moments arising from anisotropic spin density distributions vary between positive and negative values, yielding increased or decreased effective moments. Depending on the cluster geometry, the easy axis of magnetization of the Fe clusters shows in-plane or out-of-plane behavior.

  4. Spin-spin interactions of electrons and also of nucleons create atomic molecular and nuclear structures

    International Nuclear Information System (INIS)

    Kaliambos, L.A.

    2008-01-01

    Fundamental interactions of spinning electrons at an interelectron separation less than 578.8 fm yield attractive electromagnetic forces with S = 0 creating vibrations under a motional emf. They explain the indistinguishability of electrons and give a vibration energy able for calculating the ground-state energies of many-electron atoms without using any perturbative approximation. Such forces create two-electron orbitals able to account for the exclusion principal and the mechanism of covalent bonds. In the outer subshells of atoms the penetrating orbitals interact also as pair-pair systems and deform drastically the probability densities of the quantum mechanical electron clouds. Such a dynamics of deformation removes the degeneracy and leads to the deviation from the shell scheme. However in the interior of atoms the large nuclear charge leads to a spherically symmetric potential with non-interacting pairs for creating shells of degenerate states giving an accurate explanation of the X-ray lines. On the other hand, considerable charge distributions in nucleons as multiples of 2e/3 and - e/3 determined by the magnetic moments, interact for creating the nuclear structure with p-n bonds. Such spin-spin interactions show that the dominant concept of the untisymmetric wave function for fermions is inapplicable not only in the simple p-n, p-p, and n-n systems but also in the LS coupling of atoms in which the electrons interact from different quantum states giving either S = 0 or S = l. (author)

  5. Manipulating the spin states in a double molecular magnets tunneling junction

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Liang; Liu, Xi [National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093 (China); Zhang, Zhengzhong, E-mail: zeikeezhang@126.com [National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093 (China); Nano Science and Technology Institute, University of Science and Technology of China, Suzhou 215123 (China); Wang, Ruiqiang [Laboratory of Quantum Engineering and Quantum Materials, South China Normal University, Guangzhou 510006 (China)

    2014-01-17

    We theoretically explore the spin transport through nano-structures consisting of two serially coupled single-molecular magnets (SMM) sandwiched between two nonmagnetic electrodes. We find that the magnetization of SMM can be controlled by the spin transfer torque with respect to the bias voltage direction, and the electron current can be switched on/off in different magnetic structures. Such a manipulation is performed by full electrical manner, and needs neither external magnetic field nor ferromagnetic electrodes in the tunneling junction. The proposal device scheme can be realized with the use of the present technology and has potential applications in molecular spintronics or quantum information processing.

  6. Magnetic surfactants as molecular based-magnets with spin glass-like properties

    International Nuclear Information System (INIS)

    Brown, Paul; Hatton, T Alan; Smith, Gregory N; Hernández, Eduardo Padrón; James, Craig; Eastoe, Julian; Nunes, Wallace C; Settens, Charles M; Baker, Peter J

    2016-01-01

    This paper reports the use of muon spin relaxation spectroscopy to study how the aggregation behavior of magnetic surfactants containing lanthanide counterions may be exploited to create spin glass-like materials. Surfactants provide a unique approach to building in randomness, frustration and competing interactions into magnetic materials without requiring a lattice of ordered magnetic species or intervening ligands and elements. We demonstrate that this magnetic behavior may also be manipulated via formation of micelles rather than simple dilution, as well as via design of surfactant molecular architecture. This somewhat unexpected result indicates the potential of using novel magnetic surfactants for the generation and tuning of molecular magnets. (paper)

  7. Manipulating the spin states in a double molecular magnets tunneling junction

    Science.gov (United States)

    Jiang, Liang; Liu, Xi; Zhang, Zhengzhong; Wang, Ruiqiang

    2014-01-01

    We theoretically explore the spin transport through nano-structures consisting of two serially coupled single-molecular magnets (SMM) sandwiched between two nonmagnetic electrodes. We find that the magnetization of SMM can be controlled by the spin transfer torque with respect to the bias voltage direction, and the electron current can be switched on/off in different magnetic structures. Such a manipulation is performed by full electrical manner, and needs neither external magnetic field nor ferromagnetic electrodes in the tunneling junction. The proposal device scheme can be realized with the use of the present technology [6] and has potential applications in molecular spintronics or quantum information processing.

  8. Don't spin the pen: two alternative methods for second-stage sampling in urban cluster surveys

    Directory of Open Access Journals (Sweden)

    Rose Angela MC

    2007-06-01

    Full Text Available Abstract In two-stage cluster surveys, the traditional method used in second-stage sampling (in which the first household in a cluster is selected is time-consuming and may result in biased estimates of the indicator of interest. Firstly, a random direction from the center of the cluster is selected, usually by spinning a pen. The houses along that direction are then counted out to the boundary of the cluster, and one is then selected at random to be the first household surveyed. This process favors households towards the center of the cluster, but it could easily be improved. During a recent meningitis vaccination coverage survey in Maradi, Niger, we compared this method of first household selection to two alternatives in urban zones: 1 using a superimposed grid on the map of the cluster area and randomly selecting an intersection; and 2 drawing the perimeter of the cluster area using a Global Positioning System (GPS and randomly selecting one point within the perimeter. Although we only compared a limited number of clusters using each method, we found the sampling grid method to be the fastest and easiest for field survey teams, although it does require a map of the area. Selecting a random GPS point was also found to be a good method, once adequate training can be provided. Spinning the pen and counting households to the boundary was the most complicated and time-consuming. The two methods tested here represent simpler, quicker and potentially more robust alternatives to spinning the pen for cluster surveys in urban areas. However, in rural areas, these alternatives would favor initial household selection from lower density (or even potentially empty areas. Bearing in mind these limitations, as well as available resources and feasibility, investigators should choose the most appropriate method for their particular survey context.

  9. Thermal Fluctuations in the Magnetic Ground State of the Molecular Cluster Mn12O12 Acetate from μSR and Proton NMR Relaxation

    International Nuclear Information System (INIS)

    Lascialfari, A.; Borsa, F.; Carretta, P.; Jang, Z.H.; Borsa, F.; Gatteschi, D.

    1998-01-01

    Measurements of the spin-lattice relaxation rate are reported for muons and protons as a function of temperature for different values of the applied magnetic field in the Mn 12 O 12 molecular cluster. Strongly field dependent maxima in the relaxation rate versus temperature are observed below 50thinspthinspK. The results are explained in terms of thermal fluctuations of the total magnetization of the cluster among the different orientations with respect to the anisotropy axis. The lifetimes of the different m components of the total spin, S T =10 , of the molecule are obtained from the experiment and shown to be consistent with the ones expected from a spin-phonon coupling mechanism. No clear evidence for macroscopic quantum tunneling was observed in the field dependence of the proton relaxation rate at low T . copyright 1998 The American Physical Society

  10. Spin-driven structural effects in alkali doped (4)He clusters from quantum calculations.

    Science.gov (United States)

    Bovino, S; Coccia, E; Bodo, E; Lopez-Durán, D; Gianturco, F A

    2009-06-14

    In this paper, we carry out variational Monte Carlo and diffusion Monte Carlo (DMC) calculations for Li(2)((1)Sigma(g) (+))((4)He)(N) and Li(2)((3)Sigma(u) (+))((4)He)(N) with N up to 30 and discuss in detail the results of our computations. After a comparison between our DMC energies with the "exact" discrete variable representation values for the species with one (4)He, in order to test the quality of our computations at 0 K, we analyze the structural features of the whole range of doped clusters. We find that both species reside on the droplet surface, but that their orientation is spin driven, i.e., the singlet molecule is perpendicular and the triplet one is parallel to the droplet's surface. We have also computed quantum vibrational relaxation rates for both dimers in collision with a single (4)He and we find them to differ by orders of magnitude at the estimated surface temperature. Our results therefore confirm the findings from a great number of experimental data present in the current literature and provide one of the first attempts at giving an accurate, fully quantum picture for the nanoscopic properties of alkali dimers in (4)He clusters.

  11. Clustering Effects on Dynamics in Ionomer Solutions: A Neutron Spin Echo Insight

    Science.gov (United States)

    Perahia, Dvora; Wijesinghe, Sidath; Senanayake, Manjula; Wickramasinghe, Anuradhi; Mohottalalage, Supun S.; Ohl, Michael

    Ionizable blocks in ionomers associate into aggregates serving as physical cross-links and concurrently form transport pathways. The dynamics of ionomers underline their functionality. Incorporating small numbers of ionic groups into polymers significantly constraint their dynamics. Recent computational studies demonstrated a direct correlation between ionic cluster morphology and polymer dynamics. Here using neutron spin echo, we probe the segmental dynamics of polystyrene sulfonate (PSS) as the degree of sulfonation of the PSS and the solution dielectrics are varied. Specifically, 20Wt% PSS of 11,000 g/mol with polydispersity of 1.02 with 3% and 9% sulfonation were studies in toluene (dielectric constant ɛ = 2.8), a good solvent for polystyrene, and with 5Wt% of ethanol (ɛ = 24.3l) added. The dynamic structure factor S(q,t) was analyzed with a single exponential except for a limited q range where two time constants associated with constraint and mobile segments were detected. S(q,t) exhibits several distinctive time and length scales for the dynamics with a crossover appearing at the length scale of the ionic clusters. NSF DMR 1611136.

  12. Molecular clusters in zirconium and thorium tetrachloride melts

    International Nuclear Information System (INIS)

    Akdeniz, Z.; Tosi, M.P.

    2000-08-01

    We evaluate within a microscopic ionic model the structure and the binding of small clusters which may exist as structural units in molten ThCl 4 and ZrCl 4 and in their mixtures with alkali halides, according to Raman scattering studies of Photiadis and Papatheodorou. The model is adjusted to the two isolated tetrahedral molecules. Appreciably higher ionicity is found for ThCl 4 than for ZrCl 4 , and this fact underlies the strikingly different structures of the two systems in the dense liquid state - in particular, a molecular-type structure for molten ZrCl 4 against a structure including charged oligomers in molten ThCl 4 . (author)

  13. Generalized extended Navier-Stokes theory: multiscale spin relaxation in molecular fluids.

    Science.gov (United States)

    Hansen, J S

    2013-09-01

    This paper studies the relaxation of the molecular spin angular velocity in the framework of generalized extended Navier-Stokes theory. Using molecular dynamics simulations, it is shown that for uncharged diatomic molecules the relaxation time decreases with increasing molecular moment of inertia per unit mass. In the regime of large moment of inertia the fast relaxation is wave-vector independent and dominated by the coupling between spin and the fluid streaming velocity, whereas for small inertia the relaxation is slow and spin diffusion plays a significant role. The fast wave-vector-independent relaxation is also observed for highly packed systems. The transverse and longitudinal spin modes have, to a good approximation, identical relaxation, indicating that the longitudinal and transverse spin viscosities have same value. The relaxation is also shown to be isomorphic invariant. Finally, the effect of the coupling in the zero frequency and wave-vector limit is quantified by a characteristic length scale; if the system dimension is comparable to this length the coupling must be included into the fluid dynamical description. It is found that the length scale is independent of moment of inertia but dependent on the state point.

  14. Clustering the Orion B giant molecular cloud based on its molecular emission

    Science.gov (United States)

    Bron, Emeric; Daudon, Chloé; Pety, Jérôme; Levrier, François; Gerin, Maryvonne; Gratier, Pierre; Orkisz, Jan H.; Guzman, Viviana; Bardeau, Sébastien; Goicoechea, Javier R.; Liszt, Harvey; Öberg, Karin; Peretto, Nicolas; Sievers, Albrecht; Tremblin, Pascal

    2018-02-01

    Context. Previous attempts at segmenting molecular line maps of molecular clouds have focused on using position-position-velocity data cubes of a single molecular line to separate the spatial components of the cloud. In contrast, wide field spectral imaging over a large spectral bandwidth in the (sub)mm domain now allows one to combine multiple molecular tracers to understand the different physical and chemical phases that constitute giant molecular clouds (GMCs). Aims: We aim at using multiple tracers (sensitive to different physical processes and conditions) to segment a molecular cloud into physically/chemically similar regions (rather than spatially connected components), thus disentangling the different physical/chemical phases present in the cloud. Methods: We use a machine learning clustering method, namely the Meanshift algorithm, to cluster pixels with similar molecular emission, ignoring spatial information. Clusters are defined around each maximum of the multidimensional probability density function (PDF) of the line integrated intensities. Simple radiative transfer models were used to interpret the astrophysical information uncovered by the clustering analysis. Results: A clustering analysis based only on the J = 1-0 lines of three isotopologues of CO proves sufficient to reveal distinct density/column density regimes (nH 100 cm-3, 500 cm-3, and >1000 cm-3), closely related to the usual definitions of diffuse, translucent and high-column-density regions. Adding two UV-sensitive tracers, the J = 1-0 line of HCO+ and the N = 1-0 line of CN, allows us to distinguish two clearly distinct chemical regimes, characteristic of UV-illuminated and UV-shielded gas. The UV-illuminated regime shows overbright HCO+ and CN emission, which we relate to a photochemical enrichment effect. We also find a tail of high CN/HCO+ intensity ratio in UV-illuminated regions. Finer distinctions in density classes (nH 7 × 103 cm-3, 4 × 104 cm-3) for the densest regions are also

  15. Size effects in van der Waals clusters studied by spin and angle-resolved electron spectroscopy and multi-coincidence ion imaging

    International Nuclear Information System (INIS)

    Rolles, D; Pesic, Z D; Zhang, H; Bilodeau, R C; Bozek, J D; Berrah, N

    2007-01-01

    We have studied the valence and inner-shell photoionization of free rare-gas clusters by means of angle and spin resolved photoelectron spectroscopy and momentum resolving electron-multi-ion coincidence spectroscopy. The electron measurements probe the evolution of the photoelectron angular distribution and spin polarization parameters as a function of photon energy and cluster size, and reveal a strong cluster size dependence of the photoelectron angular distributions in certain photon energy regions. In contrast, the spin polarization parameter of the cluster photoelectrons is found to be very close to the atomic value for all covered photon energies and cluster sizes. The ion imaging measurements, which probe the fragmentation dynamics of multiply charged van der Waals clusters, also exhibit a pronounced cluster size dependence

  16. Hydrogen cluster/network in tobermorite as studied by multiple-quantum spin counting {sup 1}H NMR

    Energy Technology Data Exchange (ETDEWEB)

    Mogami, Yuuki [Division of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); Yamazaki, Satoru; Matsuno, Shinya [Analysis and Simulation Center, Asahi Kasei Corporation, Fuji, Shizuoka 416-8501 (Japan); Matsui, Kunio [Products and Marketing Development Dept., Asahi Kasei Construction Materials Corporation, Sakai-machi, Ibaraki 306-0493 (Japan); Noda, Yasuto [Division of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); Takegoshi, K., E-mail: takeyan@kuchem.kyoto-u.ac.jp [Division of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan)

    2014-12-15

    Proton multiple-quantum (MQ) spin-counting experiment has been employed to study arrangement of hydrogen atoms in 9 Å/11 Å natural/synthetic tobermorites. Even though all tobermorite samples give similar characterless, broad static-powder {sup 1}H NMR spectra, their MQ spin-counting spectra are markedly different; higher quanta in 11 Å tobermorite do not grow with the MQ excitation time, while those in 9 Å one do. A statistical analysis of the MQ results recently proposed [26] is applied to show that hydrogens align in 9 Å tobermorite one dimensionally, while in 11 Å tobermorite they exist as a cluster of 5–8 hydrogen atoms.

  17. Direct calculation of the spin stiffness on square, triangular and cubic lattices using the coupled cluster method

    OpenAIRE

    Krüger, S. E.; Darradi, R.; Richter, J.; Farnell, D. J. J

    2006-01-01

    We present a method for the direct calculation of the spin stiffness by means of the coupled cluster method. For the spin-half Heisenberg antiferromagnet on the square, the triangular and the cubic lattices we calculate the stiffness in high orders of approximation. For the square and the cubic lattices our results are in very good agreement with the best results available in the literature. For the triangular lattice our result is more precise than any other result obtained so far by other a...

  18. Fulde-Ferrell-Like Molecular States in Spin-Orbit Coupled Ultracold Fermi Gases

    Science.gov (United States)

    Ye, Chong; Fu, Li-Bin

    2017-08-01

    We study the molecular state in three-component Fermi gases with a single impurity of 6 Li immersing in a no-interacting Fermi sea of 40 K in the presence of an equal weight combination of Rashba-type and Dresselhaus-type spin-orbit coupling. In the region where the Fermi sea has two disjointed Fermi surfaces, we find that there are two Fulde-Ferrell-like molecular states with dominating contributions from the lower helicity branch. Decreasing the scattering length or the spin-orbit coupled Fermi energy, we find the Fulde-Ferrell-like molecular state with small center-of-mass momentum is always energy favored and the other one will suddenly disappear. Supported by the National Basic Research Program of China (973 Program) under Grant Nos. 2013CBA01502, 2013CB834100, and the National Natural Science Foundation of China under Grant Nos. 11374040, 11475027, 11575027, 11274051, and 11075020

  19. Molecular dynamics calculation of half-lives for thermal decay of Lennard-Jones clusters

    International Nuclear Information System (INIS)

    Smith, R.W.

    1991-01-01

    Molecular dynamics has been used with a Lenard-Jones (6-12) potential in order to study the decay behavior of neutral Argon clusters containing between 12 and 14 atoms. The clusters were heated to temperatures well above their melting points and then tracked in time via molecular dynamics until evaporation of one or more atoms was observed. In each simulation, the mode of evaporation, energy released during evaporation, and cluster lifetime were recorded. Results from roughly 2000 simulation histories were combined in order to compute statistically significant values of cluster half-lives and decay energies. It was found that cluster half-life decreases with increasing energy and that for a given value of excess energy (defined as E=(E tot -E gnd )/n), the 13 atom cluster is more stable against decay than clusters containing either 12 or 14 atoms. The dominant decay mechanism for all clusters was determined to be single atom emission. (orig.)

  20. Heat-induced changes to lipid molecular structure in Vimy flaxseed: Spectral intensity and molecular clustering

    Science.gov (United States)

    Yu, Peiqiang; Damiran, Daalkhaijav

    2011-06-01

    Autoclaving was used to manipulate nutrient utilization and availability. The objectives of this study were to characterize any changes of the functional groups mainly associated with lipid structure in flaxseed ( Linum usitatissimum, cv. Vimy), that occurred on a molecular level during the treatment process using infrared Fourier transform molecular spectroscopy. The parameters included lipid CH 3 asymmetric (ca. 2959 cm -1), CH 2 asymmetric (ca. 2928 cm -1), CH 3 symmetric (ca. 2871 cm -1) and CH 2 symmetric (ca. 2954 cm -1) functional groups, lipid carbonyl C dbnd O ester group (ca. 1745 cm -1), lipid unsaturation group (CH attached to C dbnd C) (ca. 3010 cm -1) as well as their ratios. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were conducted to identify molecular spectral differences. Flaxseed samples were kept raw for the control or autoclaved in batches at 120 °C for 20, 40 or 60 min for treatments 1, 2 and 3, respectively. Molecular spectral analysis of lipid functional group ratios showed a significant decrease ( P 0.05) on lipid carbonyl C dbnd O ester group and lipid unsaturation group (CH attached to C dbnd C) (with average spectral peak area intensities of 138.3 and 68.8 IR intensity units, respectively). Multivariate molecular spectral analyses, CLA and PCA, were unable to make distinctions between the different treatment original spectra at the CH 3 and CH 2 asymmetric and symmetric region (ca. 2988-2790 cm -1). The results indicated that autoclaving had an impact to the mid-infrared molecular spectrum of flaxseed to identify heat-induced changes in lipid conformation. A future study is needed to quantify the relationship between lipid molecular structure changes and functionality/availability.

  1. Magnetic switching of a single molecular magnet due to spin-polarized current

    Science.gov (United States)

    Misiorny, Maciej; Barnaś, Józef

    2007-04-01

    Magnetic switching of a single molecular magnet (SMM) due to spin-polarized current flowing between ferromagnetic metallic leads (electrodes) is investigated theoretically. Magnetic moments of the leads are assumed to be collinear and parallel to the magnetic easy axis of the molecule. Electrons tunneling through the barrier between magnetic leads are coupled to the SMM via exchange interaction. The current flowing through the system, as well as the spin relaxation times of the SMM, are calculated from the Fermi golden rule. It is shown that spin of the SMM can be reversed by applying a certain voltage between the two magnetic electrodes. Moreover, the switching may be visible in the corresponding current-voltage characteristics.

  2. Atomistic interactions of clusters on surfaces using molecular dynamics and hyper molecular dynamics

    International Nuclear Information System (INIS)

    Sanz-Navarro, Carlos F.

    2002-01-01

    The work presented in this thesis describes the results of Molecular Dynamics (MD) simulations applied to the interaction of silver clusters with graphite surfaces and some numerical and theoretical methods concerning the extension of MD simulations to longer time scales (hyper-MD). The first part of this thesis studies the implantation of clusters at normal incidence onto a graphite surface in order to determine the scaling of the penetration depth (PD) against the impact energy. A comparison with experimental results is made with good agreement. The main physical observations of the impact process are described and analysed. It is shown that there is a threshold impact velocity above which the linear dependence on PD on impact energy changes to a linear dependence on velocity. Implantation of silver clusters at oblique incidence is also considered. The second part of this work analyses the validity and feasibility of the three minimisation methods for the hyper-MD simulation method whereby time scales of an MD simulation can be extended. A correct mathematical basis for the iterative method is derived. It is found that one of the iterative methods, upon which hyper-lD is based, is very likely to fail in high-dimensional situations because it requires a too expensive convergence. Two new approximations to the hyper-MD approach are proposed, which reduce the computational effort considerably. Both approaches, although not exact, can help to search for some of the most likely transitions in the system. Some examples are given to illustrate this. (author)

  3. Boosting spin-caloritronic effects by attractive correlations in molecular junctions.

    Science.gov (United States)

    Weymann, Ireneusz

    2016-01-25

    In nanoscopic systems quantum confinement and interference can lead to an enhancement of thermoelectric properties as compared to conventional bulk materials. For nanostructures, such as molecules or quantum dots coupled to external leads, the thermoelectric figure of merit can reach or even exceed unity. Moreover, in the presence of external magnetic field or when the leads are ferromagnetic, an applied temperature gradient can generate a spin voltage and an associated spin current flow in the system, which makes such nanostructures particularly interesting for future thermoelectric applications. In this study, by using the numerical renormalization group method, we examine the spin-dependent thermoelectric transport properties of a molecular junction involving an orbital level with attractive Coulomb correlations coupled to ferromagnetic leads. We analyze how attractive correlations affect the spin-resolved transport properties of the system and find a nontrivial dependence of the conductance and tunnel magnetoresistance on the strength and sign of those correlations. We also demonstrate that attractive correlations can lead to an enhancement of the spin thermopower and the figure of merit, which can be controlled by a gate voltage.

  4. A photoionization study of hydrogen-bound clusters in a supersonic molecular beam

    International Nuclear Information System (INIS)

    Cook, K.D.; Jones, G.G.; Taylor, J.W.

    1980-01-01

    Hydrogen bonding of methanol, methanol-d, ethanol, and trifluoroethanol is investigated with a supersonic molecular beam as a sampling system for a photoionization quadrupole mass spectrometer. Monochromatized vacuum ultraviolet synchrotron radiation is used as the ionizing source. Cluster ions belonging to the series (ROH)sub(n)H + are detected when sampling up to 100-torr alcohol vapor with the molecular beam. No parent cluster molecular ions are detected. Experiments are described which exclude ion-molecule reactions in the mass spectrometer ion source as a possible origin of the cluster ions. Experimental evidence shows that nozzle temperature primarily influences the equilibrium distribution of clusters present in the nozzle source. From the dependences of relative cluster ion intensities on nozzle source temperature, the heats of formation of oligomers of the alcohols are estimated. Cooperative hydrogen bonding is not detected, expect for trifluoroethanol, where the trimer is found to be the most stable cluster. (orig.)

  5. Correction of auto interaction in the formalism of the local spin density: molecular systems

    International Nuclear Information System (INIS)

    Figueiredo, S.K. de.

    1987-01-01

    The auto-insertion correction proposed by Perdew and Zunger is introduced in the multiple scattering. The orbital spin relaxation is analyzed and this model is applied to the molecules = CH 4 , SiH 4 , GeH 4 as well as for the molecular compound GaAs with seventeen atoms in the [1Ga4As12Ga] configuration. (A.C.A.S.) [pt

  6. The enhanced spin-polarized transport behaviors through cobalt benzene-porphyrin-benzene molecular junctions: the effect of functional groups

    Science.gov (United States)

    Cheng, Jue-Fei; Zhou, Liping; Wen, Zhongqian; Yan, Qiang; Han, Qin; Gao, Lei

    2017-05-01

    The modification effects of the groups amino (NH2) and nitro (NO2) on the spin polarized transport properties of the cobalt benzene-porphyrin-benzene (Co-BPB) molecule coupled to gold (Au) nanowire electrodes are investigated by the nonequilibrium Green’s function method combined with the density functional theory. The calculation results show that functional groups can lead to the significant spin-filter effect, enhanced low-bias negative differential resistance (NDR) behavior and novel reverse rectifying effect in Co-BPB molecular junction. The locations and types of functional groups have distinct influences on spin-polarized transport performances. The configuration with NH2 group substituting H atom in central porphyrin ring has larger spin-down current compared to that with NO2 substitution. And Co-BPB molecule junction with NH2 group substituting H atom in side benzene ring shows reverse rectifying effect. Detailed analyses confirm that NH2 and NO2 group substitution change the spin-polarized transferred charge, which makes the highest occupied molecular orbitals (HOMO) of spin-down channel of Co-BPB closer to the Fermi level. And the shift of HOMO strengthens the spin-polarized coupling between the molecular orbitals and the electrodes, leading to the enhanced spin-polarized behavior. Our findings might be useful in the design of multi-functional molecular devices in the future.

  7. Anisotropic Rotational Diffusion Studied by Nuclear Spin Relaxation and Molecular Dynamics Simulation: An Undergraduate Physical Chemistry Laboratory

    Science.gov (United States)

    Fuson, Michael M.

    2017-01-01

    Laboratories studying the anisotropic rotational diffusion of bromobenzene using nuclear spin relaxation and molecular dynamics simulations are described. For many undergraduates, visualizing molecular motion is challenging. Undergraduates rarely encounter laboratories that directly assess molecular motion, and so the concept remains an…

  8. Spin-polarized transport properties of a pyridinium-based molecular spintronics device

    Science.gov (United States)

    Zhang, J.; Xu, B.; Qin, Z.

    2018-05-01

    By applying a first-principles approach based on non-equilibrium Green's functions combined with density functional theory, the transport properties of a pyridinium-based "radical-π-radical" molecular spintronics device are investigated. The obvious negative differential resistance (NDR) and spin current polarization (SCP) effect, and abnormal magnetoresistance (MR) are obtained. Orbital reconstruction is responsible for novel transport properties such as that the MR increases with bias and then decreases and that the NDR being present for both parallel and antiparallel magnetization configurations, which may have future applications in the field of molecular spintronics.

  9. bcl::Cluster : A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System.

    Science.gov (United States)

    Alexander, Nathan; Woetzel, Nils; Meiler, Jens

    2011-02-01

    Clustering algorithms are used as data analysis tools in a wide variety of applications in Biology. Clustering has become especially important in protein structure prediction and virtual high throughput screening methods. In protein structure prediction, clustering is used to structure the conformational space of thousands of protein models. In virtual high throughput screening, databases with millions of drug-like molecules are organized by structural similarity, e.g. common scaffolds. The tree-like dendrogram structure obtained from hierarchical clustering can provide a qualitative overview of the results, which is important for focusing detailed analysis. However, in practice it is difficult to relate specific components of the dendrogram directly back to the objects of which it is comprised and to display all desired information within the two dimensions of the dendrogram. The current work presents a hierarchical agglomerative clustering method termed bcl::Cluster. bcl::Cluster utilizes the Pymol Molecular Graphics System to graphically depict dendrograms in three dimensions. This allows simultaneous display of relevant biological molecules as well as additional information about the clusters and the members comprising them.

  10. Deformation of Ag clusters deposited on Au(111) - Experiment and molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Miroslawski, Natalie; Groenhagen, Niklas; Hoevel, Heinz [TU Dortmund, Experimentelle Physik I (Germany); Issendorff, Bernd von [Universitaet Freiburg, Fakultaet Physik (Germany); Jaervi, Tommi [Fraunhofer Institut fuer Werkstoffmechanik, Freiburg (Germany); Moseler, Michael [Universitaet Freiburg, Fakultaet Physik (Germany); Fraunhofer Institut fuer Werkstoffmechanik, Freiburg (Germany); Freiburger Materialforschungszentrum (Germany)

    2011-07-01

    Mass selected clusters from Ag{sup +}{sub 55} to Ag{sup +}{sub 147{+-}}{sub 2} were deposited with different deposition energies at 77 K on Au(111) and imaged with STM at 77 K. We observed a deformation of the cluster shape due to the strong metallic interaction between the cluster and the substrate. The clusters became epitaxial and developed a structure composed of several Ag monolayers. The number of these monolayers depends on the number of atoms in the cluster and the deposition energy. The larger the cluster mass the more monolayers the cluster develops on Au(111) and the larger the deposition energy the fewer monolayers occur. These results were verified by molecular dynamic simulations. Additionally the behaviour of Ag{sub N} clusters on Au(111) after different annealing steps was investigated.

  11. Molecular detection using Rydberg, autoionizing, and cluster states. Progress report

    Energy Technology Data Exchange (ETDEWEB)

    Wessel, J.

    1989-08-17

    Continuing investigations of multiphoton ionization processes in naphthalene have established the geometry and spectroscopy of trimer and tetramer cluster states. A new, highly efficient ionization mechanism has been identified in the trimer. It is closely related to autoionization of 2-electron atoms by resonant 2-photon excitation and to exciton fusion in larger clusters.

  12. Low energy Cu clusters slow deposition on a Fe (001) surface investigated by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Shixu [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Laboratory of Advanced Nuclear Materials, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Gong, Hengfeng [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Division of Nuclear Materials Science and Engineering, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); Chen, Xuanzhi [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Li, Gongping, E-mail: ligp@lzu.edu.cn [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Wang, Zhiguang, E-mail: zhgwang@impcas.ac.cn [Laboratory of Advanced Nuclear Materials, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China)

    2014-09-30

    Highlights: • We study the deposition of low energy Cu clusters on Fe (001) surface by molecular dynamics. • The interaction between low energy cluster and substrate can be divided to the landing and the thermal diffusion phases. • The phenomenon of contact epitaxy of cluster occurred. • The thermal diffusion of cluster atoms was analyzed. - Abstract: The slow deposition of low energy Cu clusters on a Fe (001) surface was investigated by molecular dynamics simulation. A many-body potential based on Finnis–Sinclair model was used to describe the interactions among atoms. Three clusters comprising of 13, 55 and 147 atoms, respectively, were deposited with incident energies ranging from 0.0 to 1.0 eV/atom at various substrate temperatures (0, 300 and 800 K). The rearrangement and the diffusion of cluster can occur, only when the cluster atoms are activated and obtained enough migration energy. The interaction between low energy cluster and substrate can be divided to the landing and the thermal diffusion phases. In the former, the migration energy originates from the latent heat of binding energy for the soft deposition regime and primarily comes from the incident energy of cluster for the energetic cluster deposition regime. In the latter, the thermal vibration would result in some cluster atoms activated again at medium and high substrate temperatures. Also, the effects of incident energy, cluster size and substrate temperature on the interaction potential energy between cluster and substrate, the final deposition morphology of cluster, the spreading index and the structure parameter of cluster are analyzed.

  13. Endohedral Metallofullerene as Molecular High Spin Qubit: Diverse Rabi Cycles in Gd2@C79N.

    Science.gov (United States)

    Hu, Ziqi; Dong, Bo-Wei; Liu, Zheng; Liu, Jun-Jie; Su, Jie; Yu, Changcheng; Xiong, Jin; Shi, Di-Er; Wang, Yuanyuan; Wang, Bing-Wu; Ardavan, Arzhang; Shi, Zujin; Jiang, Shang-Da; Gao, Song

    2018-01-24

    An anisotropic high-spin qubit with long coherence time could scale the quantum system up. It has been proposed that Grover's algorithm can be implemented in such systems. Dimetallic aza[80]fullerenes M 2 @C 79 N (M = Y or Gd) possess an unpaired electron located between two metal ions, offering an opportunity to manipulate spin(s) protected in the cage for quantum information processing. Herein, we report the crystallographic determination of Gd 2 @C 79 N for the first time. This molecular magnet with a collective high-spin ground state (S = 15/2) generated by strong magnetic coupling (J Gd-Rad = 350 ± 20 cm -1 ) has been unambiguously validated by magnetic susceptibility experiments. Gd 2 @C 79 N has quantum coherence and diverse Rabi cycles, allowing arbitrary superposition state manipulation between each adjacent level. The phase memory time reaches 5 μs at 5 K by dynamic decoupling. This molecule fulfills the requirements of Grover's searching algorithm proposed by Leuenberger and Loss.

  14. Enhanced Magnetoresistance in Molecular Junctions by Geometrical Optimization of Spin-Selective Orbital Hybridization.

    Science.gov (United States)

    Rakhmilevitch, David; Sarkar, Soumyajit; Bitton, Ora; Kronik, Leeor; Tal, Oren

    2016-03-09

    Molecular junctions based on ferromagnetic electrodes allow the study of electronic spin transport near the limit of spintronics miniaturization. However, these junctions reveal moderate magnetoresistance that is sensitive to the orbital structure at their ferromagnet-molecule interfaces. The key structural parameters that should be controlled in order to gain high magnetoresistance have not been established, despite their importance for efficient manipulation of spin transport at the nanoscale. Here, we show that single-molecule junctions based on nickel electrodes and benzene molecules can yield a significant anisotropic magnetoresistance of up to ∼200% near the conductance quantum G0. The measured magnetoresistance is mechanically tuned by changing the distance between the electrodes, revealing a nonmonotonic response to junction elongation. These findings are ascribed with the aid of first-principles calculations to variations in the metal-molecule orientation that can be adjusted to obtain highly spin-selective orbital hybridization. Our results demonstrate the important role of geometrical considerations in determining the spin transport properties of metal-molecule interfaces.

  15. Iron-sulfur cluster biogenesis in mammalian cells: new insights into the molecular mechanisms of cluster delivery

    Science.gov (United States)

    Maio, Nunziata; Rouault, Tracey. A.

    2014-01-01

    Iron-sulfur (Fe-S) clusters are ancient, ubiquitous cofactors composed of iron and inorganic sulfur. The combination of the chemical reactivity of iron and sulfur, together with many variations of cluster composition, oxidation states and protein environments, enables Fe-S clusters to participate in numerous biological processes. Fe-S clusters are essential to redox catalysis in nitrogen fixation, mitochondrial respiration and photosynthesis, to regulatory sensing in key metabolic pathways (i. e. cellular iron homeostasis and oxidative stress response), and to the replication and maintenance of the nuclear genome. Fe-S cluster biogenesis is a multistep process that involves a complex sequence of catalyzed protein- protein interactions and coupled conformational changes between the components of several dedicated multimeric complexes. Intensive studies of the assembly process have clarified key points in the biogenesis of Fe-S proteins. However several critical questions still remain, such as: what is the role of frataxin? Why do some defects of Fe-S cluster biogenesis cause mitochondrial iron overload? How are specific Fe-S recipient proteins recognized in the process of Fe-S transfer? This review focuses on the basic steps of Fe-S cluster biogenesis, drawing attention to recent advances achieved on the identification of molecular features that guide selection of specific subsets of nascent Fe-S recipients by the cochaperone HSC20. Additionally, it outlines the distinctive phenotypes of human diseases due to mutations in the components of the basic pathway. PMID:25245479

  16. The Role of Antisymmetric Exchange on the Quantum Interference between States of Different Spin Length in a dimeric Molecular Nanomagnet.

    Science.gov (United States)

    Del Barco, Enrique

    2009-03-01

    We report direct evidence of quantum oscillations of the total spin length of a dimeric molecular nanomagnet through the observation of quantum interference associated with tunneling trajectories between states having different spin quantum numbers. As we outline, this is a consequence of the unique characteristics of a molecular Mn12 wheel which behaves as a (weak) ferromagnetic exchange-coupled molecular dimer: each half of the molecule acts as a single-molecule magnet (SMM), while the weak coupling between the two halves gives rise to an additional internal spin degree of freedom within the molecule, namely that its total spin may fluctuate. This extra degree of freedom accounts for several magnetization tunneling resonances that cannot be explained within the usual giant spin approximation. More importantly, the observation of quantum interference provides unambiguous evidence for the quantum mechanical superposition involving entangled states of both halves of the wheel. Magnetization results obtained in two other versions of this compound, in which the ligands have been modified, show that slight variations of the relative distance between the Mn ions determine whether the molecule behaves as a rigid magnetic unit of spin S = 7 or as two exchange-coupled halves of spin S = 7/2. We analyze the effect of the Dzyaloshinskii-Moriya antisymmetric exchange interaction in a molecule with a centre of inversion symmetry and propose a formal model to account for the observed broken degeneracy that preserves the molecular inversion symmetry.

  17. Equilibrium Structures and Absorption Spectra for SixOy Molecular Clusters using Density Functional Theory

    Science.gov (United States)

    2017-05-05

    Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/6390--17-9724 Equilibrium Structures and Absorption Spectra for SixOy Molecular Clusters...TELEPHONE NUMBER (include area code) b. ABSTRACT c. THIS PAGE 18. NUMBER OF PAGES 17. LIMITATION OF ABSTRACT Equilibrium Structures and Absorption...and electronic excited-state absorption spectra for eqilibrium structures of SixOy molecular clusters using density function theory (DFT) and time

  18. Discovery of Multiseeded Multimode Formation of Embedded Clusters in the Rosette Molecular Complex

    Science.gov (United States)

    Li, Jin Zeng; Smith, Michael D.

    2005-02-01

    An investigation based on data from the spatially complete Two Micron All Sky Survey (2MASS) reveals that a remarkable burst of clustered star formation is taking place throughout the southeast quadrant of the Rosette Molecular Cloud. Compact clusters are forming in a multiseeded mode, in parallel and at various places. In addition, sparse aggregates of embedded young stars are extensively distributed. In this study we report the primary results and implications for high-mass and clustered star formation in giant molecular clouds. In particular, we incorporate for the first time the birth of medium- to low-mass stars into the scenario of sequential formation of OB clusters. Following the emergence of the young OB cluster NGC 2244, a variety of manifestations of forming clusters of medium to high mass appears in the vicinity of the swept-up layer of the H II region as well as farther into the molecular cloud. The embedded clusters appear to form in a structured manner, which suggests they follow tracks laid out by the decay of macroturbulence. We address the possible origins of the turbulence. This leads us to propose a tree model to interpret the neat spatial distribution of clusters within a large section of the Rosette complex. Prominent new-generation OB clusters are identified at the root of the tree pattern.

  19. 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.

  20. Molecular organization and dynamics of micellar phase of polyelectrolyte-surfactant complexes: ESR spin probe study

    Science.gov (United States)

    Wasserman, A. M.; Kasaikin, V. A.; Zakharova, Yu. A.; Aliev, I. I.; Baranovsky, V. Yu.; Doseva, V.; Yasina, L. L.

    2002-04-01

    Molecular dynamics and organization of the micellar phase of complexes of linear polyelectrolytes with ionogenic and non-ionogenic surfactants was studied by the ESR spin probe method. Complexes of polyacrylic acid (PAA) and sodium polystyrenesulfonate (PSS) with alkyltrimethylammonium bromides (ATAB), as well as complexes of poly- N, N'-dimethyldiallylammonium chloride (PDACL) with sodium dodecylsulfate (SDS) were studied. The micellar phase of such complexes is highly organized molecular system, molecular ordering of which near the polymeric chain is much higher than in the 'center' of the micelle, it depends on the polymer-detergent interaction, flexibility of polymeric chain and length of carbonic part of the detergent molecule. Complexes of polymethacrylic acid (PMAA) with non-ionic detergent (dodecyl-substituted polyethyleneglycol), show that the local mobility of surfactant in such complexes is significantly lower than in 'free' micelles and depends on the number of micellar particles participating in formation of complexes.

  1. A new apparatus for the study of electron impact fragmentation of molecular clusters

    International Nuclear Information System (INIS)

    Barrett, G; Burgt, P J M van der

    2008-01-01

    This paper reports on the development of a new experiment for the study of electron-impact induced dissociation and fragmentation of molecular clusters and biomolecules and other species solvated in water clusters. The purpose is to look at clusters that are of interest to biophysics, atmospheric physics, and other fields. The experiment consists of a differentially pumped vacuum system, with an expansion chamber to generate a pulsed supersonic beam of clusters, and a collision chamber where the cluster beam intersects with an electron beam. Water clusters can be seeded with biomolecules emerging from a resistively heated oven. Investigation will be possible into both ion yields and long-lived neutral metastable yields produced by electron-impact fragmentation of relevant clusters and biomolecules

  2. Antisymmetrized molecular dynamics studies for exotic clustering phenomena in neutron-rich nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Kimura, M. [Hokkaido University, Department of Physics, Sapporo (Japan); Hokkaido University, Nuclear Reaction Data Centre, Faculty of Science, Sapporo (Japan); Suhara, T. [Matsue College of Technology, Matsue (Japan); Kanada-En' yo, Y. [Kyoto University, Department of Physics, Kyoto (Japan)

    2016-12-15

    We present a review of recent works on clustering phenomena in unstable nuclei studied by antisymmetrized molecular dynamics (AMD). The AMD studies in these decades have uncovered novel types of clustering phenomena brought about by the excess neutrons. Among them, this review focuses on the molecule-like structure of unstable nuclei. One of the earliest discussions on the clustering in unstable nuclei was made for neutron-rich Be and B isotopes. AMD calculations predicted that the ground state clustering is enhanced or reduced depending on the number of excess neutrons. Today, the experiments are confirming this prediction as the change of the proton radii. Behind this enhancement and reduction of the clustering, there are underlying shell effects called molecular and atomic orbits. These orbits form covalent and ionic bonding of the clusters analogous to the atomic molecules. It was found that this ''molecular-orbit picture'' reasonably explains the low-lying spectra of Be isotopes. The molecular-orbit picture is extended to other systems having parity asymmetric cluster cores and to the three cluster systems. O and Ne isotopes are the candidates of the former, while the 3α linear chains in C isotopes are the latter. For both subjects, many intensive studies are now in progress. We also pay a special attention to the observables which are the fingerprint of the clustering. In particular, we focus on the monopole and dipole transitions which are recently regarded as good probe for the clustering. We discuss how they have and will reveal the exotic clustering. (orig.)

  3. Low-field spin dynamics of Cr7Ni and Cr7Ni-Cu-Cr7Ni molecular rings as detected by μsR

    OpenAIRE

    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.

    2017-01-01

    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...

  4. Adiabatic demagnetization of the antiferromagnetic spin-1/2 Heisenberg hexagonal cluster

    International Nuclear Information System (INIS)

    Deb, Moumita; Ghosh, Asim Kumar

    2016-01-01

    Exact analytic expressions of eigenvalues of the antiferromagnetic spin-1/2 Heisenberg hexagon in the presence of uniform magnetic field have been obtained. Magnetization process, nature of isentrops and properties of magneto caloric effect in terms of adiabatic demagnetization have been investigated. Theoretical results have been used to study the magneto caloric effect of the spin-1/2 Heisenberg hexagonal compound Cu_3WO_6.

  5. Molecular dynamics modelling of EGCG clusters on ceramide bilayers

    Energy Technology Data Exchange (ETDEWEB)

    Yeo, Jingjie; Cheng, Yuan; Li, Weifeng; Zhang, Yong-Wei [Institute of High Performance Computing, A*STAR, 138632 (Singapore)

    2015-12-31

    A novel method of atomistic modelling and characterization of both pure ceramide and mixed lipid bilayers is being developed, using only the General Amber ForceField. Lipid bilayers modelled as pure ceramides adopt hexagonal packing after equilibration, and the area per lipid and bilayer thickness are consistent with previously reported theoretical results. Mixed lipid bilayers are modelled as a combination of ceramides, cholesterol, and free fatty acids. This model is shown to be stable after equilibration. Green tea extract, also known as epigallocatechin-3-gallate, is introduced as a spherical cluster on the surface of the mixed lipid bilayer. It is demonstrated that the cluster is able to bind to the bilayers as a cluster without diffusing into the surrounding water.

  6. Molecular Gas Reservoirs in Cluster Galaxies at z = 1.46

    Science.gov (United States)

    Hayashi, Masao; Tadaki, Ken-ichi; Kodama, Tadayuki; Kohno, Kotaro; Yamaguchi, Yuki; Hatsukade, Bunyo; Koyama, Yusei; Shimakawa, Rhythm; Tamura, Yoichi; Suzuki, Tomoko L.

    2018-04-01

    We present molecular gas reservoirs of 18 galaxies associated with the XMMXCS J2215.9–1738 cluster at z = 1.46. From Band 7 and Band 3 data of the Atacama Large Millimeter/submillimeter Array, we detect dust continuum emission at 870 μm and the CO J = 2–1 emission line from 8 and 17 member galaxies, respectively, within a clustercentric radius of R 200. The molecular gas masses derived from the CO and/or dust continuum luminosities show that the fraction of molecular gas mass and the depletion timescale for the cluster galaxies are larger than expected from the scaling relations of molecular gas on stellar mass and offset from the main sequence of star-forming galaxies in general fields. The galaxies closer to the cluster center in terms of both projected position and accretion phase seem to show a larger deviation from the scaling relations. We speculate that the environment of the galaxy cluster helps feed the gas through inflow to the member galaxies and reduce the efficiency of star formation. The stacked Band 3 spectrum of 12 quiescent galaxies with M stellar ∼ 1011 M ⊙ within 0.5R 200 shows no detection of a CO emission line, giving the upper limit of molecular gas mass and molecular gas fraction to be ≲1010 M ⊙ and ≲10%, respectively. Therefore, the massive galaxies in the cluster core quench the star formation activity while consuming most of the gas reservoirs.

  7. Strong spin-filtering and spin-valve effects in a molecular V–C60–V contact

    Directory of Open Access Journals (Sweden)

    Mohammad Koleini

    2012-08-01

    Full Text Available Motivated by the recent achievements in the manipulation of C60 molecules in STM experiments, we study theoretically the structure and electronic properties of a C60 molecule in an STM tunneljunction with a magnetic tip and magnetic adatom on a Cu(111 surface using first-principles calculations. For the case of a vanadium tip/adatom, we demonstrate how spin coupling between the magnetic V atoms, mediated by the C60, can be observed in the electronic transport, which display a strong spin-filtering effect, allowing mainly majority-spin electrons to pass (>95%. Moreover, we find a significant change in the conductance between parallel and anti-parallel spin polarizations in the junction (86% which suggests that STM experiments should be able to characterize the magnetism and spin coupling for these systems.

  8. Strong spin-filtering and spin-valve effects in a molecular V-C-60-V contact

    DEFF Research Database (Denmark)

    Koleini, Mohammad; Brandbyge, Mads

    2012-01-01

    Motivated by the recent achievements in the manipulation of C-60 molecules in STM experiments, we study theoretically the structure and electronic properties of a C-60 molecule in an STM tunneljunction with a magnetic tip and magnetic adatom on a Cu(111) surface using first-principles calculations....... For the case of a vanadium tip/adatom, we demonstrate how spin coupling between the magnetic V atoms, mediated by the C-60, can be observed in the electronic transport, which display a strong spin-filtering effect, allowing mainly majority-spin electrons to pass (>95%). Moreover, we find a significant change...... in the conductance between parallel and anti-parallel spin polarizations in the junction (86%) which suggests that STM experiments should be able to characterize the magnetism and spin coupling for these systems....

  9. Molecular dynamic simulation on boron cluster implantation for shallow junction formation

    International Nuclear Information System (INIS)

    Yuan Li; Yu Min; Li Wei; Ji Huihui; Ren Liming; Zhan Kai; Huang Ru; Zhang Xing; Wang Yangyuan; Zhang Jinyu; Oka, Hideki

    2006-01-01

    Boron cluster ion implantation is a potential technology for shallow junction formation in integrated circuits manufacture. A molecular dynamic method for cluster implantation simulation, aiming at microelectronics application, is presented in this paper. Accurate geometric structures of boron clusters are described by the model, and the H atoms in clusters are included. A potential function taking the form of combining the ZBL and the SW potentials is presented here to model interaction among the atoms in the boron cluster. The impact of these models on cluster implantation simulation is investigated. There are notable impact on dopant distribution and amount of implantation defects with consideration of these models. The simulation on the distributions of B and H are verified by SIMS data

  10. The tunneling magnetoresistance and spin-polarized optoelectronic properties of graphyne-based molecular magnetic tunnel junctions

    International Nuclear Information System (INIS)

    Yang, Zhi; Ouyang, Bin; Lan, Guoqing; Xu, Li-Chun; Liu, Ruiping; Liu, Xuguang

    2017-01-01

    Using density functional theory and the non-equilibrium Green’s function method, we investigate the spin-dependent transport and optoelectronic properties of the graphyne-based molecular magnetic tunnel junctions (MMTJs). We find that these MMTJs exhibit an outstanding tunneling magnetoresistance (TMR) effect. The TMR value is as high as 10 6 %. When the magnetization directions of two electrodes are antiparallel under positive or negative bias voltages, two kinds of pure spin currents can be obtained in the systems. Furthermore, under the irradiation of infrared, visible or ultraviolet light, spin-polarized photocurrents can be generated in the MMTJs, but the corresponding microscopic mechanisms are different. More importantly, if the magnetization directions of two electrodes are antiparallel, the photocurrents with different spins are spatially separated, appearing at different electrodes. This phenomenon provides a new way to simultaneously generate two spin currents. (paper)

  11. The mobilies of chiral molecular cluster ions in He gas

    International Nuclear Information System (INIS)

    Saito, Kazuyuki; Matoba, Shiro; Koizumi, Tetsuo; Kojima, Takao M; Tanuma, Hajime; Shiromaru, Haruo

    2012-01-01

    We measured the mobilities of Li + -(2-butanol) and Li + -(limonene) ions in He gas at room temperature using a drift tube mass spectrometer. The zero field mobilities of Li + -(2-Butanol) and Li + -(Limonene) were much lower than the polarization limit, indicating that the geometric collision cross-sections between the cluster ions and He atom were larger than the cross-sections predicted by the presence of a polarization force alone.

  12. Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?

    NARCIS (Netherlands)

    Odong, T.L.; Heerwaarden, van J.; Jansen, J.; Hintum, van T.J.L.; Eeuwijk, van F.A.

    2011-01-01

    Despite the availability of newer approaches, traditional hierarchical clustering remains very popular in genetic diversity studies in plants. However, little is known about its suitability for molecular marker data. We studied the performance of traditional hierarchical clustering techniques using

  13. Local spin dynamics at low temperature in the slowly relaxing molecular chain [Dy(hfac)3{NIT(C6H4OPh)}]: A μ+ spin relaxation study

    Science.gov (United States)

    Arosio, Paolo; Corti, Maurizio; Mariani, Manuel; Orsini, Francesco; Bogani, Lapo; Caneschi, Andrea; Lago, Jorge; Lascialfari, Alessandro

    2015-05-01

    The spin dynamics of the molecular magnetic chain [Dy(hfac)3{NIT(C6H4OPh)}] were investigated by means of the Muon Spin Relaxation (μ+SR) technique. This system consists of a magnetic lattice of alternating Dy(III) ions and radical spins, and exhibits single-chain-magnet behavior. The magnetic properties of [Dy(hfac)3{NIT(C6H4OPh)}] have been studied by measuring the magnetization vs. temperature at different applied magnetic fields (H = 5, 3500, and 16500 Oe) and by performing μ+SR experiments vs. temperature in zero field and in a longitudinal applied magnetic field H = 3500 Oe. The muon asymmetry P(t) was fitted by the sum of three components, two stretched-exponential decays with fast and intermediate relaxation times, and a third slow exponential decay. The temperature dependence of the spin dynamics has been determined by analyzing the muon longitudinal relaxation rate λinterm(T), associated with the intermediate relaxing component. The experimental λinterm(T) data were fitted with a corrected phenomenological Bloembergen-Purcell-Pound law by using a distribution of thermally activated correlation times, which average to τ = τ0 exp(Δ/kBT), corresponding to a distribution of energy barriers Δ. The correlation times can be associated with the spin freezing that occurs when the system condenses in the ground state.

  14. Local spin dynamics at low temperature in the slowly relaxing molecular chain [Dy(hfac)3(NIT(C6H4OPh))]: A μ+ spin relaxation study

    International Nuclear Information System (INIS)

    Arosio, Paolo; Orsini, Francesco; Corti, Maurizio; Mariani, Manuel; Bogani, Lapo; Caneschi, Andrea; Lago, Jorge; Lascialfari, Alessandro

    2015-01-01

    The spin dynamics of the molecular magnetic chain [Dy(hfac) 3 (NIT(C 6 H 4 OPh))] were investigated by means of the Muon Spin Relaxation (μ + SR) technique. This system consists of a magnetic lattice of alternating Dy(III) ions and radical spins, and exhibits single-chain-magnet behavior. The magnetic properties of [Dy(hfac) 3 (NIT(C 6 H 4 OPh))] have been studied by measuring the magnetization vs. temperature at different applied magnetic fields (H = 5, 3500, and 16500 Oe) and by performing μ + SR experiments vs. temperature in zero field and in a longitudinal applied magnetic field H = 3500 Oe. The muon asymmetry P(t) was fitted by the sum of three components, two stretched-exponential decays with fast and intermediate relaxation times, and a third slow exponential decay. The temperature dependence of the spin dynamics has been determined by analyzing the muon longitudinal relaxation rate λ interm (T), associated with the intermediate relaxing component. The experimental λ interm (T) data were fitted with a corrected phenomenological Bloembergen-Purcell-Pound law by using a distribution of thermally activated correlation times, which average to τ = τ 0 exp(Δ/k B T), corresponding to a distribution of energy barriers Δ. The correlation times can be associated with the spin freezing that occurs when the system condenses in the ground state

  15. Novel spin dynamics in ferrimagnetic molecular chains from 1H NMR and μSR spin-lattice relaxation measurements

    International Nuclear Information System (INIS)

    Micotti, E.; Lascialfari, A.; Rigamonti, A.; Aldrovandi, S.; Caneschi, A.; Gatteschi, D.; Bogani, L.

    2004-01-01

    The spin dynamics in the helical chain Co(hfac) 2 NITPhOMe has been investigated by 1 H NMR and μSR relaxation. In the temperature range 15< T<60 K, the results are consistent with the relaxation of the homogeneous magnetization. For T≤15 K, NMR and μSR evidence a second spin relaxation mechanism, undetected by the magnetization measurements. From the analysis of these data, insights on this novel relaxation process are derived

  16. Novel spin dynamics in ferrimagnetic molecular chains from 1H NMR and μSR spin-lattice relaxation measurements

    Science.gov (United States)

    Micotti, E.; Lascialfari, A.; Rigamonti, A.; Aldrovandi, S.; Caneschi, A.; Gatteschi, D.; Bogani, L.

    2004-05-01

    The spin dynamics in the helical chain Co(hfac) 2NITPhOMe has been investigated by 1H NMR and μSR relaxation. In the temperature range 15spin relaxation mechanism, undetected by the magnetization measurements. From the analysis of these data, insights on this novel relaxation process are derived.

  17. A graph-clustering approach to search important molecular markers ...

    African Journals Online (AJOL)

    Here, we performed a comprehensive gene level assessment of Parkinson's disease using 16 colorectal cancer samples and nine normal samples. The results show that SLC6A3, SLC18A2, and EN1, etc., are related to Parkinson's disease. Besides, we further mined the underlying molecular mechanism within these ...

  18. Quantum and semiclassical spin networks: from atomic and molecular physics to quantum computing and gravity

    Science.gov (United States)

    Aquilanti, Vincenzo; Bitencourt, Ana Carla P.; Ferreira, Cristiane da S.; Marzuoli, Annalisa; Ragni, Mirco

    2008-11-01

    The mathematical apparatus of quantum-mechanical angular momentum (re)coupling, developed originally to describe spectroscopic phenomena in atomic, molecular, optical and nuclear physics, is embedded in modern algebraic settings which emphasize the underlying combinatorial aspects. SU(2) recoupling theory, involving Wigner's 3nj symbols, as well as the related problems of their calculations, general properties, asymptotic limits for large entries, nowadays plays a prominent role also in quantum gravity and quantum computing applications. We refer to the ingredients of this theory—and of its extension to other Lie and quantum groups—by using the collective term of 'spin networks'. Recent progress is recorded about the already established connections with the mathematical theory of discrete orthogonal polynomials (the so-called Askey scheme), providing powerful tools based on asymptotic expansions, which correspond on the physical side to various levels of semi-classical limits. These results are useful not only in theoretical molecular physics but also in motivating algorithms for the computationally demanding problems of molecular dynamics and chemical reaction theory, where large angular momenta are typically involved. As for quantum chemistry, applications of these techniques include selection and classification of complete orthogonal basis sets in atomic and molecular problems, either in configuration space (Sturmian orbitals) or in momentum space. In this paper, we list and discuss some aspects of these developments—such as for instance the hyperquantization algorithm—as well as a few applications to quantum gravity and topology, thus providing evidence of a unifying background structure.

  19. Molecular dynamics simulation of nanoscale surface diffusion of heterogeneous adatoms clusters

    International Nuclear Information System (INIS)

    Imran, Muhammad; Hussain, Fayyaz; Ullah, Hafeez; Ahmad, Ejaz; Rashid, Muhammad; Ismail, Muhammad; Cai, Yongqing; Javid, M Arshad; Ahmad, S A

    2016-01-01

    Molecular dynamics simulation employing the embedded atom method potential is utilized to investigate nanoscale surface diffusion mechanisms of binary heterogeneous adatoms clusters at 300 K, 500 K, and 700 K. Surface diffusion of heterogeneous adatoms clusters can be vital for the binary island growth on the surface and can be useful for the formation of alloy-based thin film surface through atomic exchange process. The results of the diffusion process show that at 300 K, the diffusion of small adatoms clusters shows hopping, sliding, and shear motion; whereas for large adatoms clusters (hexamer and above), the diffusion is negligible. At 500 K, small adatoms clusters, i.e., dimer, show almost all possible diffusion mechanisms including the atomic exchange process; however no such exchange is observed for adatoms clusters greater than dimer. At 700 K, the exchange mechanism dominates for all types of clusters, where Zr adatoms show maximum tendency and Ag adatoms show minimum or no tendency toward the exchange process. Separation and recombination of one or more adatoms are also observed at 500 K and 700 K. The Ag adatoms also occupy pop-up positions over the adatoms clusters for short intervals. At 700 K, the vacancies are also generated in the vicinity of the adatoms cluster, vacancy formation, filling, and shifting can be observed from the results. (paper)

  20. Ab Initio Molecular Dynamics Studies of Pb m Sb n ( m + n ≤ 9) Alloy Clusters

    Science.gov (United States)

    Song, Bingyi; Xu, Baoqiang; Yang, Bin; Jiang, Wenlong; Chen, Xiumin; Xu, Na; Liu, Dachun; Dai, Yongnian

    2017-10-01

    Structure, stability, and dynamics of Pb m Sb n ( m + n ≤ 9) clusters were investigated using ab initio molecular dynamics. Size dependence of binding energies, the second-order energy difference of clusters, dissociation energy, HOMO-LUMO gaps, Mayer bond order, and the diffusion coefficient of Pb m Sb n clusters were discussed. Results suggest that Pb3Sb2, Pb4Sb2, and Pb5Sb4 ( n = 2 or 4) clusters have higher stability than other clusters, which is consistent with previous findings. In case of Pb-Sb alloy, the dynamics results show that Pb4Sb2 (Pb-22.71 wt pct Sb) can exist in gas phase at 1073 K (800 °C), which reasonably explains the azeotropic phenomenon, and the calculated values are in agreement with the experimental results (Pb-22 wt pct Sb).

  1. Molecular growth in clusters of polycyclic aromatic hydrocarbons induced by collisions with ions

    International Nuclear Information System (INIS)

    Delaunay, Rudy

    2016-01-01

    This thesis concerns the experimental study of the interaction between low energy ions (keV range) and neutral isolated molecules or clusters of polycyclic aromatic hydrocarbons (PAH) in the gas phase. The use of ionising radiations on these complex molecular systems of astrophysical interest allowed to highlight processes of statistical fragmentation, corresponding to the redistribution of the energy through the degrees of freedom of the target, and non-statistical fragmentation, linked to binary collisions of the ions on the nuclei of the target. A mechanism of intermolecular growth in clusters of PAH is observed. It is associated to the ultrafast (≤ ps) formation of fragments inside the clusters following binary collisions. The presence of a molecular environment around the fragments formed during the interaction may initiate a process of reactivity between the fragments and the molecules of the clusters. More precisely, the study focusses on the importance of the electronic stopping power SE and the nuclear stopping power SN of the projectile ion. It shows that the molecular growth is enhanced when SN is higher than SE. This can be explained by the fact that the deposit of energy is mainly due to the interaction with the nuclei of the target. The process of growth has been observed for all the molecules of PAH studied during this thesis and also for nitrogenated analogues of the molecule of anthracene. This demonstrates that molecular growth may be efficiently induced by collisions of low energy ions with clusters of PAH. (author) [fr

  2. Accommodating error analysis in comparison and clustering of molecular fingerprints.

    OpenAIRE

    Salamon, H.; Segal, M. R.; Ponce de Leon, A.; Small, P. M.

    1998-01-01

    Molecular epidemiologic studies of infectious diseases rely on pathogen genotype comparisons, which usually yield patterns comprising sets of DNA fragments (DNA fingerprints). We use a highly developed genotyping system, IS6110-based restriction fragment length polymorphism analysis of Mycobacterium tuberculosis, to develop a computational method that automates comparison of large numbers of fingerprints. Because error in fragment length measurements is proportional to fragment length and is ...

  3. Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement

    Energy Technology Data Exchange (ETDEWEB)

    Bibby, Jaclyn [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Keegan, Ronan M. [Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); Mayans, Olga [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Winn, Martyn D. [Science and Technology Facilities Council Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Rigden, Daniel J., E-mail: drigden@liv.ac.uk [University of Liverpool, Liverpool L69 7ZB (United Kingdom)

    2013-11-01

    Processing of NMR structures for molecular replacement by AMPLE works well. AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models. Rosetta remodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided.

  4. Molecular-dynamics analysis of mobile helium cluster reactions near surfaces of plasma-exposed tungsten

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Lin; Maroudas, Dimitrios, E-mail: maroudas@ecs.umass.edu [Department of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts 01003-9303 (United States); Hammond, Karl D. [Department of Chemical Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Wirth, Brian D. [Department of Nuclear Engineering, University of Tennessee, Knoxville, Tennessee 37996 (United States)

    2015-10-28

    We report the results of a systematic atomic-scale analysis of the reactions of small mobile helium clusters (He{sub n}, 4 ≤ n ≤ 7) near low-Miller-index tungsten (W) surfaces, aiming at a fundamental understanding of the near-surface dynamics of helium-carrying species in plasma-exposed tungsten. These small mobile helium clusters are attracted to the surface and migrate to the surface by Fickian diffusion and drift due to the thermodynamic driving force for surface segregation. As the clusters migrate toward the surface, trap mutation (TM) and cluster dissociation reactions are activated at rates higher than in the bulk. TM produces W adatoms and immobile complexes of helium clusters surrounding W vacancies located within the lattice planes at a short distance from the surface. These reactions are identified and characterized in detail based on the analysis of a large number of molecular-dynamics trajectories for each such mobile cluster near W(100), W(110), and W(111) surfaces. TM is found to be the dominant cluster reaction for all cluster and surface combinations, except for the He{sub 4} and He{sub 5} clusters near W(100) where cluster partial dissociation following TM dominates. We find that there exists a critical cluster size, n = 4 near W(100) and W(111) and n = 5 near W(110), beyond which the formation of multiple W adatoms and vacancies in the TM reactions is observed. The identified cluster reactions are responsible for important structural, morphological, and compositional features in the plasma-exposed tungsten, including surface adatom populations, near-surface immobile helium-vacancy complexes, and retained helium content, which are expected to influence the amount of hydrogen re-cycling and tritium retention in fusion tokamaks.

  5. Cluster-spin dynamics in a GaMo{sub 4}S{sub 8}-type compound: {sup 27}Al nuclear magnetic resonance study of AlMo{sub 4}S{sub 8}

    Energy Technology Data Exchange (ETDEWEB)

    Ikeno, R; Nakamura, H; Kohara, T [Graduate School of Material Science, University of Hyogo, Kamigori, Ako-gun, Hyogo 678-1297 (Japan)

    2007-01-31

    The cluster-spin dynamics of the tetrahedral Mo{sub 4} cluster, involved in AlMo{sub 4}S{sub 8} with a cubic GaMo{sub 4}S{sub 8} type structure, was investigated by NMR of the nonmagnetic {sup 27}Al site located outside the cluster. The nuclear spin-lattice relaxation is described well by the conventional local moment model assuming the presence of S=1/2 at each cluster, indicating that each Mo{sub 4} cluster behaves like a local spin with rigid magnitude. This behaviour is in contrast to the in-cluster relaxation, which reflects the spin-density fluctuations inside the cluster as a small unit of metal.

  6. Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement.

    Science.gov (United States)

    Dahms, Sven O; Kuester, Miriam; Streb, Carsten; Roth, Christian; Sträter, Norbert; Than, Manuel E

    2013-02-01

    Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradecabromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome.

  7. Design of a 15N Molecular Unit to Achieve Long Retention of Hyperpolarized Spin State

    Science.gov (United States)

    Nonaka, Hiroshi; Hirano, Masashi; Imakura, Yuki; Takakusagi, Yoichi; Ichikawa, Kazuhiro; Sando, Shinsuke

    2017-01-01

    Nuclear hyperpolarization is a phenomenon that can be used to improve the sensitivity of magnetic resonance molecular sensors. However, such sensors typically suffer from short hyperpolarization lifetime. Herein we report that [15N, D14]trimethylphenylammonium (TMPA) has a remarkably long spin-lattice relaxation time (1128 s, 14.1 T, 30 °C, D2O) on its 15N nuclei and achieves a long retention of the hyperpolarized state. [15N, D14]TMPA-based hyperpolarized sensor for carboxylesterase allowed the highly sensitive analysis of enzymatic reaction by 15N NMR for over 40 min in phophate-buffered saline (H2O, pH 7.4, 37 °C).

  8. Condensation and dissociation rates for gas phase metal clusters from molecular dynamics trajectory calculations

    Science.gov (United States)

    Yang, Huan; Goudeli, Eirini; Hogan, Christopher J.

    2018-04-01

    In gas phase synthesis systems, clusters form and grow via condensation, in which a monomer binds to an existing cluster. While a hard-sphere equation is frequently used to predict the condensation rate coefficient, this equation neglects the influences of potential interactions and cluster internal energy on the condensation process. Here, we present a collision rate theory-molecular dynamics simulation approach to calculate condensation probabilities and condensation rate coefficients. We use this approach to examine atomic condensation onto 6-56-atom Au and Mg clusters. The probability of condensation depends upon the initial relative velocity (v) between atom and cluster and the initial impact parameter (b). In all cases, there is a well-defined region of b-v space where condensation is highly probable, and outside of which the condensation probability drops to zero. For Au clusters with more than 10 atoms, we find that at gas temperatures in the 300-1200 K range, the condensation rate coefficient exceeds the hard-sphere rate coefficient by a factor of 1.5-2.0. Conversely, for Au clusters with 10 or fewer atoms and for 14- and 28-atom Mg clusters, as cluster equilibration temperature increases, the condensation rate coefficient drops to values below the hard-sphere rate coefficient. Calculations also yield the self-dissociation rate coefficient, which is found to vary considerably with gas temperature. Finally, calculations results reveal that grazing (high b) atom-cluster collisions at elevated velocity (>1000 m s-1) can result in the colliding atom rebounding (bounce) from the cluster surface or binding while another atom dissociates (replacement). The presented method can be applied in developing rate equations to predict material formation and growth rates in vapor phase systems.

  9. MOLECULAR CLUMPS AND INFRARED CLUSTERS IN THE S247, S252, AND BFS52 REGIONS

    Energy Technology Data Exchange (ETDEWEB)

    Shimoikura, Tomomi; Dobashi, Kazuhito [Department of Astronomy and Earth Sciences, Tokyo Gakugei University, Koganei, Tokyo 184-8501 (Japan); Saito, Hiro; Nakamura, Fumitaka [National Astronomical Observatory of Japan, Mitaka, Tokyo 181-8588 (Japan); Matsumoto, Tomoaki [Hosei University, Fujimi, Chiyoda-ku, Tokyo 102-8160 (Japan); Nishimura, Atsushi; Kimura, Kimihiro; Onishi, Toshikazu; Ogawa, Hideo, E-mail: ikura@u-gakugei.ac.jp [Department of Physical Science, Osaka Prefecture University, Sakai, Osaka 599-8531 (Japan)

    2013-05-01

    We present results of the observations carried out toward the S247, S252, and BFS52 H II regions with various molecular lines using the 1.85 m radio telescope and the 45 m telescope at Nobeyama Radio Observatory. There are at least 11 young infrared clusters (IR clusters) within the observed region. We found that there are two velocity components in {sup 12}CO (J = 2-1), and also that their spatial distributions show an anti-correlation. The IR clusters are located at their interfaces, suggesting that two distinct clouds with different velocities are colliding with each other, which may have induced the cluster formation. Based on {sup 13}CO (J = 1-0) and C{sup 18}O (J = 1-0) observations, we identified 16 clumps in and around the three H II regions. Eleven of the clumps are associated with the IR clusters and the other five clumps are not associated with any known young stellar objects. We investigated variations in the velocity dispersions of the 16 clumps as a function of the distance from the center of the clusters or the clumps. Clumps with clusters tend to have velocity dispersions that increase with distance from the cluster center, while clumps without clusters show a flat velocity dispersion over the clump extents. A {sup 12}CO outflow has been found in some of the clumps with IR clusters but not in the other clumps, supporting a strong relation of these clumps to the broader velocity dispersion region. We also estimated a mean star formation efficiency of {approx}30% for the clumps with IR clusters in the three H II regions.

  10. Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement

    International Nuclear Information System (INIS)

    Dahms, Sven O.; Kuester, Miriam; Streb, Carsten; Roth, Christian; Sträter, Norbert; Than, Manuel E.

    2013-01-01

    A new approach is presented that allows the efficient localization and orientation of heavy-atom cluster compounds used in experimental phasing by a molecular replacement procedure. This permits the calculation of meaningful phases up to the highest resolution of the diffraction data. Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradecabromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome

  11. Protein rotational dynamics investigated with a dual EPR/optical molecular probe. Spin-labeled eosin.

    Science.gov (United States)

    Cobb, C E; Hustedt, E J; Beechem, J M; Beth, A H

    1993-01-01

    An acyl spin-label derivative of 5-aminoeosin (5-SLE) was chemically synthesized and employed in studies of rotational dynamics of the free probe and of the probe when bound noncovalently to bovine serum albumin using the spectroscopic techniques of fluorescence anisotropy decay and electron paramagnetic resonance (EPR) and their long-lifetime counterparts phosphorescence anisotropy decay and saturation transfer EPR. Previous work (Beth, A. H., Cobb, C. E., and J. M. Beechem, 1992. Synthesis and characterization of a combined fluorescence, phosphorescence, and electron paramagnetic resonance probe. Society of Photo-Optical Instrumentation Engineers. Time-Resolved Laser Spectroscopy III. 504-512) has shown that the spin-label moiety only slightly altered the fluorescence and phosphorescence lifetimes and quantum yields of 5-SLE when compared with 5-SLE whose nitroxide had been reduced with ascorbate and with the diamagnetic homolog 5-acetyleosin. In the present work, we have utilized time-resolved fluorescence anisotropy decay and linear EPR spectroscopies to observe and quantitate the psec motions of 5-SLE in solution and the nsec motions of the 5-SLE-bovine serum albumin complex. Time-resolved phosphorescence anisotropy decay and saturation transfer EPR studies have been carried out to observe and quantitate the microseconds motions of the 5-SLE-albumin complex in glycerol/buffer solutions of varying viscosity. These latter studies have enabled a rigorous comparison of rotational correlation times obtained from these complementary techniques to be made with a single probe. The studies described demonstrate that it is possible to employ a single molecular probe to carry out the full range of fluorescence, phosphorescence, EPR, and saturation transfer EPR studies. It is anticipated that "dual" molecular probes of this general type will significantly enhance capabilities for extracting dynamics and structural information from macromolecules and their functional

  12. Molecular order and T1-relaxation, cross-relaxation in nitroxide spin labels

    Science.gov (United States)

    Marsh, Derek

    2018-05-01

    Interpretation of saturation-recovery EPR experiments on nitroxide spin labels whose angular rotation is restricted by the orienting potential of the environment (e.g., membranes) currently concentrates on the influence of rotational rates and not of molecular order. Here, I consider the dependence on molecular ordering of contributions to the rates of electron spin-lattice relaxation and cross relaxation from modulation of N-hyperfine and Zeeman anisotropies. These are determined by the averages and , where θ is the angle between the nitroxide z-axis and the static magnetic field, which in turn depends on the angles that these two directions make with the director of uniaxial ordering. For saturation-recovery EPR at 9 GHz, the recovery rate constant is predicted to decrease with increasing order for the magnetic field oriented parallel to the director, and to increase slightly for the perpendicular field orientation. The latter situation corresponds to the usual experimental protocol and is consistent with the dependence on chain-labelling position in lipid bilayer membranes. An altered dependence on order parameter is predicted for saturation-recovery EPR at high field (94 GHz) that is not entirely consistent with observation. Comparisons with experiment are complicated by contributions from slow-motional components, and an unexplained background recovery rate that most probably is independent of order parameter. In general, this analysis supports the interpretation that recovery rates are determined principally by rotational diffusion rates, but experiments at other spectral positions/field orientations could increase the sensitivity to order parameter.

  13. Kinetic methods for measuring the temperature of clusters and nanoparticles in molecular beams

    International Nuclear Information System (INIS)

    Makarov, Grigorii N

    2011-01-01

    The temperature (internal energy) of clusters and nanoparticles is an important physical parameter which affects many of their properties and the character of processes they are involved in. At the same time, determining the temperature of free clusters and nanoparticles in molecular beams is a rather complicated problem because the temperature of small particles depends on their size. In this paper, recently developed kinetic methods for measuring the temperature of clusters and nanoparticles in molecular beams are reviewed. The definition of temperature in the present context is given, and how the temperature affects the properties of and the processes involving the particles is discussed. The temperature behavior of clusters and nanoparticles near a phase transition point is analyzed. Early methods for measuring the temperature of large clusters are briefly described. It is shown that, compared to other methods, new kinetic methods are more universal and applicable for determining the temperature of clusters and nanoparticles of practically any size and composition. The future development and applications of these methods are outlined. (reviews of topical problems)

  14. Mobility of hydrogen-helium clusters in tungsten studied by molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Grigorev, Petr, E-mail: grigorievpit@gmail.com [SCK-CEN, Nuclear Materials Science Institute, Boeretang 200, Mol, 2400 (Belgium); Ghent University, Applied Physics EA17 FUSION-DC, St.Pietersnieuwstraat, 41 B4, B-9000, Gent (Belgium); Department of Experimental Nuclear Physics K-89, Institute of Physics, Nanotechnologies, and Telecommunications, Peter the Great St.Petersburg Polytechnic University, St. Petersburg (Russian Federation); Terentyev, Dmitry; Bonny, Giovanni [SCK-CEN, Nuclear Materials Science Institute, Boeretang 200, Mol, 2400 (Belgium); Zhurkin, Evgeny E. [Department of Experimental Nuclear Physics K-89, Institute of Physics, Nanotechnologies, and Telecommunications, Peter the Great St.Petersburg Polytechnic University, St. Petersburg (Russian Federation); Oost, Guido van [Ghent University, Applied Physics EA17 FUSION-DC, St.Pietersnieuwstraat, 41 B4, B-9000, Gent (Belgium); Noterdaeme, Jean-Marie [Ghent University, Applied Physics EA17 FUSION-DC, St.Pietersnieuwstraat, 41 B4, B-9000, Gent (Belgium); Max-Planck-Institut für Plasmaphysik, Garching (Germany)

    2016-06-15

    Tungsten is a primary candidate material for plasma facing components in fusion reactors. Interaction of plasma components with the material is unavoidable and will lead to degradation of the performance and the lifetime of the in-vessel components. In order to gain better understanding the mechanisms driving the material degradation at atomic level, atomistic simulations are employed. In this work we study migration, stability and self-trapping properties of pure helium and mixed helium-hydrogen clusters in tungsten by means of molecular dynamics simulations. We test two versions of an embedded atom model interatomic potential by comparing it with ab initio data regarding the binding properties of He clusters. By analysing the trajectories of the clusters during molecular dynamics simulations at finite temperatures we obtain the diffusion parameters. The results show that the diffusivity of mixed clusters is significantly lower, than that of pure helium clusters. The latter suggest that the formation of mixed clusters during mixed hydrogen helium plasma exposure will affect the helium diffusivity in the material.

  15. Star cluster formation in a turbulent molecular cloud self-regulated by photoionization feedback

    Science.gov (United States)

    Gavagnin, Elena; Bleuler, Andreas; Rosdahl, Joakim; Teyssier, Romain

    2017-12-01

    Most stars in the Galaxy are believed to be formed within star clusters from collapsing molecular clouds. However, the complete process of star formation, from the parent cloud to a gas-free star cluster, is still poorly understood. We perform radiation-hydrodynamical simulations of the collapse of a turbulent molecular cloud using the RAMSES-RT code. Stars are modelled using sink particles, from which we self-consistently follow the propagation of the ionizing radiation. We study how different feedback models affect the gas expulsion from the cloud and how they shape the final properties of the emerging star cluster. We find that the star formation efficiency is lower for stronger feedback models. Feedback also changes the high-mass end of the stellar mass function. Stronger feedback also allows the establishment of a lower density star cluster, which can maintain a virial or sub-virial state. In the absence of feedback, the star formation efficiency is very high, as well as the final stellar density. As a result, high-energy close encounters make the cluster evaporate quickly. Other indicators, such as mass segregation, statistics of multiple systems and escaping stars confirm this picture. Observations of young star clusters are in best agreement with our strong feedback simulation.

  16. Semiclassical Hybrid Approach to Condensed Phase Molecular Dynamics: Application to the I2Kr17 Cluster

    Czech Academy of Sciences Publication Activity Database

    Buchholz, M.; Goletz, Ch. M.; Grossman, F.; Schmidt, B.; Heyda, J.; Jungwirth, Pavel

    2012-01-01

    Roč. 116, č. 46 (2012), s. 11199-11210 ISSN 1089-5639 R&D Projects: GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : semiclassical molecular dynamics * cluster * wavepacket * coherence * spectra Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.771, year: 2012

  17. Molecular dynamics simulations of sputtering of organic overlayers by slow, large clusters

    International Nuclear Information System (INIS)

    Rzeznik, L.; Czerwinski, B.; Garrison, B.J.; Winograd, N.; Postawa, Z.

    2008-01-01

    The ion-stimulated desorption of organic molecules by impact of large and slow clusters is examined using molecular dynamics (MDs) computer simulations. The investigated system, represented by a monolayer of benzene deposited on Ag{1 1 1}, is irradiated with projectiles composed of thousands of noble gas atoms having a kinetic energy of 0.1-20 eV/atom. The sputtering yield of molecular species and the kinetic energy distributions are analyzed and compared to the results obtain for PS4 overlayer. The simulations demonstrate quite clearly that the physics of ejection by large and slow clusters is distinct from the ejection events stimulated by the popular SIMS clusters, like C 60 , Au 3 and SF 5 at tens of keV energies.

  18. Spin-canting magnetization in an unusual Co4 cluster-based layer compound from a 2,3-dihydroxyquinoxaline ligand.

    Science.gov (United States)

    Yang, Chen-I; Chuang, Po-Hsiang; Lee, Gene-Hsiang; Peng, Shie-Ming; Lu, Kuang-Lieh

    2012-01-16

    The self-assembly of Co(O(2)CPh)(2) with a 2,3-dihydroxyquinoxaline (H(2)dhq) linker has revealed a new two-dimensional cluster-based compound, [Co(4)(OMe)(2)(O(2)CPh)(2)(dhq)(2)(MeOH)(2)](n), which shows spin-canted magnetization and a definite magnetic hysteresis loop.

  19. Spin orbit coupling for molecular ab initio density matrix renormalization group calculations: Application to g-tensors

    Energy Technology Data Exchange (ETDEWEB)

    Roemelt, Michael, E-mail: michael.roemelt@theochem.rub.de [Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany and Max-Planck Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany)

    2015-07-28

    Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.

  20. Spin-orbit splitted excited states using explicitly-correlated equation-of-motion coupled-cluster singles and doubles eigenvectors

    Science.gov (United States)

    Bokhan, Denis; Trubnikov, Dmitrii N.; Perera, Ajith; Bartlett, Rodney J.

    2018-04-01

    An explicitly-correlated method of calculation of excited states with spin-orbit couplings, has been formulated and implemented. Developed approach utilizes left and right eigenvectors of equation-of-motion coupled-cluster model, which is based on the linearly approximated explicitly correlated coupled-cluster singles and doubles [CCSD(F12)] method. The spin-orbit interactions are introduced by using the spin-orbit mean field (SOMF) approximation of the Breit-Pauli Hamiltonian. Numerical tests for several atoms and molecules show good agreement between explicitly-correlated results and the corresponding values, calculated in complete basis set limit (CBS); the highly-accurate excitation energies can be obtained already at triple- ζ level.

  1. Melting behaviour of gold-platinum nanoalloy clusters by molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Ong, Yee Pin; Yoon, Tiem Leong [School of Physics, Universiti Sains Malaysia, 11800 USM, Penang (Malaysia); Lim, Thong Leng [Faculty of Engineering and Technology, Multimedia University, Melaka Campus, 75450 Melaka (Malaysia)

    2015-04-24

    The melting behavior of bimetallic gold-platinum nanoclusters is studied by applying Brownian-type isothermal molecular dynamics (MD) simulation, a program modified from the cubic coupling scheme (CCS). The process begins with the ground-state structures obtained from global minimum search algorithm and proceeds with the investigation of the effect of temperature on the thermal properties of gold-platinum nanoalloy clusters. N-body Gupta potential has been employed in order to account for the interactions between gold and platinum atoms. The ground states of the nanoalloy clusters, which are core-shell segregated, are heated until they become thermally segregated. The detailed melting mechanism of the nanoalloy clusters is studied via this approach to provide insight into the thermal stability of the nanoalloy clusters.

  2. Water droplet excess free energy determined by cluster mitosis using guided molecular dynamics

    Science.gov (United States)

    Lau, Gabriel V.; Hunt, Patricia A.; Müller, Erich A.; Jackson, George; Ford, Ian J.

    2015-12-01

    Atmospheric aerosols play a vital role in affecting climate by influencing the properties and lifetimes of clouds and precipitation. Understanding the underlying microscopic mechanisms involved in the nucleation of aerosol droplets from the vapour phase is therefore of great interest. One key thermodynamic quantity in nucleation is the excess free energy of cluster formation relative to that of the saturated vapour. In our current study, the excess free energy is extracted for clusters of pure water modelled with the TIP4P/2005 intermolecular potential using a method based on nonequilibrium molecular dynamics and the Jarzynski relation. The change in free energy associated with the "mitosis" or division of a cluster of N water molecules into two N/2 sub-clusters is evaluated. This methodology is an extension of the disassembly procedure used recently to calculate the excess free energy of argon clusters [H. Y. Tang and I. J. Ford, Phys. Rev. E 91, 023308 (2015)]. Our findings are compared to the corresponding excess free energies obtained from classical nucleation theory (CNT) as well as internally consistent classical theory (ICCT). The values of the excess free energy that we obtain with the mitosis method are consistent with CNT for large cluster sizes but for the smallest clusters, the results tend towards ICCT; for intermediate sized clusters, we obtain values between the ICCT and CNT predictions. Furthermore, the curvature-dependent surface tension which can be obtained by regarding the clusters as spherical droplets of bulk density is found to be a monotonically increasing function of cluster size for the studied range. The data are compared to other values reported in the literature, agreeing qualitatively with some but disagreeing with the values determined by Joswiak et al. [J. Phys. Chem. Lett. 4, 4267 (2013)] using a biased mitosis approach; an assessment of the differences is the main motivation for our current study.

  3. Water droplet excess free energy determined by cluster mitosis using guided molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Lau, Gabriel V.; Müller, Erich A.; Jackson, George [Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Hunt, Patricia A. [Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Ford, Ian J. [Department of Physics and Astronomy and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT (United Kingdom)

    2015-12-28

    Atmospheric aerosols play a vital role in affecting climate by influencing the properties and lifetimes of clouds and precipitation. Understanding the underlying microscopic mechanisms involved in the nucleation of aerosol droplets from the vapour phase is therefore of great interest. One key thermodynamic quantity in nucleation is the excess free energy of cluster formation relative to that of the saturated vapour. In our current study, the excess free energy is extracted for clusters of pure water modelled with the TIP4P/2005 intermolecular potential using a method based on nonequilibrium molecular dynamics and the Jarzynski relation. The change in free energy associated with the “mitosis” or division of a cluster of N water molecules into two N/2 sub-clusters is evaluated. This methodology is an extension of the disassembly procedure used recently to calculate the excess free energy of argon clusters [H. Y. Tang and I. J. Ford, Phys. Rev. E 91, 023308 (2015)]. Our findings are compared to the corresponding excess free energies obtained from classical nucleation theory (CNT) as well as internally consistent classical theory (ICCT). The values of the excess free energy that we obtain with the mitosis method are consistent with CNT for large cluster sizes but for the smallest clusters, the results tend towards ICCT; for intermediate sized clusters, we obtain values between the ICCT and CNT predictions. Furthermore, the curvature-dependent surface tension which can be obtained by regarding the clusters as spherical droplets of bulk density is found to be a monotonically increasing function of cluster size for the studied range. The data are compared to other values reported in the literature, agreeing qualitatively with some but disagreeing with the values determined by Joswiak et al. [J. Phys. Chem. Lett. 4, 4267 (2013)] using a biased mitosis approach; an assessment of the differences is the main motivation for our current study.

  4. Dynamics and molecular determinants of cytoplasmic lipid droplet clustering and dispersion.

    Directory of Open Access Journals (Sweden)

    David J Orlicky

    Full Text Available Perilipin-1 (Plin1, a prominent cytoplasmic lipid droplet (CLD binding phosphoprotein and key physiological regulator of triglyceride storage and lipolysis in adipocytes, is thought to regulate the fragmentation and dispersion of CLD that occurs in response to β-adrenergic activation of adenylate cyclase. Here we investigate the dynamics and molecular determinants of these processes using cell lines stably expressing recombinant forms of Plin1 and/or other members of the perilipin family. Plin1 and a C-terminal CLD-binding fragment of Plin1 (Plin1CT induced formation of single dense CLD clusters near the microtubule organizing center, whereas neither an N-terminal CLD-binding fragment of Plin1, nor Plin2 or Plin3 induced clustering. Clustered CLD coated by Plin1, or Plin1CT, dispersed in response to isoproterenol, or other agents that activate adenylate cyclase, in a process inhibited by the protein kinase A inhibitor, H89, and blocked by microtubule disruption. Isoproterenol-stimulated phosphorylation of CLD-associated Plin1 on serine 492 preceded their dispersion, and live cell imaging showed that cluster dispersion involved initial fragmentation of tight clusters into multiple smaller clusters, which then fragmented into well-dispersed individual CLD. siRNA knockdown of the cortical actin binding protein, moesin, induced disaggregation of tight clusters into multiple smaller clusters, and inhibited the reaggregation of dispersed CLD into tight clusters. Together these data suggest that the clustering and dispersion processes involve a complex orchestration of phosphorylation-dependent, microtubule-dependent and independent, and microfilament dependent steps.

  5. Dynamics and molecular determinants of cytoplasmic lipid droplet clustering and dispersion.

    Science.gov (United States)

    Orlicky, David J; Monks, Jenifer; Stefanski, Adrianne L; McManaman, James L

    2013-01-01

    Perilipin-1 (Plin1), a prominent cytoplasmic lipid droplet (CLD) binding phosphoprotein and key physiological regulator of triglyceride storage and lipolysis in adipocytes, is thought to regulate the fragmentation and dispersion of CLD that occurs in response to β-adrenergic activation of adenylate cyclase. Here we investigate the dynamics and molecular determinants of these processes using cell lines stably expressing recombinant forms of Plin1 and/or other members of the perilipin family. Plin1 and a C-terminal CLD-binding fragment of Plin1 (Plin1CT) induced formation of single dense CLD clusters near the microtubule organizing center, whereas neither an N-terminal CLD-binding fragment of Plin1, nor Plin2 or Plin3 induced clustering. Clustered CLD coated by Plin1, or Plin1CT, dispersed in response to isoproterenol, or other agents that activate adenylate cyclase, in a process inhibited by the protein kinase A inhibitor, H89, and blocked by microtubule disruption. Isoproterenol-stimulated phosphorylation of CLD-associated Plin1 on serine 492 preceded their dispersion, and live cell imaging showed that cluster dispersion involved initial fragmentation of tight clusters into multiple smaller clusters, which then fragmented into well-dispersed individual CLD. siRNA knockdown of the cortical actin binding protein, moesin, induced disaggregation of tight clusters into multiple smaller clusters, and inhibited the reaggregation of dispersed CLD into tight clusters. Together these data suggest that the clustering and dispersion processes involve a complex orchestration of phosphorylation-dependent, microtubule-dependent and independent, and microfilament dependent steps.

  6. Oxidation of ligand-protected aluminum clusters: An ab initio molecular dynamics study

    International Nuclear Information System (INIS)

    Alnemrat, Sufian; Hooper, Joseph P.

    2014-01-01

    We report Car-Parrinello molecular dynamics simulations of the oxidation of ligand-protected aluminum clusters that form a prototypical cluster-assembled material. These clusters contain a small aluminum core surrounded by a monolayer of organic ligand. The aromatic cyclopentadienyl ligands form a strong bond with surface Al atoms, giving rise to an organometallic cluster that crystallizes into a low-symmetry solid and is briefly stable in air before oxidizing. Our calculations of isolated aluminum/cyclopentadienyl clusters reacting with oxygen show minimal reaction between the ligand and O 2 molecules at simulation temperatures of 500 and 1000 K. In all cases, the reaction pathway involves O 2 diffusing through the ligand barrier, splitting into atomic oxygen upon contact with the aluminum, and forming an oxide cluster with aluminum/ligand bonds still largely intact. Loss of individual aluminum-ligand units, as expected from unimolecular decomposition calculations, is not observed except following significant oxidation. These calculations highlight the role of the ligand in providing a steric barrier against oxidizers and in maintaining the large aluminum surface area of the solid-state cluster material

  7. CO near the Pleiades: encounter of a star cluster with a small molecular cloud

    International Nuclear Information System (INIS)

    Bally, J.; White, R.E.

    1986-01-01

    Although there is a large amount of interstellar matter near the Pleiades star cluster, the observed dust and gas is not a remnant of the placental molecular cloud from which the star cluster was formed. Carbon monoxide (CO) associated with the visible reflection nebulae was discovered by Cohen (1975). Its radial velocity differs from that of the cluster by many times the cluster escape velocity, which implies that the cloud-cluster association is the result of a chance encounter. This circumstance and the proximity of the Pleiades to the sun creates an unique opportunity for study of interstellar processes at high spatial resolution. To study the molecular component of the gas, a 1.7 square degree field was mapped with the ATandT Bell Laboratories 7-meter antenna (1.7' beam) on a 1' grid in the J=1.0 C(12)O line, obtaining over 6000 spectra with 50 kHz resolution. The cloud core was mapped in the J=1-0 line of C(13)O. Further observations include an unsuccessful search for CS (J=2-1) at ATandT BL, and some C(12)O J=2-1 spectra obtained at the Millimeter Wave Observatory of the University of Texas

  8. CO near the Pleiades: Encounter of a star cluster with a small molecular cloud

    Science.gov (United States)

    Bally, J.; White, R. E.

    1986-01-01

    Although there is a large amount of interstellar matter near the Pleiades star cluster, the observed dust and gas is not a remnant of the placental molecular cloud from which the star cluster was formed. Carbon monoxide (CO) associated with the visible reflection nebulae was discovered by Cohen (1975). Its radial velocity differs from that of the cluster by many times the cluster escape velocity, which implies that the cloud-cluster association is the result of a chance encounter. This circumstance and the proximity of the Pleiades to the sun creates an unique opportunity for study of interstellar processes at high spatial resolution. To study the molecular component of the gas, a 1.7 square degree field was mapped with the AT&T Bell Laboratories 7-meter antenna (1.7' beam) on a 1' grid in the J=1.0 C(12)O line, obtaining over 6,000 spectra with 50 kHz resolution. The cloud core was mapped in the J=1-0 line of C(13)O. Further observations include an unsuccessful search for CS (J=2-1) at AT&T BL, and some C(12)O J=2-1 spectra obtained at the Millimeter Wave Observatory of the University of Texas.

  9. 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.

  10. Spin-orbit couplings within the equation-of-motion coupled-cluster framework: Theory, implementation, and benchmark calculations

    Energy Technology Data Exchange (ETDEWEB)

    Epifanovsky, Evgeny [Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482 (United States); Department of Chemistry, University of California, Berkeley, California 94720 (United States); Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588 (United States); Klein, Kerstin; Gauss, Jürgen [Institut für Physikalische Chemie, Universität Mainz, D-55099 Mainz (Germany); Stopkowicz, Stella [Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Oslo, N-0315 Oslo (Norway); Krylov, Anna I. [Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482 (United States)

    2015-08-14

    We present a formalism and an implementation for calculating spin-orbit couplings (SOCs) within the EOM-CCSD (equation-of-motion coupled-cluster with single and double substitutions) approach. The following variants of EOM-CCSD are considered: EOM-CCSD for excitation energies (EOM-EE-CCSD), EOM-CCSD with spin-flip (EOM-SF-CCSD), EOM-CCSD for ionization potentials (EOM-IP-CCSD) and electron attachment (EOM-EA-CCSD). We employ a perturbative approach in which the SOCs are computed as matrix elements of the respective part of the Breit-Pauli Hamiltonian using zeroth-order non-relativistic wave functions. We follow the expectation-value approach rather than the response-theory formulation for property calculations. Both the full two-electron treatment and the mean-field approximation (a partial account of the two-electron contributions) have been implemented and benchmarked using several small molecules containing elements up to the fourth row of the periodic table. The benchmark results show the excellent performance of the perturbative treatment and the mean-field approximation. When used with an appropriate basis set, the errors with respect to experiment are below 5% for the considered examples. The findings regarding basis-set requirements are in agreement with previous studies. The impact of different correlation treatment in zeroth-order wave functions is analyzed. Overall, the EOM-IP-CCSD, EOM-EA-CCSD, EOM-EE-CCSD, and EOM-SF-CCSD wave functions yield SOCs that agree well with each other (and with the experimental values when available). Using an EOM-CCSD approach that provides a more balanced description of the target states yields more accurate results.

  11. Deuteron spin-flip reactions and supermultiplet potential model of interaction of the lightest clusters

    CERN Document Server

    Lebedev, V M; Struzhko, B G

    2002-01-01

    Heterogeneous data on the double and triple differential cross sections of d + p -> np + p and d + t(h) -> np + t(h) or d + t -> nn + h nuclear reactions are reduced by Migdal-Watson approximation to the unified shape of the differential cross section angular dependence having in mind just singlet nucleon-nucleon pair formation. The results are compared with the supermultiplet potential model of the lightest nuclei interaction. The d + t(h) collision is characterized by the fact that the power of V sup [ sup 4 sup 1 sup ] (r) potential is 50% higher than that of the V sup [ sup 3 sup 2 sup ] (r) one ([f] = [41] and [f] = [32] are the orbital Young patterns. This is why the theory is able to describe quantitatively both the above experiment and the elastic scattering one. However, for d + p collision the difference of potential powers for the [f] = [3] and [f] = [21] patterns equals 20% only and the agreement of theory with experiment on deuteron spin-flip is merely qualitative

  12. Nuclear spin bath effects in molecular nanomagnets: Direct quantum mechanical simulations

    Science.gov (United States)

    Sinitsyn, N. A.; Dobrovitski, V. V.

    2004-11-01

    We investigate the influence of nuclear spins on the electronic spin tunneling in magnetic molecules such as Fe8 , focusing on the role of the spin diffusion in the nuclear spin bath. We simulate the quantum spin dynamics by numerically solving the time-dependent Schrödinger equation for the compound system (the electronic spin plus the bath spins). Our results demonstrate that the effect of the spin bath cannot always be modeled as a randomly varying magnetic field acting on the electronic spin. We consider two dynamical regimes: the spin relaxation in a constant magnetic field, and the spin tunneling in the linearly varying magnetic field passing the avoided level crossing, so-called Landau-Zener-Stückelberg (LZS) transition. For the first regime, we confirmed that the hole in the magnetization distribution has the width of the hyperfine fields distribution. For the second regime, we found that the transition probability for moderately slow sweeps deviates from the standard LZS prediction, while for the fast sweeps the deviation is negligible.

  13. Spin-glass-like dynamics of ferromagnetic clusters in La0.75Ba0.25CoO3

    International Nuclear Information System (INIS)

    Kumar, Devendra

    2014-01-01

    We report a magnetization study of the compound La 0.75 Ba 0.25 CoO 3 where the Ba 2+ doping is just above the critical limit for percolation of ferromagnetic clusters. The field cooled and zero-field cooled (ZFC) magnetization exhibit thermomagnetic irreversibility and the ac susceptibility shows a frequency dependent peak at the ferromagnetic ordering temperature (T C  ≈ 203 K) of the clusters. These features indicate the presence of a non-equilibrium state below T C . For the non-equilibrium state, the dynamic scaling of the imaginary part of the ac susceptibility and the static scaling of the nonlinear susceptibility clearly establish a spin-glass-like cooperative freezing of ferromagnetic clusters at 200.9(2) K. The assertion of the occurrence of spin-glass-like freezing of ferromagnetic clusters is further substantiated by ZFC ageing and memory experiments. We also observe certain dynamical features which are not present in a typical spin glass, such as: the initial magnetization after ZFC ageing first increases and then decreases with the waiting time; and there is an imperfect recovery of relaxation in negative temperature cycling experiments. This imperfect recovery transforms to perfect recovery for concurrent field cycling. Our analysis suggests that these additional dynamical features have their origin in the inter-cluster exchange interaction and cluster size distribution. The inter-cluster exchange interaction above the magnetic percolation level gives a superferromagnetic state in some granular thin films, but our results show the absence of a typical superferromagnetic-like state in La 0.75 Ba 0.25 CoO 3 . (paper)

  14. Production and characterization of protonated molecular clusters containing a given number of water molecules with the DIAM set-up

    International Nuclear Information System (INIS)

    Bruny, G.

    2010-01-01

    nano-scale characterization of irradiation in bio-molecular systems requires observation of novel features which are now achievable with the recent technical progress. This work is a central part in the development of DIAM which is a new experimental set-up devoted to irradiation of bio-molecular clusters at the Institut de Physique Nucleaire de Lyon. The development of the cluster source and of a double focusing mass spectrometer leads to the production of intense beams of mass selected protonated molecular clusters. Combined with this mass selected cluster beams an innovative detection technique is demonstrated in collision induced dissociation experiments. The results contribute to the knowledge of the stability and the structure of the small protonated water clusters and mixed clusters of water and pyridine. (author)

  15. Low-relaxation spin waves in laser-molecular-beam epitaxy grown nanosized yttrium iron garnet films

    Energy Technology Data Exchange (ETDEWEB)

    Lutsev, L. V., E-mail: l-lutsev@mail.ru; Korovin, A. M.; Bursian, V. E.; Gastev, S. V.; Fedorov, V. V.; Suturin, S. M.; Sokolov, N. S. [Ioffe Physical-Technical Institute, Russian Academy of Sciences, 194021 St. Petersburg (Russian Federation)

    2016-05-02

    Synthesis of nanosized yttrium iron garnet (Y{sub 3}Fe{sub 5}O{sub 12}, YIG) films followed by the study of ferromagnetic resonance (FMR) and spin wave propagation in these films is reported. The YIG films were grown on gadolinium gallium garnet substrates by laser molecular beam epitaxy. It has been shown that spin waves propagating in YIG deposited at 700 °C have low damping. At the frequency of 3.29 GHz, the spin-wave damping parameter is less than 3.6 × 10{sup −5}. Magnetic inhomogeneities of the YIG films give the main contribution to the FMR linewidth. The contribution of the relaxation processes to the FMR linewidth is as low as 1.2%.

  16. The Association of Molecular Gas and Natal Super Star Clusters in Henize 2–10

    Science.gov (United States)

    Johnson, Kelsey E.; Brogan, Crystal L.; Indebetouw, Remy; Testi, Leonardo; Wilner, David J.; Reines, Amy E.; Chen, C.-H. Rosie; Vanzi, Leonardo

    2018-02-01

    We present ALMA observations of the dwarf starburst galaxy He 2–10 in combination with previous SMA CO observations to probe the molecular environments of natal super star clusters (SSCs). These observations include the HCO+(1-0), HCN(1-0), HNC(1-0), and CCH(1-0) molecular lines, as well as 88 GHz continuum with a spatial resolution of 1\\buildrel{\\prime\\prime}\\over{.} 7× 1\\buildrel{\\prime\\prime}\\over{.} 6. After correcting for the contribution from free–free emission to the 88 GHz continuum flux density (∼60% of the 88 GHz emission), we derive a total gas mass for He 2–10 of {M}{gas}=4{--}6× {10}8 M ⊙, roughly 5%–20% of the dynamical mass. Based on a principle component analysis, HCO+ is found to be the best “general” tracer of molecular emission. The line widths and luminosities of the CO emission suggests that the molecular clouds could either be as small as ∼8 pc, or alternately have enhanced line widths. The CO emission and 88 GHz continuum are anti-correlated, suggesting that either the dust and molecular gas are not cospatial, which could reflect that the 88 GHz continuum is dominated by free–free emission. The CO and CCH emission are also relatively anti-correlated, which is consistent with the CCH being photo-enhanced, and/or the CO being dissociated in the regions near the natal SSCs. The molecular line ratios of regions containing the natal star clusters are different from the line ratios observed for regions elsewhere in the galaxy. In particular, the regions with thermal radio emission all have {CO}(2{--}1)/{{HCO}}+(1-0)correlated with the evolutionary stage of the clusters.

  17. Molecular dynamics computer simulation study of Pdn (n=13, 19, 38 and 55) clusters

    International Nuclear Information System (INIS)

    Karabacak, M.; Oezcelik, S.; Guevenc, Z.B.

    2002-01-01

    Using constant-energy molecular dynamics and thermal quenching simulations, we have studied minimum-energy structures and energetics, Pd n (n=13, 19, 38, and 55) clusters employing the Voter and Chen's version of parameterisation of the embedded-atom potential surface. Isomer statistics for Pdn ( n = 13 and 19 ) is obtained from 10000 initial independent configurations, which have been generated along high-energy trajectories (chosen energy values are high enough to melt the clusters). The thermal quenching technique is employed to remove the internal kinetic energy of the clusters. The locally stable isomers are separated from metastable ones. Probabilities belonging to sampling the basins of attractions of each isomers are computed, and then, isomers' energy spectra are analyzed

  18. 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.

  19. Neutral molecular cluster formation of sulfuric acid–dimethylamine observed in real time under atmospheric conditions

    CERN Document Server

    Kürten, Andreas; Simon, Mario; Sipilä, Mikko; Sarnela, Nina; Junninen, Heikki; Adamov, Alexey; Almeida, João; Amorim, Antonio; Bianchi, Federico; Breitenlechner, Martin; Dommen, Josef; Donahue, Neil M; Duplissy, Jonathan; Ehrhart, Sebastian; Flagan, Richard C; Franchin, Alessandro; Hakala, Jani; Hansel, Armin; Heinritzi, Martin; Hutterli, Manuel; Kangasluoma, Juha; Kirkby, Jasper; Laaksonen, Ari; Lehtipalo, Katrianne; Leiminger, Markus; Makhmutov, Vladimir; Mathot, Serge; Onnela, Antti; Petäjä, Tuukka; Praplan, Arnaud P; Riccobono, Francesco; Rissanen, Matti P; Rondo, Linda; Schobesberger, Siegfried; Seinfeld, John H; Steiner, Gerhard; Tomé, António; Tröstl, Jasmin; Winkler, Paul M; Williamson, Christina; Wimmer, Daniela; Ye, Penglin; Baltensperger, Urs; Carslaw, Kenneth S; Kulmala, Markku; Worsnop, Douglas R; Curtius, Joachim

    2014-01-01

    For atmospheric sulfuric acid (SA) concentrations the presence of dimethylamine (DMA) at mixing ratios of several parts per trillion by volume can explain observed boundary layer new particle formation rates. However, the concentration and molecular composition of the neutral (uncharged) clusters have not been reported so far due to the lack of suitable instrumentation. Here we report on experiments from the Cosmics Leaving Outdoor Droplets chamber at the European Organization for Nuclear Research revealing the formation of neutral particles containing up to 14 SA and 16 DMA molecules, corresponding to a mobility diameter of about 2 nm, under atmospherically relevant conditions. These measurements bridge the gap between the molecular and particle perspectives of nucleation, revealing the fundamental processes involved in particle formation and growth. The neutral clusters are found to form at or close to the kinetic limit where particle formation is limited only by the collision rate of SA molecules. Even tho...

  20. True Molecular Scale Visualization of Variable Clustering Properties of Ryanodine Receptors

    Directory of Open Access Journals (Sweden)

    Isuru Jayasinghe

    2018-01-01

    Full Text Available Summary: Signaling nanodomains rely on spatial organization of proteins to allow controlled intracellular signaling. Examples include calcium release sites of cardiomyocytes where ryanodine receptors (RyRs are clustered with their molecular partners. Localization microscopy has been crucial to visualizing these nanodomains but has been limited by brightness of markers, restricting the resolution and quantification of individual proteins clustered within. Harnessing the remarkable localization precision of DNA-PAINT (<10 nm, we visualized punctate labeling within these nanodomains, confirmed as single RyRs. RyR positions within sub-plasmalemmal nanodomains revealed how they are organized randomly into irregular clustering patterns leaving significant gaps occupied by accessory or regulatory proteins. RyR-inhibiting protein junctophilin-2 appeared highly concentrated adjacent to RyR channels. Analyzing these molecular maps showed significant variations in the co-clustering stoichiometry between junctophilin-2 and RyR, even between nearby nanodomains. This constitutes an additional level of complexity in RyR arrangement and regulation of calcium signaling, intrinsically built into the nanodomains. : Jayasinghe et al. resolve the distribution of single ryanodine receptors (RyRs within intracellular signaling domains in cardiac myocytes with DNA-PAINT, a super-resolution microscopy approach. Individual RyRs are resolved within irregular cluster arrays. Quantitative imaging reveals significant variation in the co-clustering stoichiometry between RyRs and the regulatory protein junctophilin-2. Keywords: nanodomains, DNA-PAINT, single-molecule localization microscopy, ryanodine receptor, super-resolution imaging, junctophilin, heart

  1. Parallel variable selection of molecular dynamics clusters as a tool for calculation of spectroscopic properties

    Czech Academy of Sciences Publication Activity Database

    Kessler, Jiří; Dračínský, Martin; Bouř, Petr

    2013-01-01

    Roč. 34, č. 5 (2013), s. 366-371 ISSN 0192-8651 R&D Projects: GA ČR GAP208/11/0105; GA MŠk(CZ) LH11033 Grant - others:GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : molecular dynamics * clusters * density functional theory * Raman optical activity * NMR Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.601, year: 2013

  2. Acceleration of cluster and molecular ions by TIARA 3 MV tandem accelerator

    CERN Document Server

    Saitoh, Y; Tajima, S

    2000-01-01

    We succeeded in accelerating molecular and cluster ions (B sub 2 sub - sub 4 , C sub 2 sub - sub 1 sub 0 , O sub 2 , Al sub 2 sub - sub 4 , Si sub 2 sub - sub 4 , Cu sub 2 sub - sub 3 , Au sub 2 sub - sub 3 , LiF, and AlO) to MeV energies with high-intensity beam currents by means of a 3 MV tandem accelerator in the TIARA facility. These cluster ions were generated by a cesium sputter-type negative ion source. We tested three types of carbon sputter cathodes in which graphite powder was compressed with different pressures. The pressure difference affected the generating ratio of clusters generated to single atom ions extracted from the source and it appeared that the high-density cathode was suitable. We also investigated the optimum gas pressure for charge exchange in the tandem high-voltage terminal. Clusters of larger size tend to require lower pressure than do smaller ones. In addition, we were able to obtain doubly charged AlO molecular ions. (authors)

  3. Nuclear magnetic resonance in solids: evolution of spin temperature under multipulse irradiation and high symmetry molecular motions

    International Nuclear Information System (INIS)

    Quiroga, Luis

    1982-01-01

    In a first part, autocorrelation functions are calculated taking into account the symmetry of molecular motions by group theoretical techniques. This very general calculation method is then used to evaluate the NMR spin-lattice relaxation times T 1 and T 1 p as a function of the relative orientations of the magnetic field, the crystal and the rotation axis, in particular for cyclic, dihedral and cubic groups. Models of molecular reorientations such as jumps between a finite number of allowed orientations, rotational diffusion and superimposed reorientations are all investigated with the same formalism. In part two, the effect of the coherent excitation of spins, by multipulse sequences of the WHH-4 type, on the evolution of the heat capacity and spin temperature of the dipolar reservoir is analysed. It is shown both theoretically and experimentally that adiabatic (reversible) reduction of the dipolar Hamiltonian and its spin temperature is obtained when the amplitude of pulses (rotation angle) is slowly raised. The sudden switching on and off of the HW-8 sequence is then shown to lead to the same reversible reduction in a shorter time. It is also shown that, by this way, sensibility and selectivity of double resonance measurements of weak gyromagnetic ratio nuclei are strongly increased. This is experimentally illustrated in some cases. (author) [fr

  4. Thermodynamics of spin ice in staggered and direct (along the [111] axis) fields in the cluster approximation

    Energy Technology Data Exchange (ETDEWEB)

    Zinenko, V. I., E-mail: zvi@iph.krasn.ru; Pavlovskii, M. S. [Russian Academy of Sciences, Kirensky Institute of Physics, Siberian Branch (Russian Federation)

    2017-02-15

    We have analyzed the low-temperature thermodynamic properties of spin ice in the staggered and direct (acting along the [111] axis) fields for rare-earth oxides with the chalcolamprite structure and general formula Re{sub 2}{sup 3+}Me{sub 2}{sup 4+}O{sub 7}{sup 2-}. Calculations have been performed in the cluster approximation. The results have been compared with experimental temperature dependences of heat capacity and entropy for Dy{sub 2}Ti{sub 2}O{sub 7} compound for different values of the external field in the [111] direction. The experimental data and calculated results have also been compared for the Pr{sub 2}Ru{sub 2}O{sub 7} compound with the antiferromagnetic ordering of magnetic moments of ruthenium ions, which gives rise to the staggered field acting on the system of rare-earth ions. The calculated temperature dependences of heat capacity and entropy are in good agreement with experimental data.

  5. The molecular epidemiology of HIV-1 in the Comunidad Valenciana (Spain): analysis of transmission clusters.

    Science.gov (United States)

    Patiño-Galindo, Juan Ángel; Torres-Puente, Manoli; Bracho, María Alma; Alastrué, Ignacio; Juan, Amparo; Navarro, David; Galindo, María José; Ocete, Dolores; Ortega, Enrique; Gimeno, Concepción; Belda, Josefina; Domínguez, Victoria; Moreno, Rosario; González-Candelas, Fernando

    2017-09-14

    HIV infections are still a very serious concern for public heath worldwide. We have applied molecular evolution methods to study the HIV-1 epidemics in the Comunidad Valenciana (CV, Spain) from a public health surveillance perspective. For this, we analysed 1804 HIV-1 sequences comprising protease and reverse transcriptase (PR/RT) coding regions, sampled between 2004 and 2014. These sequences were subtyped and subjected to phylogenetic analyses in order to detect transmission clusters. In addition, univariate and multinomial comparisons were performed to detect epidemiological differences between HIV-1 subtypes, and risk groups. The HIV epidemic in the CV is dominated by subtype B infections among local men who have sex with men (MSM). 270 transmission clusters were identified (>57% of the dataset), 12 of which included ≥10 patients; 11 of subtype B (9 affecting MSMs) and one (n = 21) of CRF14, affecting predominately intravenous drug users (IDUs). Dated phylogenies revealed these large clusters to have originated from the mid-80s to the early 00 s. Subtype B is more likely to form transmission clusters than non-B variants and MSMs to cluster than other risk groups. Multinomial analyses revealed an association between non-B variants, which are not established in the local population yet, and different foreign groups.

  6. Resolving the anomalous infrared spectrum of the MeCN-HCl molecular cluster using ab Initio molecular dynamics

    DEFF Research Database (Denmark)

    Bork, Nicolai Christian; Loukonen, Ville; Kjærgaard, Henrik Grum

    2014-01-01

    We present a molecular dynamics (MD) based study of the acetonitrile-hydrogen chloride molecular cluster in the gas phase, aimed at resolving the anomalous features often seen in infrared spectra of hydrogen bonded complexes. We find that the infrared spectrum obtained from the Fourier transform...... of the electric dipole moment autocorrelation function converges very slowly due to the floppy nature of the complex. Even after 55 picoseconds of simulation, significant differences in the modelled and experimental spectrum are seen, likely due to insufficient configurational sampling. Instead, we utilize the MD...... trajectory for a structural based analysis. We find that the most populated values of the N-H-Cl angle are around 162°. The global minimum energy conformation at 180.0° is essentially unpopulated. We re-model the spectrum by combining population data from the MD simulations with optimizations constraining...

  7. Similarity transformed equation of motion coupled-cluster theory based on an unrestricted Hartree-Fock reference for applications to high-spin open-shell systems.

    Science.gov (United States)

    Huntington, Lee M J; Krupička, Martin; Neese, Frank; Izsák, Róbert

    2017-11-07

    The similarity transformed equation of motion coupled-cluster approach is extended for applications to high-spin open-shell systems, within the unrestricted Hartree-Fock (UHF) formalism. An automatic active space selection scheme has also been implemented such that calculations can be performed in a black-box fashion. It is observed that both the canonical and automatic active space selecting similarity transformed equation of motion (STEOM) approaches perform about as well as the more expensive equation of motion coupled-cluster singles doubles (EOM-CCSD) method for the calculation of the excitation energies of doublet radicals. The automatic active space selecting UHF STEOM approach can therefore be employed as a viable, lower scaling alternative to UHF EOM-CCSD for the calculation of excited states in high-spin open-shell systems.

  8. Similarity transformed equation of motion coupled-cluster theory based on an unrestricted Hartree-Fock reference for applications to high-spin open-shell systems

    Science.gov (United States)

    Huntington, Lee M. J.; Krupička, Martin; Neese, Frank; Izsák, Róbert

    2017-11-01

    The similarity transformed equation of motion coupled-cluster approach is extended for applications to high-spin open-shell systems, within the unrestricted Hartree-Fock (UHF) formalism. An automatic active space selection scheme has also been implemented such that calculations can be performed in a black-box fashion. It is observed that both the canonical and automatic active space selecting similarity transformed equation of motion (STEOM) approaches perform about as well as the more expensive equation of motion coupled-cluster singles doubles (EOM-CCSD) method for the calculation of the excitation energies of doublet radicals. The automatic active space selecting UHF STEOM approach can therefore be employed as a viable, lower scaling alternative to UHF EOM-CCSD for the calculation of excited states in high-spin open-shell systems.

  9. Massively parallel implementations of coupled-cluster methods for electron spin resonance spectra. I. Isotropic hyperfine coupling tensors in large radicals

    Energy Technology Data Exchange (ETDEWEB)

    Verma, Prakash; Morales, Jorge A., E-mail: jorge.morales@ttu.edu [Department of Chemistry and Biochemistry, Texas Tech University, P.O. Box 41061, Lubbock, Texas 79409-1061 (United States); Perera, Ajith [Department of Chemistry and Biochemistry, Texas Tech University, P.O. Box 41061, Lubbock, Texas 79409-1061 (United States); Department of Chemistry, Quantum Theory Project, University of Florida, Gainesville, Florida 32611 (United States)

    2013-11-07

    Coupled cluster (CC) methods provide highly accurate predictions of molecular properties, but their high computational cost has precluded their routine application to large systems. Fortunately, recent computational developments in the ACES III program by the Bartlett group [the OED/ERD atomic integral package, the super instruction processor, and the super instruction architecture language] permit overcoming that limitation by providing a framework for massively parallel CC implementations. In that scheme, we are further extending those parallel CC efforts to systematically predict the three main electron spin resonance (ESR) tensors (A-, g-, and D-tensors) to be reported in a series of papers. In this paper inaugurating that series, we report our new ACES III parallel capabilities that calculate isotropic hyperfine coupling constants in 38 neutral, cationic, and anionic radicals that include the {sup 11}B, {sup 17}O, {sup 9}Be, {sup 19}F, {sup 1}H, {sup 13}C, {sup 35}Cl, {sup 33}S,{sup 14}N, {sup 31}P, and {sup 67}Zn nuclei. Present parallel calculations are conducted at the Hartree-Fock (HF), second-order many-body perturbation theory [MBPT(2)], CC singles and doubles (CCSD), and CCSD with perturbative triples [CCSD(T)] levels using Roos augmented double- and triple-zeta atomic natural orbitals basis sets. HF results consistently overestimate isotropic hyperfine coupling constants. However, inclusion of electron correlation effects in the simplest way via MBPT(2) provides significant improvements in the predictions, but not without occasional failures. In contrast, CCSD results are consistently in very good agreement with experimental results. Inclusion of perturbative triples to CCSD via CCSD(T) leads to small improvements in the predictions, which might not compensate for the extra computational effort at a non-iterative N{sup 7}-scaling in CCSD(T). The importance of these accurate computations of isotropic hyperfine coupling constants to elucidate

  10. The use of a versatile o-vanilloyl hydrazone ligand to prepare SMM-like Dy3 molecular cluster pair.

    Science.gov (United States)

    Xue, Shufang; Zhao, Lang; Guo, Yun-Nan; Zhang, Peng; Tang, Jinkui

    2012-09-14

    A novel lanthanide molecular cluster pair (MCP), displaying single molecule magnet behaviour, was assembled using the novel o-vanilloyl hydrazone ligand, versatile in terms of denticity, tautomerism and the rotatable C-C bond.

  11. THE PHYSICAL CONDITIONS IN A PRE-SUPER STAR CLUSTER MOLECULAR CLOUD IN THE ANTENNAE GALAXIES

    International Nuclear Information System (INIS)

    Johnson, K. E.; Indebetouw, R.; Evans, A. S.; Leroy, A. K.; Brogan, C. L.; Hibbard, J.; Sheth, K.; Whitmore, B. C.

    2015-01-01

    We present an analysis of the physical conditions in an extreme molecular cloud in the Antennae merging galaxies. This cloud has properties consistant with those required to form a globular cluster. We have obtained ALMA CO and 870 μm observations of the Antennae galaxy system with ∼0.″5 resolution. This cloud stands out in the data with a radius of ≲24 pc and mass of >5 × 10 6 M ⊙ . The cloud appears capable of forming a globular cluster, but the lack of associated thermal radio emission indicates that star formation has not yet altered the environment. The lack of thermal radio emission places the cloud in an early stage of evolution, which we expect to be short-lived (≲1 Myr) and thus rare. Given its mass and kinetic energy, for the cloud to be confined (as its appearance strongly suggests) it must be subject to an external pressure of P/k B ≳ 10 8 K cm −3 –10,000 times higher than typical interstellar pressure. This would support theories that high pressures are required to form globular clusters and may explain why extreme environments like the Antennae are preferred environments for generating such objects. Given the cloud temperature of ∼25 K, the internal pressure must be dominated by non-thermal processes, most likely turbulence. We expect the molecular cloud to collapse and begin star formation in ≲1 Myr

  12. Molecular dynamics study of B18H22 cluster implantation into silicon

    International Nuclear Information System (INIS)

    Marques, Luis A.; Pelaz, Lourdes; Santos, Ivan

    2007-01-01

    We have carried out molecular dynamics simulations of monatomic B and octadecaborane cluster implantations into Si in order to make a comparative study and determine the advantages and drawbacks of each approach when used to fabricate shallow junctions. We have simulated a total of 1000 cascades of monatomic boron and an equivalent of 56 cascades of octadecaborane in order to have good statistics. We have obtained and analyzed the doping profiles and the amount and morphology of the damage produced within the target. Our simulation results indicate that the use of octadecaborane clusters for the implantation process shows several advantages with respect to monatomic B beams, mainly related to the reduction of channeling and the lower amount of residual damage at the end of range

  13. Ab initio molecular-orbital study on electron correlation effects in CuO6 clusters relating to high-Tc superconductivity

    International Nuclear Information System (INIS)

    Yamamoto, S.; Yamaguchi, K.; Nasu, K.

    1990-01-01

    Ab initio molecular-orbital calculations for CuO 6 clusters have been performed to elucidate the electronic structures of undoped and doped copper oxides, which are of current interest in relation to high-T c superconductivity. The electron correlation effects for these species are thoroughly investigated by the full-valence configuration-interaction method and the complete-active-space self-consistent-field method. The electron correlation effect is relatively simple for the A g state (σ hole), whereas pair excitations and spin-flip excitations give sizable contributions to the configuration-interaction wave function for the B state (in-plane π hole). Implications of these results are discussed in relation to the mechanisms of the high-T c superconductivity

  14. ULTRAVIOLET ESCAPE FRACTIONS FROM GIANT MOLECULAR CLOUDS DURING EARLY CLUSTER FORMATION

    Energy Technology Data Exchange (ETDEWEB)

    Howard, Corey; Pudritz, Ralph [Department of Physics and Astronomy, McMaster University, 1280 Main St. W, Hamilton, ON L8S 4M1 (Canada); Klessen, Ralf [Zentrum für Astronomie der Universität Heidelberg, Institut für Theoretische Astrophysik Albert-Ueberle-Str. 2, D-69120 Heidelberg (Germany)

    2017-01-01

    The UV photon escape fraction from molecular clouds is a key parameter for understanding the ionization of the interstellar medium and extragalactic processes such as cosmic reionization. We present the ionizing photon flux and the corresponding photon escape fraction ( f {sub esc}) arising as a consequence of star cluster formation in a turbulent, 10{sup 6} M {sub ⊙} giant molecular cloud, simulated using the code FLASH. We make use of sink particles to represent young, star-forming clusters coupled with a radiative transfer scheme to calculate the emergent UV flux. We find that the ionizing photon flux across the cloud boundary is highly variable in time and space due to the turbulent nature of the intervening gas. The escaping photon fraction remains at ∼5% for the first 2.5 Myr, followed by two pronounced peaks at 3.25 and 3.8 Myr with a maximum f {sub esc} of 30% and 37%, respectively. These peaks are due to the formation of large H ii regions that expand into regions of lower density, some of which reaching the cloud surface. However, these phases are short-lived, and f {sub esc} drops sharply as the H ii regions are quenched by the central cluster passing through high-density material due to the turbulent nature of the cloud. We find an average f {sub esc} of 15% with factor of two variations over 1 Myr timescales. Our results suggest that assuming a single value for f {sub esc} from a molecular cloud is in general a poor approximation, and that the dynamical evolution of the system leads to large temporal variation.

  15. Spin interactions in Graphene-Single Molecule Magnets Hybrids

    Science.gov (United States)

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

    2014-03-01

    Graphene is a potential component of novel spintronics devices owing to its long spin diffusion length. Besides its use as spin-transport channel, graphene can be employed for the detection and manipulation of molecular spins. This requires an appropriate coupling between the sheets and the single molecular magnets (SMM). Here, we present a comprehensive characterization of graphene-Fe4 SMM hybrids. The Fe4 clusters are anchored non-covalently to the graphene following a diffusion-limited assembly and can reorganize into random networks when subjected to slightly elevated temperature. Molecules anchored on graphene sheets show unaltered static magnetic properties, whilst the quantum dynamics is profoundly modulated. Interaction with Dirac fermions becomes the dominant spin-relaxation channel, with observable effects produced by graphene phonons and reduced dipolar interactions. Coupling to graphene drives the spins over Villain's threshold, allowing the first observation of strongly-perturbative tunneling processes. Preliminary spin-transport experiments at low-temperature are further presented.

  16. Magnetic properties of free alkali and transition metal clusters

    International Nuclear Information System (INIS)

    Heer, W. de; Milani, P.; Chatelain, A.

    1991-01-01

    The Stern-Gerlach deflections of small alkali clusters (N<6) and iron clusters (10< N<500) show that the paramagnetic alkali clusters always have a nondeflecting component, while the iron clusters always deflect in the high field direction. Both of these effects appear to be related to spin relaxation however in the case of alkali clusters it is shown that they are in fact caused by avoided level crossing in the Zeeman diagram. For alkali clusters the relatively weak couplings cause reduced magnetic moments where levels cross. For iron clusters however the total spin is strongly coupled to the molecular framework. Consequently this coupling is responsible for avoided level crossing which ultimately cause the total energy of the cluster to decrease with increasing magnetic field so that the iron clusters will deflect in one direction when introduced in an inhomogeneous magnetic field. Experiment and theory are discussed for both cases. (orig.)

  17. Nuclear spin transitions in the kHz range in Rydberg matter clusters give precise values of the internal magnetic field from orbiting Rydberg electrons

    International Nuclear Information System (INIS)

    Holmlid, Leif

    2009-01-01

    Clusters of the electronically excited condensed matter Rydberg matter (RM) are planar and sixfold symmetric with specific magic numbers N as shown by rotational spectroscopy of potassium K N clusters [L. Holmlid, Mol. Phys. 105 (2007) 933; L. Holmlid, J. Mol. Struct. 885 (2008) 122]. In radio frequency emission spectra from such clusters, features are observed that are due to the hyperfine interaction between the atomic nucleus 39 K and two Rydberg electrons. These electrons exist in a doubly excited K atom at n'' = 5 or 6 in a 'sleeping-top' type rotating cluster. Such low excited electrons were observed recently in optical intra-cavity experiments in K(RM), where the electrons in the conduction band are involved in the angular momentum conservation in the stimulated emission. Here we show that the agreement with the theoretical description of circular Rydberg states is excellent within ±0.2% in the magnetic field, invoking angular momentum conservation by electrons in the condensed phase. Sleeping-top clusters may form stacks of clusters, and it is likely that such stacks are the emitting entities involved in the two nuclear spin series observed.

  18. The spin-dependent electronic transport properties of M(dcdmp)2 (M = Cu, Au, Co, Ni) molecular devices based on zigzag graphene nanoribbon electrodes

    Science.gov (United States)

    Li, Dongde; Wu, Di; Zhang, Xiaojiao; Zeng, Bowen; Li, Mingjun; Duan, Haiming; Yang, Bingchu; Long, Mengqiu

    2018-05-01

    The spin-dependent electronic transport properties of M(dcdmp)2 (M = Cu, Au, Co, Ni; dcdmp = 2,3-dicyano-5,6-dimercaptopyrazyne) molecular devices based on zigzag graphene nanoribbon (ZGNR) electrodes were investigated by density functional theory combined nonequilibrium Green's function method (DFT-NEGF). Our results show that the spin-dependent transport properties of the M(dcdmp)2 molecular devices can be controlled by the spin configurations of the ZGNR electrodes, and the central 3d-transition metal atom can introduce a larger magnetism than that of the nonferrous metal one. Moreover, the perfect spin filtering effect, negative differential resistance, rectifying effect and magnetic resistance phenomena can be observed in our proposed M(dcdmp)2 molecular devices.

  19. Molecular dynamics simulations of the interaction between 60 deg. dislocation and self-interstitial cluster in silicon

    International Nuclear Information System (INIS)

    Jing Yuhang; Meng Qingyuan; Zhao Wei

    2009-01-01

    Molecular dynamics simulations are performed to investigate the interaction between 60 deg. shuffle dislocation and tetrainterstitial (I 4 ) cluster in silicon, using Stillinger-Weber (SW) potential to calculate the interatomic forces. Based on Parrinello-Rahman method, shear stress is exerted on the model to move the dislocation. Simulation results show that the I 4 cluster can bend the dislocation line and delay the dislocation movement. During the course of intersection the dislocation line sections relatively far away from the I 4 cluster accelerate first, and then decelerate. The critical shear stress unpinning the 60 deg. dislocation from the I 4 cluster decreases as the temperature increases in the models.

  20. The anchoring effect on the spin transport properties and I-V characteristics of pentacene molecular devices suspended between nickel electrodes.

    Science.gov (United States)

    Caliskan, S; Laref, A

    2014-07-14

    Spin-polarized transport properties are determined for pentacene sandwiched between Ni surface electrodes with various anchoring ligands. These calculations are carried out using spin density functional theory in tandem with a non-equilibrium Green's function technique. The presence of a Se atom at the edge of the pentacene molecule significantly modifies the transport properties of the device because Se has a different electronegativity than S. Our theoretical results clearly show a larger current for spin-up electrons than for spin-down electrons in the molecular junction that is attached asymmetrically across the Se linker at one side of the Ni electrodes (in an APL magnetic orientation). Moreover, this molecular junction exhibits pronounced NDR as the bias voltage is increased from 0.8 to 1.0 V. However, this novel NDR behavior is only detected in this promising pentacene molecular device. The NDR in the current-voltage (I-V) curve results from the narrowness of the density of states for the molecular states. The feasibility of controlling the TMR is also predicted in these molecular device nanostructures. Spin-dependent transmission calculations show that the sign and strength of the current-bias voltage characteristics and the TMR could be tailored for the organic molecule devices. These molecular junctions are joined symmetrically and asymmetrically between Ni metallic probes across the S and Se atoms (at the ends of the edges of the pentacene molecule). Our theoretical findings show that spin-valve phenomena can occur in these prototypical molecular junctions. The TMR and NDR results show that nanoscale junctions with spin valves could play a vital role in the production of novel functional molecular devices.

  1. Studies of the charge instabilities in the complex nano-objects: clusters and bio-molecular systems

    International Nuclear Information System (INIS)

    Manil, B.

    2007-11-01

    For the last 6 years, my main research works focused on i) the Coulomb instabilities and the fragmentation processes of fullerenes and clusters of fullerenes ii) the stability and the reactivity of complex bio-molecular systems. Concerning the clusters of fullerenes, which are van der Waals type clusters, we have shown that the multiply charged species, obtained in collisions with slow highly charged ions, keep their structural properties but become very good electric conductor. In another hand, with the aim to understand the role of the biologic environment at the molecular scale in the irradiation damage of complex biomolecules, we have studied the charge stabilities of clusters of small biomolecules and the dissociation processes of larger nano-hydrated biomolecules. Theses studies have shown that first, specific molecular recognition mechanisms continue to exist in gas phase and secondly, a small and very simple biochemical environment is enough to change the dynamics of instabilities. (author)

  2. Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles

    Science.gov (United States)

    Huang, Rao; Lo, Li-Ta; Wen, Yuhua; Voter, Arthur F.; Perez, Danny

    2017-10-01

    Modern molecular-dynamics-based techniques are extremely powerful to investigate the dynamical evolution of materials. With the increase in sophistication of the simulation techniques and the ubiquity of massively parallel computing platforms, atomistic simulations now generate very large amounts of data, which have to be carefully analyzed in order to reveal key features of the underlying trajectories, including the nature and characteristics of the relevant reaction pathways. We show that clustering algorithms, such as the Perron Cluster Cluster Analysis, can provide reduced representations that greatly facilitate the interpretation of complex trajectories. To illustrate this point, clustering tools are used to identify the key kinetic steps in complex accelerated molecular dynamics trajectories exhibiting shape fluctuations in Pt nanoclusters. This analysis provides an easily interpretable coarse representation of the reaction pathways in terms of a handful of clusters, in contrast to the raw trajectory that contains thousands of unique states and tens of thousands of transitions.

  3. Effects of incident cluster size, substrate temperature, and incident energy on bombardment of Ni clusters onto Cu (0 0 1) surface studied using molecular dynamics simulation

    International Nuclear Information System (INIS)

    Lin, Shiang-Jiun; Wu, Cheng-Da; Fang, Te-Hua; Chen, Guan-Hung

    2012-01-01

    The bombardment process of a Ni cluster onto a Cu (0 0 1) surface is studied using molecular dynamics (MD) simulations based on the tight-binding second-moment approximation (TB-SMA) many-body potential. The effects of incident cluster size, substrate temperature, and incident energy are evaluated in terms of molecular trajectories, kinetic energy, stress, self-diffusion coefficient, and sputtering yield. The simulation results clearly show that the penetration depth and Cu surface damage increase with increasing incident cluster size for a given incident energy per atom. The self-diffusion coefficient and the penetration depth of a cluster significantly increase with increasing substrate temperature. An incident cluster can be scattered into molecules or atoms that become embedded in the surface after incidence. When the incident energy is increased, the number of volcano-like defects and the penetration depth increase. A high sputtering yield can be obtained by increasing the incident energy at high temperature. The sputtering yield significantly increases with cluster size when the incident energy is above 5 eV/atom.

  4. Measuring the Density of a Molecular Cluster Injector via Visible Emission from an Electron Beam

    Energy Technology Data Exchange (ETDEWEB)

    Lundberg, D. P.; Kaita, R.; Majeski, R. M.; Stotler, D. P.

    2010-06-28

    A method to measure the density distribution of a dense hydrogen gas jet is pre- sented. A Mach 5.5 nozzle is cooled to 80K to form a flow capable of molecular cluster formation. A 250V, 10mA electron beam collides with the jet and produces Hα emission that is viewed by a fast camera. The high density of the jet, several 1016cm-3, results in substantial electron depletion, which attenuates the Hα emission. The attenuated emission measurement, combined with a simplified electron-molecule collision model, allows us to determine the molecular density profile via a simple iterative calculation.

  5. Efficient organometallic spin filter between single-wall carbon nanotube or graphene electrodes

    DEFF Research Database (Denmark)

    Koleini, Mohammad; Paulsson, Magnus; Brandbyge, Mads

    2007-01-01

    We present a theoretical study of spin transport in a class of molecular systems consisting of an organometallic benzene-vanadium cluster placed in between graphene or single-wall carbon-nanotube-model contacts. Ab initio modeling is performed by combining spin density functional theory...

  6. The energy and stability of helium-related cluster in nickel: A study of molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Gong, Hengfeng, E-mail: gonghengfeng@sinap.ac.cn [Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Division of Nuclear Materials and Engineering, Shanghai 201800 (China); Key Laboratory of Interfacial Physics and Technology, Chinese Academy of Sciences, Shanghai 201800 (China); Wang, Chengbin; Zhang, Wei; Xu, Jian [Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Division of Nuclear Materials and Engineering, Shanghai 201800 (China); Key Laboratory of Interfacial Physics and Technology, Chinese Academy of Sciences, Shanghai 201800 (China); Huai, Ping, E-mail: huaiping@sinap.ac.cn [Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Division of Nuclear Materials and Engineering, Shanghai 201800 (China); Key Laboratory of Nuclear Radiation and Nuclear Energy Technology, Chinese Academy of Sciences, Shanghai 201800 (China); Deng, Huiqiu; Hu, Wangyu [Hunan University, Department of Applied Physics, Changsha 410082 (China)

    2016-02-01

    Highlights: • The He-related clusters exhibit the very high symmetry. • The trapping capability of vacancy to defects becomes weak due to the pre-existed SIA. • The average length of He{sub N}V{sub 1} clusters is longer than one of He{sub N} and He{sub N}V{sub 1}SIA{sub 1} cluster. - Abstract: Using molecular dynamics simulation, we investigated the energy and stability of helium-related cluster in nickel. All the binding energies of the He-related clusters are demonstrated to be positive and increase with the cluster sizes. Due to the pre-existed self-interstitial nickel atom, the trapping capability of vacancy to defects becomes weak. Besides, the minimum energy configurations of He-related clusters exhibit the very high symmetry in the local atomistic environment. And for the He{sub N} and He{sub N}V{sub 1}SIA{sub 1} clusters, the average length of He–He bonds shortens, but it elongates for the He{sub N}V{sub 1} clusters with helium cluster sizes. The helium-to-vacancy ratio plays a decisive role on the binding energies of He{sub N}V{sub M} cluster. These results can provide some excellent clues to insight the initial stage of helium bubbles nucleation and growth in the Ni-based alloys for the Generation-IV Molten Salt Reactor.

  7. clusters

    Indian Academy of Sciences (India)

    2017-09-27

    Sep 27, 2017 ... Author for correspondence (zh4403701@126.com). MS received 15 ... lic clusters using density functional theory (DFT)-GGA of the DMOL3 package. ... In the process of geometric optimization, con- vergence thresholds ..... and Postgraduate Research & Practice Innovation Program of. Jiangsu Province ...

  8. clusters

    Indian Academy of Sciences (India)

    environmental as well as technical problems during fuel gas utilization. ... adsorption on some alloys of Pd, namely PdAu, PdAg ... ried out on small neutral and charged Au24,26,27, Cu,28 ... study of Zanti et al.29 on Pdn (n = 1–9) clusters.

  9. Characterization-Based Molecular Design of Bio-Fuel Additives Using Chemometric and Property Clustering Techniques

    International Nuclear Information System (INIS)

    Hada, Subin; Solvason, Charles C.; Eden, Mario R.

    2014-01-01

    In this work, multivariate characterization data such as infrared spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis allowed capturing important features of the molecular architecture from enormous amount of complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods based on characterization (cGCM) data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive, which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.

  10. Characterization-Based Molecular Design of Bio-Fuel Additives Using Chemometric and Property Clustering Techniques

    Energy Technology Data Exchange (ETDEWEB)

    Hada, Subin; Solvason, Charles C.; Eden, Mario R., E-mail: edenmar@auburn.edu [Department of Chemical Engineering, Auburn University, Auburn, AL (United States)

    2014-06-10

    In this work, multivariate characterization data such as infrared spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis allowed capturing important features of the molecular architecture from enormous amount of complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods based on characterization (cGCM) data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive, which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.

  11. Characterization-Based Molecular Design of Biofuel Additives Using Chemometric and Property Clustering Techniques

    Directory of Open Access Journals (Sweden)

    Subin eHada

    2014-06-01

    Full Text Available In this work, multivariate characterization data such as infrared (IR spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis (PCA allowed capturing important features of the molecular architecture from complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods (GCM based on characterization data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.

  12. Molecular depth profiling of multi-layer systems with cluster ion sources

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Juan [Department of Chemistry, Penn State University, University Park, PA 16802 (United States); Winograd, Nicholas [Department of Chemistry, Penn State University, University Park, PA 16802 (United States)]. E-mail: nxw@psu.edu

    2006-07-30

    Cluster bombardment of molecular films has created new opportunities for SIMS research. To more quantitatively examine the interaction of cluster beams with organic materials, we have developed a reproducible platform consisting of a well-defined sugar film (trehalose) doped with peptides. Molecular depth profiles have been acquired with these systems using C{sub 60} {sup +} bombardment. In this study, we utilize this platform to determine the feasibility of examining buried interfaces for multi-layer systems. Using C{sub 60} {sup +} at 20 keV, several systems have been tested including Al/trehalose/Si, Al/trehalose/Al/Si, Ag/trehalose/Si and ice/trehalose/Si. The results show that there can be interactions between the layers during the bombardment process that prevent a simple interpretation of the depth profile. We find so far that the best results are obtained when the mass of the overlayer atoms is less than or nearly equal to the mass of the atoms in buried molecules. In general, these observations suggest that C{sub 60} {sup +} bombardment can be successfully applied to interface characterization of multi-layer systems if the systems are carefully chosen.

  13. Electron and nuclear dynamics of molecular clusters in ultraintense laser fields. IV. Coulomb explosion of molecular heteroclusters.

    Science.gov (United States)

    Last, Isidore; Jortner, Joshua

    2004-11-01

    In this paper we present a theoretical and computational study of the temporal dynamics and energetics of Coulomb explosion of (CD4)(n) and (CH4)(n) (n=55-4213) molecular heteroclusters in ultraintense (I=10(16)-10(19) W cm(-2)) laser fields, addressing the manifestation of electron dynamics, together with nuclear energetic and kinematic effects on the heterocluster Coulomb instability. The manifestations of the coupling between electron and nuclear dynamics were explored by molecular dynamics simulations for these heteroclusters coupled to Gaussian laser fields (pulse width tau=25 fs), elucidating outer ionization dynamics, nanoplasma screening effects (being significant for Icharges and masses. Nonuniform heterocluster Coulomb explosion (eta >1) manifests an overrun effect of the light ions relative to the heavy ions, exhibiting the expansion of two spatially separated subclusters, with the light ions forming the outer subcluster at the outer edge of the spatial distribution. Important features of the energetics of heterocluster Coulomb explosion originate from energetic triggering effects of the driving of the light ions by the heavy ions (C(4+) for I=10(17)-10(18) W cm(-2) and C(6+) for I=10(19) W cm(-2)), as well as for kinematic effects. Based on the CVI assumption, scaling laws for the cluster size (radius R(0)) dependence of the energetics of uniform Coulomb explosion of heteroclusters (eta=1) were derived, with the size dependence of the average (E(j,av)) and maximal (E(j,M)) ion energies being E(j,av)=aR(0) (2) and E(j,M)=(5a/3)R(0) (2), as well as for the ion energy distributions P(E(j)) proportional to E(j) (1/2); E(j)1) result in an isotope effect, predicting the enhancement (by 9%-11%) of E(H,av) for Coulomb explosion of (C(4+)H(4) (+))(eta) (eta=3) relative to E(D,av) for Coulomb explosion of (C(4+)D(4) (+))(eta) (eta=1.5), with the isotope effect being determined by the ratio of the kinematic parameters for the pair of Coulomb exploding clusters

  14. Influence of molecular clustering on the interpretation of diffractograms of hydrocarbon films from tokamak T-10

    Energy Technology Data Exchange (ETDEWEB)

    Neverov, V. S., E-mail: vs-never@hotmail.com [National Research Center Kurchatov Institute, Tokamak Physics Institute (Russian Federation); Voloshinov, V. V., E-mail: vladimir.voloshinov@gmail.com [Russian Academy of Science, Institute for Information Transmission Problems (Kharkevich Institute) (Russian Federation); Kukushkin, A. B., E-mail: kukushkin-ab@nrcki.ru [National Research Center Kurchatov Institute, Tokamak Physics Institute (Russian Federation); Tarasov, A. S., E-mail: tarasov.alexey@gmail.com [Russian Academy of Science, Institute for Information Transmission Problems (Kharkevich Institute) (Russian Federation)

    2015-12-15

    The influence of molecular clustering on the formerly suggested interpretation of diffraction patterns of hydrocarbon films formed in the vacuum vessel of the tokamak T-10 is analyzed numerically. The simulation of clustering of simple hydrocarbon molecules C(D, H){sub 4}, C{sub 2}(D, H){sub 4}, and C{sub 6}(D, H){sub 6} and molecules composed of curved graphene (fullerenes and toroidal nanotubes) is carried out with the rigid body molecular dynamics method. It is shown that formerly neglected atomic correlations C–C and C–D(H) in the amorphous hydrocarbon component decrease the calculated values of the scattered intensity in the range of scattering vector modulus 5 < q < 20 nm{sup –1} because of homogenization of scatters on the spatial scale of ∼1 nm. The allowance for these correlations does not change the diffraction patterns in the range q > 20 nm{sup –1}. The results suggest the necessity to introduce to the procedure of determining the structural content of the films, similar to those from the tokamak T-10, the clusters formed by the van der Waals adhesion of hydrocarbon molecules to “graphene” nanoparticles. This simplifies the mathematical optimization to the former level of complexity—but for an extended ensemble of objects—and makes it possible to calculate the diffraction patterns of these objects using the distributed computing resources. A modified algorithm of structural content identification on the basis of joint X-ray and neutron diffractometry is suggested.

  15. Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane

    Energy Technology Data Exchange (ETDEWEB)

    Zarycz, M. Natalia C., E-mail: mnzarycz@gmail.com; Provasi, Patricio F., E-mail: patricio@unne.edu.ar [Department of Physics, University of Northeastern - CONICET, Av. Libertad 5500, Corrientes W3404AAS (Argentina); Sauer, Stephan P. A., E-mail: sauer@kiku.dk [Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø (Denmark)

    2014-10-21

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the {sup 1}J(C–H) coupling constant of CH{sub 4} using a decomposition into contributions from localized molecular orbitals and compare with the {sup 1}J(N–H) coupling constant in NH{sub 3}. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes—SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.

  16. On the representation matrices of the spin permutation group. [for atomic and molecular electronic structures

    Science.gov (United States)

    Wilson, S.

    1977-01-01

    A method is presented for the determination of the representation matrices of the spin permutation group (symmetric group), a detailed knowledge of these matrices being required in the study of the electronic structure of atoms and molecules. The method is characterized by the use of two different coupling schemes. Unlike the Yamanouchi spin algebraic scheme, the method is not recursive. The matrices for the fundamental transpositions can be written down directly in one of the two bases. The method results in a computationally significant reduction in the number of matrix elements that have to be stored when compared with, say, the standard Young tableaux group theoretical approach.

  17. Molecular clouds toward the super star cluster NGC 3603; possible evidence for a cloud-cloud collision in triggering the cluster formation

    Energy Technology Data Exchange (ETDEWEB)

    Fukui, Y.; Ohama, A.; Hanaoka, N.; Furukawa, N.; Torii, K.; Hasegawa, K.; Fukuda, T.; Soga, S.; Moribe, N.; Kuroda, Y.; Hayakawa, T.; Kuwahara, T.; Yamamoto, H.; Okuda, T. [Department of Astrophysics, Nagoya University, Chikusa-ku, Nagoya 464-8602 (Japan); Dawson, J. R. [School of Mathematics and Physics, University of Tasmania, Sandy Bay Campus, Churchill Avenue, Sandy Bay, TAS 7005 (Australia); Mizuno, N.; Kawamura, A. [National Astronomical Observatory of Japan, Mitaka, Tokyo 181-8588 (Japan); Onishi, T.; Maezawa, H. [Department of Astrophysics, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, Osaka 599-8531 (Japan); Mizuno, A., E-mail: fukui@a.phys.nagoya-u.ac.jp [Solar-terrestrial Environment Laboratory, Nagoya University, Chikusa-ku, Nagoya 464-8601 (Japan)

    2014-01-01

    We present new large field observations of molecular clouds with NANTEN2 toward the super star cluster NGC 3603 in the transitions {sup 12}CO(J = 2-1, J = 1-0) and {sup 13}CO(J = 2-1, J = 1-0). We suggest that two molecular clouds at 13 km s{sup –1} and 28 km s{sup –1} are associated with NGC 3603 as evidenced by higher temperatures toward the H II region, as well as morphological correspondence. The mass of the clouds is too small to gravitationally bind them, given their relative motion of ∼20 km s{sup –1}. We suggest that the two clouds collided with each other 1 Myr ago to trigger the formation of the super star cluster. This scenario is able to explain the origin of the highest mass stellar population in the cluster, which is as young as 1 Myr and is segregated within the central sub-pc of the cluster. This is the second super star cluster along with Westerlund 2 where formation may have been triggered by a cloud-cloud collision.

  18. Fullerene/layered antiferromagnetic reconstructed spinterface: Subsurface layer dominates molecular orbitals' spin-split and large induced magnetic moment

    Science.gov (United States)

    Shao, Yangfan; Pang, Rui; Pan, Hui; Shi, Xingqiang

    2018-03-01

    The interfaces between organic molecules and magnetic metals have gained increasing interest for both fundamental reasons and applications. Among them, the C60/layered antiferromagnetic (AFM) interfaces have been studied only for C60 bonded to the outermost ferromagnetic layer [S. L. Kawahara et al., Nano Lett. 12, 4558 (2012) and D. Li et al., Phys. Rev. B 93, 085425 (2016)]. Here, via density functional theory calculations combined with evidence from the literature, we demonstrate that C60 adsorption can reconstruct the layered-AFM Cr(001) surface at elevated annealing temperatures so that C60 bonds to both the outermost and the subsurface Cr layers in opposite spin directions. Surface reconstruction drastically changes the adsorbed molecule spintronic properties: (1) the spin-split p-d hybridization involves multi-orbitals of C60 and top two layers of Cr with opposite spin-polarization, (2) the subsurface Cr atom dominates the C60 electronic properties, and (3) the reconstruction induces a large magnetic moment of 0.58 μB in C60 as a synergistic effect of the top two Cr layers. The induced magnetic moment in C60 can be explained by the magnetic direct-exchange mechanism, which can be generalized to other C60/magnetic metal systems. Understanding these complex hybridization behaviors is a crucial step for molecular spintronic applications.

  19. Infrared investigation of the phonon spectrum in the frustrated spin cluster compound FeTe{sub 2}O{sub 5}Cl

    Energy Technology Data Exchange (ETDEWEB)

    Pfuner, F; Degiorgi, L [Laboratorium fuer Festkoerperphysik, ETH Zuerich, CH-8093 Zuerich (Switzerland); Berger, H; Forro, L [Institut de Physique de la Matiere Complexe (IPMC), EPF Lausanne, CH-1015 Lausanne (Switzerland)

    2009-09-16

    We present our optical investigations on the frustrated spin cluster compound FeTe{sub 2}O{sub 5}Cl, which develops a long-range antiferromagnetic order below 10 K. We measure the optical reflectivity from the far-infrared to the ultraviolet with polarized light. We focus our attention on the lattice dynamics by discussing the infrared-active modes. Our findings reveal a polarization dependence of the vibrational modes but which do not seem to be affected by structural anomalies linked to the magnetically ordered state at low temperatures.

  20. All-atom molecular dynamics simulations of spin labelled double and single-strand DNA for EPR studies.

    Science.gov (United States)

    Prior, C; Danilāne, L; Oganesyan, V S

    2018-05-16

    We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of electron paramagnetic resonance (EPR) spectra of spin labelled DNA. Models for two structurally different DNA spin probes with either the rigid or flexible position of the nitroxide group in the base pair, employed in experimental studies previously, have been developed. By the application of the combined MD-EPR simulation methodology we aimed at the following. Firstly, to provide a test bed against a sensitive spectroscopic technique for the recently developed improved version of the parmbsc1 force field for MD modelling of DNA. The predicted EPR spectra show good agreement with the experimental ones available from the literature, thus confirming the accuracy of the currently employed DNA force fields. Secondly, to provide a quantitative interpretation of the motional contributions into the dynamics of spin probes in both duplex and single-strand DNA fragments and to analyse their perturbing effects on the local DNA structure. Finally, a combination of MD and EPR allowed us to test the validity of the application of the Model-Free (M-F) approach coupled with the partial averaging of magnetic tensors to the simulation of EPR spectra of DNA systems by comparing the resultant EPR spectra with those simulated directly from MD trajectories. The advantage of the M-F based EPR simulation approach over the direct propagation techniques is that it requires motional and order parameters that can be calculated from shorter MD trajectories. The reported MD-EPR methodology is transferable to the prediction and interpretation of EPR spectra of higher order DNA structures with novel types of spin labels.

  1. The role of binary and many-centre molecular interactions in spin crossover in the solid state. Part II. Non-ideality parameters defined via binary molecular potentials

    International Nuclear Information System (INIS)

    Koudriavtsev, A.B.; Linert, W.

    2005-01-01

    Parameters of the formalism [1-6] describing spin crossover in the solid state have been defined via molecular potentials in model systems of neutral and ionic complexes. In the first instance Lennard-Jones and electric dipole-dipole potentials have been used whereas in ionic systems Lennard-Jones and electric point-charge potentials have been used. Electric dipole-dipole interaction of neutral complexes brings about a positive excess energy controlled by the difference of electric dipole moments of HS and LS molecules. Differences of the order of Δμ = 1-2D cause an abrupt spin crossover in systems with T 1/2 = 100-150K. Magnetic coupling contributes both to the excess energy and excess entropy, however the overall effect is equivalent to a modest positive excess energy. Ionic systems in the absence of specific interactions are characterized by very small excess energies corresponding to practically linear van't Hoff plots. Detectable positive and negative excess energies in these systems may arise from interactions of ligands belonging to neighbouring complexes. The HOMO-LUMO overlap in HS-LS pairs can bring about a nontrivial variation of the shape of transition curves. Examples of regression analysis of experimental transition curves in terms of molecular potentials are given. (author)

  2. Structure and binding of molecular clusters of trivalent metal halides in an ionic model

    International Nuclear Information System (INIS)

    Akdeniz, Z.; Pastore, G.; Tosi, M.P.

    1997-10-01

    A model of ionic interactions first proposed for the molecular monomers of alkaline earth dihalides (G. Galli and M. P. Tosi, N. Ciemento D 4,413 (1984)) is used in a systematic study of the structure and binding of monomeric and dimeric units of Al, Fe ad Ga chlorides, bromides and iodides. Ionized states obtained by stripping or adding a halogen ion are considered in addition to neutral states. The main motivation for this work comes from recent studies of liquid structure in several of these systems by neutron and X-ray diffraction and Raman scattering. Main attention is consequently given in the present calculations to (i) bond lengths and bond angles in isolated clusters as precursors of local structures in melts, and (ii) stability of local structures against fluctuations into ionized states. The results are discussed in comparison with the available experimental data as well as with the results from Hartree-Fock and density functional calculations. (author)

  3. Molecular Characterization and Cluster Analysis of Field Isolates of Avian Infectious Laryngotracheitis Virus from Argentina

    Directory of Open Access Journals (Sweden)

    María I. Craig

    2017-12-01

    Full Text Available Avian infectious laryngotracheitis (ILT is a worldwide infectious disease that causes important economic losses in the poultry industry. Although it is known that ILT virus (ILTV is present in Argentina, there is no information about the circulating strains. With the aim to characterize them, seven different genomic regions (thymidine kinase, glycoproteins D, G, B, C, and J, and infected cell polypeptide 4 were partially sequenced and compared between field samples. The gJ sequence resulted to be the most informative segment, it allowed the differentiation among field sample strains, and also, between wild and vaccine viruses. Specific changes in selected nucleotidic positions led to the definition of five distinct haplotypes. Tests for detection of clustering were run to test the null hypothesis that ILTV haplotypes were randomly distributed in time in Argentina and in space in the most densely populated poultry region of this country, Entre Rios. From this study, it was possible to identify a 46 km radius cluster in which higher proportions of haplotypes 4 and 5 were observed, next to a provincial route in Entre Rios and a significant decline of haplotype 5 between 2009 and 2011. Results here provide an update on the molecular epidemiology of ILT in Argentina, including data on specific genome segments that may be used for rapid characterization of the virus in the field. Ultimately, results will contribute to the surveillance of ILT in the country.

  4. Lipid clustering correlates with membrane curvature as revealed by molecular simulations of complex lipid bilayers.

    Directory of Open Access Journals (Sweden)

    Heidi Koldsø

    2014-10-01

    Full Text Available Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2, in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins.

  5. Coupled cluster theory of strongly correlated spin- and electron-lattice systems: an illustration via a model exhibiting competition between magnetic order and dimerization

    International Nuclear Information System (INIS)

    Bishop, Raymond F; Krueger, Sven E

    2003-01-01

    The coupled cluster method (CCM) of microscopic quantum many-body theory has become an ab initio method of first choice in quantum chemistry and many fields of nuclear, subnuclear and condensed matter physics, when results of high accuracy are required. In recent years it has begun to be applied with equal success to strongly correlated systems of electrons or quantum spins defined on a regular spatial lattice. One regularly finds that the CCM is able to describe accurately the various zero-temperature phases and the quantum phase transitions between them, even when frustration is present and other methods such as quantum Monte Carlo often fail. We illustrate the use and powerfulness of the method here by applying it to a square-lattice spin-half Heisenberg model where frustration is introduced by competing nearest neighbour bonds. The model exhibits the physically interesting phenomenon of competition between magnetic order and dimerization. Results obtained for the model with the CCM are compared with those found from spin-wave theory and from extrapolating the results of exact diagonalizations of small lattices. We show that the CCM is essentially unique among available methods in being able both to describe accurately all phases of this complex model and to provide accurate predictions of the various phase boundaries and the order of the corresponding transitions

  6. Analytic first derivatives for a spin-adapted open-shell coupled cluster theory: Evaluation of first-order electrical properties

    Energy Technology Data Exchange (ETDEWEB)

    Datta, Dipayan, E-mail: datta@uni-mainz.de; Gauss, Jürgen, E-mail: gauss@uni-mainz.de [Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz (Germany)

    2014-09-14

    An analytic scheme is presented for the evaluation of first derivatives of the energy for a unitary group based spin-adapted coupled cluster (CC) theory, namely, the combinatoric open-shell CC (COSCC) approach within the singles and doubles approximation. The widely used Lagrange multiplier approach is employed for the derivation of an analytical expression for the first derivative of the energy, which in combination with the well-established density-matrix formulation, is used for the computation of first-order electrical properties. Derivations of the spin-adapted lambda equations for determining the Lagrange multipliers and the expressions for the spin-free effective density matrices for the COSCC approach are presented. Orbital-relaxation effects due to the electric-field perturbation are treated via the Z-vector technique. We present calculations of the dipole moments for a number of doublet radicals in their ground states using restricted open-shell Hartree-Fock (ROHF) and quasi-restricted HF (QRHF) orbitals in order to demonstrate the applicability of our analytic scheme for computing energy derivatives. We also report calculations of the chlorine electric-field gradients and nuclear quadrupole-coupling constants for the CCl, CH{sub 2}Cl, ClO{sub 2}, and SiCl radicals.

  7. G0.253 + 0.016: A MOLECULAR CLOUD PROGENITOR OF AN ARCHES-LIKE CLUSTER

    International Nuclear Information System (INIS)

    Longmore, Steven N.; Ascenso, Joana; Testi, Leonardo; Bressert, Eli; Rathborne, Jill; Bastian, Nate; Alves, Joao; Meingast, Stefan; Bally, John; Battersby, Cara; Longmore, Andy; Purcell, Cormac; Walsh, Andrew; Jackson, James; Foster, Jonathan; Molinari, Sergio; Amorim, A.; Lima, J.; Marques, R.; Moitinho, A.

    2012-01-01

    Young massive clusters (YMCs) with stellar masses of 10 4 -10 5 M ☉ and core stellar densities of 10 4 -10 5 stars per cubic pc are thought to be the 'missing link' between open clusters and extreme extragalactic super star clusters and globular clusters. As such, studying the initial conditions of YMCs offers an opportunity to test cluster formation models across the full cluster mass range. G0.253 + 0.016 is an excellent candidate YMC progenitor. We make use of existing multi-wavelength data including recently available far-IR continuum (Herschel/Herschel Infrared Galactic Plane Survey) and mm spectral line (H 2 O Southern Galactic Plane Survey and Millimetre Astronomy Legacy Team 90 GHz Survey) data and present new, deep, multiple-filter, near-IR (Very Large Telescope/NACO) observations to study G0.253 + 0.016. These data show that G0.253 + 0.016 is a high-mass (1.3 × 10 5 M ☉ ), low-temperature (T dust ∼ 20 K), high-volume, and column density (n ∼ 8 × 10 4 cm –3 ; N H 2 ∼4×10 23 cm –2 ) molecular clump which is close to virial equilibrium (M dust ∼ M virial ) so is likely to be gravitationally bound. It is almost devoid of star formation and, thus, has exactly the properties expected for the initial conditions of a clump that may form an Arches-like massive cluster. We compare the properties of G0.253 + 0.016 to typical Galactic cluster-forming molecular clumps and find it is extreme, and possibly unique in the Galaxy. This uniqueness makes detailed studies of G0.253 + 0.016 extremely important for testing massive cluster formation models.

  8. Simulations of the low-dimensional molecular-based spin systems: dodecanuclear nickel ring

    International Nuclear Information System (INIS)

    Kamieniarz, G.; Haglauer, M.; Caramico D'Auria, A.; Esposito, F.; Gatteschi, D.

    2005-01-01

    The numerical exact diagonalization technique exploiting the point-group symmetry is worked out for the anisotropic Heisenberg spin Hamiltonian with the ring geometry. It is applied in large-scale simulations to the supramolecule Ni 12 (O 2 CMe) 12 (chp) 12 (H 2 O) 6 (THF) 6 , yielding the low-level energy spectra as a function of the single-ion anisotropy D and the thermodynamic functions. The strength of the constant D is analysed and estimated at D/k B =1.5K. The results for the zero-field susceptibility and the field-dependent magnetization are presented and compared with experimental data

  9. Fen (n=1–6) clusters chemisorbed on vacancy defects in graphene: Stability, spin-dipole moment, and magnetic anisotropy

    KAUST Repository

    Haldar, Soumyajyoti; Pujari, Bhalchandra S.; Bhandary, Sumanta; Cossu, Fabrizio; Eriksson, Olle; Kanhere, Dilip G.; Sanyal, Biplab

    2014-01-01

    In this work, we have studied the chemical and magnetic interactions of Fen (n=1–6) clusters with vacancy defects (monovacancy to correlated vacancies with six missing C atoms) in a graphene sheet by ab initio density functional calculations

  10. Modelling the molecular composition and nuclear-spin chemistry of collapsing prestellar sources

    Science.gov (United States)

    Hily-Blant, P.; Faure, A.; Rist, C.; Pineau des Forêts, G.; Flower, D. R.

    2018-04-01

    We study the gravitational collapse of prestellar sources and the associated evolution of their chemical composition. We use the University of Grenoble Alpes Astrochemical Network (UGAN), which includes reactions involving the different nuclear-spin states of H2, H+3, and of the hydrides of carbon, nitrogen, oxygen, and sulfur, for reactions involving up to seven protons. In addition, species-to-species rate coefficients are provided for the ortho/para interconversion of the H_3^+ + H2 system and isotopic variants. The composition of the medium is followed from an initial steady state through the early phase of isothermal gravitational collapse. Both the freeze-out of the molecules on to grains and the coagulation of the grains were incorporated in the model. The predicted abundances and column densities of the spin isomers of ammonia and its deuterated forms are compared with those measured recently towards the prestellar cores H-MM1, L16293E, and Barnard B1. We find that gas-phase processes alone account satisfactorily for the observations, without recourse to grain-surface reactions. In particular, our model reproduces both the isotopologue abundance ratios and the ortho:para ratios of NH2D and NHD2 within observational uncertainties. More accurate observations are necessary to distinguish between full scrambling processes—as assumed in our gas-phase network—and direct nucleus- or atom-exchange reactions.

  11. Magnetic materials at finite temperatures: thermodynamics and combined spin and molecular dynamics derived from first principles calculations

    International Nuclear Information System (INIS)

    Eisenbach, Markus; Perera, Meewanage Dilina N.; Landau, David P; Nicholson, Don M.; Yin, Junqi; Brown, Greg

    2015-01-01

    We present a unified approach to describe the combined behavior of the atomic and magnetic degrees of freedom in magnetic materials. Using Monte Carlo simulations directly combined with first principles the Curie temperature can be obtained ab initio in good agreement with experimental values. The large scale constrained first principles calculations have been used to construct effective potentials for both the atomic and magnetic degrees of freedom that allow the unified study of influence of phonon-magnon coupling on the thermodynamics and dynamics of magnetic systems. The MC calculations predict the specific heat of iron in near perfect agreement with experimental results from 300K to above Tc and allow the identification of the importance of the magnon-phonon interaction at the phase-transition. Further Molecular Dynamics and Spin Dynamics calculations elucidate the dynamics of this coupling and open the potential for quantitative and predictive descriptions of dynamic structure factors in magnetic materials using first principles-derived simulations.

  12. Molecular dynamic simulation of interaction of low-energy Ar and Xe ions with copper clusters at graphite surface

    International Nuclear Information System (INIS)

    Kornich, G.V.; Lozovskaya, L.I.; Betts, G.; Zaporozhchenko, V.I.; Faupel, F.

    2005-01-01

    One conducted molecular and dynamic simulation of sputtering of isolated clusters consisting of 13, 27 and 195 Cu atoms from the (0001) graphite surface by 200 eV energy Ar and Xe ions. It is shown that the factors of reflection of Ar and Xe ions from copper clusters differ from one another insignificantly, though the energy of the reflected Xe ions is essentially lower than that of Ar ions. The values of the factor of cluster sputtering by Xe ions are higher in contrast to sputtering by Ar ions. One identified two mechanisms of cluster sputtering resulting in the maximum of sputtering intensity at the polar angles near the normal one, and in periodicity of maximums within the azimuth distributions of sputtering intensity with 60 deg period [ru

  13. Theoretical studies of zirconium and carbon clusters with molecular dynamics simulations

    International Nuclear Information System (INIS)

    Zhang, B.

    1993-01-01

    With the aim of understanding the anomalous phonon behavior near the martensitic phase transition in Zr, we have simulated the dynamics of atomic motion in the high temperature bcc phase of Zr using an embedded-atom potential. The calculated dynamical structure factors reproduce the strong asymmetry in the scattering cross-sections in different Brillouin zones observed in inelastic neutron scattering experiments. From the real-space atomic picture, we observed the phase fluctuations between bcc and low temperature phase hcp. The anomalous phonon behavior arises from the incompleteness of the phase fluctuations. Combining an efficient simulated annealing scheme for generating closed, hollow, spheroidal cage structures with a tight-binding molecular-dynamics method for energy optimization. We have systematically studied the ground-state structure of every even-numbered carbon fullerene from C 20 to C 100 . Clusters of sizes 60, 70, and 84 are found to be energetically more stable than their neighbors. Most ground-state structures of fullerenes have relatively low symmetries. In many cases, several isomers of a fullerene are found to have competitively low energies, which suggests that a mixture of these isomers can be observed in experimentally prepared samples. We also simulate the collisions between fullerene and the thermal disintegration of fullerenes. We observed three different regimes of behavior as the collisions become more and more energetic: bouncing, fusion and fragmentation. The critical energies for fusion and fragmentation as well as details of the energy transfer process during the collisions are investigated. In simulations of the thermal disintegration of fullerene cages, the most commonly observed fragments after the disintegration of the carbon cages are dimers, rings, and multiple rings. The fragmentation temperature increases almost linearly with cluster size for small cages (n ≤ 58), but remains constant for larger fullerenes

  14. Molecular dynamics study on the interaction of a dislocation and radiation induced defect clusters in Fcc crystals

    International Nuclear Information System (INIS)

    Hideo, Kaburaki; Tomoko, Kadoyoshi; Futoshi, Shimizu; Hajime; Kimizuka; Shiro, Jitsukawa

    2003-01-01

    Irradiation of high-energy neutrons and charged particles into solids is known to cause a significant change in mechanical properties, in particular, hardening of metals. Hardening of solids arises as a result of interactions of dislocations with irradiation induced defect clusters. Molecular dynamics method combined with the visualization method has been used to elucidate these complex pinning structures in details. In particular, we have successfully observed the transient process for the formation of a super-jog from an edge dislocation and interstitial and vacancy clusters under irradiation cascade conditions. Parallel molecular dynamics programs, called as Parallel Molecular Dynamics Stencil (PMDS), have been developed in order to perform these large scale simulations for materials simulations. The contents of the program and its parallel performance are also reported. (authors)

  15. Simulations of the low-dimensional molecular-based spin systems: dodecanuclear nickel ring

    Energy Technology Data Exchange (ETDEWEB)

    Kamieniarz, G. [Computational Physics Division, Institute of Physics, A. Mickiewicz University, ul. Umultowska 85, Poznan 61-614 (Poland)]. E-mail: gjk@amu.edu.pl; Haglauer, M. [Computational Physics Division, Institute of Physics, A. Mickiewicz University, ul. Umultowska 85, Poznan 61-614 (Poland); Caramico D' Auria, A. [Dipartimento di Scienze Fisiche, Universita di Napoli, Naples (Italy) and INFM Unita di Naples (Italy); Esposito, F. [Dipartimento di Scienze Fisiche, Universita di Napoli, Naples (Italy) and INFM Unita di Naples (Italy); Gatteschi, D. [Dipartimento di Chimica, Universita di Firenze, Sesto Fiorentino (Italy)

    2005-04-15

    The numerical exact diagonalization technique exploiting the point-group symmetry is worked out for the anisotropic Heisenberg spin Hamiltonian with the ring geometry. It is applied in large-scale simulations to the supramolecule Ni{sub 12}(O{sub 2}CMe){sub 12}(chp){sub 12}(H{sub 2}O){sub 6}(THF){sub 6}, yielding the low-level energy spectra as a function of the single-ion anisotropy D and the thermodynamic functions. The strength of the constant D is analysed and estimated at D/k{sub B}=1.5K. The results for the zero-field susceptibility and the field-dependent magnetization are presented and compared with experimental data.

  16. Effect of nuclear spin on chemical reactions and internal molecular rotation

    International Nuclear Information System (INIS)

    Sterna, L.L.

    1980-12-01

    Part I of this dissertation is a study of the magnetic isotope effect, and results are presented for the separation of 13 C and 12 C isotopes. Two models are included in the theoretical treatment of the effect. In the first model the spin states evolve quantum mechanically, and geminate recombination is calculated by numerically integrating the collision probability times the probability the radical pair is in a singlet state. In the second model the intersystem crossing is treated via first-order rate constants which are average values of the hyperfine couplings. Using these rate constants and hydrodynamic diffusion equations, an analytical solution, which accounts for all collisions, is obtained for the geminate recombination. The two reactions studied are photolysis of benzophenone and toluene and the photolytic decomposition of dibenzylketone (1,3-diphenyl-2-propanone). No magnetic isotope effect was observed in the benzophenone reaction. 13 C enrichment was observed for the dibenzylketone reaction, and this enrichment was substantially enhanced at intermediate viscosities and low temperatures. Part II of this dissertation is a presentation of theory and results for the use of Zeeman spin-lattice relaxation as a probe of methyl group rotation in the solid state. Experimental results are presented for the time and angular dependences of rotational polarization, the methyl group magnetic moment, and methyl-methyl steric interactions. The compounds studied are 2,6-dimethylphenol, methyl iodide, 1,4,5,8-tetramethylanthracene, 1,4,5,8-tetramethylnaphthalene, 1,2,4,5-tetramethylbenzene, and 2,3-dimethylmaleicanhydride

  17. Relation between molecular electronic structure and nuclear spin-induced circular dichroism

    DEFF Research Database (Denmark)

    Štěpánek, Petr; Coriani, Sonia; Sundholm, Dage

    2017-01-01

    with spatially localized, high-resolution information. To survey the factors relating the molecular and electronic structure to the NSCD signal, we theoretically investigate NSCD of twenty structures of the four most common nucleic acid bases (adenine, guanine, thymine, cytosine). The NSCD signal correlates...... with the spatial distribution of the excited states and couplings between them, reflecting changes in molecular structure and conformation. This constitutes a marked difference to the nuclear magnetic resonance (NMR) chemical shift, which only reflects the local molecular structure in the ground electronic state....... The calculated NSCD spectra are rationalized by means of changes in the electronic density and by a sum-over-states approach, which allows to identify the contributions of the individual excited states. Two separate contributions to NSCD are identified and their physical origins and relative magnitudes...

  18. Novel spin dynamics in ferrimagnetic molecular chains from {sup 1}H NMR and {mu}SR spin-lattice relaxation measurements

    Energy Technology Data Exchange (ETDEWEB)

    Micotti, E. E-mail: micotti@fisicavolta.unipv.it; Lascialfari, A.; Rigamonti, A.; Aldrovandi, S.; Caneschi, A.; Gatteschi, D.; Bogani, L

    2004-05-01

    The spin dynamics in the helical chain Co(hfac){sub 2}NITPhOMe has been investigated by {sup 1}H NMR and {mu}SR relaxation. In the temperature range 15spin relaxation mechanism, undetected by the magnetization measurements. From the analysis of these data, insights on this novel relaxation process are derived.

  19. Theoretical studies of zirconium and carbon clusters with molecular dynamics simulations

    International Nuclear Information System (INIS)

    Zhang, B.

    1993-08-01

    In this dissertation, we will present a systematic study of structures of fullerenes ranging from C 20 to C 100 by introducing a novel scheme. Using our new scheme, we not only reproduce all known fullerene structures but also successfully predicted several other fullerene structures which were confirmed by experiments. By utilizing the tight-binding molecular-dynamic (TBMD) simulation, we also studied the dynamical behavior of fullerenes: Vibrations, thermal disintegration of individual clusters as well as collisions between fullerenes. If the beauty of carbon fullerene is not enough, people found that carbon can also form tubules and even speculated that they can form three-dimensional graphite-like networks. By extending our fullerene structure searching scheme, we performed a search for the ground-state structure of three dimensional carbon network. We found the most stable structure people ever proposed for simple cubic based networks. From the difference of this new form of carbon and graphite in the electronic and vibrational properties, we propose an experimental probe to identify these novel three-dimensional carbon networks

  20. Molecular identification and cluster analysis of homofermentative thermophilic lactobacilli isolated from dairy products.

    Science.gov (United States)

    Andrighetto, C; De Dea, P; Lombardi, A; Neviani, E; Rossetti, L; Giraffa, G

    1998-10-01

    Twenty-five strains of thermophilic lactobacilli isolated from yoghurt and from semi-hard and hard cheeses (in parallel with nine type or reference strains) were identified and grouped according to their genetic relatedness. Strains were identified by sugar fermentation patterns using the "API 50 CHL" galleries, by species-specific DNA probes in dot-blot hybridization experiments, by amplification and restriction analysis of the 16S rRNA gene (ARDRA) and by polymerase chain reaction (PCR) using species-specific oligonucleotide primers. Strains were classified as Lactobacillus delbrueckii subsp. lactis and subsp. bulgaricus, L. helveticus, and L. acidophilus. Strains which were atypical by sugar fermentation patterns were also identified. Most of the strains could not be grouped using carbohydrate fermentation profiles. PCR fingerprinting was used to identify DNA profiles for the 25 lactobacilli. Experimentally obtained PCR profiles enabled discrimination of all strains, which were grouped according to the similarities in their combined patterns. In general, the clustering of the strains corresponded well with species delineation obtained by molecular identification. The dendrogram of genetic relatedness enabled the unambiguous identification of most of the strains which were shown to be atypical by the sugar fermentation profile, except for a discrepancy in one L. delbrueckii subsp. lactis strain and one atypical Lactobacillus sp. strain.

  1. An efficient implementation of parallel molecular dynamics method on SMP cluster architecture

    International Nuclear Information System (INIS)

    Suzuki, Masaaki; Okuda, Hiroshi; Yagawa, Genki

    2003-01-01

    The authors have applied MPI/OpenMP hybrid parallel programming model to parallelize a molecular dynamics (MD) method on a symmetric multiprocessor (SMP) cluster architecture. In that architecture, it can be expected that the hybrid parallel programming model, which uses the message passing library such as MPI for inter-SMP node communication and the loop directive such as OpenMP for intra-SNP node parallelization, is the most effective one. In this study, the parallel performance of the hybrid style has been compared with that of conventional flat parallel programming style, which uses only MPI, both in cases the fast multipole method (FMM) is employed for computing long-distance interactions and that is not employed. The computer environments used here are Hitachi SR8000/MPP placed at the University of Tokyo. The results of calculation are as follows. Without FMM, the parallel efficiency using 16 SMP nodes (128 PEs) is: 90% with the hybrid style, 75% with the flat-MPI style for MD simulation with 33,402 atoms. With FMM, the parallel efficiency using 16 SMP nodes (128 PEs) is: 60% with the hybrid style, 48% with the flat-MPI style for MD simulation with 117,649 atoms. (author)

  2. [Molecular characteristics of Clustered Regularly Interspaced Short Palindromic Repeat in Shigella].

    Science.gov (United States)

    Xue, Zerun; Wang, Yingfang; Duan, Guangcai; Yang, Haiyan; Xi, Yuanlin; Wang, Pengfei; Wang, Linlin; Guo, Xiangjiao

    2015-08-01

    To detect the molecular characteristics of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) in Shigella and to analyze the distribution of CRISPR related to the time of isolation. Of the 52 Shigella strains, 41 were isolated from Henan, 6 from Jiangxi and 5 isolated from Beijing. Both CRISPR locus of S1, S2, S3 and S4 in Shigella were detected by polymerase chain reaction (PCR). The PCR products were sequenced and compared. The positive rates of CRISPR locus in Shigella were 33.69% (S1), 50.00% (S2), 82.69% (S3) and 73.08% (S4), respectively. Two subtypes were discovered in S1 and S3 locus. Three subtypes were discovered in S2 locus. Four different subtypes were discovered in S4 locus. The isolates from Henan strains were divided into two groups by the time of isolation. Distributions of S1 were different, before or after 2004, on Shigella. S1 could not be detected after 2004. There were no statistical differences of S2, S3 and S4 in two groups. Different CRISPR subtypes or Shigella were discovered. A significant correlation was noticed between the CRISPR S1 related to the time of isolation but not between S2, S3 or S4 on the time of isolation.

  3. Phase transformation during silica cluster impact on crystal silicon substrate studied by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Chen Ruling; Luo Jianbin; Guo Dan; Lu Xinchun

    2008-01-01

    The process of a silica cluster impact on a crystal silicon substrate is studied by molecular dynamics simulation. At the impact loading stage, crystal silicon of the impact zone transforms to a locally ordered molten with increasing the local temperature and pressure of the impact zone. And then the transient molten forms amorphous silicon directly as the local temperature and pressure decrease at the impact unloading stage. Moreover, the phase behavior between the locally ordered molten and amorphous silicon exhibits the reversible structural transition. The transient molten contains not only lots of four-fold atom but also many three- and five-fold atoms. And the five-fold atom is similar to the mixture structure of semi-Si-II and semi-bct5-Si. The structure transformation between five- and four-fold atoms is affected by both pressure and temperature. The structure transformation between three- and four-fold atoms is affected mostly by temperature. The direct structure transformation between five- and three-fold atoms is not observed. Finally, these five- and three-fold atoms are also different from the usual five- and three-fold deficient atoms of amorphous silicon. In addition, according to the change of coordination number of atoms the impact process is divided into six stages: elastic, plastic, hysteresis, phase regressive, adhesion and cooling stages

  4. NMR study of the molecular nanomagnet [Fe8(N3C6H15)6O2(OH)12]·[Br8·9H2O] in the high-spin magnetic ground state

    International Nuclear Information System (INIS)

    Furukawa, Y.; Kumagai, K.; Lascialfari, A.; Aldrovandi, S.; Borsa, F.; Sessoli, R.; Gatteschi, D.

    2001-01-01

    The magnetic molecular cluster [Fe 8 (N 3 C 6 H 15 ) 6 O 2 (OH) 12 ] 8+ [Br 8 ·9H 2 O] 8- , in short Fe8, has been investigated at low temperature by 1 H-NMR and relaxation measurements. Some measurements of 2 D-NMR in partially deuterated Fe8 clusters will also be reported. Upon decreasing temperature the NMR spectra display a very broad and structured signal which is the result of the internal local fields at the proton sites due to the local moments of the Fe(III) ions in the total S=10 magnetic ground state. The proton and deuteron NMR spectra have been analyzed and the different resonance peaks have been attributed to the different proton groups in the molecule. The simulation of the spectra by using a dipolar hyperfine field and the accepted model for the orientation of the Fe(III) local moments do not agree with the experiments even when the magnitude of the local Fe(III) moments is allowed to vary. It is concluded that a positive contact hyperfine interaction of the same order of magnitude as the dipolar interaction is present for all proton sites except the water molecules. The temperature and magnetic field dependence of the nuclear spin-lattice relaxation rate is ascribed to the fluctuations of the local Fe(III) moments, which follow rigidly the fluctuations of the total ground state magnetization of the nanomagnet. By using a simple model already utilized for the Mn12 cluster, we derive the value of the spin phonon coupling constant which determines the lifetime broadening of the different magnetic quantum number m substates of the S=10 ground state. It is shown that the lifetime broadening decreases rapidly on lowering the temperature. When the lifetime becomes longer than the reciprocal of the frequency shift of the proton lines a structure emerges in the NMR spectrum reflecting the ''frozen'' local moment configuration

  5. Communication: spin-orbit splittings in degenerate open-shell states via Mukherjee's multireference coupled-cluster theory: a measure for the coupling contribution.

    Science.gov (United States)

    Mück, Leonie Anna; Gauss, Jürgen

    2012-03-21

    We propose a generally applicable scheme for the computation of spin-orbit (SO) splittings in degenerate open-shell systems using multireference coupled-cluster (MRCC) theory. As a specific method, Mukherjee's version of MRCC (Mk-MRCC) in conjunction with an effective mean-field SO operator is adapted for this purpose. An expression for the SO splittings is derived and implemented using Mk-MRCC analytic derivative techniques. The computed SO splittings are found to be in satisfactory agreement with experimental data. Due to the symmetry properties of the SO operator, SO splittings can be considered a quality measure for the coupling between reference determinants in Jeziorski-Monkhorst based MRCC methods. We thus provide numerical insights into the coupling problem of Mk-MRCC theory. © 2012 American Institute of Physics

  6. A WARM MOLECULAR HYDROGEN TAIL DUE TO RAM-PRESSURE STRIPPING OF A CLUSTER GALAXY

    International Nuclear Information System (INIS)

    Sivanandam, Suresh; Rieke, Marcia J.; Rieke, George H.

    2010-01-01

    We have discovered a remarkable warm (130-160 K) molecular hydrogen tail with a H 2 mass of approximately 4 x 10 7 M sun extending 20 kpc from a cluster spiral galaxy, ESO 137-001, in Abell 3627. At least half of this gas is lost permanently to the intracluster medium, as the tail extends beyond the tidal radius of the galaxy. We also detect a hot (400-550 K) component in the tail that is approximately 1% of the mass. The large H 2 line to IR continuum luminosity ratio in the tail indicates that star formation is not a major excitation source and that the gas is possibly shock-heated. This discovery confirms that the galaxy is currently undergoing ram-pressure stripping, as also indicated by its previously discovered X-ray and Hα tails. We estimate that the galaxy is losing its warm H 2 gas at a rate of ∼2-3 M sun yr -1 . The true mass-loss rate is likely higher if we account for cold molecular gas and atomic gas. We predict that the galaxy will lose most of its gas in a single pass through the core and place a strong upper limit on the ram-pressure timescale of 1 Gyr. We also study the star-forming properties of the galaxy and its tail. We identify most of the previously discovered external Hα sources within the tail in our 8 μm data but not in our 3.6 μm data; IRS spectroscopy of the region containing these Hα sources also reveals aromatic features typically associated with star formation. From the positions of these H II regions, it appears that star formation is not occurring throughout the molecular hydrogen tail but only immediately downstream of the galaxy. Some of these H II regions lie outside the tidal radius of the galaxy, indicating that ram-pressure stripping can be a source of intracluster stars.

  7. Molecular dynamics simulations of diffusion and clustering along critical isotherms of medium-chain n-alkanes.

    Science.gov (United States)

    Mutoru, J W; Smith, W; O'Hern, C S; Firoozabadi, A

    2013-01-14

    Understanding the transport properties of molecular fluids in the critical region is important for a number of industrial and natural systems. In the literature, there are conflicting reports on the behavior of the self diffusion coefficient D(s) in the critical region of single-component molecular systems. For example, D(s) could decrease to zero, reach a maximum, or remain unchanged and finite at the critical point. Moreover, there is no molecular-scale understanding of the behavior of diffusion coefficients in molecular fluids in the critical regime. We perform extensive molecular dynamics simulations in the critical region of single-component fluids composed of medium-chain n-alkanes-n-pentane, n-decane, and n-dodecane-that interact via anisotropic united-atom potentials. For each system, we calculate D(s), and average molecular cluster sizes κ(cl) and numbers N(cl) at various cluster lifetimes τ, as a function of density ρ in the range 0.2ρ(c) ≤ ρ ≤ 2.0ρ(c) at the critical temperature T(c). We find that D(s) decreases with increasing ρ but remains finite at the critical point. Moreover, for any given τ critical point.

  8. Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: Application to polycyclic aromatic hydrocarbon clusters

    Science.gov (United States)

    Rapacioli, Mathias; Spiegelman, Fernand; Talbi, Dahbia; Mineva, Tzonka; Goursot, Annick; Heine, Thomas; Seifert, Gotthard

    2009-06-01

    The density functional based tight binding (DFTB) is a semiempirical method derived from the density functional theory (DFT). It inherits therefore its problems in treating van der Waals clusters. A major error comes from dispersion forces, which are poorly described by commonly used DFT functionals, but which can be accounted for by an a posteriori treatment DFT-D. This correction is used for DFTB. The self-consistent charge (SCC) DFTB is built on Mulliken charges which are known to give a poor representation of Coulombic intermolecular potential. We propose to calculate this potential using the class IV/charge model 3 definition of atomic charges. The self-consistent calculation of these charges is introduced in the SCC procedure and corresponding nuclear forces are derived. Benzene dimer is then studied as a benchmark system with this corrected DFTB (c-DFTB-D) method, but also, for comparison, with the DFT-D. Both methods give similar results and are in agreement with references calculations (CCSD(T) and symmetry adapted perturbation theory) calculations. As a first application, pyrene dimer is studied with the c-DFTB-D and DFT-D methods. For coronene clusters, only the c-DFTB-D approach is used, which finds the sandwich configurations to be more stable than the T-shaped ones.

  9. Correlation between inter-spin interaction and molecular dynamics of organic radicals in organic 1D nanochannels

    Energy Technology Data Exchange (ETDEWEB)

    Kobayashi, Hirokazu [Department of Chemistry, College of Humanities and Sciences, Nihon University 3-25-40, Sakura-jo-sui, Setagaya-ku, Tokyo, 156-8550 (Japan)

    2015-12-31

    One-dimensional (1D) molecular chains of 4-substituted-2,2,6,6-tetramethyl-1-piperidinyloxyl (4-X-TEMPO) radicals were constructed in the crystalline 1D nanochannels of 2,4,6-tris(4-chlorophenoxy)-1,3,5-triazine (CLPOT) used as a template. The ESR spectra of CLPOT inclusion compounds (ICs) using 4-X-TEMPO were examined on the basis of spectral simulation using EasySpin program package for simulating and fitting ESR spectra. The ESR spectra of [(CLPOT){sub 2}-(TEMPO){sub 1.0}] IC were isotropic in the total range of temperatures. The peak-to-peak line width (ΔB{sub pp}) became monotonically narrower from 2.8 to 1.3 mT with increase in temperature in the range of 4.2–298 K. The effect of the rotational diffusion motion of TEMPO radicals in the CLPOT nanochannels for the inter-spin interaction of the [(CLPOT){sub 2}-(TEMPO){sub 1.0}] IC was found to be smaller than the case of [(TPP){sub 2}−(TEMPO){sub 1.0}] IC (TPP = tris(o-phenylenedioxy)cyclotriphosphazene) reported in our previous study. The ΔB{sub pp} of the [(CLPOT){sub 2}-(TEMPO){sub 1.0}] IC in the whole range of temperatures was much narrower than the estimation to be based on the Van Vleck’s formula for the second moment of the rigid lattice model where the electron spin can be considered as fixed; 11 mT of Gaussian line-width component. This suggests the possibility of exchange narrowing in the 1D organic-radical chains of the [(CLPOT){sub 2}-(TEMPO){sub 1.0}] IC. On the other hand, the ESR spectra of [(CLPOT){sub 2}-(MeO-TEMPO){sub 0.41}] IC (MeO-TEMPO = 4-methoxy-TEMPO) were reproduced by a superposition of major broad isotropic adsorption line and minor temperature-dependent modulated triplet component. This suggests that the IC has the part of 1D organic-radical chains and MeO-TEMPO molecules isolated in the CLPOT nanochannels.

  10. Growth of CdTe on Si(100) surface by ionized cluster beam technique: Experimental and molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Araghi, Houshang, E-mail: araghi@aut.ac.ir [Department of Physics, Amirkabir University of Technology, Tehran (Iran, Islamic Republic of); Zabihi, Zabiholah [Department of Physics, Amirkabir University of Technology, Tehran (Iran, Islamic Republic of); Nayebi, Payman [Department of Physics, College of Technical and Engineering, Saveh Branch, Islamic Azad University, Saveh (Iran, Islamic Republic of); Ehsani, Mohammad Mahdi [Department of Physics, Amirkabir University of Technology, Tehran (Iran, Islamic Republic of)

    2016-10-15

    II–VI semiconductor CdTe was grown on the Si(100) substrate surface by the ionized cluster beam (ICB) technique. In the ICB method, when vapors of solid materials such as CdTe were ejected through a nozzle of a heated crucible into a vacuum region, nanoclusters were created by an adiabatic expansion phenomenon. The clusters thus obtained were partially ionized by electron bombardment and then accelerated onto the silicon substrate at 473 K by high potentials. The cluster size was determined using a retarding field energy analyzer. The results of X-ray diffraction measurements indicate the cubic zinc blende (ZB) crystalline structure of the CdTe thin film on the silicon substrate. The CdTe thin film prepared by the ICB method had high crystalline quality. The microscopic processes involved in the ICB deposition technique, such as impact and coalescence processes, have been studied in detail by molecular dynamics (MD) simulation.

  11. Molecular dynamics computer simulation study of Pd{sub n} (n=13, 19, 38 and 55) clusters

    Energy Technology Data Exchange (ETDEWEB)

    Karabacak, M [Afyon Kocatepe University, Department of Physics, Afyon (Turkey); Oezcelik, S [Gazi University, Department of Physics, Ankara (Turkey); Guevenc, Z B [Cankaya University, Department of Electronics and Communication Engineering, Ankara (Turkey)

    2002-07-01

    Using constant-energy molecular dynamics and thermal quenching simulations, we have studied minimum-energy structures and energetics, Pd{sub n} (n=13, 19, 38, and 55) clusters employing the Voter and Chen's version of parameterisation of the embedded-atom potential surface. Isomer statistics for Pdn ( n = 13 and 19 ) is obtained from 10000 initial independent configurations, which have been generated along high-energy trajectories (chosen energy values are high enough to melt the clusters). The thermal quenching technique is employed to remove the internal kinetic energy of the clusters. The locally stable isomers are separated from metastable ones. Probabilities belonging to sampling the basins of attractions of each isomers are computed, and then, isomers' energy spectra are analyzed.

  12. Electron spin resonance and electron spin echo modulation spectroscopic studies on the structure and reactivity of Pd(I) species in SAPO-11 molecular sieves

    International Nuclear Information System (INIS)

    Chul Wee Lee; Jong-Sung Yu; Kevan, L.

    1992-01-01

    This paper explores the possibility of using Pd ions in SAPO-11 by adding [Pd(NH 3 ) 4 ] 2+ during the synthesis of SAPO-11 to form PdSAPO-11, which is compared with solid-state ion exchange PdSAPO-11 and impregnation PdH-SAPO-11 in which palladium is in an extraframework position. Electron spin resonance and electron spin echo modulation spectroscopies are used to determine if the palladium position in PdSAPO-11 is located in a framework or extraframework

  13. a Moessbauer Effect and Fenske-Hall Molecular Orbital Study of the Electronic Properties of Organoiron Clusters.

    Science.gov (United States)

    Buhl, Margaret Linn

    The electronic properties of trinuclear iron, tetranuclear iron butterfly, iron-cobalt, and iron-copper clusters have been studied experimentally at 78K by the Mossbauer effect and theoretically by Fenske-Hall molecular orbital calculations. The Mossbauer effect isomer shift is very sensitive to the differences in the iron s-electron densities in these clusters and, as expected, decreases as the sum of the iron 4s Mulliken population and the Clementi and Raimondi effective nuclear charge increases. The molecular orbital wave functions and the Mulliken atomic charges are used to calculate the electric field gradient at the metal nuclei and the iron Mossbauer effect quadrupole splittings. The valence contribution was found to be the major component of the electric field gradient in all the clusters studied. In general the calculated value of Delta E_ {Q} is larger than the observed value, as a result of neglect of the valence Sternheimer factor, R. The metal charge depends upon its electronegativity and upon the nature of its Lewis base ligands. The carbonyl ligand carbon charge becomes more positive as the metal electronegativity increases. The oxygen charge becomes more negative as the anionic cluster charge increases, and in so doing, yields the maximum anionic charge separation. The electronic properties of the terminal carbonyl ligands are similar to those of carbon monoxide, whereas the electronic properties of the bridging carbonyl ligands are similar to those of the carbonyl group found in aldehydes and ketones.

  14. Spin excitations in 3D molecular magnets probed by neutron scattering

    CERN Document Server

    Bordallo, H N; Chapon, L C; Manson, J L; Cook, J C; Lee, S H; Copley, J R D; Yildirim, T; Kern, S

    2002-01-01

    The emerging field of molecular magnetism constitutes a new branch of materials science that deals with the magnetic properties of molecules, or assemblies of molecules, that contain magnetic centers. The growing interest in understanding the origin of the magnetic ordering in these materials is to obtain novel multiproperty molecular magnetic materials with high transition temperatures. Molecules based on the dicyanamide ion [N ident to C-N-C ident to N], abbreviated (dca), such as M(dca) sub 2 [M=Mn, Ni], have shown interesting bulk properties that prompted our inelastic neutron scattering (INS) studies. While the Mn sup 2 sup + ion is isotropic because of its L=0 configuration, the isostructural Ni analog has S=1 and demonstrates marked single-ion anisotropy. Mn(dca) sub 2 is a canted antiferromagnet below 16 K, while Ni(dca) sub 2 is a ferromagnet below 21 K. INS has been used to investigate the magnetic excitations in Mn(dca) sub 2 and Ni(dca) sub 2. For Mn(dca) sub 2 , a Heisenberg model gives good corr...

  15. Molecular identification and characterization of clustered regularly interspaced short palindromic repeat (CRISPR) gene cluster in Taylorella equigenitalis.

    Science.gov (United States)

    Hara, Yasushi; Hayashi, Kyohei; Nakajima, Takuya; Kagawa, Shizuko; Tazumi, Akihiro; Moore, John E; Matsuda, Motoo

    2013-09-01

    Clustered regularly interspaced short palindromic repeats (CRISPRs), of approximately 10,000 base pairs (bp) in length, were shown to occur in the Japanese Taylorella equigenitalis strain, EQ59. The locus was composed of the putative CRISPRs-associated with 5 (cas5), RAMP csd1, csd2, recB, cas1, a leader region, 13 CRISPR consensus sequence repeats (each 32 bp; 5'-TCAGCCACGTTCGCGTGGCTGTGTGTTTAAAG-3'). These were in turn separated by 12 non repetitive unique spacer regions of similar length. In addition, a leader region, a transposase/IS protein, a leader region, and cas3 were also seen. All seven putative open reading frames carry their ribosome binding sites. Promoter consensus sequences at the -35 and -10 regions and putative intrinsic ρ-independent transcription terminator regions also occurred. A possible long overlap of 170 bp in length occurred between the recB and cas1 loci. Positive reverse transcription PCR signals of cas5, RAMP csd1, csd2-recB/cas1, and cas3 were generated. A putative secondary structure of the CRISPR consensus repeats was constructed. Following this, CRISPR results of the T. equigenitalis EQ59 isolate were subsequently compared with those from the Taylorella asinigenitalis MCE3 isolate.

  16. Rotational dynamics in supercooled water from nuclear spin relaxation and molecular simulations.

    Science.gov (United States)

    Qvist, Johan; Mattea, Carlos; Sunde, Erik P; Halle, Bertil

    2012-05-28

    Structural dynamics in liquid water slow down dramatically in the supercooled regime. To shed further light on the origin of this super-Arrhenius temperature dependence, we report high-precision (17)O and (2)H NMR relaxation data for H(2)O and D(2)O, respectively, down to 37 K below the equilibrium freezing point. With the aid of molecular dynamics (MD) simulations, we provide a detailed analysis of the rotational motions probed by the NMR experiments. The NMR-derived rotational correlation time τ(R) is the integral of a time correlation function (TCF) that, after a subpicosecond librational decay, can be described as a sum of two exponentials. Using a coarse-graining algorithm to map the MD trajectory on a continuous-time random walk (CTRW) in angular space, we show that the slowest TCF component can be attributed to large-angle molecular jumps. The mean jump angle is ∼48° at all temperatures and the waiting time distribution is non-exponential, implying dynamical heterogeneity. We have previously used an analogous CTRW model to analyze quasielastic neutron scattering data from supercooled water. Although the translational and rotational waiting times are of similar magnitude, most translational jumps are not synchronized with a rotational jump of the same molecule. The rotational waiting time has a stronger temperature dependence than the translation one, consistent with the strong increase of the experimentally derived product τ(R) D(T) at low temperatures. The present CTRW jump model is related to, but differs in essential ways from the extended jump model proposed by Laage and co-workers. Our analysis traces the super-Arrhenius temperature dependence of τ(R) to the rotational waiting time. We present arguments against interpreting this temperature dependence in terms of mode-coupling theory or in terms of mixture models of water structure.

  17. 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.

  18. Ab-initio molecular dynamics studies of magnesium-doped sodium clusters

    International Nuclear Information System (INIS)

    Roethlisberger, U.; Andreoni, W.

    1993-01-01

    Structural, electronic, and vibrational properties of magnesium-doped sodium clusters have been determined using the Car-Parrinello method. It is found that in the energetically preferred structures the magnesium impurity never is located at the centre of the cluster. The validity of spherical jellium models and the effects of temperature are discussed. 9 refs, 3 figs, 1 tab

  19. Competetive clustering in a bidisperse granular gas : experiment, molecular dynamics, and flux model

    NARCIS (Netherlands)

    Mikkelsen, René; van der Meer, Devaraj; van der Weele, Ko; Lohse, Detlef

    2004-01-01

    A compartmentalized bidisperse granular gas clusters competitively [R. Mikkelsen, D. van der Meer, K. van der Weele, and D. Lohse, Phys. Rev. Lett. 89, 214301 (2002)]: By tuning the shaking strength, the clustering can be directed either towards the compartment initially containing mainly small

  20. Resonances in field-cycling NMR on molecular crystals. (reversible) Spin dynamics or (irreversible) relaxation?; Resonanzen in Field-Cycling-NMR an Molekuelkristallen. (reversible) Spindynamik oder (irreversible) Relaxation?

    Energy Technology Data Exchange (ETDEWEB)

    Tacke, Christian

    2015-07-01

    Multi spin systems with spin 1/2 nuclei and dipolar coupled quadrupolar nuclei can show so called ''quadrupolar dips''. There are two main reasons for this behavior: polarization transfer and relaxation. They look quite alike and without additional research cannot be differentiated easily in most cases. These two phenomena have quite different physical and theoretical backgrounds. For no or very slow dynamics, polarization transfer will take place, which is energy conserving inside the spin system. This effect can entirely be described using quantum mechanics on the spin system. Detailed knowledge about the crystallography is needed, because this affects the relevant hamiltonians directly. For systems with fast enough dynamics, relaxation takes over, and the energy flows from the spin system to the lattice; thus a more complex theoretical description is needed. This description has to include a dynamic model, usually in the form of a spectral density function. Both models should include detailed modelling of the complete spin system. A software library was developed to be able to model complex spin systems. It allows to simulate polarization transfer or relaxation effects. NMR measurements were performed on the protonic conductor K{sub 3}H(SO{sub 4}){sub 2}. A single crystal shows sharp quadrupolar dips at room temperature. Dynamics could be excluded using relaxation measurements and literature values. Thus, a polarization transfer analysis was used to describe those dips with good agreement. As a second system, imidazolium based molecular crystals were analyzed. The quadrupolar dips were expected to be caused by polarization transfer; this was carefully analyzed and found not to be true. A relaxation based analysis shows good agreement with the measured data in the high temperature area. It leverages a two step spectral density function, which indicates two distinct dynamic processes happening in this system.

  1. Non-adiabatic Landau-Zener transitions in low-spin molecular magnet V sub 1 sub 5

    CERN Document Server

    Chiorescu, I; Müller, A; Bögge, H; Barbara, B

    2000-01-01

    The V sub 1 sub 5 polyoxovanadate molecule is made of 15 spins ((1)/(2)) with antiferromagnetic couplings. It belongs to the class of molecules with very large Hilbert space dimension (2 sup 1 sup 5 in V sub 1 sub 5 , 10 sup 8 in Mn sub 1 sub 2 -AC). It is a low spin/large molecule with spin S=((1)/(2)). Contrary to large spins/large molecules of the Mn sub 1 sub 2 -AC type, V sub 1 sub 5 has no energy barrier against spin rotation. Magnetization measurements have been performed and despite the absence of a barrier, magnetic hysteresis is observed over a timescale of several seconds. This new phenomenon characterized by a 'butterfly' hysteresis loop is due to the effect of the environment on the quantum rotation of the entangled 15 spins of the molecule, in which the phonon density of states is not at its equilibrium (phonon bottleneck).

  2. Leakage and sweet spots in triple-quantum-dot spin qubits: A molecular-orbital study

    Science.gov (United States)

    Zhang, Chengxian; Yang, Xu-Chen; Wang, Xin

    2018-04-01

    A triple-quantum-dot system can be operated as either an exchange-only qubit or a resonant-exchange qubit. While it is generally believed that the decisive advantage of the resonant-exchange qubit is the suppression of charge noise because it is operated at a sweet spot, we show that the leakage is also an important factor. Through molecular-orbital-theoretic calculations, we show that when the system is operated in the exchange-only scheme, the leakage to states with double electron occupancy in quantum dots is severe when rotations around the axis 120∘ from z ̂ is performed. While this leakage can be reduced by either shrinking the dots or separating them further, the exchange interactions are also suppressed at the same time, making the gate operations unfavorably slow. When the system is operated as a resonant-exchange qubit, the leakage is three to five orders of magnitude smaller. We have also calculated the optimal detuning point which minimizes the leakage for the resonant-exchange qubit, and have found that although it does not coincide with the double sweet spot for the charge noise, they are rather close. Our results suggest that the resonant-exchange qubit has another advantage, that leakage can be greatly suppressed compared to the exchange-only qubit, and operating at the double sweet spot point should be optimal both for reducing charge noise and suppressing leakage.

  3. Generalized approximate spin projection calculations of effective exchange integrals of the CaMn4O5 cluster in the S1 and S3 states of the oxygen evolving complex of photosystem II.

    Science.gov (United States)

    Isobe, H; Shoji, M; Yamanaka, S; Mino, H; Umena, Y; Kawakami, K; Kamiya, N; Shen, J-R; Yamaguchi, K

    2014-06-28

    Full geometry optimizations followed by the vibrational analysis were performed for eight spin configurations of the CaMn4O4X(H2O)3Y (X = O, OH; Y = H2O, OH) cluster in the S1 and S3 states of the oxygen evolution complex (OEC) of photosystem II (PSII). The energy gaps among these configurations obtained by vertical, adiabatic and adiabatic plus zero-point-energy (ZPE) correction procedures have been used for computation of the effective exchange integrals (J) in the spin Hamiltonian model. The J values are calculated by the (1) analytical method and the (2) generalized approximate spin projection (AP) method that eliminates the spin contamination errors of UB3LYP solutions. Using J values derived from these methods, exact diagonalization of the spin Hamiltonian matrix was carried out, yielding excitation energies and spin densities of the ground and lower-excited states of the cluster. The obtained results for the right (R)- and left (L)-opened structures in the S1 and S3 states are found to be consistent with available optical and magnetic experimental results. Implications of the computational results are discussed in relation to (a) the necessity of the exact diagonalization for computations of reliable energy levels, (b) magneto-structural correlations in the CaMn4O5 cluster of the OEC of PSII, (c) structural symmetry breaking in the S1 and S3 states, and (d) the right- and left-handed scenarios for the O-O bond formation for water oxidation.

  4. Intensities and cross sections of Ne, H2, N2, NO and O2 clusters in a molecular beam, ch. 4

    International Nuclear Information System (INIS)

    Deursen, A.P.J. van; Reuss, J.

    1976-01-01

    Molecular beams of Ne, H 2 , N 2 , NO, and O 2 clusters have been investigated. The temperature and pressure dependence of the ion signals have been measured for masses up to three times the monomer mass. (Auth.)

  5. Local spin dynamics at low temperature in the slowly relaxing molecular chain [Dy(hfac)3(NIT(C6H4OPh))]: A μ{sup +} spin relaxation study

    Energy Technology Data Exchange (ETDEWEB)

    Arosio, Paolo, E-mail: paolo.arosio@guest.unimi.it; Orsini, Francesco [Department of Physics, Università degli Studi di Milano, and INSTM, Milano (Italy); Corti, Maurizio [Department of Physics, Università degli Studi di Pavia and INSTM, Pavia (Italy); Mariani, Manuel [Department of Physics and Astronomy, Università degli Studi di Bologna, Bologna (Italy); Bogani, Lapo [Physikalisches Institut, Universität Stuttgart, Stuttgart (Germany); Caneschi, Andrea [INSTM and Department of Chemistry, University of Florence, Firenze (Italy); Lago, Jorge [Departamento de Quimica Inorganica, Universidad del Pais Vasco, Bilbao (Spain); Lascialfari, Alessandro [Department of Physics, Università degli Studi di Milano, and INSTM, Milano (Italy); Centro S3, Istituto Nanoscienze - CNR, Modena (Italy)

    2015-05-07

    The spin dynamics of the molecular magnetic chain [Dy(hfac){sub 3}(NIT(C{sub 6}H{sub 4}OPh))] were investigated by means of the Muon Spin Relaxation (μ{sup +}SR) technique. This system consists of a magnetic lattice of alternating Dy(III) ions and radical spins, and exhibits single-chain-magnet behavior. The magnetic properties of [Dy(hfac){sub 3}(NIT(C{sub 6}H{sub 4}OPh))] have been studied by measuring the magnetization vs. temperature at different applied magnetic fields (H = 5, 3500, and 16500 Oe) and by performing μ{sup +}SR experiments vs. temperature in zero field and in a longitudinal applied magnetic field H = 3500 Oe. The muon asymmetry P(t) was fitted by the sum of three components, two stretched-exponential decays with fast and intermediate relaxation times, and a third slow exponential decay. The temperature dependence of the spin dynamics has been determined by analyzing the muon longitudinal relaxation rate λ{sub interm}(T), associated with the intermediate relaxing component. The experimental λ{sub interm}(T) data were fitted with a corrected phenomenological Bloembergen-Purcell-Pound law by using a distribution of thermally activated correlation times, which average to τ = τ{sub 0} exp(Δ/k{sub B}T), corresponding to a distribution of energy barriers Δ. The correlation times can be associated with the spin freezing that occurs when the system condenses in the ground state.

  6. Influence of local molecular motions on the determination of 1H-1H internuclear distances measured by 2D 1H spin-exchange experiments

    Czech Academy of Sciences Publication Activity Database

    Brus, Jiří; Petříčková, H.; Dybal, Jiří

    2003-01-01

    Roč. 23, č. 4 (2003), s. 183-197 ISSN 0926-2040 R&D Projects: GA AV ČR IAB4050203; GA AV ČR IAA4050208; GA ČR GA203/99/0067 Institutional research plan: CEZ:AV0Z4050913 Keywords : H-1-H-1 spin exchange * interatomic distances * molecular motion Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.453, year: 2003

  7. Neutron Scattering studies of magnetic molecular magnets

    International Nuclear Information System (INIS)

    Chaboussant, G.

    2009-01-01

    This work deals with inelastic neutron scattering studies of magnetic molecular magnets and focuses on their magnetic properties at low temperature and low energies. Several molecular magnets (Mn 12 , V 15 , Ni 12 , Mn 4 , etc.) are reviewed. Inelastic neutron scattering is shown to be a perfectly suited spectroscopy tool to -a) probe magnetic energy levels in such systems and -b) provide key information to understand the quantum tunnel effect of the magnetization in molecular spin clusters. (author)

  8. Quantum molecular dynamics: Numerical methods and physical study of the structure, thermodynamics, stability and fragmentation of sodium metallic clusters

    International Nuclear Information System (INIS)

    Blaise, Philippe

    1998-01-01

    The aim of this thesis is to study metallic sodium clusters by numerical simulation. We have developed two ab initio molecular dynamics programs within the formalism of density functional theory. The first is based on the semi-classical extended Thomas-Fermi approach. We use a real-space grid and a Car-Parrinello-like scheme. The computational cost is O(N), and we have built a pseudopotential that speeds up the calculations. By neglecting quantum shell effects, we are able to study a very large set of clusters. We show that sodium cluster energies fit well a liquid drop formula, by adjusting a few parameters. We have investigated breathing modes, surface oscillations and the net charge density. We have shown that the surface energy varies strongly with temperature, and that clusters have a lower melting point than bulk material. We have calculated fission barriers by a constraint method. The second program is based on the quantum Kohn-Sham approach. We use a real-space grid, and combine a generalized Broyden scheme for assuring self-consistency with an iterative Davidson-Lanczos algorithm for solving the Eigen-problem. The cost of the method is much higher. First of all, we have calculated some stable structures for small clusters and their energetics. We obtained very good agreement with previous works. Then, we have investigated highly charged cluster dynamics. We have identified a chaotic fission process. For high fissility systems, we observe a multi-fragmentation dynamics and we find preferential emission of monomers on a characteristic time scale less than a pico-second. This has been simulated for the first time, with the help of our adaptive grid method which follows each fragment as they move apart during the fragmentation. (author)

  9. Non-flipping 13C spins near an NV center in diamond: hyperfine and spatial characteristics by density functional theory simulation of the C510[NV]H252 cluster

    Science.gov (United States)

    Nizovtsev, A. P.; Kilin, S. Ya; Pushkarchuk, A. L.; Pushkarchuk, V. A.; Kuten, S. A.; Zhikol, O. A.; Schmitt, S.; Unden, T.; Jelezko, F.

    2018-02-01

    Single NV centers in diamond coupled by hyperfine interaction (hfi) to neighboring 13C nuclear spins are now widely used in emerging quantum technologies as elements of quantum memory adjusted to a nitrogen-vacancy (NV) center electron spin qubit. For nuclear spins with low flip-flop rate, single shot readout was demonstrated under ambient conditions. Here we report on a systematic search for such stable NV-13C systems using density functional theory to simulate the hfi and spatial characteristics of all possible NV-13C complexes in the H-terminated cluster C510[NV]-H252 hosting the NV center. Along with the expected stable ‘NV-axial-13C’ systems wherein the 13C nuclear spin is located on the NV axis, we found for the first time new families of positions for the 13C nuclear spin exhibiting negligible hfi-induced flipping rates due to near-symmetric local spin density distribution. Spatially, these positions are located in the diamond bilayer passing through the vacancy of the NV center and being perpendicular to the NV axis. Analysis of available publications showed that, apparently, some of the predicted non-axial near-stable NV-13C systems have already been observed experimentally. A special experiment performed on one of these systems confirmed the prediction made.

  10. Genetic diversity of K-antigen gene clusters of Escherichia coli and their molecular typing using a suspension array.

    Science.gov (United States)

    Yang, Shuang; Xi, Daoyi; Jing, Fuyi; Kong, Deju; Wu, Junli; Feng, Lu; Cao, Boyang; Wang, Lei

    2018-04-01

    Capsular polysaccharides (CPSs), or K-antigens, are the major surface antigens of Escherichia coli. More than 80 serologically unique K-antigens are classified into 4 groups (Groups 1-4) of capsules. Groups 1 and 4 contain the Wzy-dependent polymerization pathway and the gene clusters are in the order galF to gnd; Groups 2 and 3 contain the ABC-transporter-dependent pathway and the gene clusters consist of 3 regions, regions 1, 2 and 3. Little is known about the variations among the gene clusters. In this study, 9 serotypes of K-antigen gene clusters (K2ab, K11, K20, K24, K38, K84, K92, K96, and K102) were sequenced and correlated with their CPS chemical structures. On the basis of sequence data, a K-antigen-specific suspension array that detects 10 distinct CPSs, including the above 9 CPSs plus K30, was developed. This is the first report to catalog the genetic features of E. coli K-antigen variations and to develop a suspension array for their molecular typing. The method has a number of advantages over traditional bacteriophage and serum agglutination methods and lays the foundation for straightforward identification and detection of additional K-antigens in the future.

  11. Influence of Molecular Structure on O2-Binding Properties and Blood Circulation of Hemoglobin‒Albumin Clusters.

    Directory of Open Access Journals (Sweden)

    Kana Yamada

    Full Text Available A hemoglobin wrapped covalently by three human serum albumins, a Hb-HSA3 cluster, is an artificial O2-carrier with the potential to function as a red blood cell substitute. This paper describes the synthesis and O2-binding properties of new hemoglobin‒albumin clusters (i bearing four HSA units at the periphery (Hb-HSA4, large-size variant and (ii containing an intramolecularly crosslinked Hb in the center (XLHb-HSA3, high O2-affinity variant. Dynamic light scattering measurements revealed that the Hb-HSA4 diameter is greater than that of either Hb-HSA3 or XLHb-HSA3. The XLHb-HSA3 showed moderately high O2-affinity compared to the others because of the chemical linkage between the Cys-93(β residues in Hb. Furthermore, the blood circulation behavior of 125I-labeled clusters was investigated by assay of blood retention and tissue distribution after intravenous administration into anesthetized rats. The XLHb-HSA3 was metabolized faster than Hb-HSA3 and Hb-HSA4. Results suggest that the molecular structure of the protein cluster is a factor that can influence in vivo circulation behavior.

  12. Pressure and cooling rate effect on polyhedron clusters in Cu-Al alloy by using molecular dynamics simulation

    Science.gov (United States)

    Celik, Fatih Ahmet

    2014-10-01

    In this study, the microstructural evolution of crystal-type and icosahedral (icos)-type polyhedrons in Cu-50 at%Al alloy based on the embedded atom method (EAM) model is studied at two cooling rates under normal and high pressures by using the molecular dynamics (MD) simulation method. The cluster-type index method (CTIM) which describes icos and defective icos polyhedrons and the new cluster-type index method (CTIM-2) which describes crystal-type polyhedrons have been used to perform polyhedron analysis in the model alloy system. The results of our simulations demonstrate that the effects of the cooling rate and pressure play an important role in the numbers of polyhedrons and their structures in the system.

  13. Pressure and cooling rate effect on polyhedron clusters in Cu–Al alloy by using molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Celik, Fatih Ahmet, E-mail: facelik@beu.edu.tr

    2014-10-01

    In this study, the microstructural evolution of crystal-type and icosahedral (icos)-type polyhedrons in Cu–50 at%Al alloy based on the embedded atom method (EAM) model is studied at two cooling rates under normal and high pressures by using the molecular dynamics (MD) simulation method. The cluster-type index method (CTIM) which describes icos and defective icos polyhedrons and the new cluster-type index method (CTIM-2) which describes crystal-type polyhedrons have been used to perform polyhedron analysis in the model alloy system. The results of our simulations demonstrate that the effects of the cooling rate and pressure play an important role in the numbers of polyhedrons and their structures in the system.

  14. Differential cross-sections of a double spin-flip In d + d reactions and supermultiplet potential model of the interaction of clusters

    CERN Document Server

    Lebedev, V M; Struzhko, B G

    2002-01-01

    The experimental two-dimensional proton-proton coincidence spectra of the four-particle reaction d + d -> p + p + n + n are simulated with regard to dominant quasi-binary processes, viz. a quasi-free scattering of protons and final-state interaction of nucleons. Differential cross-sections d sigma (nu,E)/d OMEGA of a deuteron charge exchange sup 2 H(d, sup 2 n) sup 2 p reaction (0,57 +- 0.03 mb/sr at THETA sub c sub m 62,5 degree, 1,01 +- 0,05 mb /sr at THETA sub c sub m = 79,6 degree, E sub c sub m = 11,6 MeV) and spin-isospin flip sup 2 H(d,d sup *)d sup * one (1,1 +- 0,3 mb /sr at THETA sub c sub m = 90 degree E sub c sub m 23,4 MeV) are defined. They are compared to the cross-sections calculated in the approach of generalized (supermultiplet) potential model where the problem of the interaction of clusters A and B can be reduced to a set of one-channel scattering problems with potentials V sup [ f], where [f] are the allowed Young schemes for the system A + B. This is important for channels with minimum t...

  15. Mapping the influence of molecular structure on rates of electron transfer using direct measurements of the electron spin-spin exchange interaction.

    Science.gov (United States)

    Lukas, Aaron S; Bushard, Patrick J; Weiss, Emily A; Wasielewski, Michael R

    2003-04-02

    The spin-spin exchange interaction, 2J, in a radical ion pair produced by a photoinduced electron transfer reaction can provide a direct measure of the electronic coupling matrix element, V, for the subsequent charge recombination reaction. We have developed a series of dyad and triad donor-acceptor molecules in which 2J is measured directly as a function of incremental changes in their structures. In the dyads the chromophoric electron donors 4-(N-pyrrolidinyl)- and 4-(N-piperidinyl)naphthalene-1,8-dicarboximide, 5ANI and 6ANI, respectively, and a naphthalene-1,8:4,5-bis(dicarboximide) (NI) acceptor are linked to the meta positions of a phenyl spacer to yield 5ANI-Ph-NI and 6ANI-Ph-NI. In the triads the same structure is used, except that the piperidine in 6ANI is replaced by a piperazine in which a para-X-phenyl, where X = H, F, Cl, MeO, and Me(2)N, is attached to the N' nitrogen to form a para-X-aniline (XAn) donor to give XAn-6ANI-Ph-NI. Photoexcitation yields the respective 5ANI(+)-Ph-NI(-), 6ANI(+)-Ph-NI(-), and XAn(+)-6ANI-Ph-NI(-) singlet radical ion pair states, which undergo subsequent radical pair intersystem crossing followed by charge recombination to yield (3)NI. The radical ion pair distances within the dyads are about 11-12 A, whereas those in the triads are about approximately 16-19 A. The degree of delocalization of charge (and spin) density onto the aniline, and therefore the average distance between the radical ion pairs, is modulated by the para substituent. The (3)NI yields monitored spectroscopically exhibit resonances as a function of magnetic field, which directly yield 2J for the radical ion pairs. A plot of ln 2J versus r(DA), the distance between the centroids of the spin distributions of the two radicals that comprise the pair, yields a slope of -0.5 +/- 0.1. Since both 2J and k(CR), the rate of radical ion pair recombination, are directly proportional to V(2), the observed distance dependence of 2J shows directly that the recombination

  16. Simulations of the dissociation of small helium clusters with ab initio molecular dynamics in electronically excited states

    International Nuclear Information System (INIS)

    Closser, Kristina D.; Head-Gordon, Martin; Gessner, Oliver

    2014-01-01

    The dynamics resulting from electronic excitations of helium clusters were explored using ab initio molecular dynamics. The simulations were performed with configuration interaction singles and adiabatic classical dynamics coupled to a state-following algorithm. 100 different configurations of He 7 were excited into the 2s and 2p manifold for a total of 2800 trajectories. While the most common outcome (90%) was complete fragmentation to 6 ground state atoms and 1 excited state atom, 3% of trajectories yielded bound, He 2 * , and <0.5% yielded an excited helium trimer. The nature of the dynamics, kinetic energy release, and connections to experiments are discussed

  17. Cluster radioactivity and very asymmetric fission through quasi-molecular shapes

    International Nuclear Information System (INIS)

    Royer, G.

    1997-01-01

    The decay of radioactive nuclei which emit heavy clusters like C, O, Ne, Mg and Si has been studied in the fission valley which leads one spherical nucleus towards two spherical touching nuclei before crossing the barrier. Assuming volume conservation, the deformation energy has been calculated within a generalized liquid drop model taking into account the proximity effects between the cluster and the daughter nucleus. The theoretical partial half-lives obtained within the WKB barrier penetration probability are in good agreement with the experimental data for the heaviest clusters. The Ne, Mg and Si emission looks like a very-asymmetric spontaneous fission. The 14 C radioactivity is not correctly described within the fission hypothesis. The 14 C and apparently also the 20 O are probably pre-born in the parent nucleus, the emission being similar to the α decay process. (author)

  18. Investigation of the Influence of PLA Molecular Structure on the Crystalline Forms (α’ and α and Mechanical Properties of Wet Spinning Fibres

    Directory of Open Access Journals (Sweden)

    Michał Puchalski

    2017-01-01

    Full Text Available In this paper, the influence of the molecular structure of polylactide (PLA—characterised by its molar mass and content of d-lactide isomer—on the molecular ordering and α’–α form transition during fibre manufacturing by the wet spinning method is described. Fibres were studied by wide-angle X-ray diffraction (WAXD and differential scanning calorimetry (DSC. Additionally, the physical and mechanical properties of the fibres were determined. This study also examines the preliminary molecular ordering and crystallisation of PLA fibres at various draw ratios. The performed experiments clearly show the dependence of the molecular ordering of PLA on the molar mass and d-lactide content during the wet spinning process. The fibres manufactured from PLA with the lowest content of d-lactide and the lowest molar mass were characterised by a higher tendency for crystallisation and a higher possibility to undergo the disorder-to-order phase transition (α’ to α form. The structural changes in PLA explain the observed changes in the physical and mechanical properties of the obtained fibres.

  19. Comparison of combinatorial clustering methods on pharmacological data sets represented by machine learning-selected real molecular descriptors.

    Science.gov (United States)

    Rivera-Borroto, Oscar Miguel; Marrero-Ponce, Yovani; García-de la Vega, José Manuel; Grau-Ábalo, Ricardo del Corazón

    2011-12-27

    Cluster algorithms play an important role in diversity related tasks of modern chemoinformatics, with the widest applications being in pharmaceutical industry drug discovery programs. The performance of these grouping strategies depends on various factors such as molecular representation, mathematical method, algorithmical technique, and statistical distribution of data. For this reason, introduction and comparison of new methods are necessary in order to find the model that best fits the problem at hand. Earlier comparative studies report on Ward's algorithm using fingerprints for molecular description as generally superior in this field. However, problems still remain, i.e., other types of numerical descriptions have been little exploited, current descriptors selection strategy is trial and error-driven, and no previous comparative studies considering a broader domain of the combinatorial methods in grouping chemoinformatic data sets have been conducted. In this work, a comparison between combinatorial methods is performed,with five of them being novel in cheminformatics. The experiments are carried out using eight data sets that are well established and validated in the medical chemistry literature. Each drug data set was represented by real molecular descriptors selected by machine learning techniques, which are consistent with the neighborhood principle. Statistical analysis of the results demonstrates that pharmacological activities of the eight data sets can be modeled with a few of families with 2D and 3D molecular descriptors, avoiding classification problems associated with the presence of nonrelevant features. Three out of five of the proposed cluster algorithms show superior performance over most classical algorithms and are similar (or slightly superior in the most optimistic sense) to Ward's algorithm. The usefulness of these algorithms is also assessed in a comparative experiment to potent QSAR and machine learning classifiers, where they perform

  20. Cluster-cluster clustering

    International Nuclear Information System (INIS)

    Barnes, J.; Dekel, A.; Efstathiou, G.; Frenk, C.S.; Yale Univ., New Haven, CT; California Univ., Santa Barbara; Cambridge Univ., England; Sussex Univ., Brighton, England)

    1985-01-01

    The cluster correlation function xi sub c(r) is compared with the particle correlation function, xi(r) in cosmological N-body simulations with a wide range of initial conditions. The experiments include scale-free initial conditions, pancake models with a coherence length in the initial density field, and hybrid models. Three N-body techniques and two cluster-finding algorithms are used. In scale-free models with white noise initial conditions, xi sub c and xi are essentially identical. In scale-free models with more power on large scales, it is found that the amplitude of xi sub c increases with cluster richness; in this case the clusters give a biased estimate of the particle correlations. In the pancake and hybrid models (with n = 0 or 1), xi sub c is steeper than xi, but the cluster correlation length exceeds that of the points by less than a factor of 2, independent of cluster richness. Thus the high amplitude of xi sub c found in studies of rich clusters of galaxies is inconsistent with white noise and pancake models and may indicate a primordial fluctuation spectrum with substantial power on large scales. 30 references

  1. Intensities and cross-sections of Ar clusters in a molecular beam, ch. 3

    International Nuclear Information System (INIS)

    Deursen, A.P.J. van; Lumig, A. van; Reuss, J.

    1976-01-01

    Ar-cluster beams were produced by supersonic expansion under various source conditions. The experimental intensities have been scaled such that universal curves are obtained, up to moderate source pressures. The ratio of dimer/monomer cross-sections has been determined. (Auth.)

  2. Molecular population genetics of the β-esterase gene cluster of ...

    Indian Academy of Sciences (India)

    We suggest that the demographic history (bottleneck and admixture of genetically differentiated populations) is the major factor shaping the pattern of nucleotide polymorphism in the -esterase gene cluster. However there are some 'footprints' of directional and balancing selection shaping specific distribution of nucleotide ...

  3. From molecular clusters to nanoparticles: second-generation ion-mediated nucleation model

    Directory of Open Access Journals (Sweden)

    F. Yu

    2006-01-01

    Full Text Available Ions, which are generated in the atmosphere by galactic cosmic rays and other ionization sources, may play an important role in the formation of atmospheric aerosols. In the paper, a new second-generation ion-mediated nucleation (IMN model is presented. The new model explicitly treats the evaporation of neutral and charged clusters and it describes the evolution of the size spectra and composition of both charged and neutral clusters/particles ranging from small clusters of few molecules to large particles of several micrometers in diameter. Schemes used to calculate the evaporation coefficients for small neutral and charged clusters are consistent with the experimental data within the uncertainty range. The present IMN model, which is size-, composition-, and type-resolved, is a powerful tool for investigating the dominant mechanisms and key parameters controlling the formation and subsequent growth of nanoparticles in the atmosphere. This model can be used to analyze simultaneous measurements of the ion-mobility spectra and particle size distributions, which became available only recently. General features of the spectra for ions smaller than the critical size, size-dependent fractions of charged nanoparticles, and asymmetrical charging of freshly nucleated particles predicted by the new IMN model are consistent with recent measurements. Results obtained using the second generation IMN model, in which the most recent thermodynamic data for neutral and charged H2SO4-H2O clusters were used, suggest that ion-mediated nucleation of H2SO4-H2O can lead to a significant production of new particles in the lower atmosphere (including the boundary layer under favorable conditions. It has been shown that freshly nucleated particles of few nanometers in size can grow by the condensation of low volatile organic compounds to the size of cloud condensation nuclei. In such cases, the chemical composition of nucleated particles larger than ~10 nm is dominated

  4. Comparison of Molecular Typing Methods Useful for Detecting Clusters of Campylobacter jejuni and C. coli Isolates through Routine Surveillance

    Science.gov (United States)

    Taboada, Eduardo; Grant, Christopher C. R.; Blakeston, Connie; Pollari, Frank; Marshall, Barbara; Rahn, Kris; MacKinnon, Joanne; Daignault, Danielle; Pillai, Dylan; Ng, Lai-King

    2012-01-01

    Campylobacter spp. may be responsible for unreported outbreaks of food-borne disease. The detection of these outbreaks is made more difficult by the fact that appropriate methods for detecting clusters of Campylobacter have not been well defined. We have compared the characteristics of five molecular typing methods on Campylobacter jejuni and C. coli isolates obtained from human and nonhuman sources during sentinel site surveillance during a 3-year period. Comparative genomic fingerprinting (CGF) appears to be one of the optimal methods for the detection of clusters of cases, and it could be supplemented by the sequencing of the flaA gene short variable region (flaA SVR sequence typing), with or without subsequent multilocus sequence typing (MLST). Different methods may be optimal for uncovering different aspects of source attribution. Finally, the use of several different molecular typing or analysis methods for comparing individuals within a population reveals much more about that population than a single method. Similarly, comparing several different typing methods reveals a great deal about differences in how the methods group individuals within the population. PMID:22162562

  5. Determination of size of molecular clusters of ethanol by means of NMR diffusometry and hydrodynamic calculations

    Czech Academy of Sciences Publication Activity Database

    Šoltésová, M.; Benda, L.; Peksa, M.; Czernek, Jiří; Lang, J.

    2014-01-01

    Roč. 118, č. 24 (2014), s. 6864-6874 ISSN 1520-6106 Institutional support: RVO:61389013 Keywords : diffusion * NMR * molecular Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.302, year: 2014

  6. An Effective Approach for Clustering InhA Molecular Dynamics Trajectory Using Substrate-Binding Cavity Features.

    Directory of Open Access Journals (Sweden)

    Renata De Paris

    Full Text Available Protein receptor conformations, obtained from molecular dynamics (MD simulations, have become a promising treatment of its explicit flexibility in molecular docking experiments applied to drug discovery and development. However, incorporating the entire ensemble of MD conformations in docking experiments to screen large candidate compound libraries is currently an unfeasible task. Clustering algorithms have been widely used as a means to reduce such ensembles to a manageable size. Most studies investigate different algorithms using pairwise Root-Mean Square Deviation (RMSD values for all, or part of the MD conformations. Nevertheless, the RMSD only may not be the most appropriate gauge to cluster conformations when the target receptor has a plastic active site, since they are influenced by changes that occur on other parts of the structure. Hence, we have applied two partitioning methods (k-means and k-medoids and four agglomerative hierarchical methods (Complete linkage, Ward's, Unweighted Pair Group Method and Weighted Pair Group Method to analyze and compare the quality of partitions between a data set composed of properties from an enzyme receptor substrate-binding cavity and two data sets created using different RMSD approaches. Ensembles of representative MD conformations were generated by selecting a medoid of each group from all partitions analyzed. We investigated the performance of our new method for evaluating binding conformation of drug candidates to the InhA enzyme, which were performed by cross-docking experiments between a 20 ns MD trajectory and 20 different ligands. Statistical analyses showed that the novel ensemble, which is represented by only 0.48% of the MD conformations, was able to reproduce 75% of all dynamic behaviors within the binding cavity for the docking experiments performed. Moreover, this new approach not only outperforms the other two RMSD-clustering solutions, but it also shows to be a promising strategy to

  7. Explaining the luminosity spread in young clusters: proto and pre-main sequence stellar evolution in a molecular cloud environment

    Science.gov (United States)

    Jensen, Sigurd S.; Haugbølle, Troels

    2018-02-01

    Hertzsprung-Russell diagrams of star-forming regions show a large luminosity spread. This is incompatible with well-defined isochrones based on classic non-accreting protostellar evolution models. Protostars do not evolve in isolation of their environment, but grow through accretion of gas. In addition, while an age can be defined for a star-forming region, the ages of individual stars in the region will vary. We show how the combined effect of a protostellar age spread, a consequence of sustained star formation in the molecular cloud, and time-varying protostellar accretion for individual protostars can explain the observed luminosity spread. We use a global magnetohydrodynamic simulation including a sub-scale sink particle model of a star-forming region to follow the accretion process of each star. The accretion profiles are used to compute stellar evolution models for each star, incorporating a model of how the accretion energy is distributed to the disc, radiated away at the accretion shock, or incorporated into the outer layers of the protostar. Using a modelled cluster age of 5 Myr, we naturally reproduce the luminosity spread and find good agreement with observations of the Collinder 69 cluster, and the Orion Nebular Cluster. It is shown how stars in binary and multiple systems can be externally forced creating recurrent episodic accretion events. We find that in a realistic global molecular cloud model massive stars build up mass over relatively long time-scales. This leads to an important conceptual change compared to the classic picture of non-accreting stellar evolution segmented into low-mass Hayashi tracks and high-mass Henyey tracks.

  8. HIV-TRACE (Transmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens.

    Science.gov (United States)

    Kosakovsky Pond, Sergei L; Weaver, Steven; Leigh Brown, Andrew J; Wertheim, Joel O

    2018-01-31

    In modern applications of molecular epidemiology, genetic sequence data are routinely used to identify clusters of transmission in rapidly evolving pathogens, most notably HIV-1. Traditional 'shoeleather' epidemiology infers transmission clusters by tracing chains of partners sharing epidemiological connections (e.g., sexual contact). Here, we present a computational tool for identifying a molecular transmission analog of such clusters: HIV-TRACE (TRAnsmission Cluster Engine). HIV-TRACE implements an approach inspired by traditional epidemiology, by identifying chains of partners whose viral genetic relatedness imply direct or indirect epidemiological connections. Molecular transmission clusters are constructed using codon-aware pairwise alignment to a reference sequence followed by pairwise genetic distance estimation among all sequences. This approach is computationally tractable and is capable of identifying HIV-1 transmission clusters in large surveillance databases comprising tens or hundreds of thousands of sequences in near real time, i.e., on the order of minutes to hours. HIV-TRACE is available at www.hivtrace.org and from github.com/veg/hivtrace, along with the accompanying result visualization module from github.com/veg/hivtrace-viz. Importantly, the approach underlying HIV-TRACE is not limited to the study of HIV-1 and can be applied to study outbreaks and epidemics of other rapidly evolving pathogens. © The Author 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. Molecular comparison of the structural proteins encoding gene clusters of two related Lactobacillus delbrueckii bacteriophages.

    Science.gov (United States)

    Vasala, A; Dupont, L; Baumann, M; Ritzenthaler, P; Alatossava, T

    1993-01-01

    Virulent phage LL-H and temperate phage mv4 are two related bacteriophages of Lactobacillus delbrueckii. The gene clusters encoding structural proteins of these two phages have been sequenced and further analyzed. Six open reading frames (ORF-1 to ORF-6) were detected. Protein sequencing and Western immunoblotting experiments confirmed that ORF-3 (g34) encoded the main capsid protein Gp34. The presence of a putative late promoter in front of the phage LL-H g34 gene was suggested by primer extension experiments. Comparative sequence analysis between phage LL-H and phage mv4 revealed striking similarities in the structure and organization of this gene cluster, suggesting that the genes encoding phage structural proteins belong to a highly conservative module. Images PMID:8497043

  10. New concepts for molecular magnets

    Science.gov (United States)

    Pilawa, Bernd

    1999-03-01

    Miller and Epstein (1994) define molecular magnets as magnetic materials which are prepared by the low-temperature methods of the preparative chemistry. This definition includes molecular crystals of neutral radicals, radical salts and charge transfer complexes as well as metal complexes and polymers with unpaired spins (Dormann 1995). The challenge of molecular magnets consists in tailoring magnetic properties by specific modifications of the molecular units. The combination of magnetism with mechanical or electrical properties of molecular compounds promise materials of high technical interest (Gatteschi 1994a and 1994b, Möhwald 1996) and both the chemical synthesis of new molecular materials with magnetic properties as well as the physical investigation and explanation of these properties is important, in order to achieve any progress. This work deals with the physical characterization of the magnetic properties of molecular materials. It is organized as follows. In the first part molecular crystals of neutral radicals are studied. After briefly discussing the general magnetic properties of these materials and after an overview over the physical principles of exchange interaction between organic radicals I focus on the interplay between the crystallographic structure and the magnetic properties of various derivatives of the verdazyl and nitronyl nitroxide radicals. The magnetic properties of metal complexes are the subject of the second part. After an overview over the experimental and theoretical tools which are used for the investigation of the magnetic properties I shortly discuss the exchange coupling of transition metal ions and the magnetic properties of complexes of two and three metal ions. Special emphasis is given to spin cluster compounds. Spin cluster denote complexes of many magnetic ions. They are attractive as building blocks of molecular magnets as well as magnetic model compounds for the study of spin frustration, molecular super

  11. Ground-state magnetization of the molecular cluster Mn12O12-acetate as seen by proton NMR

    International Nuclear Information System (INIS)

    Furukawa, Y.; Watanabe, K.; Kumagai, K.; Jang, Z. H.; Lascialfari, A.; Borsa, F.; Gatteschi, D.

    2000-01-01

    1 H nuclear magnetic resonance (NMR) measurements have been carried out in Mn 12 O 12 -acetate clusters at low temperature in order to investigate microscopically the static and dynamic magnetic properties of the molecule in its high-spin S=10 ground state. Below liquid helium temperature it is found that the local hyperfine fields at the proton sites are static as expected for the very slow superparamagnetic relaxation of Mn 12 O 12 at low temperature. The magnitude and distribution of the hyperfine fields can be reproduced to a good approximation by considering only the dipolar interaction of protons with the local Mn magnetic moments and by assigning the magnitude and orientation of the local moments of the different Mn 3+ and Mn 4+ ions according to an accepted coupling scheme for the total S=10 ground state. The relaxation time of the macroscopic magnetization of the cluster was measured by monitoring the change of the intensity of the 1 H-NMR shifted lines following inversion of the applied magnetic field. This is possible because the sudden change of the field orientation changes the sign of the shift of the NMR lines in the proton spectrum. Although important differences are noticed, the relaxation time of the magnetization as measured indirectly by the 1 H-NMR method is comparable to the one obtained directly with a superconducting quantum interference device magnetometer. In particular we could reproduce the minima in the relaxation time as a function of magnetic field at the fields for level crossing, minima which are considered to be a signature of the quantum tunneling of the magnetization

  12. Synthesis of molecular hexatechnetium clusters by means of dimensional reduction of their polymeric complexes

    International Nuclear Information System (INIS)

    Ikai, T.; Yoshimura, T.; Shinohara, A.; Takayama, T.; Sekine, T.

    2006-01-01

    Selenide capping hexatechnetium cluster complex [Tc 6 (μ 3 -Se) 8 CN 6 ] 4- (1) was prepared by the reactions of one-dimensional polymer complex [Tc 6 (μ 3 -Se) 8 Br 4 ] 2- and cyanides at high temperature. Similar reaction of sulfide capping hexatechnetium cluster complex, [Tc 6 (μ 3 -S) 8 Br 6 ] 4- with cyanide gave the terminal substituted complex [Tc 6 (μ 3 -S) 8 CN 6 ] 4- (2). The single-crystal X-ray analysis of 1 and 2, showed that the Tc-Tc bond lengths become longer with lager ionic radius of the face capping ligands in the order S -1 , and that of 2 showed it at 2119 cm -1 . Each of cyclic voltammogram of 1 and 2 showed a reversible one electron redox wave assignable to the Tc 6 III /Tc 5 III Tc IV process. These redox potentials shift to the positive about 0.4V compared to those of the Re cluster analogs. (author)

  13. Energy spectra of vibron and cluster models in molecular and nuclear systems

    Science.gov (United States)

    Jalili Majarshin, A.; Sabri, H.; Jafarizadeh, M. A.

    2018-03-01

    The relation of the algebraic cluster model, i.e., of the vibron model and its extension, to the collective structure, is discussed. In the first section of the paper, we study the energy spectra of vibron model, for diatomic molecule then we derive the rotation-vibration spectrum of 2α, 3α and 4α configuration in the low-lying spectrum of 8Be, 12C and 16O nuclei. All vibrational and rotational states with ground and excited A, E and F states appear to have been observed, moreover the transitional descriptions of the vibron model and α-cluster model were considered by using an infinite-dimensional algebraic method based on the affine \\widehat{SU(1,1)} Lie algebra. The calculated energy spectra are compared with experimental data. Applications to the rotation-vibration spectrum for the diatomic molecule and many-body nuclear clusters indicate that there are solvable models and they can be approximated very well using the transitional theory.

  14. Molecular oxygen adsorption and dissociation on Au12M clusters with M = Cu, Ag or Ir

    Science.gov (United States)

    Jiménez-Díaz, Laura M.; Pérez, Luis A.

    2018-03-01

    In this work, we present a density functional theory study of the structural and electronic properties of isolated neutral clusters of the type Au12M, with M = Cu, Ag, or Ir. On the other hand, there is experimental evidence that gold-silver, gold-copper and gold-iridium nanoparticles have an enhanced catalytic activity for the CO oxidation reaction. In order to address these phenomena, we also performed density functional calculations of the adsorption and dissociation of O2 on these nanoparticles. Moreover, to understand the effects of Cu, Ag, and Ir impurity atoms on the dissociation of O2, we also analyze this reaction in the corresponding pure gold cluster. The results indicate that the substitution of one gold atom in a Au13 cluster by Ag, Cu or Ir diminishes the activation energy barrier for the O2 dissociation by nearly 1 eV. This energy barrier is similar for Au12Ag and Au12Cu, whereas for Au12Ir is even lower. These results suggest that the addition of other transition metal atoms to gold nanoclusters can enhance their catalytic activity towards the CO oxidation reaction, independently of the effect that the substrate could have on supported nanoclusters.

  15. Photoelectron angular distributions for states of any mixed character: An experiment-friendly model for atomic, molecular, and cluster anions

    International Nuclear Information System (INIS)

    Khuseynov, Dmitry; Blackstone, Christopher C.; Culberson, Lori M.; Sanov, Andrei

    2014-01-01

    We present a model for laboratory-frame photoelectron angular distributions in direct photodetachment from (in principle) any molecular orbital using linearly polarized light. A transparent mathematical approach is used to generalize the Cooper-Zare central-potential model to anionic states of any mixed character. In the limit of atomic-anion photodetachment, the model reproduces the Cooper-Zare formula. In the case of an initial orbital described as a superposition of s and p-type functions, the model yields the previously obtained s-p mixing formula. The formalism is further advanced using the Hanstorp approximation, whereas the relative scaling of the partial-wave cross-sections is assumed to follow the Wigner threshold law. The resulting model describes the energy dependence of photoelectron anisotropy for any atomic, molecular, or cluster anions, usually without requiring a direct calculation of the transition dipole matrix elements. As a benchmark case, we apply the p-d variant of the model to the experimental results for NO − photodetachment and show that the observed anisotropy trend is described well using physically meaningful values of the model parameters. Overall, the presented formalism delivers insight into the photodetachment process and affords a new quantitative strategy for analyzing the photoelectron angular distributions and characterizing mixed-character molecular orbitals using photoelectron imaging spectroscopy of negative ions

  16. Photoelectron angular distributions for states of any mixed character: An experiment-friendly model for atomic, molecular, and cluster anions

    Science.gov (United States)

    Khuseynov, Dmitry; Blackstone, Christopher C.; Culberson, Lori M.; Sanov, Andrei

    2014-09-01

    We present a model for laboratory-frame photoelectron angular distributions in direct photodetachment from (in principle) any molecular orbital using linearly polarized light. A transparent mathematical approach is used to generalize the Cooper-Zare central-potential model to anionic states of any mixed character. In the limit of atomic-anion photodetachment, the model reproduces the Cooper-Zare formula. In the case of an initial orbital described as a superposition of s and p-type functions, the model yields the previously obtained s-p mixing formula. The formalism is further advanced using the Hanstorp approximation, whereas the relative scaling of the partial-wave cross-sections is assumed to follow the Wigner threshold law. The resulting model describes the energy dependence of photoelectron anisotropy for any atomic, molecular, or cluster anions, usually without requiring a direct calculation of the transition dipole matrix elements. As a benchmark case, we apply the p-d variant of the model to the experimental results for NO- photodetachment and show that the observed anisotropy trend is described well using physically meaningful values of the model parameters. Overall, the presented formalism delivers insight into the photodetachment process and affords a new quantitative strategy for analyzing the photoelectron angular distributions and characterizing mixed-character molecular orbitals using photoelectron imaging spectroscopy of negative ions.

  17. Electron induced formation and stability of molecular and cluster ions in gas phase and superfluid helium nanodroplets

    International Nuclear Information System (INIS)

    Aleem, M. A.

    2010-01-01

    The present PhD thesis represents a broad range study of electron induced formation and stability of positive and negative ions in gas phase and superfluid helium nanodroplets. The molecules studied are of industrial, environmental, plasma and biological relevance. The knowledge obtained from the study provides new insight for the proper understanding and control on energetics and dynamics of the reactions involved in the formation and fragmentation processes of the studied molecules and clusters. The experiments are accomplished and investigated using mass spectrometric techniques for the formation of molecular and cluster ions using different mass spectrometers available in our laboratory. One part of the work is focused on electron-induced reactions of the molecules in gas phase. Especially focus is laid to electron attachment to the isomers of mononitrotolouene used as an additive to explosives. The fragile nature and high internal energy of these molecules has lead to extensive fragmentation following the ionisation process. Dissociative electron attachment to the three different isomers has shown different resonances and therefore this process can be utilized to explicitly distinguish these isomers. Anion efficiency curves of the isomers have been studied using effusive molecular beam source in combination with a hemispherical electron monochromator as well as a Nier-type ion source attached to a sector field mass spectrometer. The outcome of the experiment is a reliable and effective detection method highly desirable for environmental and security reasons. Secondly, dissociative electron ionization of acetylene and propene is studied and their data is directly related to the plasma modelling for plasma fusion and processing reactors. Temperature effects for dissociative electron attachment to halo-hydrocarbons are also measured using a trochoidal electron monochromator. The second part of the work is concerned with the investigation of electron

  18. Linkage of molecular units in the chemistry of niobium and tantalum cluster halides

    International Nuclear Information System (INIS)

    Perrin, C.; Sergent, M.

    1991-01-01

    In low valency niobium and tantalum halides, interunit linkages are observed between the (Me 6 X 12 )X 6 units. They are insulators and interesting magnetic properties are observed, due to the intrinsic potential magnetism of the Me 6 cluster and depending on the inserted cations, for instance rare earths in MM'Nb 6 Cl 18 (M = monovalent cation, M' = rare earth). Of special interest are the niobium iodides which exhibit (Me 6 X 8 )X 6 units, an exception in the niobium chemistry; interesting properties have been reported for some of these iodides

  19. Implementation of Molecular Surveillance After a Cluster of Fatal Toxoplasmosis at 2 Neighboring Transplant Centers.

    Science.gov (United States)

    Isa, Flonza; Saito, Kohta; Huang, Yao-Ting; Schuetz, Audrey; Babady, N Esther; Salvatore, Steven; Pessin, Melissa; van Besien, Koen; Perales, Miguel-Angel; Giralt, Sergio; Sepkowitz, Kent; Papanicolaou, Genovefa A; Soave, Rosemary; Kamboj, Mini

    2016-08-15

    After a cluster of fatal toxoplasmosis among stem cell transplant recipients at 2 hospitals, surveillance with polymerase chain reaction (PCR) (blood) was instituted. Rate of reactivation among seropositive recipients was 2.2 and 16%. Parasitemia was successfully managed with preemptive treatment. For seropositive recipients unable to take prophylaxis, toxoplasma PCR surveillance should be routinely performed. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  20. Unconventional Current Scaling and Edge Effects for Charge Transport through Molecular Clusters

    DEFF Research Database (Denmark)

    Obersteiner, Veronika; Huhs, Georg; Papior, Nick Rübner

    2017-01-01

    Metal-molecule-metal junctions are the key components of molecular electronics circuits. Gaining a microscopic understanding of their conducting properties is central to advancing the field. In the present contribution we highlight the fundamental differences between single-molecule and ensemble ...

  1. Classical description of dynamical many-body systems with central forces, spin-orbit forces and spin-spin forces

    International Nuclear Information System (INIS)

    Goepfert, A.

    1994-01-01

    This thesis develops a new model, and related numerical methods, to describe classical time-dependent many-body systems interacting through central forces, spin-orbit forces and spin-spin forces. The model is based on two-particle interactions. The two-body forces consist of attractive and repulsive parts. In this model the investigated multi-particle systems are self-bound. Also the total potential of the whole ensemble is derived from the two-particle potential and is not imposed 'from outside'. Each particle has the three degrees of freedom of its centre-of-mass motion and the spin degree of freedom. The model allows for the particles to be either charged or uncharged. Furthermore, each particle has an angular momentum, an intrinsic spin, and a magnetic dipole moment. Through the electromagnetic forces between these charges and moments there arise dynamical couplings between them. The internal interactions between the charges and moments are well described by electromagnetic coupling mechanisms. In fact, compared to conventional classical molecular dynamics calculations in van der Waals clusters, which have no spin degrees of freedom, or for Heisenberg spin Systems, which have no orbital degrees of freedom, the model presented here contains both types of degrees of freedom with a highly non-trivial coupling. The model allows to study the fundamental effects resulting from the dynamical coupling of the spin and the orbital-motion sub-systems. In particular, the dynamics of the particle mass points show a behaviour basically different from the one of particles in a potential with only central forces. Furthermore, a special type of quenching procedure was invented, which tends to drive the multi-particle Systems into states with highly periodic, non-ergodic behaviour. Application of the model to cluster simulations has provided evidence that the model can also be used to investigate items like solid-to-liquid phase transitions (melting), isomerism and specific heat

  2. Molecular geometries and relative stabilities of titanium oxide and gold-titanium oxide clusters

    Energy Technology Data Exchange (ETDEWEB)

    Hudson, Rohan J.; Falcinella, Alexander; Metha, Gregory F., E-mail: greg.metha@adelaide.edu.au

    2016-09-30

    Titanium oxide and gold-titanium oxide clusters of stoichiometry M{sub x}O{sub y} (M{sub x} = Ti{sub 3}, Ti{sub 4} & AuTi{sub 3}; y = 0 − (2x + 2)) have been investigated using density functional theory. Geometries of determined global energy minimum structures are reported and other isomers predicted up to 0.5 eV higher in energy. The Ti{sub 3}O{sub n} geometries build upon a triangular Ti{sub 3} motif, while Ti{sub 4}O{sub n} stoichiometries template upon a pseudo-tetrahedral Ti{sub 4} structure. Addition of a gold atom to the Ti{sub 3}O{sub n} series does not significantly alter the cluster geometry, with the gold atom preferentially binding to titanium atoms over oxygen atoms. Adiabatic ionization energies, electron affinities and HOMO/LUMO energies increase in magnitude with increasing oxygenation. The HOMO-LUMO energy gaps reach the bulk anatase band gap energy at stoichiometry (Au)Ti{sub m}O{sub 2m−1}, and increase above this upon further oxygen addition. The most stable structural moieties are found to be a cage-like, C{sub 3v} symmetric Ti{sub 4}O{sub 6/7} geometry and a Ti{sub 3}O{sub 6} structure with an η{sup 3}-bound oxygen atom.

  3. Theory vs. experiment for molecular clusters: Spectra of OCS trimers and tetramers

    Energy Technology Data Exchange (ETDEWEB)

    Evangelisti, Luca [Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904 (United States); Dipartimento di Chimica “G. Ciamician,” University of Bologna, Via Selmi 2, Bologna 40126 (Italy); Perez, Cristobal; Seifert, Nathan A.; Pate, Brooks H. [Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904 (United States); Dehghany, M.; Moazzen-Ahmadi, N. [Department of Physics and Astronomy, University of Calgary, 2500 University Drive North West, Calgary, Alberta T2N 1N4 (Canada); McKellar, A. R. W. [National Research Council of Canada, Ottawa, Ontario K1A 0R6 (Canada)

    2015-03-14

    All singly substituted {sup 13}C, {sup 18}O, and {sup 34}S isotopomers of the previously known OCS trimer are observed in natural abundance in a broad-band spectrum measured with a chirped-pulse Fourier transform microwave spectrometer. The complete substitution structure thus obtained critically tests (and confirms) the common assumption that monomers tend to retain their free structure in a weakly bound cluster. A new OCS trimer isomer is also observed, and its structure is determined to be barrel-shaped but with the monomers all approximately aligned, in contrast to the original trimer which is barrel-shaped with two monomers aligned and one anti-aligned. An OCS tetramer spectrum is assigned for the first time, and the tetramer structure resembles an original trimer with an OCS monomer added at the end with two sulfur atoms. Infrared spectra observed in the region of the OCS ν{sub 1} fundamental (≈2060 cm{sup −1}) are assigned to the same OCS tetramer, and another infrared band is tentatively assigned to a different tetramer isomer. The experimental results are compared and contrasted with theoretical predictions from the literature and from new cluster calculations which use an accurate OCS pair potential and assume pairwise additivity.

  4. Molecular dynamics simulations to examine structure, energetics, and evaporation/condensation dynamics in small charged clusters of water or methanol containing a single monatomic ion.

    Science.gov (United States)

    Daub, Christopher D; Cann, Natalie M

    2012-11-01

    We study small clusters of water or methanol containing a single Ca(2+), Na(+), or Cl(-) ion with classical molecular dynamics simulations, using models that incorporate polarizability via the Drude oscillator framework. Evaporation and condensation of solvent from these clusters is examined in two systems, (1) for isolated clusters initially prepared at different temperatures and (2) those with a surrounding inert (Ar) gas of varying temperature. We examine these clusters over a range of sizes, from almost bare ions up to 40 solvent molecules. We report data on the evaporation and condensation of solvent from the clusters and argue that the observed temperature dependence of evaporation in the smallest clusters demonstrates that the presence of heated gas alone cannot, in most cases, solely account for bare ion production in electrospray ionization (ESI), neglecting the key contribution of the electric field. We also present our findings on the structure and energetics of the clusters as a function of size. Our data agree well with the abundant literature on hydrated ion clusters and offer some novel insight into the structure of methanol and ion clusters, especially those with a Cl(-) anion, where we observe the presence of chain-like structures of methanol molecules. Finally, we provide some data on the reparameterizations necessary to simulate ions in methanol using the separately developed Drude oscillator models for methanol and for ions in water.

  5. Molecular dynamics studies of the transient nucleation regime in the freezing of (RbCl)108 clusters

    International Nuclear Information System (INIS)

    Huang, Jinfan; Bartell, L.S.Lawrence S.

    2004-01-01

    The freezing of supercooled liquids in the transient period before a steady state of nucleation is attained has been the subject of a number of theoretical treatments. To our knowledge, no published experimental studies or computer simulations have been carried out in sufficient detail to test definitively the behavior predicted by the various theories. The present molecular dynamics (MD) simulation of 375 nucleation events in small, liquid RbCl clusters, however, yields a reasonably accurate account of the transient region. Despite published criticisms of a 1969 treatment by Kashchiev, it turns out that the behavior observed in the present study agrees with that predicted by Kashchiev. The study also obtains a much more accurate nucleation rate and time lag than reported for MD studies of RbCl previously published in this journal. In addition, it provides estimates of the solid-liquid interfacial free energy and the Granasy thickness of the diffuse solid-liquid interface

  6. Molecular depth profiling of trehalose using a C{sub 60} cluster ion beam

    Energy Technology Data Exchange (ETDEWEB)

    Wucher, Andreas [Department of Physics, University of Duisburg-Essen, D-47048 Duisburg (Germany)], E-mail: andreas.wucher@uni-due.de; Cheng Juan; Winograd, Nicholas [Department of Chemistry, Pennsylvania State University, University Park, PA 16802 (United States)

    2008-12-15

    Molecular depth profiling of organic overlayers was performed using a mass selected fullerene ion beam in conjunction with time-of-flight (TOF-SIMS) mass spectrometry. The characteristics of depth profiles acquired on a 300-nm trehalose film on Si were studied as a function of the impact kinetic energy and charge state of the C{sub 60} projectile ions. We find that the achieved depth resolution depends only weakly upon energy.

  7. Molecular dynamics simulations with electronic stopping can reproduce experimental sputtering yields of metals impacted by large cluster ions

    Science.gov (United States)

    Tian, Jiting; Zhou, Wei; Feng, Qijie; Zheng, Jian

    2018-03-01

    An unsolved problem in research of sputtering from metals induced by energetic large cluster ions is that molecular dynamics (MD) simulations often produce sputtering yields much higher than experimental results. Different from the previous simulations considering only elastic atomic interactions (nuclear stopping), here we incorporate inelastic electrons-atoms interactions (electronic stopping, ES) into MD simulations using a friction model. In this way we have simulated continuous 45° impacts of 10-20 keV C60 on a Ag(111) surface, and found that the calculated sputtering yields can be very close to the experimental results when the model parameter is appropriately assigned. Conversely, when we ignore the effect of ES, the yields are much higher, just like the previous studies. We further expand our research to the sputtering of Au induced by continuous keV C60 or Ar100 bombardments, and obtain quite similar results. Our study indicates that the gap between the experimental and the simulated sputtering yields is probably induced by the ignorance of ES in the simulations, and that a careful treatment of this issue is important for simulations of cluster-ion-induced sputtering, especially for those aiming to compare with experiments.

  8. 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.

  9. Effects of incident energy and angle on carbon cluster ions implantation on silicon substrate: a molecular dynamics study

    Science.gov (United States)

    Wei, Ye; Sang, Shengbo; Zhou, Bing; Deng, Xiao; Chai, Jing; Ji, Jianlong; Ge, Yang; Huo, Yuanliang; Zhang, Wendong

    2017-09-01

    Carbon cluster ion implantation is an important technique in fabricating functional devices at micro/nanoscale. In this work, a numerical model is constructed for implantation and implemented with a cutting-edge molecular dynamics method. A series of simulations with varying incident energies and incident angles is performed for incidence on silicon substrate and correlated effects are compared in detail. Meanwhile, the behavior of the cluster during implantation is also examined under elevated temperatures. By mapping the nanoscopic morphology with variable parameters, numerical formalism is proposed to explain the different impacts on phrase transition and surface pattern formation. Particularly, implantation efficiency (IE) is computed and further used to evaluate the performance of the overall process. The calculated results could be properly adopted as the theoretical basis for designing nano-structures and adjusting devices’ properties. Project supported by the National Natural Science Foundation of China (Nos. 51622507, 61471255, 61474079, 61403273, 51502193, 51205273), the Natural Science Foundation of Shanxi (Nos. 201601D021057, 201603D421035), the Youth Foundation Project of Shanxi Province (Nos. 2015021097), the Doctoral Fund of MOE of China (No. 20131402110013), the National High Technology Research and Development Program of China (No. 2015AA042601), and the Specialized Project in Public Welfare from The Ministry of Water Resources of China (Nos. 1261530110110).

  10. Fe-Mo double perovskite: From small clusters to bulk material

    Energy Technology Data Exchange (ETDEWEB)

    Carvajal, E., E-mail: ecarvajalq@ipn.mx [Instituto Politecnico Nacional, ESIME-Culhuacan, Av. Santa Ana 1000, C.P. 04430 Mexico, D.F. (Mexico); Oviedo-Roa, R. [Programa de Investigacion en Ingenieria Molecular, Instituto Mexicano del Petroleo, Eje Central Lazaro Cardenas Norte 152, 07730 Mexico, D.F. (Mexico); Cruz-Irisson, M. [Instituto Politecnico Nacional, ESIME-Culhuacan, Av. Santa Ana 1000, C.P. 04430 Mexico, D.F. (Mexico); Navarro, O. [Instituto de Investigaciones en Materiales, Universidad Nacional Autonoma de Mexico, A.P. 70-360, 04510 Mexico, D.F. (Mexico)

    2012-09-20

    To understand the differences in behaviour between up- and down-spin electrons observed in the half-metallic Sr{sub 2}FeMoO{sub 6} double perovskite, the density of states (DOS) was studied for the (FeO{sub 6}){sup -4} and (MoO{sub 6}){sup -6} octahedral clusters using first-principles density functional theory within the generalised gradient approximation (GGA) scheme and the Perdew-Burke-Ernzerhof (PBE) functional. Our results reveal that half-metallic character is present, even starting from an isolated (FeO{sub 6}){sup -4} cluster, and is a consequence of spin decoupling of antibonding hybridisations between iron t{sub 2g} states and oxygen p states (t{sub 2g}{sup a} states), i.e., t{sub 2g}{sup a} states lie below the Highest Occupied Molecular Orbital (HOMO) in the up-spin channel, whereas they lie above the HOMO level in the down-spin channel. The spin-induced shifting between up-spin and down-spin DOS situates the HOMO in such a way that the molecular orbitals oxygen p states (p bands) are fully spin-paired by octet electrons. Thus, the down-spin channel has metallic character because the HOMO lies just at the p bands, and the up-spin channel is semiconducting because the HOMO falls within the energy gap between the t{sub 2g}{sup a} and e{sub g}{sup a} bands. Finally, the (MoO{sub 6}){sup -6} octahedron does not inhibit the perovskite half-metallic character since this cluster has a zero total spin.

  11. Structure and properties of molecular and ionic clusters in vapour over caesium fluoride

    Science.gov (United States)

    Mwanga, Stanley F.; Pogrebnaya, Tatiana P.; Pogrebnoi, Alexander M.

    2015-06-01

    The properties of neutral molecules Cs2F2, Cs3F3, and Cs4F4, and positive and negative cluster ions Cs2F+, CsF2-, Cs3F2+, Cs2F3-, Cs4F3+, and Cs5F4+ were studied by several of quantum chemical methods implementing density function theory and Möller-Plesset perturbation theory of second and fourth orders. For all species, the equilibrium geometrical structure and vibrational spectra were determined. Different isomers have been revealed for the trimer neutral molecule Cs3F3; pentaatomic, both positive and negative, Cs3F2+, Cs2F3-; and heptaatomic Cs4F3+ ions. The most abundant isomers in the saturated vapour were determined. Enthalpies of dissociation reactions and enthalpies of formation of the species were obtained.

  12. Molecular Dynamics Simulation of Solidification of Pd-Ni Clusters with Different Nickel Content

    Directory of Open Access Journals (Sweden)

    Chen Gang

    2014-01-01

    Full Text Available Molecular dynamics simulation has been performed for investigating the glass transition of Pd-Ni alloy nanoparticles in the solidification process. The results showed that the Pd-Ni nanoparticles with composition far from pure metal should form amorphous structure more easily, which is in accordance with the results of the thermodynamic calculation. There are some regular and distorted fivefold symmetry in the amorphous Pd-Ni alloy nanoparticles. The nanoclusters with bigger difference value between formation enthalpies of solutions and glasses will transform to glass more easily than the other Pd-Ni alloy nanoclusters.

  13. SHORT- AND LONG-TERM RADIO VARIABILITY OF YOUNG STARS IN THE ORION NEBULA CLUSTER AND MOLECULAR CLOUD

    International Nuclear Information System (INIS)

    Rivilla, V. M.; Martín-Pintado, J.; Chandler, C. J.; Sanz-Forcada, J.; Jiménez-Serra, I.; Forbrich, J.

    2015-01-01

    We have used the Karl G. Jansky Very Large Array (VLA) to carry out multi-epoch radio continuum monitoring of the Orion Nebula Cluster (ONC) and the background Orion Molecular Cloud (OMC; 3 epochs at Q band and 11 epochs at Ka band). Our new observations reveal the presence of 19 radio sources, mainly concentrated in the Trapezium Cluster and the Orion Hot Core (OHC) regions. With the exception of the Becklin–Neugebauer object and source C (which we identify here as dust emission associated with a proplyd) the sources all show radio variability between the different epochs. We have found tentative evidence of variability in the emission from the massive object related to source I. Our observations also confirm radio flux density variations of a factor >2 on timescales of hours to days in five sources. One of these flaring sources, OHC-E, has been detected for the first time. We conclude that the radio emission can be attributed to two different components: (i) highly variable (flaring) non-thermal radio gyrosynchrotron emission produced by electrons accelerated in the magnetospheres of pre-main-sequence low-mass stars and (ii) thermal emission due to free–free radiation from ionized gas and/or heated dust around embedded massive objects and proplyds. Combining our sample with other radio monitoring at 8.3 GHz and the X-ray catalog provided by Chandra, we have studied the properties of the entire sample of radio/X-ray stars in the ONC/OMC region (51 sources). We have found several hints of a relation between the X-ray activity and the mechanisms responsible for (at least some fraction of) the radio emission. We have estimated a radio flaring rate of ∼0.14 flares day −1 in the dense stellar cluster embedded in the OHC region. This suggests that radio flares are more common events during the first stages of stellar evolution than previously thought. The advent of improved sensitivity with the new VLA and ALMA will dramatically increase the number of stars in

  14. Vicinage forces between molecular and atomic fragments dissociated from small hydrogen clusters and their effects on energy distributions

    International Nuclear Information System (INIS)

    Barriga-Carrasco, Manuel D.; Garcia-Molina, Rafael

    2003-01-01

    In this paper we analyze the dynamic evolution of molecular and atomic fragments of small hydrogen clusters interacting with thin solid foils. We compare the vicinage forces, calculated within the dielectric formalism, for H + , H 0 , and H 2 + fragments. Using a molecular dynamics numerical code we determine the energy distribution of the fragments after interacting with the target. This distribution is compared to experimental results for protons coming from the fragmentation of v=2.02 a.u. H 2 + ions impinging on an aluminum foil; a fraction of neutral H 0 is needed to be included in the simulation to get a good agreement with the experimental results. The H 2 + energy spectra for v=5.42 a.u. H 3 + interacting with amorphous carbon is also determined. The asymmetry in the Coulomb peaks appearing in the energy spectra both experimentally and in our calculation is opposite for H 2 + than in H + ; kinematic effects and differences in the electronic stopping are enough to reproduce the difference in the alignment of H 2 + and H + fragments

  15. Synthesis and characterization of osmium carbonyl cluster compounds with molecular oxygen electroreduction capacity

    Energy Technology Data Exchange (ETDEWEB)

    Castellanos, R.H.; Ocampo, A.L.; Moreira-Acosta, J.; Sebastian, P.J. [CIE-UNAM Solar Energy Laboratory, Morelos (Mexico). Photovoltaic Systems Group, Solar-Hydrogen-Fuel Cell

    2001-12-01

    A transition metal cluster electrocatalyst based on Os{sub x}(CO){sub n} was synthesized by pyrolysis of Os{sub 3} (CO){sub 12} in 1,2-Dichlorobenzene (b.p.{approx_equal}180{sup o}C) under inert atmosphere (N{sub 2}). The electrocatalytic parameters of the oxygen reduction reaction (ORR) for an Os{sub x}(CO){sub n} catalyst were studied with a rotating disk electrode in 0.5 MH{sub 2}SO{sub 4} electrolyte. The diffusion coefficient and solubility of O{sub 2} in 0.5 MH{sub 2}SO{sub 4} were calculated. Koutecky-Levich analysis of the linear voltamperometry data showed that the reaction follows first-order kinetics and the value of the Koutecky-Levich slope indicates a multielectron charge transfer during the ORR. The value of the Tafel slope obtained from the mass transfer corrected Tafel plots is 131 mV/decade. The performance of the catalyst in a H{sub 2}/O{sub 2} PEM fuel cell cathode was evaluated and found to be nearly as good as that of Pt. (author)

  16. "Divide-and-conquer" semiclassical molecular dynamics: An application to water clusters

    Science.gov (United States)

    Di Liberto, Giovanni; Conte, Riccardo; Ceotto, Michele

    2018-03-01

    We present an investigation of vibrational features in water clusters performed by means of our recently established divide-and-conquer semiclassical approach [M. Ceotto, G. Di Liberto, and R. Conte, Phys. Rev. Lett. 119, 010401 (2017)]. This technique allows us to simulate quantum vibrational spectra of high-dimensional systems starting from full-dimensional classical trajectories and projection of the semiclassical propagator onto a set of lower dimensional subspaces. The potential energy surface employed is a many-body representation up to three-body terms, in which monomers and two-body interactions are described by the high level Wang-Huang-Braams-Bowman (WHBB) water potential, while, for three-body interactions, calculations adopt a fast permutationally invariant ab initio surface at the same level of theory of the WHBB 3-body potential. Applications range from the water dimer up to the water decamer, a system made of 84 vibrational degrees of freedom. Results are generally in agreement with previous variational estimates in the literature. This is particularly true for the bending and the high-frequency stretching motions, while estimates of modes strongly influenced by hydrogen bonding are red shifted, in a few instances even substantially, as a consequence of the dynamical and global picture provided by the semiclassical approach.

  17. Mitochondrial iron-sulfur cluster biogenesis from molecular understanding to clinical disease

    Science.gov (United States)

    Alfadhel, Majid; Nashabat, Marwan; Ali, Qais Abu; Hundallah, Khalid

    2017-01-01

    Iron–sulfur clusters (ISCs) are known to play a major role in various protein functions. Located in the mitochondria, cytosol, endoplasmic reticulum and nucleus, they contribute to various core cellular functions. Until recently, only a few human diseases related to mitochondrial ISC biogenesis defects have been described. Such diseases include Friedreich ataxia, combined oxidative phosphorylation deficiency 19, infantile complex II/III deficiency defect, hereditary myopathy with lactic acidosis and mitochondrial muscle myopathy, lipoic acid biosynthesis defects, multiple mitochondrial dysfunctions syndromes and non ketotic hyperglycinemia due to glutaredoxin 5 gene defect. Disorders of mitochondrial import, export and translation, including sideroblastic anemia with ataxia, EVEN-PLUS syndrome and mitochondrial complex I deficiency due to nucleotide-binding protein-like protein gene defect, have also been implicated in ISC biogenesis defects. With advances in next generation sequencing technologies, more disorders related to ISC biogenesis defects are expected to be elucidated. In this article, we aim to shed the light on mitochondrial ISC biogenesis, related proteins and their function, pathophysiology, clinical phenotypes of related disorders, diagnostic approach, and future implications. PMID:28064324

  18. Pulsed EPR for studying silver clusters

    International Nuclear Information System (INIS)

    Michalik, J.; Wasowicz, T.; Sadlo, J.; Reijerse, E.J.; Kevan, L.

    1996-01-01

    The cationic silver clusters of different nuclearity have been produced by radiolysis of zeolite A and SAPO molecular sieves containing Ag + as exchangeable cations. The pulsed EPR spectroscopy has been applied for studying the local environment of silver cluster in order to understand the mechanism of cluster formation and stabilization. the electron spin echo modulation (ESEM) results on Ag 6 n+ cluster in dehydration zeolite A indicate that the hexameric silver is stabilized only in sodalite cages which are surrounded by α-cages containing no water molecules. Trimeric silver clusters formed in hydrated A zeolites strongly interact with water, thus the paramagnetic center can be considered as a cluster-water adduct. In SAPO-molecular sieves, silver clusters are formed only in the presence of adsorbed alcohol molecules. From ESEM it is determined that Ag 4 n+ in SAPO-42 is stabilized in α cages, where it is directly coordinated by two methanol molecules. Dimeric silver, Ag 2 + in SAPO-5 and SAPO-11 is located in 6-ring channels and interacts with three CH 3 OH molecules, each in different 10 ring or 12 ring channels. The differences of Ag 2 + stability in SAPO-5 and SAPO-11 are also discussed. (Author)

  19. Molecular dynamics simulation investigations of H2/D2 dissocitive chemisorption dynamics on Cun(n=13-14) Rigid/nonrigid clusters

    International Nuclear Information System (INIS)

    Elzein, N.

    2004-01-01

    In this work with a use of molecular dynamic simulations we have reported the results of a quasiclassical simulation study of the interaction of H2/(D2) with Cu N (N=13-14) atoms in both rigid /(non rigid) clusters.The geometry of the cluster is obtained by an embedded-atom (EA) mode potential, and the interaction between the molecule and cIuster is described by a LEPS -London-Eyring -Polanyi-Sato) potential energy function.Both channels the reactive dissociative adsorption of the molecule on the cIuster) and non reactive (scattering of the molecule from the cluster) are considered. The dissociative chemisorption probability, cross section and rate constant are studied as functions of the initial quantal rovibrational state of the molecule, collision energy, impact parameter and the temperature (OK,296K,834K ,1014K,1554K) of the clusters

  20. Facility for low-temperature spin-polarized-scanning tunneling microscopy studies of magnetic/spintronic materials prepared in situ by nitride molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Wenzhi; Foley, Andrew; Alam, Khan; Wang, Kangkang; Liu, Yinghao; Chen, Tianjiao; Pak, Jeongihm; Smith, Arthur R., E-mail: smitha2@ohio.edu [Department of Physics and Astronomy, Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, Ohio 45701 (United States)

    2014-04-15

    Based on the interest in, as well as exciting outlook for, nitride semiconductor based structures with regard to electronic, optoelectronic, and spintronic applications, it is compelling to investigate these systems using the powerful technique of spin-polarized scanning tunneling microscopy (STM), a technique capable of achieving magnetic resolution down to the atomic scale. However, the delicate surfaces of these materials are easily corrupted by in-air transfers, making it unfeasible to study them in stand-alone ultra-high vacuum STM facilities. Therefore, we have carried out the development of a hybrid system including a nitrogen plasma assisted molecular beam epitaxy/pulsed laser epitaxy facility for sample growth combined with a low-temperature, spin-polarized scanning tunneling microscope system. The custom-designed molecular beam epitaxy growth system supports up to eight sources, including up to seven effusion cells plus a radio frequency nitrogen plasma source, for epitaxially growing a variety of materials, such as nitride semiconductors, magnetic materials, and their hetero-structures, and also incorporating in situ reflection high energy electron diffraction. The growth system also enables integration of pulsed laser epitaxy. The STM unit has a modular design, consisting of an upper body and a lower body. The upper body contains the coarse approach mechanism and the scanner unit, while the lower body accepts molecular beam epitaxy grown samples using compression springs and sample skis. The design of the system employs two stages of vibration isolation as well as a layer of acoustic noise isolation in order to reduce noise during STM measurements. This isolation allows the system to effectively acquire STM data in a typical lab space, which during its construction had no special and highly costly elements included, (such as isolated slabs) which would lower the environmental noise. The design further enables tip exchange and tip coating without

  1. Facility for low-temperature spin-polarized-scanning tunneling microscopy studies of magnetic/spintronic materials prepared in situ by nitride molecular beam epitaxy.

    Science.gov (United States)

    Lin, Wenzhi; Foley, Andrew; Alam, Khan; Wang, Kangkang; Liu, Yinghao; Chen, Tianjiao; Pak, Jeongihm; Smith, Arthur R

    2014-04-01

    Based on the interest in, as well as exciting outlook for, nitride semiconductor based structures with regard to electronic, optoelectronic, and spintronic applications, it is compelling to investigate these systems using the powerful technique of spin-polarized scanning tunneling microscopy (STM), a technique capable of achieving magnetic resolution down to the atomic scale. However, the delicate surfaces of these materials are easily corrupted by in-air transfers, making it unfeasible to study them in stand-alone ultra-high vacuum STM facilities. Therefore, we have carried out the development of a hybrid system including a nitrogen plasma assisted molecular beam epitaxy/pulsed laser epitaxy facility for sample growth combined with a low-temperature, spin-polarized scanning tunneling microscope system. The custom-designed molecular beam epitaxy growth system supports up to eight sources, including up to seven effusion cells plus a radio frequency nitrogen plasma source, for epitaxially growing a variety of materials, such as nitride semiconductors, magnetic materials, and their hetero-structures, and also incorporating in situ reflection high energy electron diffraction. The growth system also enables integration of pulsed laser epitaxy. The STM unit has a modular design, consisting of an upper body and a lower body. The upper body contains the coarse approach mechanism and the scanner unit, while the lower body accepts molecular beam epitaxy grown samples using compression springs and sample skis. The design of the system employs two stages of vibration isolation as well as a layer of acoustic noise isolation in order to reduce noise during STM measurements. This isolation allows the system to effectively acquire STM data in a typical lab space, which during its construction had no special and highly costly elements included, (such as isolated slabs) which would lower the environmental noise. The design further enables tip exchange and tip coating without

  2. Facility for low-temperature spin-polarized-scanning tunneling microscopy studies of magnetic/spintronic materials prepared in situ by nitride molecular beam epitaxy

    International Nuclear Information System (INIS)

    Lin, Wenzhi; Foley, Andrew; Alam, Khan; Wang, Kangkang; Liu, Yinghao; Chen, Tianjiao; Pak, Jeongihm; Smith, Arthur R.

    2014-01-01

    Based on the interest in, as well as exciting outlook for, nitride semiconductor based structures with regard to electronic, optoelectronic, and spintronic applications, it is compelling to investigate these systems using the powerful technique of spin-polarized scanning tunneling microscopy (STM), a technique capable of achieving magnetic resolution down to the atomic scale. However, the delicate surfaces of these materials are easily corrupted by in-air transfers, making it unfeasible to study them in stand-alone ultra-high vacuum STM facilities. Therefore, we have carried out the development of a hybrid system including a nitrogen plasma assisted molecular beam epitaxy/pulsed laser epitaxy facility for sample growth combined with a low-temperature, spin-polarized scanning tunneling microscope system. The custom-designed molecular beam epitaxy growth system supports up to eight sources, including up to seven effusion cells plus a radio frequency nitrogen plasma source, for epitaxially growing a variety of materials, such as nitride semiconductors, magnetic materials, and their hetero-structures, and also incorporating in situ reflection high energy electron diffraction. The growth system also enables integration of pulsed laser epitaxy. The STM unit has a modular design, consisting of an upper body and a lower body. The upper body contains the coarse approach mechanism and the scanner unit, while the lower body accepts molecular beam epitaxy grown samples using compression springs and sample skis. The design of the system employs two stages of vibration isolation as well as a layer of acoustic noise isolation in order to reduce noise during STM measurements. This isolation allows the system to effectively acquire STM data in a typical lab space, which during its construction had no special and highly costly elements included, (such as isolated slabs) which would lower the environmental noise. The design further enables tip exchange and tip coating without

  3. DFT Calculation of IR Absorption Spectra for PCE-nH2O, TCE-nH2O, DCE-nH2O, VC-nH2O for Small and Water-Dominated Molecular Clusters

    Science.gov (United States)

    2017-10-31

    VC-nH2O for Small and Water-Dominated Molecular Clusters October 31, 2017 Approved for public release; distribution is unlimited. L. Huang S.g...Calculation of IR Absorption Spectra for PCE-nH2O, TCE-nH2O, DCE-nH2O, VC-nH2O for Small and Water-Dominated Molecular Clusters L. Huang,1 S.G...nH2O molecular clusters using density function theory (DFT). DFT can provide interpretation of absorption spectra with respect to molecular

  4. Spin current

    CERN Document Server

    Valenzuela, Sergio O; Saitoh, Eiji; Kimura, Takashi

    2012-01-01

    In a new branch of physics and technology called spin-electronics or spintronics, the flow of electrical charge (usual current) as well as the flow of electron spin, the so-called 'spin current', are manipulated and controlled together. This book provides an introduction and guide to the new physics and application of spin current.

  5. Vibronic coupling in molecular crystals: A Franck-Condon Herzberg-Teller model of H-aggregate fluorescence based on quantum chemical cluster calculations

    Energy Technology Data Exchange (ETDEWEB)

    Wykes, M., E-mail: mikewykes@gmail.com; Parambil, R.; Gierschner, J. [Madrid Institute for Advanced Studies, IMDEA Nanoscience, Calle Faraday 9, Campus Cantoblanco, 28049 Madrid (Spain); Beljonne, D. [Laboratory for Chemistry of Novel Materials, University of Mons, Place du Parc 20, 7000 Mons (Belgium)

    2015-09-21

    Here, we present a general approach to treating vibronic coupling in molecular crystals based on atomistic simulations of large clusters. Such clusters comprise model aggregates treated at the quantum chemical level embedded within a realistic environment treated at the molecular mechanics level. As we calculate ground and excited state equilibrium geometries and vibrational modes of model aggregates, our approach is able to capture effects arising from coupling to intermolecular degrees of freedom, absent from existing models relying on geometries and normal modes of single molecules. Using the geometries and vibrational modes of clusters, we are able to simulate the fluorescence spectra of aggregates for which the lowest excited state bears negligible oscillator strength (as is the case, e.g., ideal H-aggregates) by including both Franck-Condon (FC) and Herzberg-Teller (HT) vibronic transitions. The latter terms allow the adiabatic excited state of the cluster to couple with vibrations in a perturbative fashion via derivatives of the transition dipole moment along nuclear coordinates. While vibronic coupling simulations employing FC and HT terms are well established for single-molecules, to our knowledge this is the first time they are applied to molecular aggregates. Here, we apply this approach to the simulation of the low-temperature fluorescence spectrum of para-distyrylbenzene single-crystal H-aggregates and draw comparisons with coarse-grained Frenkel-Holstein approaches previously extensively applied to such systems.

  6. Dynamics of water clusters confined in proteins: a molecular dynamics simulation study of interfacial waters in a dimeric hemoglobin.

    Science.gov (United States)

    Gnanasekaran, Ramachandran; Xu, Yao; Leitner, David M

    2010-12-23

    Water confined in proteins exhibits dynamics distinct from the dynamics of water in the bulk or near the surface of a biomolecule. We examine the water dynamics at the interface of the two globules of the homodimeric hemoglobin from Scapharca inaequivalvis (HbI) by molecular dynamics (MD) simulations, with focus on water-protein hydrogen bond lifetimes and rotational anisotropy of the interfacial waters. We find that relaxation of the waters at the interface of both deoxy- and oxy-HbI, which contain a cluster of 17 and 11 interfacial waters, respectively, is well described by stretched exponentials with exponents from 0.1 to 0.6 and relaxation times of tens to thousands of picoseconds. The interfacial water molecules of oxy-HbI exhibit slower rotational relaxation and hydrogen bond rearrangement than those of deoxy-HbI, consistent with an allosteric transition from unliganded to liganded conformers involving the expulsion of several water molecules from the interface. Though the interfacial waters are translationally and rotationally static on the picosecond time scale, they contribute to fast communication between the globules via vibrations. We find that the interfacial waters enhance vibrational energy transport across the interface by ≈10%.

  7. Investigating the significance of zero-point motion in small molecular clusters of sulphuric acid and water

    International Nuclear Information System (INIS)

    Stinson, Jake L.; Ford, Ian J.; Kathmann, Shawn M.

    2014-01-01

    The nucleation of particles from trace gases in the atmosphere is an important source of cloud condensation nuclei, and these are vital for the formation of clouds in view of the high supersaturations required for homogeneous water droplet nucleation. The methods of quantum chemistry have increasingly been employed to model nucleation due to their high accuracy and efficiency in calculating configurational energies; and nucleation rates can be obtained from the associated free energies of particle formation. However, even in such advanced approaches, it is typically assumed that the nuclei have a classical nature, which is questionable for some systems. The importance of zero-point motion (also known as quantum nuclear dynamics) in modelling small clusters of sulphuric acid and water is tested here using the path integral molecular dynamics method at the density functional level of theory. The general effect of zero-point motion is to distort the mean structure slightly, and to promote the extent of proton transfer with respect to classical behaviour. In a particular configuration of one sulphuric acid molecule with three waters, the range of positions explored by a proton between a sulphuric acid and a water molecule at 300 K (a broad range in contrast to the confinement suggested by geometry optimisation at 0 K) is clearly affected by the inclusion of zero point motion, and similar effects are observed for other configurations

  8. Antibiotic discovery throughout the Small World Initiative: A molecular strategy to identify biosynthetic gene clusters involved in antagonistic activity.

    Science.gov (United States)

    Davis, Elizabeth; Sloan, Tyler; Aurelius, Krista; Barbour, Angela; Bodey, Elijah; Clark, Brigette; Dennis, Celeste; Drown, Rachel; Fleming, Megan; Humbert, Allison; Glasgo, Elizabeth; Kerns, Trent; Lingro, Kelly; McMillin, MacKenzie; Meyer, Aaron; Pope, Breanna; Stalevicz, April; Steffen, Brittney; Steindl, Austin; Williams, Carolyn; Wimberley, Carmen; Zenas, Robert; Butela, Kristen; Wildschutte, Hans

    2017-06-01

    The emergence of bacterial pathogens resistant to all known antibiotics is a global health crisis. Adding to this problem is that major pharmaceutical companies have shifted away from antibiotic discovery due to low profitability. As a result, the pipeline of new antibiotics is essentially dry and many bacteria now resist the effects of most commonly used drugs. To address this global health concern, citizen science through the Small World Initiative (SWI) was formed in 2012. As part of SWI, students isolate bacteria from their local environments, characterize the strains, and assay for antibiotic production. During the 2015 fall semester at Bowling Green State University, students isolated 77 soil-derived bacteria and genetically characterized strains using the 16S rRNA gene, identified strains exhibiting antagonistic activity, and performed an expanded SWI workflow using transposon mutagenesis to identify a biosynthetic gene cluster involved in toxigenic compound production. We identified one mutant with loss of antagonistic activity and through subsequent whole-genome sequencing and linker-mediated PCR identified a 24.9 kb biosynthetic gene locus likely involved in inhibitory activity in that mutant. Further assessment against human pathogens demonstrated the inhibition of Bacillus cereus, Listeria monocytogenes, and methicillin-resistant Staphylococcus aureus in the presence of this compound, thus supporting our molecular strategy as an effective research pipeline for SWI antibiotic discovery and genetic characterization. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  9. Proton affinity of the histidine-tryptophan cluster motif from the influenza A virus from ab initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Bankura, Arindam; Klein, Michael L.; Carnevale, Vincenzo, E-mail: vincenzo.carnevale@temple.edu

    2013-08-30

    Highlights: • The estimated pK{sub a} is in agreement with the experimental one. • The affinity for protons is similar to that of a histidine residue in aqueous solution. • The electrostatic environment is responsible for the stabilization of the charged imidazolium moiety. - Abstract: Ab initio molecular dynamics calculations have been used to compare and contrast the deprotonation reaction of a histidine residue in aqueous solution with the situation arising in a histidine-tryptophan cluster. The latter is used as a model of the proton storage unit present in the pore of the M2 proton conducting ion channel. We compute potentials of mean force for the dissociation of a proton from the Nδ and N∊ positions of the imidazole group to estimate the pK{sub a}s. Anticipating our results, we will see that the estimated pK{sub a} for the first protonation event of the M2 channel is in good agreement with experimental estimates. Surprisingly, despite the fact that the histidine is partially desolvated in the M2 channel, the affinity for protons is similar to that of a histidine in aqueous solution. Importantly, the electrostatic environment provided by the indoles is responsible for the stabilization of the charged imidazolium.

  10. Spins in chemistry

    CERN Document Server

    McWeeny, Roy

    2004-01-01

    Originally delivered as a series of lectures, this volume systematically traces the evolution of the ""spin"" concept from its role in quantum mechanics to its assimilation into the field of chemistry. Author Roy McWeeny presents an in-depth illustration of the deductive methods of quantum theory and their application to spins in chemistry, following the path from the earliest concepts to the sophisticated physical methods employed in the investigation of molecular structure and properties. Starting with the origin and development of the spin concept, the text advances to an examination of sp

  11. Finite-temperature coupled-cluster, many-body perturbation, and restricted and unrestricted Hartree-Fock study on one-dimensional solids: Luttinger liquids, Peierls transitions, and spin- and charge-density waves.

    Science.gov (United States)

    Hermes, Matthew R; Hirata, So

    2015-09-14

    One-dimensional (1D) solids exhibit a number of striking electronic structures including charge-density wave (CDW) and spin-density wave (SDW). Also, the Peierls theorem states that at zero temperature, a 1D system predicted by simple band theory to be a metal will spontaneously dimerize and open a finite fundamental bandgap, while at higher temperatures, it will assume the equidistant geometry with zero bandgap (a Peierls transition). We computationally study these unique electronic structures and transition in polyyne and all-trans polyacetylene using finite-temperature generalizations of ab initio spin-unrestricted Hartree-Fock (UHF) and spin-restricted coupled-cluster doubles (CCD) theories, extending upon previous work [He et al., J. Chem. Phys. 140, 024702 (2014)] that is based on spin-restricted Hartree-Fock (RHF) and second-order many-body perturbation (MP2) theories. Unlike RHF, UHF can predict SDW as well as CDW and metallic states, and unlike MP2, CCD does not diverge even if the underlying RHF reference wave function is metallic. UHF predicts a gapped SDW state with no dimerization at low temperatures, which gradually becomes metallic as the temperature is raised. CCD, meanwhile, confirms that electron correlation lowers the Peierls transition temperature. Furthermore, we show that the results from all theories for both polymers are subject to a unified interpretation in terms of the UHF solutions to the Hubbard-Peierls model using different values of the electron-electron interaction strength, U/t, in its Hamiltonian. The CCD wave function is shown to encompass the form of the exact solution of the Tomonaga-Luttinger model and is thus expected to describe accurately the electronic structure of Luttinger liquids.

  12. Nuclear inelastic scattering and density functional theory studies of a one-dimensional spin crossover [Fe(1,2,4-triazole)2(1,2,4-triazolato)](BF4) molecular chain.

    Science.gov (United States)

    Jenni, Kevin; Scherthan, Lena; Faus, Isabelle; Marx, Jennifer; Strohm, Cornelius; Herlitschke, Marcus; Wille, Hans-Christian; Würtz, Peter; Schünemann, Volker; Wolny, Juliusz A

    2017-07-26

    Nuclear inelastic scattering (NIS) experiments have been performed in order to study the vibrational dynamics of the low- and high-spin states of the polynuclear 1D spin crossover compound [Fe(1,2,4-triazole) 2 (1,2,4-triazolato)](BF 4 ) (1). Density functional theory (DFT) calculations using the functional B3LYP* and the basis set CEP-31G for heptameric and nonameric models of the compound yielded the normal vibrations and electronic energies for high-spin and low-spin isomers of three models differing in the distribution of anionic trz - ligands and BF 4 - anions. On the basis of the obtained energies a structural model with a centrosymmetric Fe(trzH) 4 (trz - ) 2 coordination core of the mononuclear unit of the chain is proposed. The obtained distribution of the BF 4 - counteranions in the proposed structure is similar to that obtained on the basis of X-ray powder diffraction studies by Grossjean et al. (Eur. J. Inorg. Chem., 2013, 796). The NIS data of the system diluted to 10% Fe(ii) content in a 90% Zn(ii) matrix (compound (2)) show a characteristic change of the spectral pattern of the low-spin centres, compared to the low-spin phase of the parent Fe(ii) complex (1). DFT calculations reveal that this is caused by a change of the structure of the neighbours of the low-spin centres. The spectral pattern of the high-spin centres in (2) is within a good approximation identical to that of the high-spin Fe(ii) isomer of (1). The inspection of the molecular orbitals of the monomeric model systems of [Fe(trzH) 4 (trz - ) 2 ] and [Fe(trzH) 6 ], together with calculations of spin transition energies, point towards the importance of an electrostatic effect caused by the negatively charged ligands. This results in the stabilisation of the low-spin state of the complex containing the anionic ligand and shortening of the Fe-N(trz - ) compared to the Fe-N(trzH) bond in high-spin, but not in low-spin [Fe(trzH) 4 (trz - ) 2 ].

  13. Studies on electronic spectrum and electron spin resonance of vanadium (IV) complexes with organophosphorus compounds and high molecular weight amines

    International Nuclear Information System (INIS)

    Sato, Taichi; Nakamura, Takato

    1981-01-01

    In the extraction of vanadium (IV) from aqueous solutions containing hydrochloric acid and/or a mixture of hydrochloric acid and lithium chloride by bis(2-ethylhexyl) hydrogenphosphate (DEHPA; HX), trioctylmethylammonium chloride (Aliquat-336), trioctylamine (TOA), trioctylphosphine oxide (TOPO) and tributyl phosphate (TBP), the complexes formed in the organic phases have been examined by spectrophotometry and electron spin resonance spectroscopy. It is found that in the extraction by DEHPA, the vanadium in the organic phase exists as the monomeric species, VO(X 2 H) 2 , or the polymeric one, (VOX 2 )sub(n), and that in the extractions by Aliquat-336, TOA, TOPO, and TBP, tetravalent vanadium complexes are stable in the organic phases extracted from a mixed solution of hydrochloric acid and lithium chloride, while complexes containing pentavalent vanadium and VOV 4+ ions are formed in the organic phases extracted from hydrochloric acid solutions. (author)

  14. THE TWO MOLECULAR CLOUDS IN RCW 38: EVIDENCE FOR THE FORMATION OF THE YOUNGEST SUPER STAR CLUSTER IN THE MILKY WAY TRIGGERED BY CLOUD–CLOUD COLLISION

    Energy Technology Data Exchange (ETDEWEB)

    Fukui, Y.; Torii, K.; Ohama, A.; Hasegawa, K.; Hattori, Y.; Sano, H.; Yamamoto, H.; Tachihara, K. [Department of Physics, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8601 (Japan); Ohashi, S.; Fujii, K.; Kuwahara, S. [Department of Astronomy, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 133-0033 (Japan); Mizuno, N.; Okuda, T. [National Astronomical Observatory of Japan, Mitaka, Tokyo 181-8588 (Japan); Dawson, J. R. [Department of Physics and Astronomy and MQ Research Centre in Astronomy, Astrophysics and Astrophotonics, Macquarie University, NSW 2109 (Australia); Onishi, T. [Department of Astrophysics, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka 599-8531 (Japan); Mizuno, A., E-mail: torii@a.phys.nagoya-u.ac.jp [Solar-Terrestrial Environment Laboratory, Nagoya University, Chikusa-ku, Nagoya 464-8601 (Japan)

    2016-03-20

    We present distributions of two molecular clouds having velocities of 2 and 14 km s{sup −1} toward RCW 38, the youngest super star cluster in the Milky Way, in the {sup 12}CO J = 1–0 and 3–2 and {sup 13}CO J = 1–0 transitions. The two clouds are likely physically associated with the cluster as verified by the high intensity ratio of the J = 3–2 emission to the J = 1–0 emission, the bridging feature connecting the two clouds in velocity, and their morphological correspondence with the infrared dust emission. The velocity difference is too large for the clouds to be gravitationally bound. We frame a hypothesis that the two clouds are colliding with each other by chance to trigger formation of the ∼20 O stars that are localized within ∼0.5 pc of the cluster center in the 2 km s{sup −1} cloud. We suggest that the collision is currently continuing toward part of the 2 km s{sup −1} cloud where the bridging feature is localized. This is the third super star cluster alongside Westerlund 2 and NGC 3603 where cloud–cloud collision has triggered the cluster formation. RCW 38 is the youngest super star cluster in the Milky Way, holding a possible sign of on-going O star formation, and is a promising site where we may be able to witness the moment of O star formation.

  15. Percolation and spin glass transition

    International Nuclear Information System (INIS)

    Sadiq, A.; Tahir-Kheli, R.A.; Wortis, M.; Bhatti, N.A.

    1980-10-01

    The behaviour of clusters of curved and normal plaquette particles in a bond random, +-J, Ising model is studied in finite square and triangular lattices. Computer results for the concentration of antiferromagnetic bonds when percolating clusters first appears are found to be close to those reported for the occurrence and disappearance of spin glass phases in these systems. (author)

  16. Geometrical spin symmetry and spin

    International Nuclear Information System (INIS)

    Pestov, I. B.

    2011-01-01

    Unification of General Theory of Relativity and Quantum Mechanics leads to General Quantum Mechanics which includes into itself spindynamics as a theory of spin phenomena. The key concepts of spindynamics are geometrical spin symmetry and the spin field (space of defining representation of spin symmetry). The essence of spin is the bipolar structure of geometrical spin symmetry induced by the gravitational potential. The bipolar structure provides a natural derivation of the equations of spindynamics. Spindynamics involves all phenomena connected with spin and provides new understanding of the strong interaction.

  17. Aggregation Number in Water/n-Hexanol Molecular Clusters Formed in Cyclohexane at Different Water/n-Hexanol/Cyclohexane Compositions Calculated by Titration 1H NMR.

    Science.gov (United States)

    Flores, Mario E; Shibue, Toshimichi; Sugimura, Natsuhiko; Nishide, Hiroyuki; Moreno-Villoslada, Ignacio

    2017-11-09

    Upon titration of n-hexanol/cyclohexane mixtures of different molar compositions with water, water/n-hexanol clusters are formed in cyclohexane. Here, we develop a new method to estimate the water and n-hexanol aggregation numbers in the clusters that combines integration analysis in one-dimensional 1 H NMR spectra, diffusion coefficients calculated by diffusion-ordered NMR spectroscopy, and further application of the Stokes-Einstein equation to calculate the hydrodynamic volume of the clusters. Aggregation numbers of 5-15 molecules of n-hexanol per cluster in the absence of water were observed in the whole range of n-hexanol/cyclohexane molar fractions studied. After saturation with water, aggregation numbers of 6-13 n-hexanol and 0.5-5 water molecules per cluster were found. O-H and O-O atom distances related to hydrogen bonds between donor/acceptor molecules were theoretically calculated using density functional theory. The results show that at low n-hexanol molar fractions, where a robust hydrogen-bond network is held between n-hexanol molecules, addition of water makes the intermolecular O-O atom distance shorter, reinforcing molecular association in the clusters, whereas at high n-hexanol molar fractions, where dipole-dipole interactions dominate, addition of water makes the intermolecular O-O atom distance longer, weakening the cluster structure. This correlates with experimental NMR results, which show an increase in the size and aggregation number in the clusters upon addition of water at low n-hexanol molar fractions, and a decrease of these magnitudes at high n-hexanol molar fractions. In addition, water produces an increase in the proton exchange rate between donor/acceptor molecules at all n-hexanol molar fractions.

  18. Hydration structure and dynamics of a hydroxide ion in water clusters of varying size and temperature: Quantum chemical and ab initio molecular dynamics studies

    International Nuclear Information System (INIS)

    Bankura, Arindam; Chandra, Amalendu

    2012-01-01

    Highlights: ► A theoretical study of hydroxide ion-water clusters is carried for varying cluster size and temperature. ► The structures of OH − (H 2 O) n are found out through quantum chemical calculations for n = 4, 8, 16 and 20. ► The finite temperature behavior of the clusters is studied through ab initio dynamical simulations. ► The spectral features of OH modes (deuterated) and their dependence on hydrogen bonding states of water are discussed. ► The mechanism and kinetics of proton transfer processes in these anionic clusters are also investigated. - Abstract: We have investigated the hydration structure and dynamics of OH − (H 2 O) n clusters (n = 4, 8, 16 and 20) by means of quantum chemical and ab initio molecular dynamics calculations. Quantum chemical calculations reveal that the solvation structure of the hydroxide ion transforms from three and four-coordinated surface states to five-coordinated interior state with increase in cluster size. Several other isomeric structures with energies not very different from the most stable isomer are also found. Ab initio simulations show that the most probable configurations at higher temperatures need not be the lowest energy isomeric structure. The rates of proton transfer in these clusters are found to be slower than that in bulk water. The vibrational spectral calculations reveal distinct features for free OH (deuterated) stretch modes of water in different hydrogen bonding states. Effects of temperature on the structural and dynamical properties are also investigated for the largest cluster considered here.

  19. Theoretical investigation of molecular hydrogen reactions with active centres in B6H5- and AlB6H5- clusters

    International Nuclear Information System (INIS)

    Mebel', A.M.; Charkin, O.P.

    1991-01-01

    Nonempirical calculations of sections of potential surface (PS) along the shortest way of reaction of hydrogen interaction with different active centres in AlB 5 H 5 - cluster were conducted. Mechanisms of reactions of valent-saturated hydrides (BH, AlH) and clusters (B 6 H 5 - , AlB 5 H 5 - ) with molecular hydrogen are correlated. Qualitative model enabling to form an opinion about the presence or the absence of barrier on PS of the shortest way of reactions of breaking σ-bond of H-H type on the active centre of cluster, is suggested. The model is based on analysis of the character of canonical MO reagents and products

  20. Surface Solvation of Halogen Anions in Water Clusters: An ab initio Molecular Dynamics Study of the Cl-(H.sub.2./sub.O).sub.6./sub. Complex

    Czech Academy of Sciences Publication Activity Database

    Tobias, D. J.; Jungwirth, Pavel; Parrinello, M.

    2001-01-01

    Roč. 114, č. 16 (2001), s. 7036-7044 ISSN 0021-9606 R&D Projects: GA MŠk LN00A032 Grant - others:NATO Science Program(XE) CLG-974459 Institutional research plan: CEZ:AV0Z4040901 Keywords : cluster * ab initio molecular dynamics * anionic solvation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.147, year: 2001

  1. Molecular analysis of HIV strains from a cluster of worker infections in the adult film industry, Los Angeles 2004.

    Science.gov (United States)

    Brooks, John T; Robbins, Kenneth E; Youngpairoj, Ae S; Rotblatt, Harlan; Kerndt, Peter R; Taylor, Melanie M; Daar, Eric S; Kalish, Marcia L

    2006-04-04

    In April 2004, 13 susceptible women were exposed to a single acutely HIV-1-infected man while employed to perform various sex acts for the production of adult films; three women were subsequently found to have acquired HIV infection (23% attack rate). As part of the investigation of this infection cluster, we evaluated whether viral strains collected from infected individuals were significantly related. We determined nucleotide sequences from the C2V3C3 and gp41 region of env and the p17 region of gag in viruses from the three infected individuals from whom specimens were available. We then compared these sequences phylogenetically to comparable sequences from available reference strains. Genotypic and phenotypic antiretroviral drug resistance was determined for plasma virus from the male index case and one female contact at a separate commercial laboratory. The env and gag sequences of the HIV strains from the male index case and two of the infected women were 100% similar. Genotyping of the male index case's virus identified 12 mutations, which represented known naturally occurring polymorphisms in the subtype B consensus sequence that are not associated with antiretroviral drug resistance. Genotyping of the virus from the female contact identified 10 mutations, all of which were shared by the virus from the male index case. Phenotyping demonstrated that both viruses were susceptible to all antiretroviral drugs tested. Molecular and virological data strongly support the epidemiological conclusion that these women were infected with an identical strain of HIV through occupational exposure to an individual with an acute HIV infection.

  2. The Validity of 21 cm Spin Temperature as a Kinetic Temperature Indicator in Atomic and Molecular Gas

    Energy Technology Data Exchange (ETDEWEB)

    Shaw, Gargi [Dept. of Physics, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Mumbai 400098 (India); Ferland, G. J. [Department of Physics and Astronomy, University of Kentucky, Lexington, KY 40506 (United States); Hubeny, I., E-mail: gargishaw@gmail.com, E-mail: gary@uky.edu, E-mail: hubeny@as.arizona.edu [Steward Observatory, University of Arizona, Tucson, AZ 85721 (United States)

    2017-07-10

    The gas kinetic temperature ( T {sub K} ) of various interstellar environments is often inferred from observations that can deduce level populations of atoms, ions, or molecules using spectral line observations; H i 21 cm is perhaps the most widely used, and has a long history. Usually the H i 21 cm line is assumed to be in thermal equilibrium and the populations are given by the Boltzmann distribution. A variety of processes, many involving Ly α , can affect the 21 cm line. Here we show how this is treated in the spectral simulation code Cloudy, and present numerical simulations of environments where this temperature indicator is used, with a detailed treatment of the physical processes that determine level populations within H{sup 0}. We discuss situations where this temperature indicator traces T {sub K}, cases where it fails, as well as the effects of Ly α pumping on the 21 cm spin temperature. We also show that the Ly α excitation temperature rarely traces the gas kinetic temperature.

  3. Formation of atomic clusters through the laser ablation of refractory materials in a supersonic molecular beam source

    International Nuclear Information System (INIS)

    Haufler, R.E.; Puretzky, A.A.; Compton, R.N.

    1993-01-01

    Concepts which guide the design of atomic cluster supersonic beam sources have been developed. These ideas are founded on the knowledge of laser ablation dynamics and are structured in order to take advantage of certain features of the ablation event. Some of the drawbacks of previous cluster source designs become apparent when the sequence of events following laser ablation are clarified. Key features of the new cluster source design include control of the cluster size distribution, uniform performance with a variety of solid materials and elements, high beam intensity, and significant removal of internal energy during the supersonic expansion

  4. Nuclear spin conversion in formaldehyde

    OpenAIRE

    Chapovsky, Pavel L.

    2000-01-01

    Theoretical model of the nuclear spin conversion in formaldehyde (H2CO) has been developed. The conversion is governed by the intramolecular spin-rotation mixing of molecular ortho and para states. The rate of conversion has been found equal 1.4*10^{-4}~1/s*Torr. Temperature dependence of the spin conversion has been predicted to be weak in the wide temperature range T=200-900 K.

  5. Molecular [(Fe3)–(Fe3)] and [(Fe4)–(Fe4)] coordination cluster pairs as single or composite arrays.

    Science.gov (United States)

    Sañudo, E Carolina; Uber, Jorge Salinas; Pons Balagué, Alba; Roubeau, Olivier; Aromí, Guillem

    2012-08-06

    The synthesis of molecular cluster pairs is a challenge for coordination chemists due to the potential applications of these species in molecular spintronics or quantum computing. The ligand H(4)L, 1,3-bis-(3-oxo-3-(2-hydroxyphenyl)-propionyl)-2-methoxybenzene, has been successfully used to obtain a series of such complexes using the basic Fe(III) trinuclear carboxylates as starting materials. Synthetic control has allowed the isolation of the two molecular cluster pairs that form the composite [Fe(4)O(2)(PhCO(2))(6)(H(2)L)(pz)](2)[Fe(3)O(PhCO(2))(5)(py)(H(2)L)](2) (1). The dimers of trinuclear units, [Fe(3)O(PhCO(2))(5)(H(2)O)(H(2)L)](2) (2) and [Fe(3)O(o-MePhCO(2))(5)(H(2)L)(py)](2) (3), and the dimers of tetranuclear units, [Fe(4)O(2)(PhCO(2))(6)(H(2)L)(pz)](2) (4) and [Fe(4)O(2)(o-MePhCO(2))(6)(H(2)L)(pz)](2) (5), are presented here. The magnetic properties of the reported aggregates show that they are pairs of semi-independent clusters weakly interacting magnetically as required for two-qubit quantum gates.

  6. Spacer type mediated tunable spin crossover (SCO) characteristics of pyrene decorated 2,6-bis(pyrazol-1-yl)pyridine (bpp) based Fe(ii) molecular spintronic modules.

    Science.gov (United States)

    Kumar, Kuppusamy Senthil; Šalitroš, Ivan; Moreno-Pineda, Eufemio; Ruben, Mario

    2017-08-14

    A simple "isomer-like" variation of the spacer group in a set of Fe(ii) spin crossover (SCO) complexes designed to probe spin state dependence of electrical conductivity in graphene-based molecular spintronic junctions led to the observation of remarkable variations in the thermal- and light-induced magnetic characteristics, paving a simple route for the design of functional SCO complexes with different temperature switching regimes based on a 2,6-bis(pyrazol-1-yl)pyridine ligand skeleton.

  7. Vibration dependence of the tensor spin-spin and scalar spin-spin hyperfine interactions by precision measurement of hyperfine structures of 127I2 near 532 nm

    International Nuclear Information System (INIS)

    Hong Fenglei; Zhang Yun; Ishikawa, Jun; Onae, Atsushi; Matsumoto, Hirokazu

    2002-01-01

    Hyperfine structures of the R(87)33-0, R(145)37-0, and P(132)36-0 transitions of molecular iodine near 532 nm are measured by observing the heterodyne beat-note signal of two I 2 -stabilized lasers, whose frequencies are bridged by an optical frequency comb generator. The measured hyperfine splittings are fit to a four-term Hamiltonian, which includes the electric quadrupole, spin-rotation, tensor spin-spin, and scalar spin-spin interactions, with an accuracy of ∼720 Hz. High-accurate hyperfine constants are obtained from this fit. Vibration dependences of the tensor spin-spin and scalar spin-spin hyperfine constants are determined for molecular iodine, for the first time to our knowledge. The observed hyperfine transitions are good optical frequency references in the 532-nm region

  8. A full-potential linear-muffin-tin-orbital molecular-dynamics study of B{sub 7}, B{sub 10} and B{sub 13} clusters

    Energy Technology Data Exchange (ETDEWEB)

    Cao Peilin Cao; Zhao Wei; Li Baoxing; Song Bin; Zhou Xuyan [Department of Physics and State Key Laboratory of Silicon Material, Zhejiang University, Hangzhou, Zhejiang (China)

    2001-06-04

    The structures of B{sub 7}, B{sub 10} and B{sub 13} boron clusters are studied using the full-potential linear-muffin-tin-orbital molecular-dynamics method. Seven stable structures for B{sub 7} and fifteen for B{sub 10} have been obtained. C{sub 2h}-B{sub 10} is the most stable among the 15 structures, but C{sub 2v}-B{sub 10} is not stable. For B{sub 13}, three degenerate ground-state structures have been found. The potential surface near C{sub 2v}-B{sub 7} (ground state) and D{sub 6h}-B{sub 7} is very flat. As a fundamental unit in constructing bigger clusters, C{sub 2v}-B{sub 7} will change its form easily. The most stable structures for B{sub 7}, B{sub 10} and B{sub 13} clusters are two-dimensional (quasi-) planar clusters, rather than the three-dimensional ones. General speaking, these clusters obey the 'Aufbau principle'. (author)

  9. Nuclear spin-spin coupling in a van der Waals-bonded system: xenon dimer.

    Science.gov (United States)

    Vaara, Juha; Hanni, Matti; Jokisaari, Jukka

    2013-03-14

    Nuclear spin-spin coupling over van der Waals bond has recently been observed via the frequency shift of solute protons in a solution containing optically hyperpolarized (129)Xe nuclei. We carry out a first-principles computational study of the prototypic van der Waals-bonded xenon dimer, where the spin-spin coupling between two magnetically non-equivalent isotopes, J((129)Xe - (131)Xe), is observable. We use relativistic theory at the four-component Dirac-Hartree-Fock and Dirac-density-functional theory levels using novel completeness-optimized Gaussian basis sets and choosing the functional based on a comparison with correlated ab initio methods at the nonrelativistic level. J-coupling curves are provided at different levels of theory as functions of the internuclear distance in the xenon dimer, demonstrating cross-coupling effects between relativity and electron correlation for this property. Calculations on small Xe clusters are used to estimate the importance of many-atom effects on J((129)Xe - (131)Xe). Possibilities of observing J((129)Xe - (131)Xe) in liquid xenon are critically examined, based on molecular dynamics simulation. A simplistic spherical model is set up for the xenon dimer confined in a cavity, such as in microporous materials. It is shown that the on the average shorter internuclear distance enforced by the confinement increases the magnitude of the coupling as compared to the bulk liquid case, rendering J((129)Xe - (131)Xe) in a cavity a feasible target for experimental investigation.

  10. Nuclear spins in nanostructures

    International Nuclear Information System (INIS)

    Coish, W.A.; Baugh, J.

    2009-01-01

    We review recent theoretical and experimental advances toward understanding the effects of nuclear spins in confined nanostructures. These systems, which include quantum dots, defect centers, and molecular magnets, are particularly interesting for their importance in quantum information processing devices, which aim to coherently manipulate single electron spins with high precision. On one hand, interactions between confined electron spins and a nuclear-spin environment provide a decoherence source for the electron, and on the other, a strong effective magnetic field that can be used to execute local coherent rotations. A great deal of effort has been directed toward understanding the details of the relevant decoherence processes and to find new methods to manipulate the coupled electron-nuclear system. A sequence of spectacular new results have provided understanding of spin-bath decoherence, nuclear spin diffusion, and preparation of the nuclear state through dynamic polarization and more general manipulation of the nuclear-spin density matrix through ''state narrowing.'' These results demonstrate the richness of this physical system and promise many new mysteries for the future. (Abstract Copyright [2009], Wiley Periodicals, Inc.)

  11. Spin-orbit-induced spin splittings in polar transition metal dichalcogenide monolayers

    KAUST Repository

    Cheng, Yingchun; Zhu, Zhiyong; Tahir, Muhammad; Schwingenschlö gl, Udo

    2013-01-01

    . We present ab initio electronic structure, phonon, and molecular-dynamics calculations to study the structural stability and spin-orbit-induced spin splitting in the transition metal dichalcogenide monolayers MXY (M = Mo, W and X, Y = S, Se, Te

  12. Molecular limit of a bulk semiconductor: size dependent optical spectroscopy study of CdSe cluster molecules

    Energy Technology Data Exchange (ETDEWEB)

    Soloviev, V.N.; Banin, U. [Hebrew Univ., Jerusalem (Israel). Dept. of Physical Chemistry; Eichhoefer, A. [Forschungszentrum Karlsruhe GmbH Technik und Umwelt (Germany). Inst. fuer Nanotechnologie; Fenske, D. [Forschungszentrum Karlsruhe GmbH Technik und Umwelt (Germany). Inst. fuer Nanotechnologie; Karlsruhe Univ. (T.H.) (Germany). Inst. fuer Anorganische Chemie

    2001-03-01

    Steady state and time-resolved photoluminescence measurements of a homologous series of CdSe cluster molecules were performed over a broad temperature range (T = 5-200 K). The absorption and low temperature PLE onset of the clusters shifts systematically to the blue in smaller clusters, manifesting the quantum confinement effect. The emission in all cluster molecules is observed only at low temperatures and is red-shifted significantly from the absorption onset. It is assigned to optically forbidden transitions involving surface states, as substantiated by the {mu}s range of lifetimes and by the involvement of low frequency vibrations of capping selenophenol ligands in the nonradiative relaxation of excited cluster molecules. (orig.)

  13. THE CHEMISTRY OF POPULATION III SUPERNOVA EJECTA. II. THE NUCLEATION OF MOLECULAR CLUSTERS AS A DIAGNOSTIC FOR DUST IN THE EARLY UNIVERSE

    International Nuclear Information System (INIS)

    Cherchneff, Isabelle; Dwek, Eli

    2010-01-01

    We study the formation of molecular precursors to dust in the ejecta of Population III supernovae (Pop. III SNe) using a chemical kinetic approach to follow the evolution of small dust cluster abundances from day 100 to day 1000 after explosion. Our work focuses on zero-metallicity 20 M sun and 170 M sun progenitors, and we consider fully macroscopically mixed and unmixed ejecta. The dust precursors comprise molecular chains, rings, and small clusters of chemical composition relevant to the initial elemental composition of the ejecta under study. The nucleation stage for small silica, metal oxides and sulfides, pure metal, and carbon clusters is described with a new chemical reaction network highly relevant to the kinetic description of dust formation in hot circumstellar environments. We consider the effect of the pressure dependence of critical nucleation rates and test the impact of microscopically mixed He + on carbon dust formation. Two cases of metal depletion on silica clusters (full and no depletion) are considered to derive upper limits to the amounts of dust produced in SN ejecta at 1000 days, while the chemical composition of clusters gives a prescription for the type of dust formed in Pop. III SNe. We show that the cluster mass produced in the fully mixed ejecta of a 170 M sun progenitor is ∼ 25 M sun whereas its 20 M sun counterpart forms ∼ 0.16 M sun of clusters. The unmixed ejecta of a 170 M sun progenitor SN synthesize ∼5.6 M sun of small clusters, while its 20 M sun counterpart produces ∼0.103 M sun . Our results point to smaller amounts of dust formed in the ejecta of Pop. III SNe by a factor of ∼ 5 compared to values derived by previous studies, and to different dust chemical compositions. Such deviations result from some erroneous assumptions made, the inappropriate use of classical nucleation theory to model dust formation, and the omission of the synthesis of molecules in SN ejecta. We also find that the unmixed ejecta of massive Pop

  14. The Chemistry of Population III Supernova Ejecta. II. The Nucleation of Molecular Clusters as a Diagnostic for Dust in the Early Universe

    Science.gov (United States)

    Cherchneff, Isabelle; Dwek, Eli

    2010-04-01

    We study the formation of molecular precursors to dust in the ejecta of Population III supernovae (Pop. III SNe) using a chemical kinetic approach to follow the evolution of small dust cluster abundances from day 100 to day 1000 after explosion. Our work focuses on zero-metallicity 20 M sun and 170 M sun progenitors, and we consider fully macroscopically mixed and unmixed ejecta. The dust precursors comprise molecular chains, rings, and small clusters of chemical composition relevant to the initial elemental composition of the ejecta under study. The nucleation stage for small silica, metal oxides and sulfides, pure metal, and carbon clusters is described with a new chemical reaction network highly relevant to the kinetic description of dust formation in hot circumstellar environments. We consider the effect of the pressure dependence of critical nucleation rates and test the impact of microscopically mixed He+ on carbon dust formation. Two cases of metal depletion on silica clusters (full and no depletion) are considered to derive upper limits to the amounts of dust produced in SN ejecta at 1000 days, while the chemical composition of clusters gives a prescription for the type of dust formed in Pop. III SNe. We show that the cluster mass produced in the fully mixed ejecta of a 170 M sun progenitor is ~ 25 M sun whereas its 20 M sun counterpart forms ~ 0.16 M sun of clusters. The unmixed ejecta of a 170 M sun progenitor SN synthesize ~5.6 M sun of small clusters, while its 20 M sun counterpart produces ~0.103 M sun. Our results point to smaller amounts of dust formed in the ejecta of Pop. III SNe by a factor of ~ 5 compared to values derived by previous studies, and to different dust chemical compositions. Such deviations result from some erroneous assumptions made, the inappropriate use of classical nucleation theory to model dust formation, and the omission of the synthesis of molecules in SN ejecta. We also find that the unmixed ejecta of massive Pop. III SNe

  15. Molecular ordering of spin-coated and electrosprayed P3HT:PCBM thin films and their applications to photovoltaic cell

    Energy Technology Data Exchange (ETDEWEB)

    Fukuda, Takeshi, E-mail: fukuda@fms.saitama-u.ac.jp [Department of Functional Materials Science, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570 (Japan); Toda, Asuki; Takahira, Kazuya; Suzuki, Katsumi [Department of Functional Materials Science, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570 (Japan); Liao, Yingjie [CERMAV-CNRS, UPR5301 & Grenoble Alpes University, 601 rue de la Chimie, BP53, 38041 Grenoble Cedex 9 (France); Hirahara, Miru [Department of Functional Materials Science, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570 (Japan); Saito, Masahiko; Osaka, Itaru [Emergent Molecular Function Research Group, RIKEN Center for Emergent Matter Science (CEMS), Wako, Saitama 351-0198 (Japan)

    2016-08-01

    Poly(3-hexylthiophene-2,5-diyl) (P3HT) is one of the most popular donor polymers for organic photovoltaic cells; however, annealing-induced molecular ordering is necessary for realizing high photoconversion efficiency. In this study, the ratio of ordered-disordered P3HT Raman signals was calculated as the crystallinity parameter, which can be evaluated as the molecular ordering of P3HT. In the case of spin-coated devices, the crystallinity parameter increases with increasing annealing temperature, and this agrees with the photovoltaic performance. Furthermore, the direct molecular ordering of P3HT during electrospray deposition is reported, detailing the relation between the solvent evaporation time and the crystallinity of P3HT, and is evaluated by Raman spectroscopy and grazing incidence X-ray diffraction. To observe the solvent evaporation phenomena of the electropsray process, in situ measurement of solvent evaporation time was also successfully realized for the first time by placing a CCD camera below the substrate in electrospray deposition. The solvent evaporation time was controlled from 0.036 to 2.8 s by changing the applied voltage and solvent. By investigating the relationship between the solvent evaporation time and the molecular ordering of P3HT, the long solvent evaporation time caused the high crystallinity of P3HT. In addition, the population of P3HT crystallinity with an edge-on orientation also increased with increasing solvent evaporation time by evaluating the grazing incidence X-ray diffraction pattern, in good agreement with the estimated crystallinity from Raman spectroscopy. Finally, a photoconversion efficiency of 2.0% was achieved by electrospray deposition without post thermal annealing. - Highlights: • An orientation of P3HT was controlled due to the solvent evaporation time. • A solvent evaporation time was evaluated for the electrospray deposition. • A crystallinity parameter was evaluated from the Raman spectroscopy. • X

  16. Iron-sulfur clusters as biological sensors: the chemistry of reactions with molecular oxygen and nitric oxide.

    Science.gov (United States)

    Crack, Jason C; Green, Jeffrey; Thomson, Andrew J; Le Brun, Nick E

    2014-10-21

    Iron-sulfur cluster proteins exhibit a range of physicochemical properties that underpin their functional diversity in biology, which includes roles in electron transfer, catalysis, and gene regulation. Transcriptional regulators that utilize iron-sulfur clusters are a growing group that exploit the redox and coordination properties of the clusters to act as sensors of environmental conditions including O2, oxidative and nitrosative stress, and metabolic nutritional status. To understand the mechanism by which a cluster detects such analytes and then generates modulation of DNA-binding affinity, we have undertaken a combined strategy of in vivo and in vitro studies of a range of regulators. In vitro studies of iron-sulfur cluster proteins are particularly challenging because of the inherent reactivity and fragility of the cluster, often necessitating strict anaerobic conditions for all manipulations. Nevertheless, and as discussed in this Account, significant progress has been made over the past decade in studies of O2-sensing by the fumarate and nitrate reduction (FNR) regulator and, more recently, nitric oxide (NO)-sensing by WhiB-like (Wbl) and FNR proteins. Escherichia coli FNR binds a [4Fe-4S] cluster under anaerobic conditions leading to a DNA-binding dimeric form. Exposure to O2 converts the cluster to a [2Fe-2S] form, leading to protein monomerization and hence loss of DNA binding ability. Spectroscopic and kinetic studies have shown that the conversion proceeds via at least two steps and involves a [3Fe-4S](1+) intermediate. The second step involves the release of two bridging sulfide ions from the cluster that, unusually, are not released into solution but rather undergo oxidation to sulfane (S(0)) subsequently forming cysteine persulfides that then coordinate the [2Fe-2S] cluster. Studies of other [4Fe-4S] cluster proteins that undergo oxidative cluster conversion indicate that persulfide formation and coordination may be more common than previously

  17. Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations.

    Science.gov (United States)

    Kraus, Jodi; Gupta, Rupal; Yehl, Jenna; Lu, Manman; Case, David A; Gronenborn, Angela M; Akke, Mikael; Polenova, Tatyana

    2018-03-22

    Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic, since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for 15 N H . Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0.86 Å lactose-bound and 1.25 Å apo form) X-ray crystal structures. The resolution of the X-ray crystal structure used as an input into the AF-NMR program did not affect the accuracy of the chemical shift calculations to any significant extent. Excellent agreement between experimental and computed shifts is obtained for 13 C α , while larger scatter is observed for 15 N H chemical shifts, which are influenced to a greater extent by electrostatic interactions, hydrogen bonding, and solvation.

  18. Effects of spin orbital coupling on atomic and electronic structures in Al2Cu and Al2Au crystal and liquid phases via ab initio molecular dynamics simulations

    International Nuclear Information System (INIS)

    Wang, Y.; Lu, Y.H.; Wang, X.D.; Cao, Q.P.; Zhang, D.X.; Jiang, J.Z.

    2014-01-01

    Highlights: • The SOC effect affects the cohesion energy of crystal phase. • The effect of SOC was reduced due to random local atomic structures in liquids. • The local geometrical structures also affect the melting points. • Both SOC effect and local atomic structures are important for melting point difference. - Abstract: The origin of different melting points between Al 2 Cu and Al 2 Au has been studied using ab initio molecular dynamics simulations. Cohesive energy, electronic structures and structure information of both crystal and liquid phases have been analyzed. It is found that spin orbital coupling (SOC) plays an important role on the cohesive energy of crystal phase, consistent with the different melting points of these two alloys. Whereas, it seems that SOC has no effect on the formation energy and structure of liquid phase. Possible mechanism of reduced SOC effect at liquid phase is proposed. Our results are helpful to understand the glass formation ability difference between Al 2 Cu and Al 2 Au

  19. Analysis of spin-Hamiltonian and molecular orbital coefficients of Cu2+ doped C8H11KO8 single crystal through EPR technique

    Science.gov (United States)

    Juliet sheela, K.; Krishnan, S. Radha; Shanmugam, V. M.; Subramanian, P.

    2018-04-01

    Electron paramagnetic resonance (EPR) studies have been investigated at X-band microwave frequency on Cu2+ ion incorporated into the single crystal of potassium succinate-succinic acid (KSSA) at room temperature. The angular variation of the EPR spectra has shown two magnetically in-equivalent Cu2+ sites in the KSSA single crystal system. The spin Hamiltonian parameters g and A are determined which reveals that the site I and site II occupied in rhombic and axial local field symmetry around the impurity ion. Among the two paramagnetic impurity ions, sites one occupies at substituitional position in the place of monovalent cation (K+) in the crystal whereas the other enters in its lattice interstitially by the correlation of EPR and crystal structure data. From the calculated principle values gxx, gyy, gzz and Axx, Ayy, Azz of both the sites, the admixture coefficients and molecular orbital coefficients were evaluated which gives the information of ground state wave function and types of bonding of impurity ions with the ligands.

  20. Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent

    Science.gov (United States)

    Bryce, Richard A.; Vincent, Mark A.; Malcolm, Nathaniel O. J.; Hillier, Ian H.; Burton, Neil A.

    1998-08-01

    A new hybrid quantum mechanical/molecular mechanical model of solvation is developed and used to describe the structure and dynamics of small fluoride/water clusters, using an ab initio wave function to model the ion and a fluctuating charge potential to model the waters. Appropriate parameters for the water-water and fluoride-water interactions are derived, with the fluoride anion being described by density functional theory and a large Gaussian basis. The role of solvent polarization in determining the structure and energetics of F(H2O)4- clusters is investigated, predicting a slightly greater stability of the interior compared to the surface structure, in agreement with ab initio studies. An extended Lagrangian treatment of the polarizable water, in which the water atomic charges fluctuate dynamically, is used to study the dynamics of F(H2O)4- cluster. A simulation using a fixed solvent charge distribution indicates principally interior, solvated states for the cluster. However, a preponderance of trisolvated configurations is observed using the polarizable model at 300 K, which involves only three direct fluoride-water hydrogen bonds. Ab initio calculations confirm this trisolvated species as a thermally accessible state at room temperature, in addition to the tetrasolvated interior and surface structures. Extension of this polarizable water model to fluoride clusters with five and six waters gave less satisfactory agreement with experimental energies and with ab initio geometries. However, our results do suggest that a quantitative model of solvent polarization is fundamental for an accurate understanding of the properties of anionic water clusters.

  1. Clustering pesticides according to their molecular properties and their impacts by considering additional ecotoxicological parameters in the TyPol method

    Science.gov (United States)

    Traore, Harouna; Crouzet, Olivier; Mamy, Laure; Sireyjol, Christine; Rossard, Virginie; Servien, Remy; Latrille, Eric; Benoit, Pierre

    2017-04-01

    The understanding of the fate of pesticides and their environmental impacts largely relies on their molecular properties. We recently developed 'TyPol' (Typology of Pollutants), a clustering method based on statistical analyses combining several environmental endpoints (i.e. environmental parameters such as sorption coefficient, degradation half-life) and one ecotoxicological one (bioconcentration factor), and structural molecular descriptors (number of atoms in the molecule, molecular surface, dipole moment, energy of orbitals…). TyPol has been conceived on the available knowledge on QSAR of a wide diversity of organic compounds (Mamy et al., 2015). This approach also allows to focus on transformation products present in different clusters and to infer possible changes in environmental fate consecutively to different degradation processes (Servien et al., 2014; Benoit et al., 2016). The initial version of TyPol did not include any ecotoxicological parameters except the bioconcentration factor (BCF), which informs more on the transfer along the trophic chain rather than on the effects on non-target organisms. The objective was to implement the TyPol database with a data set of ecotoxicological data concerning pesticides and several aquatic and terrestrial organisms, in order to test the possibility to extend TyPol to ecotoxicological effects on various organisms. The data analysis (available literature and databases) revealed that relevant ecotoxicological endpoints for terrestrial organisms such as soil microorganisms and macroinvertebrates are lacking compared to aquatic organisms. We have added seven parameters for acute (EC50, LC50) and chronic (NOEC) toxicological effects for the following organisms: Daphnia, Algae, Lemna and Earthworm. In this new configuration, TyPol was used to classify about 45 pesticides in different behavioural and ecotoxicity clusters. The clustering results were analyzed to reveals relationships between molecular descriptors

  2. Experimental Tests of the Algebraic Cluster Model

    Science.gov (United States)

    Gai, Moshe

    2018-02-01

    The Algebraic Cluster Model (ACM) of Bijker and Iachello that was proposed already in 2000 has been recently applied to 12C and 16O with much success. We review the current status in 12C with the outstanding observation of the ground state rotational band composed of the spin-parity states of: 0+, 2+, 3-, 4± and 5-. The observation of the 4± parity doublet is a characteristic of (tri-atomic) molecular configuration where the three alpha- particles are arranged in an equilateral triangular configuration of a symmetric spinning top. We discuss future measurement with electron scattering, 12C(e,e’) to test the predicted B(Eλ) of the ACM.

  3. Spin current

    CERN Document Server

    Valenzuela, Sergio O; Saitoh, Eiji; Kimura, Takashi

    2017-01-01

    Since the discovery of the giant magnetoresistance effect in magnetic multilayers in 1988, a new branch of physics and technology, called spin-electronics or spintronics, has emerged, where the flow of electrical charge as well as the flow of electron spin, the so-called “spin current,” are manipulated and controlled together. The physics of magnetism and the application of spin current have progressed in tandem with the nanofabrication technology of magnets and the engineering of interfaces and thin films. This book aims to provide an introduction and guide to the new physics and applications of spin current, with an emphasis on the interaction between spin and charge currents in magnetic nanostructures.

  4. Spin doctoring

    OpenAIRE

    Vozková, Markéta

    2011-01-01

    1 ABSTRACT The aim of this text is to provide an analysis of the phenomenon of spin doctoring in the Euro-Atlantic area. Spin doctors are educated people in the fields of semiotics, cultural studies, public relations, political communication and especially familiar with the infrastructure and the functioning of the media industry. Critical reflection of manipulative communication techniques puts spin phenomenon in historical perspective and traces its practical use in today's social communica...

  5. RCW 36 in the Vela Molecular Ridge: Evidence for high-mass star-cluster formation triggered by cloud-cloud collision

    Science.gov (United States)

    Sano, Hidetoshi; Enokiya, Rei; Hayashi, Katsuhiro; Yamagishi, Mitsuyoshi; Saeki, Shun; Okawa, Kazuki; Tsuge, Kisetsu; Tsutsumi, Daichi; Kohno, Mikito; Hattori, Yusuke; Yoshiike, Satoshi; Fujita, Shinji; Nishimura, Atsushi; Ohama, Akio; Tachihara, Kengo; Torii, Kazufumi; Hasegawa, Yutaka; Kimura, Kimihiro; Ogawa, Hideo; Wong, Graeme F.; Braiding, Catherine; Rowell, Gavin; Burton, Michael G.; Fukui, Yasuo

    2018-05-01

    A collision between two molecular clouds is one possible candidate for high-mass star formation. The H II region RCW 36, located in the Vela molecular ridge, contains a young star cluster (˜ 1 Myr old) and two O-type stars. We present new CO observations of RCW 36 made with NANTEN2, Mopra, and ASTE using 12CO(J = 1-0, 2-1, 3-2) and 13CO(J = 2-1) emission lines. We have discovered two molecular clouds lying at the velocities VLSR ˜ 5.5 and 9 km s-1. Both clouds are likely to be physically associated with the star cluster, as verified by the good spatial correspondence among the two clouds, infrared filaments, and the star cluster. We also found a high intensity ratio of ˜ 0.6-1.2 for CO J = 3-2/1-0 toward both clouds, indicating that the gas temperature has been increased due to heating by the O-type stars. We propose that the O-type stars in RCW 36 were formed by a collision between the two clouds, with a relative velocity separation of 5 km s-1. The complementary spatial distributions and the velocity separation of the two clouds are in good agreement with observational signatures expected for O-type star formation triggered by a cloud-cloud collision. We also found a displacement between the complementary spatial distributions of the two clouds, which we estimate to be 0.3 pc assuming the collision angle to be 45° relative to the line-of-sight. We estimate the collision timescale to be ˜ 105 yr. It is probable that the cluster age found by Ellerbroek et al. (2013b, A&A, 558, A102) is dominated by the low-mass members which were not formed under the triggering by cloud-cloud collision, and that the O-type stars in the center of the cluster are explained by the collisional triggering independently from the low-mass star formation.

  6. [Clustering analysis of Mycobacterium tuberculosis using the JATA(12)-VNTR system for molecular epidemiological surveillance in broad areas of Japan].

    Science.gov (United States)

    Wada, Takayuki; Tamaru, Aki; Iwamoto, Tomotada; Arikawa, Kentaro; Nakanishi, Noriko; Komukai, Jun; Matsumoto, Kenji; Hase, Atsushi

    2013-04-01

    Japan Anti-Tuberculosis Association (JATA) (12)-variable numbers of tandem repeats (VNTR) is a standard method for genotyping of clinical isolates of Mycobacterium tuberculosis in Japan. As a model study for nationwide surveillance, this study aimed to describe the tendency and frequency of genotypes of M. tuberculosis in a large number of clinical samples. Clinical isolates of M. tuberculosis (n = 1,778) were obtained from patients with tuberculosis in 3 areas, i.e., Osaka City, Osaka Prefecture, and Kobe City, during 2007 and 2008. The samples were analyzed using JATA (12)-VNTR. All genotypes were subjected to clustering analysis. In total, 1,086 (61.1%) isolates showed clustering. The most common clusters were composed of 3 members. Such clusters were considered to reflect either actual transmission or low discriminatory power of JATA (12)-VNTR. Several prevalent JATA(12)-VNTR genotypes formed large clusters and were discussed in relation with epidemiological findings of other studies. The findings of this study will aid in the construction of an effective genotyping-based surveillance system of M. tuberculosis, through improvement of interpretation of VNTR types, observation of certain particular strains in an area, and efficient detection of unidentified outbreaks.

  7. Adiabatic quantum computing with spin qubits hosted by molecules.

    Science.gov (United States)

    Yamamoto, Satoru; Nakazawa, Shigeaki; Sugisaki, Kenji; Sato, Kazunobu; Toyota, Kazuo; Shiomi, Daisuke; Takui, Takeji

    2015-01-28

    A molecular spin quantum computer (MSQC) requires electron spin qubits, which pulse-based electron spin/magnetic resonance (ESR/MR) techniques can afford to manipulate for implementing quantum gate operations in open shell molecular entities. Importantly, nuclear spins, which are topologically connected, particularly in organic molecular spin systems, are client qubits, while electron spins play a role of bus qubits. Here, we introduce the implementation for an adiabatic quantum algorithm, suggesting the possible utilization of molecular spins with optimized spin structures for MSQCs. We exemplify the utilization of an adiabatic factorization problem of 21, compared with the corresponding nuclear magnetic resonance (NMR) case. Two molecular spins are selected: one is a molecular spin composed of three exchange-coupled electrons as electron-only qubits and the other an electron-bus qubit with two client nuclear spin qubits. Their electronic spin structures are well characterized in terms of the quantum mechanical behaviour in the spin Hamiltonian. The implementation of adiabatic quantum computing/computation (AQC) has, for the first time, been achieved by establishing ESR/MR pulse sequences for effective spin Hamiltonians in a fully controlled manner of spin manipulation. The conquered pulse sequences have been compared with the NMR experiments and shown much faster CPU times corresponding to the interaction strength between the spins. Significant differences are shown in rotational operations and pulse intervals for ESR/MR operations. As a result, we suggest the advantages and possible utilization of the time-evolution based AQC approach for molecular spin quantum computers and molecular spin quantum simulators underlain by sophisticated ESR/MR pulsed spin technology.

  8. Clusters in nuclei

    CERN Document Server

    Following the pioneering discovery of alpha clustering and of molecular resonances, the field of nuclear clustering is today one of those domains of heavy-ion nuclear physics that faces the greatest challenges, yet also contains the greatest opportunities. After many summer schools and workshops, in particular over the last decade, the community of nuclear molecular physicists has decided to collaborate in producing a comprehensive collection of lectures and tutorial reviews covering the field. This third volume follows the successful Lect. Notes Phys. 818 (Vol. 1) and 848 (Vol. 2), and comprises six extensive lectures covering the following topics:  - Gamma Rays and Molecular Structure - Faddeev Equation Approach for Three Cluster Nuclear Reactions - Tomography of the Cluster Structure of Light Nuclei Via Relativistic Dissociation - Clustering Effects Within the Dinuclear Model : From Light to Hyper-heavy Molecules in Dynamical Mean-field Approach - Clusterization in Ternary Fission - Clusters in Light N...

  9. Computations of the chirality-sensitive effect induced by an antisymmetric indirect spin–spin coupling

    Science.gov (United States)

    Garbacz, Piotr

    2018-05-01

    Results of quantum mechanical computations of the antisymmetric part of the indirect spin-spin coupling tensor, ?, performed using the coupled-cluster method, the second-order polarisation propagator approximation, and the density functional theory for 25 molecules and nearly 100 spin-spin couplings are reported. These results are used for an estimation of the magnitude of the recently proposed liquid-state nuclear magnetic resonance chirality-sensitive effect, which allows to determine the molecular chirality directly, i.e. without the need for the application of any chiral agent. The following were found: (i) the antisymmetry J⋆ is usually larger for the coupling between spins separated by two chemical bonds in comparison with the coupling through one bond, (ii) promising samples are those which contain fluorine, and (iii) the antisymmetry of the spin-spin coupling tensor is of the order of a few hertz for commercially available chemical compounds. Therefore, the relevant property of the experiment, the pseudoscalar Jc, for them is of the order of 1 nHz m/V.

  10. 3D molecular imaging SIMS

    Energy Technology Data Exchange (ETDEWEB)

    Gillen, Greg [Surface and Microanalysis Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8371 (United States)]. E-mail: Greg.gillen@nist.gov; Fahey, Albert [Surface and Microanalysis Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8371 (United States); Wagner, Matt [Surface and Microanalysis Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8371 (United States); Mahoney, Christine [Surface and Microanalysis Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8371 (United States)

    2006-07-30

    Thin monolayer and bilayer films of spin cast poly(methyl methacrylate) (PMMA), poly(2-hydroxyethyl methacrylate) (PHEMA), poly(lactic) acid (PLA) and PLA doped with several pharmaceuticals have been analyzed by dynamic SIMS using SF{sub 5} {sup +} polyatomic primary ion bombardment. Each of these systems exhibited minimal primary beam-induced degradation under cluster ion bombardment allowing molecular depth profiles to be obtained through the film. By combing secondary ion imaging with depth profiling, three-dimensional molecular image depth profiles have been obtained from these systems. In another approach, bevel cross-sections are cut in the samples with the SF{sub 5} {sup +} primary ion beam to produce a laterally magnified cross-section of the sample that does not contain the beam-induced damage that would be induced by conventional focussed ion beam (FIB) cross-sectioning. The bevel surface can then be examined using cluster SIMS imaging or other appropriate microanalysis technique.

  11. Molecular calculations of interplanar electronic interactions in a YBaCu2O6+δ cluster as a function of the oxygen concentration

    International Nuclear Information System (INIS)

    Cogordan, J.A.; Sansores, L.E.; Valladares, A.A.

    1991-01-01

    In this paper molecular ab initio SCF calculations on a cluster formed by Y, Cu(2)-(2)-O(3) plane, Ba-O(1) plane and Cu(1)-O(4) chains are reported. The computations were performed for five different sets of lattice parameters of YBACu 2 O 6+δ . Each of these sets correspond to a values of the oxygen stoichiometry. Mulliken population analysis results show a charge transfer to the Cu(2)-O(2)-O(3) plane when the oxygen stoichiometry is increased from six to seven

  12. Eating a planet and spinning up

    Science.gov (United States)

    Qureshi, Ahmed; Naoz, Smadar; Shkolnik, Evgenya L.

    2018-01-01

    One of the predictions of high eccentricity planetary migration is that many planets will end up plunging into their host stars. We investigate the consequence of planetary mergers on their stellar hosts’ spin-period. Energy and angular momentum conservation yield that a planet consumption by a star will spin-up of the star. We find that our calculations align with the observed bifurcation in the stellar spin-period in young clusters. After a Sun-like star has eaten a planet, it will then, spin down due to magnetic braking, consistent with the observed lack of fast rotators in old clusters. The agreement between the calculations presented here and the observed spin-period of stars in young clusters provides circumstantial evidence that planetary accretion onto their host stars is a generic feature in planetary-system evolution.

  13. Dealing with chemical reaction pathways and electronic excitations in molecular systems via renormalized and active-space coupled-cluster methods

    Energy Technology Data Exchange (ETDEWEB)

    Piecuch, Piotr; Li, Wei; Lutz, Jesse J. [Department of Chemistry, Michigan State University, East Lansing, MI 48824 (United States); Włoch, Marta [Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931 (United States); Gour, Jeffrey R. [Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA and Department of Chemistry, Stanford University, Stanford, California 94305 (United States)

    2015-01-22

    Coupled-cluster (CC) theory has become the de facto standard for high-accuracy molecular calculations, but the widely used CC and equation-of-motion (EOM) CC approaches, such as CCSD(T) and EOMCCSD, have difficulties with capturing stronger electron correlations that characterize multi-reference molecular problems. This presentation demonstrates that many of these difficulties can be addressed by exploiting the completely renormalized (CR) CC and EOMCC approaches, such as CR-CC(2,3), CR-EOMCCSD(T), and CR-EOMCC(2,3), and their local correlation counterparts applicable to systems with hundreds of atoms, and the active-space CC/EOMCC approaches, such as CCSDt and EOMCCSDt, and their extensions to valence systems via the electron-attached and ionized formalisms.

  14. Clustering of near clusters versus cluster compactness

    International Nuclear Information System (INIS)

    Yu Gao; Yipeng Jing

    1989-01-01

    The clustering properties of near Zwicky clusters are studied by using the two-point angular correlation function. The angular correlation functions for compact and medium compact clusters, for open clusters, and for all near Zwicky clusters are estimated. The results show much stronger clustering for compact and medium compact clusters than for open clusters, and that open clusters have nearly the same clustering strength as galaxies. A detailed study of the compactness-dependence of correlation function strength is worth investigating. (author)

  15. Spin 1990

    International Nuclear Information System (INIS)

    Anton, Gisela

    1990-01-01

    The idea of the intrinsic angular momentum, or 'spin', of a particle has played an essential part in fundamental physics for more than 60 years, and its continuing importance was underlined at the 9th International Symposium on High Energy Spin Physics, held in September in Bonn.

  16. Spin 1990

    Energy Technology Data Exchange (ETDEWEB)

    Anton, Gisela

    1990-12-15

    The idea of the intrinsic angular momentum, or 'spin', of a particle has played an essential part in fundamental physics for more than 60 years, and its continuing importance was underlined at the 9th International Symposium on High Energy Spin Physics, held in September in Bonn.

  17. Spin tomography

    Energy Technology Data Exchange (ETDEWEB)

    D' Ariano, G M [Quantum Optics and Information Group, INFM Udr Pavia, Dipartimento di Fisica ' Alessandro Volta' and INFM, Via Bassi 6, 27100 Pavia (Italy); Maccone, L [Quantum Optics and Information Group, INFM Udr Pavia, Dipartimento di Fisica ' Alessandro Volta' and INFM, Via Bassi 6, 27100 Pavia (Italy); Paini, M [Quantum Optics and Information Group, INFM Udr Pavia, Dipartimento di Fisica ' Alessandro Volta' and INFM, Via Bassi 6, 27100 Pavia (Italy)

    2003-02-01

    We propose a tomographic reconstruction scheme for spin states. The experimental set-up, which is a modification of the Stern-Gerlach scheme, can be easily performed with currently available technology. The method is generalized to multiparticle states, analysing the spin-1/2 case for indistinguishable particles. Some Monte Carlo numerical simulations are given to illustrate the technique.

  18. Spin tomography

    International Nuclear Information System (INIS)

    D'Ariano, G M; Maccone, L; Paini, M

    2003-01-01

    We propose a tomographic reconstruction scheme for spin states. The experimental set-up, which is a modification of the Stern-Gerlach scheme, can be easily performed with currently available technology. The method is generalized to multiparticle states, analysing the spin-1/2 case for indistinguishable particles. Some Monte Carlo numerical simulations are given to illustrate the technique

  19. Temperature Dependence in Heterogeneous Nucleation with Application to the Direct Determination of Cluster Energy on Nearly Molecular Scale.

    Science.gov (United States)

    McGraw, Robert L; Winkler, Paul M; Wagner, Paul E

    2017-12-04

    A re-examination of measurements of heterogeneous nucleation of water vapor on silver nanoparticles is presented here using a model-free framework that derives the energy of critical cluster formation directly from measurements of nucleation probability. Temperature dependence is correlated with cluster stabilization by the nanoparticle seed and previously found cases of unusual increasing nucleation onset saturation ratio with increasing temperature are explained. A necessary condition for the unusual positive temperature dependence is identified, namely that the critical cluster be more stable, on a per molecule basis, than the bulk liquid to exhibit the effect. Temperature dependence is next examined in the classical Fletcher model, modified here to make the energy of cluster formation explicit in the model.  The contact angle used in the Fletcher model is identified as the microscopic contact angle, which can be directly obtained from heterogeneous nucleation experimental data by a recently developed analysis method. Here an equivalent condition, increasing contact angle with temperature, is found necessary for occurrence of unusual temperature dependence. Our findings have immediate applications to atmospheric particle formation and nanoparticle detection in condensation particle counters (CPCs).

  20. Spin glasses

    CERN Document Server

    Bovier, Anton

    2007-01-01

    Spin glass theory is going through a stunning period of progress while finding exciting new applications in areas beyond theoretical physics, in particular in combinatorics and computer science. This collection of state-of-the-art review papers written by leading experts in the field covers the topic from a wide variety of angles. The topics covered are mean field spin glasses, including a pedagogical account of Talagrand's proof of the Parisi solution, short range spin glasses, emphasizing the open problem of the relevance of the mean-field theory for lattice models, and the dynamics of spin glasses, in particular the problem of ageing in mean field models. The book will serve as a concise introduction to the state of the art of spin glass theory, usefull to both graduate students and young researchers, as well as to anyone curious to know what is going on in this exciting area of mathematical physics.

  1. Spin symposium

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    1989-01-15

    The recent 8th International Symposium on High Energy Spin Physics at the University of Minnesota in Minneapolis, Minnesota, opened with a bang when L. Pondrom (Wisconsin), donning a hard hat borrowed from construction workers, ventured that 'spin, the notorious inessential complication of hadronic physics, is finally telling us what real QCD (quantum chromodynamics, the field theory of quarks and gluons) looks like.' He was referring to an animated discussion on the meaning of the recent spin oriented (polarized) scattering results from the European Muon Collaboration (EMC) at CERN and reported at the Symposium by R. Garnet (Liverpool) and P. Schuler (Yale) which show that the proton spin is not simply a reflection of the spins of its constituent quarks.

  2. Spin incommensurability and two phase competition in cobaltites.

    Science.gov (United States)

    Phelan, D; Louca, Despina; Kamazawa, K; Lee, S-H; Ancona, S N; Rosenkranz, S; Motome, Y; Hundley, M F; Mitchell, J F; Moritomo, Y

    2006-12-08

    The perovskite LaCoO3 evolves from a nonmagnetic Mott insulator to a spin cluster ferromagnet (FM) with the substitution of Sr2+ for La3+ in La1-xSrxCoO3. The clusters increase in size and number with x and the charge percolation through the clusters leads to a metallic state. Using elastic neutron scattering on La1-xSrxCoO3 single crystals, we show that an incommensurate spin superstructure coexists with the FM spin clusters. The incommensurability increases continuously with x, with the intensity rising in the insulating phase and dropping in the metallic phase as it directly competes with the commensurate FM, itinerant clusters. The spin incommensurability arises from local order of Co3+-Co4+ clusters but no long-range static or dynamic spin stripes develop. The coexistence and competition of the two magnetic phases explain the residual resistivity at low temperatures in samples with metalliclike transport.

  3. Extrinsic spin Hall effect in graphene

    Science.gov (United States)

    Rappoport, Tatiana

    The intrinsic spin-orbit coupling in graphene is extremely weak, making it a promising spin conductor for spintronic devices. In addition, many applications also require the generation of spin currents in graphene. Theoretical predictions and recent experimental results suggest one can engineer the spin Hall effect in graphene by greatly enhancing the spin-orbit coupling in the vicinity of an impurity. The extrinsic spin Hall effect then results from the spin-dependent skew scattering of electrons by impurities in the presence of spin-orbit interaction. This effect can be used to efficiently convert charge currents into spin-polarized currents. I will discuss recent experimental results on spin Hall effect in graphene decorated with adatoms and metallic cluster and show that a large spin Hall effect can appear due to skew scattering. While this spin-orbit coupling is small if compared with what it is found in metals, the effect is strongly enhanced in the presence of resonant scattering, giving rise to robust spin Hall angles. I will present our single impurity scattering calculations done with exact partial-wave expansions and complement the analysis with numerical results from a novel real-space implementation of the Kubo formalism for tight-binding Hamiltonians. The author acknowledges the Brazilian agencies CNPq, CAPES, FAPERJ and INCT de Nanoestruturas de Carbono for financial support.

  4. Formation of a percolating cluster in films prepared by cathodic electrodeposition of a mixture of lower and higher molecular weight epoxy-amine adducts.

    Science.gov (United States)

    Ranjbar, Zahra; Moradian, Siamak; Rastegar, Saeed

    2003-08-15

    The electrodeposition behavior of blends of primary dispersions of a lower and a higher molecular weight epoxy-amine adduct has been investigated. The throwing power of the above-mentioned blends showed a voltage-dependent critical composition at which the throwing power dropped to a much lower value. This was assigned to the formation of an infinite conducting cluster, the extension of which is dependent on the rate of the electrocoagulation process at the cathode boundary. The random resistor network approach of Stauffer (RRNS) and the random resistor network approach of Miller and Abrahams (RRNMA) were applied to the experimental data with high correlations (r2=0.9314 and 0.9699). The percolating cluster formed within the film, however, gave a critical exponent of conductivity equal to 1.1028, much less than expected from a classical three-dimensional lattice (i.e., 1.5-2.0). This discrepancy was explained in terms of the changed behavior of the film resulting from the bubbles formed near the cathode and its effect on the infinite conducting cluster.

  5. The existence of a plastic phase and a solid-liquid dynamical bistability region in small fullerene cluster (C60)7: molecular dynamics simulation

    International Nuclear Information System (INIS)

    Piatek, A; Dawid, A; Gburski, Z

    2006-01-01

    We have simulated (by the molecular dymanics (MD) method) the dynamics of fullerenes (C 60 ) in an extremely small cluster composed of only as many as seven C 60 molecules. The interaction is taken to be the full 60-site pairwise additive Lennard-Jones (LJ) potential which generates both translational and anisotropic rotational motions of each molecule. Our atomically detailed MD simulations discover the plastic phase (no translations but active reorientations of fullerenes) at low energies (temperatures) of the (C 60 ) 7 cluster. We provide the in-depth evidence of the dynamical solid-liquid bistability region in the investigated cluster. Moreover, we confirm the existence of the liquid phase in (C 60 ) 7 , the finding of Gallego et al (1999 Phys. Rev. Lett. 83 5258) obtained earlier on the basis of Girifalco's model, which assumes single-site only and spherically symmetrical interaction between C 60 molecules. We have calculated the translational and angular velocity autocorrelation functions and estimated the diffusion coefficient of fullerene in the liquid phase

  6. Interaction of the iron–sulfur cluster assembly protein IscU with the Hsc66/Hsc20 molecular chaperone system of Escherichia coli

    Science.gov (United States)

    Hoff, Kevin G.; Silberg, Jonathan J.; Vickery, Larry E.

    2000-01-01

    The iscU gene in bacteria is located in a gene cluster encoding proteins implicated in iron–sulfur cluster assembly and an hsc70-type (heat shock cognate) molecular chaperone system, iscSUA-hscBA. To investigate possible interactions between these systems, we have overproduced and purified the IscU protein from Escherichia coli and have studied its interactions with the hscA and hscB gene products Hsc66 and Hsc20. IscU and its iron–sulfur complex (IscU–Fe/S) stimulated the basal steady-state ATPase activity of Hsc66 weakly in the absence of Hsc20 but, in the presence of Hsc20, increased the ATPase activity up to 480-fold. Hsc20 also decreased the apparent Km for IscU stimulation of Hsc66 ATPase activity, and surface plasmon resonance studies revealed that Hsc20 enhances binding of IscU to Hsc66. Surface plasmon resonance and isothermal titration calorimetry further showed that IscU and Hsc20 form a complex, and Hsc20 may thereby aid in the targeting of IscU to Hsc66. These results establish a direct and specific role for the Hsc66/Hsc20 chaperone system in functioning with isc gene components for the assembly of iron–sulfur cluster proteins. PMID:10869428

  7. Molecular-based rapid inventories of sympatric diversity: a comparison of DNA barcode clustering methods applied to geography-based vs clade-based sampling of amphibians.

    Science.gov (United States)

    Paz, Andrea; Crawford, Andrew J

    2012-11-01

    Molecular markers offer a universal source of data for quantifying biodiversity. DNA barcoding uses a standardized genetic marker and a curated reference database to identify known species and to reveal cryptic diversity within wellsampled clades. Rapid biological inventories, e.g. rapid assessment programs (RAPs), unlike most barcoding campaigns, are focused on particular geographic localities rather than on clades. Because of the potentially sparse phylogenetic sampling, the addition of DNA barcoding to RAPs may present a greater challenge for the identification of named species or for revealing cryptic diversity. In this article we evaluate the use of DNA barcoding for quantifying lineage diversity within a single sampling site as compared to clade-based sampling, and present examples from amphibians. We compared algorithms for identifying DNA barcode clusters (e.g. species, cryptic species or Evolutionary Significant Units) using previously published DNA barcode data obtained from geography-based sampling at a site in Central Panama, and from clade-based sampling in Madagascar. We found that clustering algorithms based on genetic distance performed similarly on sympatric as well as clade-based barcode data, while a promising coalescent-based method performed poorly on sympatric data. The various clustering algorithms were also compared in terms of speed and software implementation. Although each method has its shortcomings in certain contexts, we recommend the use of the ABGD method, which not only performs fairly well under either sampling method, but does so in a few seconds and with a user-friendly Web interface.

  8. Performance and economic evaluation of the molecular detection of pathogens for patients with severe infections: the EVAMICA open-label, cluster-randomised, interventional crossover trial.

    Science.gov (United States)

    Cambau, Emmanuelle; Durand-Zaleski, Isabelle; Bretagne, Stéphane; Brun-Buisson, Christian; Cordonnier, Catherine; Duval, Xavier; Herwegh, Stéphanie; Pottecher, Julien; Courcol, René; Bastuji-Garin, Sylvie

    2017-11-01

    Microbiological diagnosis (MD) of infections remains insufficient. The resulting empirical antimicrobial therapy leads to multidrug resistance and inappropriate treatments. We therefore evaluated the cost-effectiveness of direct molecular detection of pathogens in blood for patients with severe sepsis (SES), febrile neutropenia (FN) and suspected infective endocarditis (SIE). Patients were enrolled in a multicentre, open-label, cluster-randomised crossover trial conducted during two consecutive periods, randomly assigned as control period (CP; standard diagnostic workup) or intervention period (IP; additional testing with LightCycler ® SeptiFast). Multilevel models used to account for clustering were stratified by clinical setting (SES, FN, SIE). A total of 1416 patients (907 SES, 440 FN, 69 SIE) were evaluated for the primary endpoint (rate of blood MD). For SES patients, the MD rate was higher during IP than during CP [42.6% (198/465) vs. 28.1% (125/442), odds ratio (OR) 1.89, 95% confidence interval (CI) 1.43-2.50; P analysis of the incremental cost-effectiveness ratio showed weak dominance of intervention in SES patients. Addition of molecular detection to standard care improves MD and thus efficiency of healthcare resource usage in patients with SES. ClinicalTrials.gov registration number: NCT00709358.

  9. Application of the finite-field coupled-cluster method to calculate molecular properties relevant to electron electric-dipole-moment searches

    Science.gov (United States)

    Abe, M.; Prasannaa, V. S.; Das, B. P.

    2018-03-01

    Heavy polar diatomic molecules are currently among the most promising probes of fundamental physics. Constraining the electric dipole moment of the electron (e EDM ), in order to explore physics beyond the standard model, requires a synergy of molecular experiment and theory. Recent advances in experiment in this field have motivated us to implement a finite-field coupled-cluster (FFCC) approach. This work has distinct advantages over the theoretical methods that we had used earlier in the analysis of e EDM searches. We used relativistic FFCC to calculate molecular properties of interest to e EDM experiments, that is, the effective electric field (Eeff) and the permanent electric dipole moment (PDM). We theoretically determine these quantities for the alkaline-earth monofluorides (AEMs), the mercury monohalides (Hg X ), and PbF. The latter two systems, as well as BaF from the AEMs, are of interest to e EDM searches. We also report the calculation of the properties using a relativistic finite-field coupled-cluster approach with single, double, and partial triples' excitations, which is considered to be the gold standard of electronic structure calculations. We also present a detailed error estimate, including errors that stem from our choice of basis sets, and higher-order correlation effects.

  10. Molecular Epidemiology of HIV-1 in Jilin Province, Northeastern China: Emergence of a New CRF07_BC Transmission Cluster and Intersubtype Recombinants

    Science.gov (United States)

    Ning, Chuanyi; Feng, Yi; Xie, Cunxin; He, Xiang; Takebe, Yutaka; Sun, Liuyan; Guo, Qi; Xing, Hui; Kalish, Marcia L.; Shao, Yiming

    2014-01-01

    Objective To investigate the HIV-1 molecular epidemiology among newly diagnosed HIV-1 infected persons living in the Jilin province of northeastern China. Methods Plasma samples from 189 newly diagnosed HIV-1 infected patients were collected between June 2010 and August 2011 from all nine cities of Jilin province. HIV-1 nucleotide sequences of gag P17–P24 and env C2–C4 gene regions were amplified using a multiplex RT-PCR method and sequenced. Phylogenetic and recombination analyses were used to determine the HIV-1 genotypes. Results Based on all sequences generated, the subtype/CFR distribution was as follows: CRF01_AE (58.1%), CRF07_BC (13.2%), subtype B’ (13.2%), recombinant viruses (8.1%), subtype B (3.7%), CRF02_AG (2.9%), subtype C (0.7%). In addition to finding CRF01_AE strains from previously reported transmission clusters 1, 4 and 5, a new transmission cluster was described within the CRF07_BC radiation. Among 11 different recombinants identified, 10 contained portions of gene regions from the CRF01_AE lineage. CRF02_AG was found to form a transmission cluster of 4 in local Jilin residents. Conclusions Our study presents a molecular epidemiologic investigation describing the complex structure of HIV-1 strains co-circulating in Jilin province. The results highlight the critical importance of continuous monitoring of HIV-infections, along with detailed socio-demographic data, in order to design appropriate prevention measures to limit the spread of new HIV infections. PMID:25356726

  11. Aqueous solvation of Mg(ii) and Ca(ii): A Born-Oppenheimer molecular dynamics study of microhydrated gas phase clusters

    Science.gov (United States)

    León-Pimentel, C. I.; Amaro-Estrada, J. I.; Hernández-Cobos, J.; Saint-Martin, H.; Ramírez-Solís, A.

    2018-04-01

    The hydration features of [Mg(H2O)n ] 2 + and [Ca(H2O)n ] 2 + clusters with n = 3-6, 8, 18, and 27 were studied by means of Born-Oppenheimer molecular dynamics simulations at the B3LYP/6-31+G** level of theory. For both ions, it is energetically more favorable to have all water molecules in the first hydration shell when n ≤ 6, but stable lower coordination average structures with one water molecule not directly interacting with the ion were found for Mg2+ at room temperature, showing signatures of proton transfer events for the smaller cation but not for the larger one. A more rigid octahedral-type structure for Mg2+ than for Ca2+ was observed in all simulations, with no exchange of water molecules to the second hydration shell. Significant thermal effects on the average structure of clusters were found: while static optimizations lead to compact, spherically symmetric hydration geometries, the effects introduced by finite-temperature dynamics yield more prolate configurations. The calculated vibrational spectra are in agreement with infrared spectroscopy results. Previous studies proposed an increase in the coordination number (CN) from six to eight water molecules for [Ca(H2O)n ] 2 + clusters when n ≥ 12; however, in agreement with recent measurements of binding energies, no transition to a larger CN was found when n > 8. Moreover, the excellent agreement found between the calculated extended X-ray absorption fine structure spectroscopy spectra for the larger cluster and the experimental data of the aqueous solution supports a CN of six for Ca2+.

  12. Photo fragmentation dynamics of small argon clusters and biological molecular: new tools by trapping and vectorial correlation

    International Nuclear Information System (INIS)

    Lepere, V.

    2006-09-01

    The present work concerns the building up of a complex set-up whose aim being the investigation of the photo fragmentation of ionised clusters and biological molecules. This new tool is based on the association of several techniques. Two ion sources are available: clusters produced in a supersonic beam are ionised by 70 eV electrons while ions of biological interest are produced in an 'electro-spray'. Ro-vibrational cooling is achieved in a 'Zajfman' electrostatic ion trap. The lifetime of ions can also be measured using the trap. Two types of lasers are used to excite the ionised species: the femtosecond laser available at the ELYSE facilities and a nanosecond laser. Both lasers have a repetition rate of 1 kHz. The neutral and ionised fragments are detected in coincidence using a sophisticated detection system allowing time and localisation of the various fragments to be determined. With such a tool, I was able to investigate in details the fragmentation dynamics of ionised clusters and bio-molecules. The first experiments deal with the measurement of the lifetime of the Ar 2+ dimer II(1/2)u metastable state. The relative population of this state was also determined. The Ar 2+ and Ar 3+ photo-fragmentation was then studied and electronic transitions responsible for their dissociation identified. The detailed analysis of our data allowed to distinguish the various fragmentation mechanisms. Finally, a preliminary investigation of the protonated tryptamine fragmentation is presented. (author)

  13. Spin systems

    CERN Document Server

    Caspers, W J

    1989-01-01

    This book is about spin systems as models for magnetic materials, especially antiferromagnetic lattices. Spin-systems are well-defined models, for which, in special cases, exact properties may be derived. These special cases are for the greater part, one- dimensional and restricted in their applicability, but they may give insight into general properties that also exist in higher dimension. This work pays special attention to qualitative differences between spin lattices of different dimensions. It also replaces the traditional picture of an (ordered) antiferromagnetic state of a Heisenberg sy

  14. Multicritical phase diagrams of the ferromagnetic spin-3/2 Blume-Emery-Griffiths model with repulsive biquadratic coupling including metastable phases: The cluster variation method and the path probability method with the point distribution

    Energy Technology Data Exchange (ETDEWEB)

    Keskin, Mustafa [Department of Physics, Erciyes University, 38039 Kayseri (Turkey)], E-mail: keskin@erciyes.edu.tr; Canko, Osman [Department of Physics, Erciyes University, 38039 Kayseri (Turkey)

    2008-01-15

    We study the thermal variations of the ferromagnetic spin-3/2 Blume-Emery-Griffiths (BEG) model with repulsive biquadratic coupling by using the lowest approximation of the cluster variation method (LACVM) in the absence and presence of the external magnetic field. We obtain metastable and unstable branches of the order parameters besides the stable branches and phase transitions of these branches are investigated extensively. The classification of the stable, metastable and unstable states is made by comparing the free energy values of these states. We also study the dynamics of the model by using the path probability method (PPM) with the point distribution in order to make sure that we find and define the metastable and unstable branches of the order parameters completely and correctly. We present the metastable phase diagrams in addition to the equilibrium phase diagrams in the (kT/J, K/J) and (kT/J, D/J) planes. It is found that the metastable phase diagrams always exist at the low temperatures, which are consistent with experimental and theoretical works.

  15. Multicritical phase diagrams of the ferromagnetic spin-3/2 Blume-Emery-Griffiths model with repulsive biquadratic coupling including metastable phases: The cluster variation method and the path probability method with the point distribution

    International Nuclear Information System (INIS)

    Keskin, Mustafa; Canko, Osman

    2008-01-01

    We study the thermal variations of the ferromagnetic spin-3/2 Blume-Emery-Griffiths (BEG) model with repulsive biquadratic coupling by using the lowest approximation of the cluster variation method (LACVM) in the absence and presence of the external magnetic field. We obtain metastable and unstable branches of the order parameters besides the stable branches and phase transitions of these branches are investigated extensively. The classification of the stable, metastable and unstable states is made by comparing the free energy values of these states. We also study the dynamics of the model by using the path probability method (PPM) with the point distribution in order to make sure that we find and define the metastable and unstable branches of the order parameters completely and correctly. We present the metastable phase diagrams in addition to the equilibrium phase diagrams in the (kT/J, K/J) and (kT/J, D/J) planes. It is found that the metastable phase diagrams always exist at the low temperatures, which are consistent with experimental and theoretical works

  16. Ab Initio Ligand Field Molecular Mechanics and the Nature of Metal-Ligand π-Bonding in Fe(II) 2,6-di(pyrazol-1-yl)pyridine Spin Crossover Complexes.

    Science.gov (United States)

    Deeth, Robert J; Halcrow, Malcolm A; Kershaw Cook, Laurence J; Raithby, Paul R

    2018-04-06

    A ligand field molecular mechanics (LFMM) force field has been constructed for the spin states of [Fe(bpp) 2 ] 2+ (bpp=2,6-di(pyrazol-1-yl)pyridine) and related complexes. A new charge scheme is employed which interpolates between partial charges for neutral bpp and protonated [H 3 bpp] 3+ to achieve a target metal charge. The LFMM angular overlap model (AOM) parameters are fitted to fully ab initio d orbital energies. However, several AOM parameter sets are possible. The ambiguity is resolved by calculating the Jahn-Teller distortion mode for high spin, which indicates that in [Fe(bpp) 2 ] 2+ pyridine is a π-acceptor and pyrazole a weak π-donor. The alternative fit, assumed previously, where both ligands act as π-donors leads to an inconsistent distortion. LFMM optimisations in the presence of [BF 4 ] - or [PF 6 ] - anions are in good agreement with experiment and the model also correctly predicts the spin state energetics for 3-pyrazolyl substituents where the interactions are mainly steric. However, for 4-pyridyl or 4-pyrazolyl substituents, LFMM only treats the electrostatic contribution which, for the pyridyl substituents, generates a fair correlation with the spin crossover transition temperatures, T 1/2 , but in the reverse sense to the dominant electronic effect. Thus, LFMM generates its smallest spin state energy difference for the substituent with the highest T 1/2 . One parameter set for all substituted bpp ligands is insufficient and further LFMM development will be required. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Electronic and atomic impacts on large clusters

    International Nuclear Information System (INIS)

    Gspann, J.

    1982-01-01

    Describing first the generation and properties of molecular beams of large Van der Waals clusters such as speed distribution, cluster size distribution, and internal temperature of the clusters, the review then features the results of electronic impacts on large clusters: metastable electronic cluster excitations, ejection of positive cluster ions of less than 100 atoms from much larger parent clusters, and ionization of the large clusters. Atomic impacts at thermal energies are treated with respect to the scattering cross section of the clusters, their drag coefficient in free molecular flow, and the peculiarities of impacts on helium clusters of either isotope. (Auth.)

  18. Connection of spin and statistics for charge--monopole composites

    International Nuclear Information System (INIS)

    Goldhaber, A.S.

    1976-01-01

    An object composed of a spinless electrically charged particle and a spinless magnetically charged particle may bear net half-integer spin, but the wave function of two such clusters must be symmetric under their interchange. Nevertheless, a careful study of the relative motion of the clusters shows that this symmetry condition implies the usual connection between spin and statistics

  19. Spin electronics

    CERN Document Server

    Buhrman, Robert; Daughton, James; Molnár, Stephan; Roukes, Michael

    2004-01-01

    This report is a comparative review of spin electronics ("spintronics") research and development activities in the United States, Japan, and Western Europe conducted by a panel of leading U.S. experts in the field. It covers materials, fabrication and characterization of magnetic nanostructures, magnetism and spin control in magnetic nanostructures, magneto-optical properties of semiconductors, and magnetoelectronics and devices. The panel's conclusions are based on a literature review and a series of site visits to leading spin electronics research centers in Japan and Western Europe. The panel found that Japan is clearly the world leader in new material synthesis and characterization; it is also a leader in magneto-optical properties of semiconductor devices. Europe is strong in theory pertaining to spin electronics, including injection device structures such as tunneling devices, and band structure predictions of materials properties, and in development of magnetic semiconductors and semiconductor heterost...

  20. Spin Conference

    International Nuclear Information System (INIS)

    Anon.

    1983-01-01

    The 5th International Symposium on High Energy Spin Physics met in September at Brookhaven. The symposium has evolved to include a number of diverse specialities: theory, including parity violations and proposed quantum chromodynamics (QCD) tests with polarized beams; experiment, including the large spin effects discovered in high transverse momentum elastic scattering and hyperon production, dibaryons, and magnetic moments; acceleration and storage of polarized protons and electrons; and development of polarized sources and targets

  1. Magnetohydrodynamic Simulations of the Formation of Molecular Clouds toward the Stellar Cluster Westerlund 2: Interaction of a Jet with a Clumpy Interstellar Medium

    International Nuclear Information System (INIS)

    Asahina, Yuta; Kawashima, Tomohisa; Furukawa, Naoko; Enokiya, Rei; Yamamoto, Hiroaki; Fukui, Yasuo; Matsumoto, Ryoji

    2017-01-01

    The formation mechanism of CO clouds observed with the NANTEN2 and Mopra telescopes toward the stellar cluster Westerlund 2 is studied by 3D magnetohydrodynamic simulations, taking into account the interstellar cooling. These molecular clouds show a peculiar shape composed of an arc-shaped cloud on one side of the TeV γ -ray source HESS J1023-575 and a linear distribution of clouds (jet clouds) on the other side. We propose that these clouds are formed by the interaction of a jet with clumps of interstellar neutral hydrogen (H i). By studying the dependence of the shape of dense cold clouds formed by shock compression and cooling on the filling factor of H i clumps, we found that the density distribution of H i clumps determines the shape of molecular clouds formed by the jet–cloud interaction: arc clouds are formed when the filling factor is large. On the other hand, when the filling factor is small, molecular clouds align with the jet. The jet propagates faster in models with small filling factors.

  2. Magnetohydrodynamic Simulations of the Formation of Molecular Clouds toward the Stellar Cluster Westerlund 2: Interaction of a Jet with a Clumpy Interstellar Medium

    Energy Technology Data Exchange (ETDEWEB)

    Asahina, Yuta; Kawashima, Tomohisa [National Astronomical Observatory of Japan, Osawa, Mitaka, Tokyo 181-8588 (Japan); Furukawa, Naoko; Enokiya, Rei; Yamamoto, Hiroaki; Fukui, Yasuo [Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan); Matsumoto, Ryoji, E-mail: asahina@cfca.jp [Department of Physics, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522 (Japan)

    2017-02-20

    The formation mechanism of CO clouds observed with the NANTEN2 and Mopra telescopes toward the stellar cluster Westerlund 2 is studied by 3D magnetohydrodynamic simulations, taking into account the interstellar cooling. These molecular clouds show a peculiar shape composed of an arc-shaped cloud on one side of the TeV γ -ray source HESS J1023-575 and a linear distribution of clouds (jet clouds) on the other side. We propose that these clouds are formed by the interaction of a jet with clumps of interstellar neutral hydrogen (H i). By studying the dependence of the shape of dense cold clouds formed by shock compression and cooling on the filling factor of H i clumps, we found that the density distribution of H i clumps determines the shape of molecular clouds formed by the jet–cloud interaction: arc clouds are formed when the filling factor is large. On the other hand, when the filling factor is small, molecular clouds align with the jet. The jet propagates faster in models with small filling factors.

  3. Formation of stable products from cluster-cluster collisions

    International Nuclear Information System (INIS)

    Alamanova, Denitsa; Grigoryan, Valeri G; Springborg, Michael

    2007-01-01

    The formation of stable products from copper cluster-cluster collisions is investigated by using classical molecular-dynamics simulations in combination with an embedded-atom potential. The dependence of the product clusters on impact energy, relative orientation of the clusters, and size of the clusters is studied. The structures and total energies of the product clusters are analysed and compared with those of the colliding clusters before impact. These results, together with the internal temperature, are used in obtaining an increased understanding of cluster fusion processes

  4. Molecular Beam Epitaxy on Gas Cluster Ion Beam Prepared GaSb Substrates: Towards Improved Surfaces and Interfaces

    National Research Council Canada - National Science Library

    Krishnaswami, Kannan; Vangala, Shivashankar R; Dauplaise, Helen M; Allen, Lisa P; Dallas, Gordon; Bakken, Daniel; Bliss, David F; Goodhue, WIlliam D

    2007-01-01

    ... at temperatures ranging 530 degrees C to 560 degrees C. Cross-sectional transmission electron microscopy of molecular beam epitaxy grown GaSb/AlGaSb layers showed that the HBr-GCIB surface produced a smooth dislocation-free substrate-to-epi transition...

  5. 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

  6. Spin-Orbit Effect on the Molecular Properties of TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4): A Density Functional Theory and Ab Initio Study.

    Science.gov (United States)

    Moon, Jiwon; Kim, Joonghan

    2016-09-29

    Density functional theory (DFT) and ab initio calculations, including spin-orbit coupling (SOC), were performed to investigate the spin-orbit (SO) effect on the molecular properties of tellurium halides, TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4). SOC elongates the Te-X bond and slightly reduces the vibrational frequencies. Consideration of SOC leads to better agreement with experimental values. Møller-Plesset second-order perturbation theory (MP2) seriously underestimates the Te-X bond lengths. In contrast, B3LYP significantly overestimates them. SO-PBE0 and multireference configuration interactions with the Davidson correction (MRCI+Q), which include SOC via a state-interaction approach, give the Te-I bond length of TeI2 that matches the experimental value. On the basis of the calculated thermochemical energy and optimized molecular structure, TeI4 is unlikely to be stable. The use of PBE0 including SOC is strongly recommended for predicting the molecular properties of Te-containing compounds.

  7. Spin-flip scattering effect on the current-induced spin torque in ferromagnet-insulator-ferromagnet tunnel junctions

    International Nuclear Information System (INIS)

    Zhu Zhengang; Su Gang; Jin Biao; Zheng Qingrong

    2003-01-01

    We have investigated the current-induced spin transfer torque of a ferromagnet-insulator-ferromagnet tunnel junction by taking the spin-flip scatterings into account. It is found that the spin-flip scattering can induce an additional spin torque, enhancing the maximum of the spin torque and giving rise to an angular shift compared to the case when the spin-flip scatterings are neglected. The effects of the molecular fields of the left and right ferromagnets on the spin torque are also studied. It is found that τ Rx /I e (τ Rx is the spin-transfer torque acting on the right ferromagnet and I e is the tunneling electrical current) does vary with the molecular fields. At two certain angles, τ Rx /I e is independent of the molecular field of the right ferromagnet, resulting in two crossing points in the curve of τ Rx /I e versus the relevant orientation for different molecular fields

  8. Efficient calculation of nuclear spin-rotation constants from auxiliary density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Zuniga-Gutierrez, Bernardo, E-mail: bzuniga.51@gmail.com [Departamento de Ciencias Computacionales, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, C.P. 44430 Guadalajara, Jalisco (Mexico); Camacho-Gonzalez, Monica [Universidad Tecnológica de Tecámac, División A2, Procesos Industriales, Carretera Federal México Pachuca Km 37.5, Col. Sierra Hermosa, C.P. 55740 Tecámac, Estado de México (Mexico); Bendana-Castillo, Alfonso [Universidad Tecnológica de Tecámac, División A3, Tecnologías de la Información y Comunicaciones, Carretera Federal México Pachuca Km 37.5, Col. Sierra Hermosa, C.P. 55740 Tecámac, Estado de México (Mexico); Simon-Bastida, Patricia [Universidad Tecnlógica de Tulancingo, División Electromecánica, Camino a Ahuehuetitla No. 301, Col. Las Presas, C.P. 43642 Tulancingo, Hidalgo (Mexico); Calaminici, Patrizia; Köster, Andreas M. [Departamento de Química, CINVESTAV, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, México D.F. 07000 (Mexico)

    2015-09-14

    The computation of the spin-rotation tensor within the framework of auxiliary density functional theory (ADFT) in combination with the gauge including atomic orbital (GIAO) scheme, to treat the gauge origin problem, is presented. For the spin-rotation tensor, the calculation of the magnetic shielding tensor represents the most demanding computational task. Employing the ADFT-GIAO methodology, the central processing unit time for the magnetic shielding tensor calculation can be dramatically reduced. In this work, the quality of spin-rotation constants obtained with the ADFT-GIAO methodology is compared with available experimental data as well as with other theoretical results at the Hartree-Fock and coupled-cluster level of theory. It is found that the agreement between the ADFT-GIAO results and the experiment is good and very similar to the ones obtained by the coupled-cluster single-doubles-perturbative triples-GIAO methodology. With the improved computational performance achieved, the computation of the spin-rotation tensors of large systems or along Born-Oppenheimer molecular dynamics trajectories becomes feasible in reasonable times. Three models of carbon fullerenes containing hundreds of atoms and thousands of basis functions are used for benchmarking the performance. Furthermore, a theoretical study of temperature effects on the structure and spin-rotation tensor of the H{sup 12}C–{sup 12}CH–DF complex is presented. Here, the temperature dependency of the spin-rotation tensor of the fluorine nucleus can be used to identify experimentally the so far unknown bent isomer of this complex. To the best of our knowledge this is the first time that temperature effects on the spin-rotation tensor are investigated.

  9. Efficient calculation of nuclear spin-rotation constants from auxiliary density functional theory

    International Nuclear Information System (INIS)

    Zuniga-Gutierrez, Bernardo; Camacho-Gonzalez, Monica; Bendana-Castillo, Alfonso; Simon-Bastida, Patricia; Calaminici, Patrizia; Köster, Andreas M.

    2015-01-01

    The computation of the spin-rotation tensor within the framework of auxiliary density functional theory (ADFT) in combination with the gauge including atomic orbital (GIAO) scheme, to treat the gauge origin problem, is presented. For the spin-rotation tensor, the calculation of the magnetic shielding tensor represents the most demanding computational task. Employing the ADFT-GIAO methodology, the central processing unit time for the magnetic shielding tensor calculation can be dramatically reduced. In this work, the quality of spin-rotation constants obtained with the ADFT-GIAO methodology is compared with available experimental data as well as with other theoretical results at the Hartree-Fock and coupled-cluster level of theory. It is found that the agreement between the ADFT-GIAO results and the experiment is good and very similar to the ones obtained by the coupled-cluster single-doubles-perturbative triples-GIAO methodology. With the improved computational performance achieved, the computation of the spin-rotation tensors of large systems or along Born-Oppenheimer molecular dynamics trajectories becomes feasible in reasonable times. Three models of carbon fullerenes containing hundreds of atoms and thousands of basis functions are used for benchmarking the performance. Furthermore, a theoretical study of temperature effects on the structure and spin-rotation tensor of the H 12 C– 12 CH–DF complex is presented. Here, the temperature dependency of the spin-rotation tensor of the fluorine nucleus can be used to identify experimentally the so far unknown bent isomer of this complex. To the best of our knowledge this is the first time that temperature effects on the spin-rotation tensor are investigated

  10. Efficient calculation of nuclear spin-rotation constants from auxiliary density functional theory.

    Science.gov (United States)

    Zuniga-Gutierrez, Bernardo; Camacho-Gonzalez, Monica; Bendana-Castillo, Alfonso; Simon-Bastida, Patricia; Calaminici, Patrizia; Köster, Andreas M

    2015-09-14

    The computation of the spin-rotation tensor within the framework of auxiliary density functional theory (ADFT) in combination with the gauge including atomic orbital (GIAO) scheme, to treat the gauge origin problem, is presented. For the spin-rotation tensor, the calculation of the magnetic shielding tensor represents the most demanding computational task. Employing the ADFT-GIAO methodology, the central processing unit time for the magnetic shielding tensor calculation can be dramatically reduced. In this work, the quality of spin-rotation constants obtained with the ADFT-GIAO methodology is compared with available experimental data as well as with other theoretical results at the Hartree-Fock and coupled-cluster level of theory. It is found that the agreement between the ADFT-GIAO results and the experiment is good and very similar to the ones obtained by the coupled-cluster single-doubles-perturbative triples-GIAO methodology. With the improved computational performance achieved, the computation of the spin-rotation tensors of large systems or along Born-Oppenheimer molecular dynamics trajectories becomes feasible in reasonable times. Three models of carbon fullerenes containing hundreds of atoms and thousands of basis functions are used for benchmarking the performance. Furthermore, a theoretical study of temperature effects on the structure and spin-rotation tensor of the H(12)C-(12)CH-DF complex is presented. Here, the temperature dependency of the spin-rotation tensor of the fluorine nucleus can be used to identify experimentally the so far unknown bent isomer of this complex. To the best of our knowledge this is the first time that temperature effects on the spin-rotation tensor are investigated.

  11. Evidence for radical anion formation during liquid secondary ion mass spectrometry analysis of oligonucleotides and synthetic oligomeric analogues: a deconvolution algorithm for molecular ion region clusters.

    Science.gov (United States)

    Laramée, J A; Arbogast, B; Deinzer, M L

    1989-10-01

    It is shown that one-electron reduction is a common process that occurs in negative ion liquid secondary ion mass spectrometry (LSIMS) of oligonucleotides and synthetic oligonucleosides and that this process is in competition with proton loss. Deconvolution of the molecular anion cluster reveals contributions from (M-2H).-, (M-H)-, M.-, and (M + H)-. A model based on these ionic species gives excellent agreement with the experimental data. A correlation between the concentration of species arising via one-electron reduction [M.- and (M + H)-] and the electron affinity of the matrix has been demonstrated. The relative intensity of M.- is mass-dependent; this is rationalized on the basis of base-stacking. Base sequence ion formation is theorized to arise from M.- radical anion among other possible pathways.

  12. Application of the Fenske-Hall molecular orbital method to the calculation of 11B NMR chemical shifts. Antipodal substituent effects in deltahedral clusters

    International Nuclear Information System (INIS)

    Fehlner, T.P.; Czech, P.T.; Fenske, R.F.

    1990-01-01

    Utilizing Fenske-Hall wave functions and eigenvalues combined with the Ramsey sum over states (SOS) approximation, it is demonstrated that the sign and magnitude of the paramagnetic contribution to the shielding correlates well with the observed 11 B chemical shifts of a substantial variety of boron- and metal-containing compounds. Analysis of the molecular orbital (MO) contributions in the SOS approximation leads to an explanation of the large downfield shifts associated with metal-rich metallaboranes. A similar analysis demonstrates the importance of selected cluster occupied and unoccupied MO's in explaining both exo-cage substituent effects in which the antipodal boron resonance is shifted upfield and endo-cage substituent effects (interchange of isolobal fragments within the cage framework) in which the antipodal boron resonance is shifted downfield. Exo- and endo-cage substitution perturbs these MO's in an understandable fashion, leading to an internally consistent explanation of the observed chemical shift changes. 36 refs., 8 figs., 4 tabs

  13. Clustering, microalloying and mechanical properties in Cu/Zr-based glassy models by molecular dynamics simulations and ab-initio computations

    Energy Technology Data Exchange (ETDEWEB)

    Lekka, Ch.E.; Bokas, G.B. [University of Ioannina, Department of Materials Science and Engineering, Ioannina 45100 (Greece); Almyras, G.A. [University of Ioannina, Department of Physics, Ioannina 45110 (Greece); Papageorgiou, D.G. [University of Ioannina, Department of Materials Science and Engineering, Ioannina 45100 (Greece); Evangelakis, G.A., E-mail: gevagel@cc.uoi.gr [University of Ioannina, Department of Physics, Ioannina 45110 (Greece)

    2012-09-25

    Highlights: Black-Right-Pointing-Pointer Cu-Zr MGs consist of interpenetrating ICO-like clusters (superclusters (SCs)). Black-Right-Pointing-Pointer The SCs participate in the accommodation of the tensile deformation. Black-Right-Pointing-Pointer The SCs may exhibit a free of bonds (FoB) plane. Black-Right-Pointing-Pointer Al microalloying changes the SCs' electronic structure inducing FoB planes. Black-Right-Pointing-Pointer Control of SCs' electronic structure may lead to control of MGs' properties. - Abstract: We present results on the microstructure of Cu-Zr metallic glasses (MGs) at equilibrium and under tensile deformation by means of large scale molecular dynamics (MD) simulations and density functional theory (DFT) calculations. We found that the MGs are composed by interpenetrating icosahedral-like (ICO) clusters forming superclusters (SCs). The deformation accommodation is associated with the destruction and recreation of these ICO clusters and SCs. DFT calculations on the Cu{sub 13}Zr{sub 10} SCs with Cu-Cu core atoms revealed the presence of a free of bonds (FoB) plane that could be viewed as analog of a slip plane of the crystalline materials. The microalloying (MA) effect in a similar SC (one of the core atoms substituted by Al) yielded that Al is associated with the formation of a FoB plane. These results provide possible explanations of the experimental findings referring to the short range order, the MA effect and could potentially be used for the design of new MGs.

  14. Scattering of a proton with the Li{sub 4} cluster: Non-adiabatic molecular dynamics description based on time-dependent density-functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Castro, A., E-mail: acastro@bifi.es [Institute for Biocomputation and Physics of Complex Systems (BIFI) and Zaragoza Scientific Center for Advanced Modelling (ZCAM), University of Zaragoza, 50018 Zaragoza (Spain); Isla, M. [Departamento de Fisica Teorica, Atomica y Optica, Universidad de Valladolid, 47005 Valladolid (Spain); Martinez, Jose I. [Departamento de Fisica Teorica de la Materia Condensada, Universidad Autonoma de Madrid, ES-28049 Madrid (Spain); Alonso, J.A. [Departamento de Fisica Teorica, Atomica y Optica, Universidad de Valladolid, 47005 Valladolid (Spain)

    2012-05-03

    Graphical abstract: Two trajectories for the collision of a proton with the Lithium tetramer. On the left, the proton is scattered away, and a Li{sub 2} molecule plus two isolated Lithium atoms result. On the right, the proton is captured and a LiH molecule is created. Highlights: Black-Right-Pointing-Pointer Scattering of a proton with Lithium clusters described from first principles. Black-Right-Pointing-Pointer Description based on non-adiabatic molecular dynamics. Black-Right-Pointing-Pointer The electronic structure is described with time-dependent density-functional theory. Black-Right-Pointing-Pointer The method allows to discern reaction channels depending on initial parameters. - Abstract: We have employed non-adiabatic molecular dynamics based on time-dependent density-functional theory to characterize the scattering behavior of a proton with the Li{sub 4} cluster. This technique assumes a classical approximation for the nuclei, effectively coupled to the quantum electronic system. This time-dependent theoretical framework accounts, by construction, for possible charge transfer and ionization processes, as well as electronic excitations, which may play a role in the non-adiabatic regime. We have varied the incidence angles in order to analyze the possible reaction patterns. The initial proton kinetic energy of 10 eV is sufficiently high to induce non-adiabatic effects. For all the incidence angles considered the proton is scattered away, except in one interesting case in which one of the Lithium atoms captures it, forming a LiH molecule. This theoretical formalism proves to be a powerful, effective and predictive tool for the analysis of non-adiabatic processes at the nanoscale.

  15. Molecular basis of the γ-aminobutyric acid A receptor α3 subunit interaction with the clustering protein gephyrin

    DEFF Research Database (Denmark)

    Tretter, Verena; Kerschner, Bernd; Milenkovic, Ivan

    2011-01-01

    The multifunctional scaffolding protein gephyrin is a key player in the formation of the postsynaptic scaffold at inhibitory synapses, clustering both inhibitory glycine receptors (GlyRs) and selected GABA(A) receptor (GABA(A)R) subtypes. We report a direct interaction between the GABA(A)R α3...... subunit and gephyrin, mapping reciprocal binding sites using mutagenesis, overlay, and yeast two-hybrid assays. This analysis reveals that critical determinants of this interaction are located in the motif FNIVGTTYPI in the GABA(A)R α3 M3-M4 domain and the motif SMDKAFITVL at the N terminus...... of the gephyrin E domain. GABA(A)R α3 gephyrin binding-site mutants were unable to co-localize with endogenous gephyrin in transfected hippocampal neurons, despite being able to traffic to the cell membrane and form functional benzodiazepine-responsive GABA(A)Rs in recombinant systems. Interestingly, motifs...

  16. Competing Spin Liquids and Hidden Spin-Nematic Order in Spin Ice with Frustrated Transverse Exchange

    Directory of Open Access Journals (Sweden)

    Mathieu Taillefumier

    2017-12-01

    Full Text Available Frustration in magnetic interactions can give rise to disordered ground states with subtle and beautiful properties. The spin ices Ho_{2}Ti_{2}O_{7} and Dy_{2}Ti_{2}O_{7} exemplify this phenomenon, displaying a classical spin-liquid state, with fractionalized magnetic-monopole excitations. Recently, there has been great interest in closely related “quantum spin-ice” materials, following the realization that anisotropic exchange interactions could convert spin ice into a massively entangled, quantum spin liquid, where magnetic monopoles become the charges of an emergent quantum electrodynamics. Here we show that even the simplest model of a quantum spin ice, the XXZ model on the pyrochlore lattice, can realize a still-richer scenario. Using a combination of classical Monte Carlo simulation, semiclassical molecular-dynamics simulation, and analytic field theory, we explore the properties of this model for frustrated transverse exchange. We find not one, but three competing forms of spin liquid, as well as a phase with hidden, spin-nematic order. We explore the experimental signatures of each of these different states, making explicit predictions for inelastic neutron scattering. These results show an intriguing similarity to experiments on a range of pyrochlore oxides.

  17. Spin modes

    International Nuclear Information System (INIS)

    Gaarde, C.

    1985-01-01

    An analysis of spectra of (p,n) reactions showed that they were very selective in exciting spin modes. Charge exchange reactions at intermediate energies give important new understanding of the M1-type of excitations and of the spin structure of continuum p spectra in general. In this paper, the author discusses three charge exchange reactions: (p,n); ( 3 H,t); and (d,2p) at several targets. Low-lying states and the Δ region are discussed separately. Finally, the charge exchange reaction with heavy ion beams is briefly discussed. (G.J.P./Auth.)

  18. Relationship between energy landscape and low-temperature dynamics of ±J spin glasses

    International Nuclear Information System (INIS)

    Kobe, S.; Krawczyk, J.

    2004-01-01

    Clusters and valleys in the exact low-energy landscape of finite Edwards-Anderson ±J spin glasses are related to the distribution of spin domains and free spins in the ground states. The time evolution of the spin correlation function reflects a walk through the landscape at a given temperature and shows typical glassy behaviour

  19. Quantum mechanics/molecular mechanics simulation of the ligand vibrations of the water-oxidizing Mn4CaO5 cluster in photosystem II.

    Science.gov (United States)

    Nakamura, Shin; Noguchi, Takumi

    2016-10-11

    During photosynthesis, the light-driven oxidation of water performed by photosystem II (PSII) provides electrons necessary to fix CO 2 , in turn supporting life on Earth by liberating molecular oxygen. Recent high-resolution X-ray images of PSII show that the water-oxidizing center (WOC) is composed of an Mn 4 CaO 5 cluster with six carboxylate, one imidazole, and four water ligands. FTIR difference spectroscopy has shown significant structural changes of the WOC during the S-state cycle of water oxidation, especially within carboxylate groups. However, the roles that these carboxylate groups play in water oxidation as well as how they should be properly assigned in spectra are unresolved. In this study, we performed a normal mode analysis of the WOC using the quantum mechanics/molecular mechanics (QM/MM) method to simulate FTIR difference spectra on the S 1 to S 2 transition in the carboxylate stretching region. By evaluating WOC models with different oxidation and protonation states, we determined that models of high-oxidation states, Mn(III) 2 Mn(IV) 2 , satisfactorily reproduced experimental spectra from intact and Ca-depleted PSII compared with low-oxidation models. It is further suggested that the carboxylate groups bridging Ca and Mn ions within this center tune the reactivity of water ligands bound to Ca by shifting charge via their π conjugation.

  20. The influence of 150-cavity binders on the dynamics of influenza A neuraminidases as revealed by molecular dynamics simulations and combined clustering.

    Directory of Open Access Journals (Sweden)

    Kyle T Greenway

    Full Text Available Neuraminidase inhibitors are the main pharmaceutical agents employed for treatments of influenza infections. The neuraminidase structures typically exhibit a 150-cavity, an exposed pocket that is adjacent to the catalytic site. This site offers promising additional contact points for improving potency of existing pharmaceuticals, as well as generating entirely new candidate inhibitors. Several inhibitors based on known compounds and designed to interact with 150-cavity residues have been reported. However, the dynamics of any of these inhibitors remains unstudied and their viability remains unknown. This work reports the outcome of long-term, all-atom molecular dynamics simulations of four such inhibitors, along with three standard inhibitors for comparison. Each is studied in complex with four representative neuraminidase structures, which are also simulated in the absence of ligands for comparison, resulting in a total simulation time of 9.6 µs. Our results demonstrate that standard inhibitors characteristically reduce the mobility of these dynamic proteins, while the 150-binders do not, instead giving rise to many unique conformations. We further describe an improved RMSD-based clustering technique that isolates these conformations--the structures of which are provided to facilitate future molecular docking studies--and reveals their interdependence. We find that this approach confers many advantages over previously described techniques, and the implications for rational drug design are discussed.

  1. Joint refinement model for the spin resolved one-electron reduced density matrix of YTiO3 using magnetic structure factors and magnetic Compton profiles data.

    Science.gov (United States)

    Gueddida, Saber; Yan, Zeyin; Kibalin, Iurii; Voufack, Ariste Bolivard; Claiser, Nicolas; Souhassou, Mohamed; Lecomte, Claude; Gillon, Béatrice; Gillet, Jean-Michel

    2018-04-28

    In this paper, we propose a simple cluster model with limited basis sets to reproduce the unpaired electron distributions in a YTiO 3 ferromagnetic crystal. The spin-resolved one-electron-reduced density matrix is reconstructed simultaneously from theoretical magnetic structure factors and directional magnetic Compton profiles using our joint refinement algorithm. This algorithm is guided by the rescaling of basis functions and the adjustment of the spin population matrix. The resulting spin electron density in both position and momentum spaces from the joint refinement model is in agreement with theoretical and experimental results. Benefits brought from magnetic Compton profiles to the entire spin density matrix are illustrated. We studied the magnetic properties of the YTiO 3 crystal along the Ti-O 1 -Ti bonding. We found that the basis functions are mostly rescaled by means of magnetic Compton profiles, while the molecular occupation numbers are mainly modified by the magnetic structure factors.

  2. Spinning worlds

    NARCIS (Netherlands)

    Schwarz, H.

    2017-01-01

    The thesis "Spinning Worlds" is about the characterisation of two types of gas-giant exoplanets: Hot Jupiters, with orbital periods of fewer than five days, and young, wide-orbit gas giants, with orbital periods as long as thousands of years. The thesis is based on near-infrared observations of 1

  3. The Spin Vector of (832) Karin

    Science.gov (United States)

    Slivan, Stephen M.; Molnar, L. A.

    2010-10-01

    We observed rotation lightcurves of Koronis family and Karin cluster member (832) Karin during its four consecutive apparitions in 2006-2009, and combined the new observations with previously published lightcurves to determine its spin vector orientation and preliminary model shape. Karin is a prograde rotator with a period of 18.352 h, spin obliquity near 41°, and pole ecliptic longitude near either 51° or 228°. Although the two ambiguous pole solutions are near the clustered pole solutions of four Koronis family members whose spins are thought to be trapped in a spin-orbit resonance (Vokrouhlický et al., 2003), Karin does not seem to be trapped in the resonance; this is consistent with the expectation that the 6 My age of Karin (Nesvorný et al., 2002) is too young for YORP torques to have modified its spin since its formation. The spin vector and shape results for Karin will constrain family formation models that include spin properties, and we discuss the Karin results in the context of the other members of the Karin cluster, the Karin parent body, and the parent body's siblings in the Koronis family.

  4. Lipid-Mediated Clusters of Guest Molecules in Model Membranes and Their Dissolving in the Presence of Lipid Rafts.

    Science.gov (United States)

    Kardash, Maria E; Dzuba, Sergei A

    2017-05-25

    The clustering of molecules is an important feature of plasma membrane organization. It is challenging to develop methods for quantifying membrane heterogeneities because of their transient nature and small size. Here, we obtained evidence that transient membrane heterogeneities can be frozen at cryogenic temperatures which allows the application of solid-state experimental techniques sensitive to the nanoscale distance range. We employed the pulsed version of electron paramagnetic resonance (EPR) spectroscopy, the electron spin echo (ESE) technique, for spin-labeled molecules in multilamellar lipid bilayers. ESE decays were refined for pure contribution of spin-spin magnetic dipole-dipolar interaction between the labels; these interactions manifest themselves at a nanometer distance range. The bilayers were prepared from different types of saturated and unsaturated lipids and cholesterol (Chol); in all cases, a small amount of guest spin-labeled substances 5-doxyl-stearic-acid (5-DSA) or 3β-doxyl-5α-cholestane (DChl) was added. The local concentration found of 5-DSA and DChl molecules was remarkably higher than the mean concentration in the bilayer, evidencing the formation of lipid-mediated clusters of these molecules. To our knowledge, formation of nanoscale clusters of guest amphiphilic molecules in biological membranes is a new phenomenon suggested only recently. Two-dimensional 5-DSA molecular clusters were found, whereas flat DChl molecules were found to be clustered into stacked one-dimensional structures. These clusters disappear when the Chol content is varied between the boundaries known for lipid raft formation at room temperatures. The room temperature EPR evidenced entrapping of DChl molecules in the rafts.

  5. Energy spectra in $p$-shell $\\Lambda$ hypernuclei and $^{19}_{\\Lambda}\\textrm{F}$ and spin-dependent $\\Lambda N$ interactions

    OpenAIRE

    Kanada-En'yo, Yoshiko; Isaka, Masahiro; Motoba, Toshio

    2018-01-01

    Energy spectra of $0s$-orbit $\\Lambda$ states in $p$-shell $\\Lambda$ hypernuclei ($^{A}_\\Lambda Z$) and those in $^{19}_{\\Lambda}\\textrm{F}$ are studied with the microscopic cluster model and antisymmetrized molecular dynamics using the $G$-matrix effective $\\Lambda N$ ($\\Lambda NG$) interactions. Spin-dependent terms of the ESC08a version of the $\\Lambda NG$ interactions are tested and phenomenologically tuned to reproduce observed energy spectra in $p$-shell $^{A}_\\Lambda Z$. Spin-dependent...

  6. Cluster induced chemistry at solid surfaces: Molecular dynamics simulations of keV C60 bombardment of Si

    International Nuclear Information System (INIS)

    Krantzman, K.D.; Kingsbury, D.B.; Garrison, Barbara J.

    2007-01-01

    Molecular dynamics simulations of the sputtering of Si by keV C 60 bombardment have been performed as a function of incident kinetic energy at two incident angles, normal incidence and 45 deg. Nearly all of the C atoms remain embedded in the surface after bombardment because the C atoms from the projectile form strong covalent bonds with the Si atoms in the target. At low incident kinetic energies, the sputtering yield of Si atoms is small and there is a net deposition of solid material from the projectile atoms. As the incident kinetic energy is increased, the yield of sputtered Si atoms increases. A transition occurs in which the yield of sputtered Si atoms exceeds the number of C atoms deposited, and there is a net erosion of the solid material. A significantly higher sputter yield is observed at an incident angle of 45 deg. than at normal incidence, and therefore, the energy value is lower for the transition from net deposition to net erosion. This phenomenon is discussed in terms of the depth distribution of deposited energy, which is found to be shallower at an incident angle of 45 deg

  7. Mixed spin Ising model with four-spin interaction and random crystal field

    International Nuclear Information System (INIS)

    Benayad, N.; Ghliyem, M.

    2012-01-01

    The effects of fluctuations of the crystal field on the phase diagram of the mixed spin-1/2 and spin-1 Ising model with four-spin interactions are investigated within the finite cluster approximation based on a single-site cluster theory. The state equations are derived for the two-dimensional square lattice. It has been found that the system exhibits a variety of interesting features resulting from the fluctuation of the crystal field interactions. In particular, for low mean value D of the crystal field, the critical temperature is not very sensitive to fluctuations and all transitions are of second order for any value of the four-spin interactions. But for relatively high D, the transition temperature depends on the fluctuation of the crystal field, and the system undergoes tricritical behaviour for any strength of the four-spin interactions. We have also found that the model may exhibit reentrance for appropriate values of the system parameters.

  8. Spin tunnelling in mesoscopic systems

    Indian Academy of Sciences (India)

    We study spin tunnelling in molecular magnets as an instance of a mesoscopic phenomenon, with special emphasis on the molecule Fe8. We show that the tunnel splitting between various pairs of Zeeman levels in this molecule oscillates as a function of applied magnetic field, vanishing completely at special points in the ...

  9. STM observations of ferromagnetic clusters

    International Nuclear Information System (INIS)

    Wawro, A.; Kasuya, A.

    1998-01-01

    Co, Fe and Ni clusters of nanometer size, deposited on silicon and graphite (highly oriented pyrolytic graphite), were observed by a scanning tunneling microscope. Deposition as well as the scanning tunneling microscope measurements were carried out in an ultrahigh vacuum system at room temperature. Detailed analysis of Co cluster height was done with the scanning tunneling microscope equipped with a ferromagnetic tip in a magnetic field up to 70 Oe. It is found that bigger clusters (few nanometers in height) exhibit a dependence of their apparent height on applied magnetic field. We propose that such behaviour originates from the ferromagnetic ordering of cluster and associate this effect to spin polarized tunneling. (author)

  10. Nuclear cluster states

    International Nuclear Information System (INIS)

    Rae, W.D.M.; Merchant, A.C.

    1993-01-01

    We review clustering in light nuclei including molecular resonances in heavy ion reactions. In particular we study the systematics, paying special attention to the relationships between cluster states and superdeformed configurations. We emphasise the selection rules which govern the formation and decay of cluster states. We review some recent experimental results from Daresbury and elsewhere. In particular we report on the evidence for a 7-α chain state in 28 Si in experiments recently performed at the NSF, Daresbury. Finally we begin to address theoretically the important question of the lifetimes of cluster states as deduced from the experimental energy widths of the resonances. (Author)

  11. Universal Mechanism of Spin Relaxation in Solids

    Science.gov (United States)

    Chudnovsky, Eugene

    2006-03-01

    Conventional elastic theory ignores internal local twists and torques. Meantime, spin-lattice relaxation is inherently coupled with local elastic twists through conservation of the total angular momentum (spin + lattice). This coupling gives universal lower bound (free of fitting parameters) on the relaxation of the atomic or molecular spin in a solid [1] and on the relaxation of the electron spin in a quantum dot [2]. [1] E. M. Chudnovsky, D. A. Garanin, and R. Schilling, Phys. Rev. B 72, 094426 (2005). [2] C. Calero, E. M. Chudnovsky, and D. A. Garanin, Phys. Rev. Lett. 95, 166603 (2005).

  12. PREFACE: Nuclear Cluster Conference; Cluster'07

    Science.gov (United States)

    Freer, Martin

    2008-05-01

    The Cluster Conference is a long-running conference series dating back to the 1960's, the first being initiated by Wildermuth in Bochum, Germany, in 1969. The most recent meeting was held in Nara, Japan, in 2003, and in 2007 the 9th Cluster Conference was held in Stratford-upon-Avon, UK. As the name suggests the town of Stratford lies upon the River Avon, and shortly before the conference, due to unprecedented rainfall in the area (approximately 10 cm within half a day), lay in the River Avon! Stratford is the birthplace of the `Bard of Avon' William Shakespeare, and this formed an intriguing conference backdrop. The meeting was attended by some 90 delegates and the programme contained 65 70 oral presentations, and was opened by a historical perspective presented by Professor Brink (Oxford) and closed by Professor Horiuchi (RCNP) with an overview of the conference and future perspectives. In between, the conference covered aspects of clustering in exotic nuclei (both neutron and proton-rich), molecular structures in which valence neutrons are exchanged between cluster cores, condensates in nuclei, neutron-clusters, superheavy nuclei, clusters in nuclear astrophysical processes and exotic cluster decays such as 2p and ternary cluster decay. The field of nuclear clustering has become strongly influenced by the physics of radioactive beam facilities (reflected in the programme), and by the excitement that clustering may have an important impact on the structure of nuclei at the neutron drip-line. It was clear that since Nara the field had progressed substantially and that new themes had emerged and others had crystallized. Two particular topics resonated strongly condensates and nuclear molecules. These topics are thus likely to be central in the next cluster conference which will be held in 2011 in the Hungarian city of Debrechen. Martin Freer Participants and Cluster'07

  13. Electron localization in water clusters

    International Nuclear Information System (INIS)

    Landman, U.; Barnett, R.N.; Cleveland, C.L.; Jortner, J.

    1987-01-01

    Electron attachment to water clusters was explored by the quantum path integral molecular dynamics method, demonstrating that the energetically favored localization mode involves a surface state of the excess electron, rather than the precursor of the hydrated electron. The cluster size dependence, the energetics and the charge distribution of these novel electron-cluster surface states are explored. 20 refs., 2 figs., 1 tab

  14. Spin Coherence in Semiconductor Nanostructures

    National Research Council Canada - National Science Library

    Flatte, Michael E

    2006-01-01

    ... dots, tuning of spin coherence times for electron spin, tuning of dipolar magnetic fields for nuclear spin, spontaneous spin polarization generation and new designs for spin-based teleportation and spin transistors...

  15. Structures, energetics, vibrational spectra of NH4+ (H2O)(n=4,6) clusters: Ab initio calculations and first principles molecular dynamics simulations.

    Science.gov (United States)

    Karthikeyan, S; Singh, Jiten N; Park, Mina; Kumar, Rajesh; Kim, Kwang S

    2008-06-28

    Important structural isomers of NH(4) (+)(H(2)O)(n=4,6) have been studied by using density functional theory, Moller-Plesset second order perturbation theory, and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The zero-point energy (ZPE) correction to the complete basis set limit of the CCSD(T) binding energies and free energies is necessary to identify the low energy structures for NH(4) (+)(H(2)O)(n=4,6) because otherwise wrong structures could be assigned for the most probable structures. For NH(4) (+)(H(2)O)(6), the cage-type structure, which is more stable than the previously reported open structure before the ZPE correction, turns out to be less stable after the ZPE correction. In first principles Car-Parrinello molecular dynamics simulations around 100 K, the combined power spectrum of three lowest energy isomers of NH(4) (+)(H(2)O)(4) and two lowest energy isomers of NH(4) (+)(H(2)O)(6) explains each experimental IR spectrum.

  16. TreeCluster: Massively scalable transmission clustering using phylogenetic trees

    OpenAIRE

    Moshiri, Alexander

    2018-01-01

    Background: The ability to infer transmission clusters from molecular data is critical to designing and evaluating viral control strategies. Viral sequencing datasets are growing rapidly, but standard methods of transmission cluster inference do not scale well beyond thousands of sequences. Results: I present TreeCluster, a cross-platform tool that performs transmission cluster inference on a given phylogenetic tree orders of magnitude faster than existing inference methods and supports multi...

  17. Clusters in nuclei. Vol. 1

    International Nuclear Information System (INIS)

    Beck, Christian

    2010-01-01

    Following the pioneering discovery of alpha clustering and of molecular resonances, the field of nuclear clustering is presently one of the domains of heavy-ion nuclear physics facing both the greatest challenges and opportunities. After many summer schools and workshops, in particular over the last decade, the community of nuclear molecular physics decided to team up in producing a comprehensive collection of lectures and tutorial reviews covering the field. This first volume, gathering seven extensive lectures, covers the follow topics: - Cluster Radioactivity - Cluster States and Mean Field Theories - Alpha Clustering and Alpha Condensates - Clustering in Neutron-rich Nuclei - Di-neutron Clustering - Collective Clusterization in Nuclei - Giant Nuclear Molecules By promoting new ideas and developments while retaining a pedagogical nature of presentation throughout, these lectures will both serve as a reference and as advanced teaching material for future courses and schools in the fields of nuclear physics and nuclear astrophysics. (orig.)

  18. Algorithm for the generation of nuclear spin species and nuclear spin statistical weights

    International Nuclear Information System (INIS)

    Balasubramanian, K.

    1982-01-01

    A set of algorithms for the computer generation of nuclear spin species and nuclear spin statistical weights potentially useful in molecular spectroscopy is developed. These algorithms generate the nuclear spin species from group structures known as generalized character cycle indices (GCCIs). Thus the required input for these algorithms is just the set of all GCCIs for the symmetry group of the molecule which can be computed easily from the character table. The algorithms are executed and illustrated with examples

  19. Inverse spin-valve effect in nanoscale Si-based spin-valve devices

    Science.gov (United States)

    Hiep, Duong Dinh; Tanaka, Masaaki; Hai, Pham Nam

    2017-12-01

    We investigated the spin-valve effect in nano-scale silicon (Si)-based spin-valve devices using a Fe/MgO/Ge spin injector/detector deposited on Si by molecular beam epitaxy. For a device with a 20 nm Si channel, we observed clear magnetoresistance up to 3% at low temperature when a magnetic field was applied in the film plane along the Si channel transport direction. A large spin-dependent output voltage of 20 mV was observed at a bias voltage of 0.9 V at 15 K, which is among the highest values in lateral spin-valve devices reported so far. Furthermore, we observed that the sign of the spin-valve effect is reversed at low temperatures, suggesting the possibility of a spin-blockade effect of defect states in the MgO/Ge tunneling barrier.

  20. High spin-filter efficiency and Seebeck effect through spin-crossover iron–benzene complex

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Qiang; Zhou, Liping, E-mail: zhoulp@suda.edu.cn; Cheng, Jue-Fei; Wen, Zhongqian; Han, Qin; Wang, Xue-Feng [College of Physics, Optoelectronics and Energy and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215006 (China)

    2016-04-21

    Electronic structures and coherent quantum transport properties are explored for spin-crossover molecule iron-benzene Fe(Bz){sub 2} using density functional theory combined with non-equilibrium Green’s function. High- and low-spin states are investigated for two different lead-molecule junctions. It is found that the asymmetrical T-shaped contact junction in the high-spin state behaves as an efficient spin filter while it has a smaller conductivity than that in the low-spin state. Large spin Seebeck effect is also observed in asymmetrical T-shaped junction. Spin-polarized properties are absent in the symmetrical H-shaped junction. These findings strongly suggest that both the electronic and contact configurations play significant roles in molecular devices and metal-benzene complexes are promising materials for spintronics and thermo-spintronics.

  1. Spin crossover and high spin filtering behavior in Co-Pyridine and Co-Pyrimidine molecules

    Science.gov (United States)

    Wen, Zhongqian; Zhou, Liping; Cheng, Jue-Fei; Li, Shu-Jin; You, Wen-Long; Wang, Xuefeng

    2018-03-01

    We present a theoretical study on a series of cobalt complexes, which are constructed with cobalt atoms and pyridine/pyrimidine rings, using density functional theory. We investigate the structural and electric transport properties of spin crossover (SCO) Co complex with two spin states, namely low-spin configuration [LS] and high-spin configuration [HS]. Energy analyses of the two spin states imply that the SCO Co-Pyridine2 and Co-Pyrimidine2 complexes may display a spin transition process accompanied by a geometric modification driven by external stimuli. A nearly perfect spin filtering effect is observed in the Co-Pyrimidine2 complex with [HS] state. In addition, we also discover the contact-dependent transmission properties of Co-Pyridine2. These findings indicate that SCO Co complexes are promising materials for molecular spintronic devices.

  2. CO dissociation on magnetic Fen clusters

    KAUST Repository

    Jedidi, Abdesslem

    2014-01-01

    This work theoretically investigates the CO dissociation on Fen nanoparticles, for n in the range of 1-65, focusing on size dependence in the context of the initial step of the Fischer-Tropsch reaction. CO adsorbs molecularly through its C-end on a triangular facet of the nanoparticle. Dissociation becomes easier when the cluster size increases. Then, the C atom is bonded to a square facet that is generated as a result of the adsorption if it does not yet exist in the bare cluster, while the O atom is adsorbed on a triangular facet. In the most stable situation, the two adsorbed atoms remain close together, both having in common one shared first-neighbor iron atom. There is a partial spin quenching of the neighboring Fe atoms, which become more positively charged than the other Fe atoms. The shared surface iron atom resembles a metal-cation from a complex. Despite the small size of the iron cluster considered, fluctuations due to specific configurations do not influence properties for n > 25 and global trends seem significant.

  3. Large resistance change on magnetic tunnel junction based molecular spintronics devices

    Science.gov (United States)

    Tyagi, Pawan; Friebe, Edward

    2018-05-01

    Molecular bridges covalently bonded to two ferromagnetic electrodes can transform ferromagnetic materials and produce intriguing spin transport characteristics. This paper discusses the impact of molecule induced strong coupling on the spin transport. To study molecular coupling effect the octametallic molecular cluster (OMC) was bridged between two ferromagnetic electrodes of a magnetic tunnel junction (Ta/Co/NiFe/AlOx/NiFe/Ta) along the exposed side edges. OMCs induced strong inter-ferromagnetic electrode coupling to yield drastic changes in transport properties of the magnetic tunnel junction testbed at the room temperature. These OMCs also transformed the magnetic properties of magnetic tunnel junctions. SQUID and ferromagnetic resonance studies provided insightful data to explain transport studies on the magnetic tunnel junction based molecular spintronics devices.

  4. Spin tunnelling in mesoscopic systems

    Science.gov (United States)

    Garg, Anupam

    2001-02-01

    We study spin tunnelling in molecular magnets as an instance of a mesoscopic phenomenon, with special emphasis on the molecule Fe8. We show that the tunnel splitting between various pairs of Zeeman levels in this molecule oscillates as a function of applied magnetic field, vanishing completely at special points in the space of magnetic fields, known as diabolical points. This phenomena is explained in terms of two approaches, one based on spin-coherent-state path integrals, and the other on a generalization of the phase integral (or WKB) method to difference equations. Explicit formulas for the diabolical points are obtained for a model Hamiltonian.

  5. Fractional Spin Fluctuations as a Precursor of Quantum Spin Liquids: Majorana Dynamical Mean-Field Study for the Kitaev Model.

    Science.gov (United States)

    Yoshitake, Junki; Nasu, Joji; Motome, Yukitoshi

    2016-10-07

    Experimental identification of quantum spin liquids remains a challenge, as the pristine nature is to be seen in asymptotically low temperatures. We here theoretically show that the precursor of quantum spin liquids appears in the spin dynamics in the paramagnetic state over a wide temperature range. Using the cluster dynamical mean-field theory and the continuous-time quantum Monte Carlo method, which are newly developed in the Majorana fermion representation, we calculate the dynamical spin structure factor, relaxation rate in nuclear magnetic resonance, and magnetic susceptibility for the honeycomb Kitaev model whose ground state is a canonical example of the quantum spin liquid. We find that dynamical spin correlations show peculiar temperature and frequency dependence even below the temperature where static correlations saturate. The results provide the experimentally accessible symptoms of the fluctuating fractionalized spins evincing the quantum spin liquids.

  6. Cluster headache

    Science.gov (United States)

    Histamine headache; Headache - histamine; Migrainous neuralgia; Headache - cluster; Horton's headache; Vascular headache - cluster ... Doctors do not know exactly what causes cluster headaches. They ... (chemical in the body released during an allergic response) or ...

  7. Spin glasses

    International Nuclear Information System (INIS)

    Mookerjee, Abhijit

    1976-01-01

    ''Spin glasses'', are entire class of magnetic alloys of moderate dilution, in which the magnetic atoms are far enough apart to be unlike the pure metal, but close enough so that the indirect exchange energy between them (mediated by the s-d interaction between local moments and conduction electrons) dominates all other energies. Characteristic critical phenomena displayed such as freezing of spin orientation at 'Tsub(c)' and spreading of magnetic ordering, are pointed out. Anomalous behaviour, associated with these critical phenomena, as reflected in : (i) Moessbauer spectroscopy giving hyperfine splitting at Tsub(c), (ii) maxima in susceptibility and remanent magnetism, (iii) thermopower maxima and change in slope, (iv) Characteristic cusp in susceptibility and its removal by very small magnetic fields, and (v) conductivity-resistivity measurements, are discussed. Theoretical developments aimed at explaining these phenomena, in particular, the ideas from percolation and localisation theories, and the approach based on the gellations of polymers, are discussed. Finally, a new approach based on renormalisation group in disordered systems is also briefly mentioned. (K.B.)

  8. General active space commutator-based coupled cluster theory of general excitation rank for electronically excited states: implementation and application to ScH.

    Science.gov (United States)

    Hubert, Mickaël; Olsen, Jeppe; Loras, Jessica; Fleig, Timo

    2013-11-21

    We present a new implementation of general excitation rank coupled cluster theory for electronically excited states based on the single-reference multi-reference formalism. The method may include active-space selected and/or general higher excitations by means of the general active space concept. It may employ molecular integrals over the four-component Lévy-Leblond Hamiltonian or the relativistic spin-orbit-free four-component Hamiltonian of Dyall. In an initial application to ground- and excited states of the scandium monohydride molecule we report spectroscopic constants using basis sets of up to quadruple-zeta quality and up to full iterative triple excitations in the cluster operators. Effects due to spin-orbit interaction are evaluated using two-component multi-reference configuration interaction for assessing the accuracy of the coupled cluster results.

  9. Heat and spin interconversion

    International Nuclear Information System (INIS)

    Ohnuma, Yuichi; Matsuo, Mamoru; Maekawa, Sadamichi; Saitoh, Eeiji

    2017-01-01

    Spin Seebeck and spin Peltier effects, which are mutual conversion phenomena of heat and spin, are discussed on the basis of the microscopic theory. First, the spin Seebeck effect, which is the spin-current generation due to heat current, is discussed. The recent progress in research on the spin Seebeck effect are introduced. We explain the origin of the observed sign changes of the spin Seebeck effect in compensated ferromagnets. Next, the spin Peltier effect, which is the heat-current generation due to spin current, is discussed. Finally, we show that the spin Seebeck and spin Peltier effects are summarized by Onsager's reciprocal relation and derive Kelvin's relation for the spin and heat transports. (author)

  10. Entangled spins and ghost-spins

    Directory of Open Access Journals (Sweden)

    Dileep P. Jatkar

    2017-09-01

    Full Text Available We study patterns of quantum entanglement in systems of spins and ghost-spins regarding them as simple quantum mechanical toy models for theories containing negative norm states. We define a single ghost-spin as in [20] as a 2-state spin variable with an indefinite inner product in the state space. We find that whenever the spin sector is disentangled from the ghost-spin sector (both of which could be entangled within themselves, the reduced density matrix obtained by tracing over all the ghost-spins gives rise to positive entanglement entropy for positive norm states, while negative norm states have an entanglement entropy with a negative real part and a constant imaginary part. However when the spins are entangled with the ghost-spins, there are new entanglement patterns in general. For systems where the number of ghost-spins is even, it is possible to find subsectors of the Hilbert space where positive norm states always lead to positive entanglement entropy after tracing over the ghost-spins. With an odd number of ghost-spins however, we find that there always exist positive norm states with negative real part for entanglement entropy after tracing over the ghost-spins.

  11. From collisions to clusters

    DEFF Research Database (Denmark)

    Loukonen, Ville; Bork, Nicolai; Vehkamaki, Hanna

    2014-01-01

    -principles molecular dynamics collision simulations of (sulphuric acid)1(water)0, 1 + (dimethylamine) → (sulphuric acid)1(dimethylamine)1(water)0, 1 cluster formation processes. The simulations indicate that the sticking factor in the collisions is unity: the interaction between the molecules is strong enough...... control. As a consequence, the clusters show very dynamic ion pair structure, which differs from both the static structure optimisation calculations and the equilibrium first-principles molecular dynamics simulations. In some of the simulation runs, water mediates the proton transfer by acting as a proton...... to overcome the possible initial non-optimal collision orientations. No post-collisional cluster break up is observed. The reasons for the efficient clustering are (i) the proton transfer reaction which takes place in each of the collision simulations and (ii) the subsequent competition over the proton...

  12. Spin transport in nanowires

    OpenAIRE

    Pramanik, S.; bandyopadhyay, S.; Cahay, M.

    2003-01-01

    We study high-field spin transport of electrons in a quasi one-dimensional channel of a $GaAs$ gate controlled spin interferometer (SPINFET) using a semiclassical formalism (spin density matrix evolution coupled with Boltzmann transport equation). Spin dephasing (or depolarization) is predominantly caused by D'yakonov-Perel' relaxation associated with momentum dependent spin orbit coupling effects that arise due to bulk inversion asymmetry (Dresselhaus spin orbit coupling) and structural inve...

  13. Spin vectors in the Koronis family: III. (832) Karin

    Science.gov (United States)

    Slivan, Stephen M.; Molnar, Lawrence A.

    2012-08-01

    Studies of asteroid families constrain models of asteroid collisions and evolution processes, and the Karin cluster within the Koronis family is among the youngest families known (Nesvorný, D., Bottke, Jr., W.F., Dones, L., Levison, H.F. [2002]. Nature 417, 720-722). (832) Karin itself is by far the largest member of the Karin cluster, thus knowledge of Karin's spin vector is important to constrain family formation and evolution models that include spin, and to test whether its spin properties are consistent with the Karin cluster being a very young family. We observed rotation lightcurves of Karin during its four consecutive apparitions in 2006-2009, and combined the new observations with previously published lightcurves to determine its spin vector orientation and preliminary model shape. Karin is a prograde rotator with a period of (18.352 ± 0.003) h, spin obliquity near (42 ± 5)°, and pole ecliptic longitude near either (52 ± 5)° or (230 ± 5)°. The spin vector and shape results for Karin will constrain models of family formation that include spin properties; in the meantime we briefly discuss Karin's own spin in the context of those of other members of the Karin cluster and the parent body's siblings in the Koronis family.

  14. Thermodynamics of Rh nuclear spins calculated by exact diagonalization

    DEFF Research Database (Denmark)

    Lefmann, K.; Ipsen, J.; Rasmussen, F.B.

    2000-01-01

    We have employed the method of exact diagonalization to obtain the full-energy spectrum of a cluster of 16 Rh nuclear spins, having dipolar and RK interactions between first and second nearest neighbours only. We have used this to calculate the nuclear spin entropy, and our results at both positi...

  15. Magnetic Nanostructures Spin Dynamics and Spin Transport

    CERN Document Server

    Farle, Michael

    2013-01-01

    Nanomagnetism and spintronics is a rapidly expanding and increasingly important field of research with many applications already on the market and many more to be expected in the near future. This field started in the mid-1980s with the discovery of the GMR effect, recently awarded with the Nobel prize to Albert Fert and Peter Grünberg. The present volume covers the most important and most timely aspects of magnetic heterostructures, including spin torque effects, spin injection, spin transport, spin fluctuations, proximity effects, and electrical control of spin valves. The chapters are written by internationally recognized experts in their respective fields and provide an overview of the latest status.

  16. Weighted Clustering

    DEFF Research Database (Denmark)

    Ackerman, Margareta; Ben-David, Shai; Branzei, Simina

    2012-01-01

    We investigate a natural generalization of the classical clustering problem, considering clustering tasks in which different instances may have different weights.We conduct the first extensive theoretical analysis on the influence of weighted data on standard clustering algorithms in both...... the partitional and hierarchical settings, characterizing the conditions under which algorithms react to weights. Extending a recent framework for clustering algorithm selection, we propose intuitive properties that would allow users to choose between clustering algorithms in the weighted setting and classify...

  17. On clusters and clustering from atoms to fractals

    CERN Document Server

    Reynolds, PJ

    1993-01-01

    This book attempts to answer why there is so much interest in clusters. Clusters occur on all length scales, and as a result occur in a variety of fields. Clusters are interesting scientifically, but they also have important consequences technologically. The division of the book into three parts roughly separates the field into small, intermediate, and large-scale clusters. Small clusters are the regime of atomic and molecular physics and chemistry. The intermediate regime is the transitional regime, with its characteristics including the onset of bulk-like behavior, growth and aggregation, a

  18. Spin dynamics in mesoscopic size magnetic systems: A 1HNMR study in rings of iron (III) ions

    International Nuclear Information System (INIS)

    Lascialfari, A.; Gatteschi, D.; Borsa, F.; Cornia, A.

    1997-01-01

    Two magnetic molecular clusters containing almost coplanar rings of iron (III) ions with spinS=5/2 have been investigated by 1 H NMR and relaxation measurements. The first system, which will be referred to as Fe6, is a molecule of general formula [NaFe 6 (OCH 3 ) 12 (C 17 O 4 H 15 ) 6 ] + ClO 4 - or [NaFe 6 (OCH 3 ) 12 (C 15 H 11 O 2 ) 6 ] + ClO 4 - or [LiFe 6 (OCH 3 ) 12 (C 15 H 11 O 2 ) 6 ] + ClO 4 - while the second type of ring, denoted Fe10, corresponds to the molecule [Fe 10 (OCH 3 ) 20 (C 2 H 2 O 2 Cl) 10 ]. The 1 H NMR linewidth is broadened by the nuclear dipolar interaction and by the dipolar coupling of the protons with the iron (III) paramagnetic moment. It is found that the nuclear spin-lattice relaxation rate, T 1 -1 , of the proton is a sensitive probe of the Fe spin dynamics. In both clusters, T 1 -1 decreases with decreasing temperatures from room temperature, goes through a peak just below about 30 K in Fe6 and 10 K in Fe10, and it drops exponentially to very small values at helium temperature. The temperature dependence of the relaxation rate is discussed in terms of the fluctuations of the local spins within the allowed total spin configurations in the framework of the weak collision theory to describe the nuclear relaxation. We use the calculated energy levels for the Fe6 ring based on a Heisenberg Hamiltonian and the value of J obtained from the fit of the magnetic susceptibility to describe semiquantitatively the behavior of T 1 -1 vs T. The exponential drop of T 1 -1 at low temperature is consistent with a nonmagnetic singlet ground state separated by an energy gap from the first excited triplet state. (Abstract Truncated)

  19. Spin-Dependent Transport through Chiral Molecules Studied by Spin-Dependent Electrochemistry

    Science.gov (United States)

    2016-01-01

    Conspectus Molecular spintronics (spin + electronics), which aims to exploit both the spin degree of freedom and the electron charge in molecular devices, has recently received massive attention. Our recent experiments on molecular spintronics employ chiral molecules which have the unexpected property of acting as spin filters, by way of an effect we call “chiral-induced spin selectivity” (CISS). In this Account, we discuss new types of spin-dependent electrochemistry measurements and their use to probe the spin-dependent charge transport properties of nonmagnetic chiral conductive polymers and biomolecules, such as oligopeptides, L/D cysteine, cytochrome c, bacteriorhodopsin (bR), and oligopeptide-CdSe nanoparticles (NPs) hybrid structures. Spin-dependent electrochemical measurements were carried out by employing ferromagnetic electrodes modified with chiral molecules used as the working electrode. Redox probes were used either in solution or when directly attached to the ferromagnetic electrodes. During the electrochemical measurements, the ferromagnetic electrode was magnetized either with its magnetic moment pointing “UP” or “DOWN” using a permanent magnet (H = 0.5 T), placed underneath the chemically modified ferromagnetic electrodes. The spin polarization of the current was found to be in the range of 5–30%, even in the case of small chiral molecules. Chiral films of the l- and d-cysteine tethered with a redox-active dye, toludin blue O, show spin polarizarion that depends on the chirality. Because the nickel electrodes are susceptible to corrosion, we explored the effect of coating them with a thin gold overlayer. The effect of the gold layer on the spin polarization of the electrons ejected from the electrode was investigated. In addition, the role of the structure of the protein on the spin selective transport was also studied as a function of bias voltage and the effect of protein denaturation was revealed. In addition to

  20. Magnetic properties of a quantum transverse spin-1 Blume-Emery-Griffiths model

    Intern