A Kirkwood-Buff derived force field for alkaline earth halide salts.

PubMed

Naleem, Nawavi; Bentenitis, Nikolaos; Smith, Paul E

2018-06-14

The activity and function of many macromolecules in cellular environments are coupled with the binding of divalent ions such as calcium or magnesium. In principle, computer simulations can be used to understand the molecular level aspects of how many important macromolecules interact with ions. However, most of the force fields currently available often fail to accurately reproduce the properties of divalent ions in aqueous environments. Here we develop classical non-polarizable force fields for the aqueous alkaline earth metal halides (MX 2 ), where M = Mg 2+ , Ca 2+ , Sr 2+ , Ba 2+ and X = Cl - , Br - , I - , which can be used in bimolecular simulations and which are compatible with the Simple Point Charge/Extended (SPC/E) water model. The force field parameters are specifically developed to reproduce the experimental Kirkwood-Buff integrals for aqueous solutions and thereby the experimental activity derivatives, partial molar volumes, and excess coordination numbers. This ensures that a reasonable balance between ion-ion, ion-water, and water-water distributions is obtained. However, this requires a scaling of the cation to water oxygen interaction strength in order to accurately reproduce the integrals. The scaling factors developed for chloride salts are successfully transferable to the bromide and iodide salts. Use of these new models leads to reasonable diffusion constants and dielectric decrements. However, the performance of the models decreases with increasing salt concentration (>4m), and simulations of the pure crystals exhibited unstable behavior.

Physical Processes in the Heliospheric Interface Region and their Implications for ENA Images

NASA Astrophysics Data System (ADS)

Gruntman, M.; Roelof, E. C.; McComas, D. J.; Funsten, H. O.; Krimigis, S. M.; Mitchell, D. G.

2009-12-01

The recent in situ measurements of particles and fields by Voyager 1 and 2 spacecraft and global heliospheric maps in fluxes of energetic neutral atoms (ENAs) obtained by IBEX and Cassini/INCA have challenged our established concepts of the heliosphere interaction with the surrounding local interstellar medium. We review the physics of the interaction in an attempt to identify most important processes determining the dynamics and properties of the heliospheric sheath region. The non-thermal ion component and interstellar magnetic field clearly play significant roles in the interaction, as well as the flow of the warm interstellar plasma. We stress here that the basic conservation laws for energetic ions and neutrals constrain the processes that must be included in any valid formulation of particle transport. The termination shock can be viewed as a continuous source of energetic ions that are transported throughout the inner heliosheath, through the heliopause, and outward through the outer heliosheath and into the local interstellar medium. ENA images integrate the ENA production by energetic ions along lines of sight (LOS) that extend in principle to infinity, and hence are quite sensitive to the way that energetic ions and ENAs eventually escape this huge (~1000AU) system. Non-thermal ion and ENA space densities can be changed by three mechanisms: spatial transport (which by itself only rearranges the numbers of energetic ions and ENAs), energy gain and loss of ions in electric field, and elastic and inelastic collisions. Thus, only if these mechanisms are properly included in computational models can the salient features observed ENA images be replicated by the model simulations.

Abrasion-ablation model for neutron production in heavy ion reactions

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Wilson, John W.; Townsend, Lawrence W.

1995-01-01

In heavy ion reactions, neutron production at forward angles is observed to occur with a Gaussian shape that is centered near the beam energy and extends to energies well above that of the beam. This paper presents an abrasion-ablation model for making quantitative predictions of the neutron spectrum. To describe neutrons produced from the abrasion step of the reaction where the projectile and target overlap, the authors use the Glauber model and include effects of final-state interactions. They then use the prefragment mass distribution from abrasion with a statistical evaporation model to estimate the neutron spectrum resulting from ablation. Measurements of neutron production from Ne and Nb beams are compared with calculations, and good agreement is found.

Quantum simulations of the Ising model with trapped ions: Devil's staircase and arbitrary lattice proposal

NASA Astrophysics Data System (ADS)

Korenblit, Simcha

A collection of trapped atomic ions represents one of the most attractive platforms for the quantum simulation of interacting spin networks and quantum magnetism. Spin-dependent optical dipole forces applied to an ion crystal create long-range effective spin-spin interactions and allow the simulation of spin Hamiltonians that possess nontrivial phases and dynamics. We trap linear chains of 171Yb+ ions in a Paul trap, and constrain the occupation of energy levels to the ground hyperne clock-states, creating a qubit or pseudo-spin 1/2 system. We proceed to implement spin-spin couplings between two ions using the far detuned Molmer-Sorenson scheme and perform adiabatic quantum simulations of Ising Hamiltonians with long-range couplings. We then demonstrate our ability to control the sign and relative strength of the interaction between three ions. Using this control, we simulate a frustrated triangular lattice, and for the first time establish an experimental connection between frustration and quantum entanglement. We then scale up our simulation to show phase transitions from paramagnetism to ferromagnetism for nine ions, and to anti-ferromagnetism for sixteen ions. The experimental work culminates with our most complicated Hamiltonian---a long range anti-ferromagnetic Ising interaction between 10 ions with a biasing axial field. Theoretical work presented in this thesis shows how the approach to quantum simulation utilized in this thesis can be further extended and improved. It is shown how appropriate design of laser fields can provide for arbitrary multidimensional spin-spin interaction graphs even for the case of a linear spatial array of ions. This scheme uses currently existing trap technology and is scalable to levels where classical methods of simulation are intractable.

Parameter-Space Survey of Linear G-mode and Interchange in Extended Magnetohydrodynamics

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

Howell, E. C.; Sovinec, C. R.

The extended magnetohydrodynamic stability of interchange modes is studied in two configurations. In slab geometry, a local dispersion relation for the gravitational interchange mode (g-mode) with three different extensions of the MHD model [P. Zhu, et al., Phys. Rev. Lett. 101, 085005 (2008)] is analyzed. Our results delineate where drifts stablize the g-mode with gyroviscosity alone and with a two-fluid Ohm’s law alone. Including the two-fluid Ohm’s law produces an ion drift wave that interacts with the g-mode. This interaction then gives rise to a second instability at finite k y. A second instability is also observed in numerical extended MHD computations of linear interchange in cylindrical screw-pinch equilibria, the second configuration. Particularly with incomplete models, this mode limits the regions of stability for physically realistic conditions. But, applying a consistent two-temperature extended MHD model that includes the diamagnetic heat flux density (more » $$\\vec{q}$$ *) makes the onset of the second mode occur at larger Hall parameter. For conditions relevant to the SSPX experiment [E.B. Hooper, Plasma Phys. Controlled Fusion 54, 113001 (2012)], significant stabilization is observed for Suydam parameters as large as unity (D s≲1).« less

Parameter-Space Survey of Linear G-mode and Interchange in Extended Magnetohydrodynamics

DOE PAGES

Howell, E. C.; Sovinec, C. R.

2017-09-11

The extended magnetohydrodynamic stability of interchange modes is studied in two configurations. In slab geometry, a local dispersion relation for the gravitational interchange mode (g-mode) with three different extensions of the MHD model [P. Zhu, et al., Phys. Rev. Lett. 101, 085005 (2008)] is analyzed. Our results delineate where drifts stablize the g-mode with gyroviscosity alone and with a two-fluid Ohm’s law alone. Including the two-fluid Ohm’s law produces an ion drift wave that interacts with the g-mode. This interaction then gives rise to a second instability at finite k y. A second instability is also observed in numerical extended MHD computations of linear interchange in cylindrical screw-pinch equilibria, the second configuration. Particularly with incomplete models, this mode limits the regions of stability for physically realistic conditions. But, applying a consistent two-temperature extended MHD model that includes the diamagnetic heat flux density (more » $$\\vec{q}$$ *) makes the onset of the second mode occur at larger Hall parameter. For conditions relevant to the SSPX experiment [E.B. Hooper, Plasma Phys. Controlled Fusion 54, 113001 (2012)], significant stabilization is observed for Suydam parameters as large as unity (D s≲1).« less

Comparing the Atmospheric Losses at Io and Europa

NASA Astrophysics Data System (ADS)

Dols, V. J.; Bagenal, F.; Crary, F. J.; Cassidy, T.

2017-12-01

At Io and Europa, the interaction of the Jovian plasma with the moon atmosphere leads to a significant loss of atomic/molecular neutrals and ions to space. The processes that lead to atmospheric escape are diverse: atmospheric sputtering, molecular dissociation, molecular ion recombination, Jeans escape etc. Each process leads to neutrals escaping at different velocities (i.e. electron impact dissociation leads to very slow atomic neutrals, sputtering might eject faster molecular neutrals). Some neutrals will be ejected out of the Jovian system; others will form extended neutral clouds along the orbit of the moons. These atomic/molecular extended neutral clouds are probably the main source of plasma for the Jovian magnetosphere. They are difficult to observe directly thus their composition and density are still poorly constrained. A future modeling of the formation of these extended clouds requires an estimate of their atmospheric sources. We estimate the atmospheric losses at Io and Europa for each loss process with a multi-species chemistry model, using a prescribed atmospheric distribution consistent with the observations. We compare the neutral losses at Io and Europa.

Cation–Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

PubMed Central

Gebala, Magdalena; Giambasu, George M.; Lipfert, Jan; Bisaria, Namita; Bonilla, Steve; Li, Guangchao; York, Darrin M.; Herschlag, Daniel

2016-01-01

The ion atmosphere is a critical structural, dynamic, and energetic component of nucleic acids that profoundly affects their interactions with proteins and ligands. Experimental methods that “count” the number of ions thermodynamically associated with the ion atmosphere allow dissection of energetic properties of the ion atmosphere, and thus provide direct comparison to theoretical results. Previous experiments have focused primarily on the cations that are attracted to nucleic acid polyanions, but have also showed that anions are excluded from the ion atmosphere. Herein, we have systematically explored the properties of anion exclusion, testing the zeroth-order model that anions of different identity are equally excluded due to electrostatic repulsion. Using a series of monovalent salts, we find, surprisingly, that the extent of anion exclusion and cation inclusion significantly depends on salt identity. The differences are prominent at higher concentrations and mirror trends in mean activity coefficients of the electrolyte solutions. Salts with lower activity coefficients exhibit greater accumulation of both cations and anions within the ion atmosphere, strongly suggesting that cation–anion correlation effects are present in the ion atmosphere and need to be accounted for to understand electrostatic interactions of nucleic acids. To test whether the effects of cation–anion correlations extend to nucleic acid kinetics and thermodynamics, we followed the folding of P4–P6, a domain of the Tetrahymena group I ribozyme, via single-molecule fluorescence resonance energy transfer in solutions with different salts. Solutions of identical concentration but lower activity gave slower and less favorable folding. Our results reveal hitherto unknown properties of the ion atmosphere and suggest possible roles of oriented ion pairs or anion-bridged cations in the ion atmosphere for electrolyte solutions of salts with reduced activity. Consideration of these new results leads to a reevaluation of the strengths and limitations of Poisson–Boltzmann theory and highlights the need for next-generation atomic-level models of the ion atmosphere. PMID:26517731

Fast, Statistical Model of Surface Roughness for Ion-Solid Interaction Simulations and Efficient Code Coupling

NASA Astrophysics Data System (ADS)

Drobny, Jon; Curreli, Davide; Ruzic, David; Lasa, Ane; Green, David; Canik, John; Younkin, Tim; Blondel, Sophie; Wirth, Brian

2017-10-01

Surface roughness greatly impacts material erosion, and thus plays an important role in Plasma-Surface Interactions. Developing strategies for efficiently introducing rough surfaces into ion-solid interaction codes will be an important step towards whole-device modeling of plasma devices and future fusion reactors such as ITER. Fractal TRIDYN (F-TRIDYN) is an upgraded version of the Monte Carlo, BCA program TRIDYN developed for this purpose that includes an explicit fractal model of surface roughness and extended input and output options for file-based code coupling. Code coupling with both plasma and material codes has been achieved and allows for multi-scale, whole-device modeling of plasma experiments. These code coupling results will be presented. F-TRIDYN has been further upgraded with an alternative, statistical model of surface roughness. The statistical model is significantly faster than and compares favorably to the fractal model. Additionally, the statistical model compares well to alternative computational surface roughness models and experiments. Theoretical links between the fractal and statistical models are made, and further connections to experimental measurements of surface roughness are explored. This work was supported by the PSI-SciDAC Project funded by the U.S. Department of Energy through contract DOE-DE-SC0008658.

X-ray Reflectivity Characterization of Ion Distribution at Biomimetic Membrane Surfaces

NASA Astrophysics Data System (ADS)

Krüger, Peter; Pittler, Jens; Vaknin, David; Lösche, Mathias

2003-03-01

Ions at cell membrane surfaces may control the function and conformation of nearby biomolecules, thus playing an important role in inter- and intracellular transport as well as in biorecognition processes. Moreover, charge patterns at membrane surfaces may direct the growth of inorganic crystals in biomineralization. Langmuir monolayers are widely employed as model systems for studying charge distribution and growth processes at the organic/inorganic interface. We present a novel x-ray reflectivity technique that provides detailed information on ion distribution at biomembrane surfaces by using monochromatic x-rays at various energies at and away from the ion x-ray absorption edges. As a model, the interaction of Ba^2+ with DMPA^- (dimyristoyl phosphatidic acid) monolayers at the aqueous surface was studied. We find an unexpectedly large concentration of the cations near the interface where they form a Stern layer of bound ions. These studies have been complemented with conventional x-ray reflectivity measurements and extended to other anionic lipid species (DMPS, DMPG) and cations (Ca^2+).

A New Poisson-Nernst-Planck Model with Ion-Water Interactions for Charge Transport in Ion Channels.

PubMed

Chen, Duan

2016-08-01

In this work, we propose a new Poisson-Nernst-Planck (PNP) model with ion-water interactions for biological charge transport in ion channels. Due to narrow geometries of these membrane proteins, ion-water interaction is critical for both dielectric property of water molecules in channel pore and transport dynamics of mobile ions. We model the ion-water interaction energy based on realistic experimental observations in an efficient mean-field approach. Variation of a total energy functional of the biological system yields a new PNP-type continuum model. Numerical simulations show that the proposed model with ion-water interaction energy has the new features that quantitatively describe dielectric properties of water molecules in narrow pores and are possible to model the selectivity of some ion channels.

Interaction of the high energy deuterons with the graphite target in the plasma focus devices based on Lee model

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

Akel, M., E-mail: pscientific2@aec.org.sy; Alsheikh Salo, S.; Ismael, Sh.

2014-07-15

Numerical experiments are systematically carried out using the Lee model code extended to compute the ion beams on various plasma focus devices operated with Deuterium gas. The deuteron beam properties of the plasma focus are studied for low and high energy plasma focus device. The energy spectral distribution for deuteron ions ejected from the pinch plasma is calculated and the ion numbers with energy around 1 MeV is then determined. The deuteron–graphite target interaction is studied for different conditions. The yield of the reaction {sup 12}C(d,n){sup 13}N and the induced radioactivity for one and multi shots plasma focus devices in themore » graphite solid target is investigated. Our results present the optimized high energy repetitive plasma focus devices as an alternative to accelerators for the production of {sup 13}N short lived radioisotopes. However, technical challenges await solutions on two fronts: (a) operation of plasma focus machines at high rep rates for a sufficient period of time (b) design of durable targets that can take the thermal load.« less

Space plasma research

NASA Technical Reports Server (NTRS)

Comfort, R. H.; Horwitz, J. L.

1986-01-01

Temperature and density analysis in the Automated Analysis Program (for the global empirical model) were modified to use flow velocities produced by the flow velocity analysis. Revisions were started to construct an interactive version of the technique for temperature and density analysis used in the automated analysis program. A sutdy of ion and electron heating at high altitudes in the outer plasmasphere was initiated. Also the analysis of the electron gun experiments on SCATHA were extended to include eclipse operations in order to test a hypothesis that there are interactions between the 50 to 100 eV beam and spacecraft generated photoelectrons. The MASSCOMP software to be used in taking and displaying data in the two-ion plasma experiment was tested and is now working satisfactorily. Papers published during the report period are listed.

A 3D Multi-fluid MHD Study of the Interaction of the Solar Wind with the Ionosphere/Atmosphere System of Mars.

NASA Astrophysics Data System (ADS)

Najib, Dalal; Nagy, Andrew; Toth, Gabor; Ma, Yingjuan

We use our new four species multi-fluid model to study the interaction of the solar wind with Mars. The lower boundary of our model is at 100 km, below the main ionospheric peak, and the radial resolution is about 10 km in the ionosphere, thus the model does a very good job in reproducing the ionosphere and the associated processes. We carry out calculations for high and low solar activity conditions and establish the importance of mass loading by the extended exosphere of Mars. We also calculate the atmospheric escape of the ionospheric species, including pick up ions. Finally, we compare our model results with the Viking, MGS and Mars Express observations.

Io's Interaction with the Jovian Magnetosphere: Models of Particle Acceleration and Scattering

NASA Astrophysics Data System (ADS)

Crary, Frank Judson

1998-09-01

I develop models of electron acceleration and ion scattering which result from Io's interaction with the jovian magnetosphere. According to my models, Io initially generates transient currents and an Alfvenic disturbance when it first encounters a jovian magnetic field line, and the interaction would eventually settle into a system of steady Birkeland currents as the field line is advected downstream past Io and into Io's wake. I derive a model of wave propagation and electron acceleration by the Alfvenic transient, due to electron inertial effects. My numerical calculations show that the power and particle energy of the resulting electron beam are consistent with observations of the Io-related auroral spot and of Jupiter's S-burst decametric emissions. In the case of the steady currents and Io's wake. I show that these currents would drive instabilities and argue that electrostatic double layers would form in the high latitudes of the Io/Io wake flux tubes. I examine the role of these double layers in producing energetic electrons and estimate the likely electron energies and power. This model agrees with observations of a long arc in the jovian aurora, extending away from the Io-related spot, the L-burst decametric radio emissions and electron beams observed by the Galileo spacecraft in Io's wake. Finally, I consider the Galileo observations of ion cyclotron waves near Io. I use the absence of waves near the S and O gyrofrequencies to place limits on the source rate of heavy ions near Io. For a sufficiently low source rate, the thermal core population prevents ion cyclotron instabilities and wave growth. I use these limits to constrain the neutral column density of Io's exosphere and amount of plasma produced within 2 to 10 body radii of Io.

The short range anion-H interaction is the driving force for crystal formation of ions in water.

PubMed

Alejandre, José; Chapela, Gustavo A; Bresme, Fernando; Hansen, Jean-Pierre

2009-05-07

The crystal formation of NaCl in water is studied by extensive molecular dynamics simulations. Ionic solutions at room temperature and various concentrations are studied using the SPC/E and TIP4P/2005 water models and seven force fields of NaCl. Most force fields of pure NaCl fail to reproduce the experimental density of the crystal, and in solution some favor dissociation at saturated conditions, while others favor crystal formation at low concentration. A new force field of NaCl is proposed, which reproduces the experimental phase diagram in the solid, liquid, and vapor regions. This force field overestimates the solubility of NaCl in water at saturation conditions when used with standard Lorentz-Berthelot combining rules for the ion-water pair potentials. It is shown that precipitation of ions is driven by the short range interaction between Cl-H pairs, a term which is generally missing in the simulation of ionic solutions. The effects of intramolecular flexibility of water on the solubility of NaCl ions are analyzed and is found to be small compared to rigid models. A flexible water model, extending the rigid SPC/E, is proposed, which incorporates Lennard-Jones interactions centered on the hydrogen atoms. This force field gives liquid-vapor coexisting densities and surface tensions in better agreement with experimental data than the rigid SPC/E model. The Cl-H, Na-O, and Cl-O pair distribution functions of the rigid and flexible models agree well with experiment. The predicted concentration dependence of the electric conductivity is in fair agreement with available experimental data.

Observing Planets and Small Bodies in Sputtered High Energy Atom (SHEA) Fluxes

NASA Technical Reports Server (NTRS)

Milillo, A.; Orsini, S.; Hsieh, K. C.; Baragiola, R.; Fama, M.; Johnson, R.; Mura, A.; Plainaki, Ch.; Sarantos, M.; Cassidy, T. A.;

Quantum molecular dynamics a microscopic model from UNILAC to CERN energies

NASA Astrophysics Data System (ADS)

Hartnack, C.; Zhuxia, Li; Neise, L.; Peilert, G.; Rosenhauer, A.; Sorge, H.; Aichelin, J.; Stöcker, H.; Greiner, W.

1989-04-01

We demonstrate that the microscopic QMD approach is useful to study heavy ion collisions from fusion fussion phenomena to the quest for signals of the quark gluon plasma. We discuss the possibilities and difficulties to determine the nuclear equation of state from heavy ion collisions. We investigate the influence of momentum dependent interactions and of in medium corrections to the nucleon-nucleon cross sections in the framework of the QMD model. The model is extended to low energies by including a Pauli potential in the nucleon-nucleon interaction. We show that it is possible to extract information on the effective cross sections from the experimental rapidity distributions of the fragments. We also investigate the transverse momentum of complex fragments with and without in medium corrections. The experimental data yield evidence for a stiff equation of state. A covariant extension of the QMD model is presented, which is applied to very high energy (10…200 AGeV) heavy ion collisions. Particle production and decay of heavy resonances are included. Predictions of the stopping power at AGS and SPS are presented. The importance of secondary scattering and nuclear stopping up to the highest energies is demonstrated. This is particularly important for the recently observed enhancement of strangeness production, which was proposed as a signal for QGP formation.

Coupled channel effects on resonance states of positronic alkali atom

NASA Astrophysics Data System (ADS)

Yamashita, Takuma; Kino, Yasushi

2018-01-01

S-wave Feshbach resonance states belonging to dipole series in positronic alkali atoms (e+Li, e+Na, e+K, e+Rb and e+Cs) are studied by coupled-channel calculations within a three-body model. Resonance energies and widths below a dissociation threshold of alkali-ion and positronium are calculated with a complex scaling method. Extended model potentials that provide positronic pseudo-alkali-atoms are introduced to investigate the relationship between the resonance states and dissociation thresholds based on a three-body dynamics. Resonances of the dipole series below a dissociation threshold of alkali-atom and positron would have some associations with atomic energy levels that results in longer resonance lifetimes than the prediction of the analytical law derived from the ion-dipole interaction.

A non-linear 4-wave resonant model for non-perturbative fast ion interactions with Alfv'enic modes in burning plasmas

NASA Astrophysics Data System (ADS)

Zonca, Fulvio; Chen, Liu

2007-11-01

We adopt the 4-wave modulation interaction model, introduced by Chen et al [1] for analyzing modulational instabilities of the radial envelope of Ion Temperature Gradient driven modes in toroidal geometry, extending it to the modulations on the fast particle distribution function due to nonlinear Alfv'enic mode dynamics, as proposed in Ref. [2]. In the case where the wave-particle interactions are non-perturbative and strongly influence the mode evolution, as in the case of Energetic Particle Modes (EPM) [3], radial distortions (redistributions) of the fast ion source dominate the mode nonlinear dynamics. In this work, we show that the resonant particle motion is secular with a time-scale inversely proportional to the mode amplitude [4] and that the time evolution of the EPM radial envelope can be cast into the form of a nonlinear Schr"odinger equation a la Ginzburg-Landau [5]. [1] L. Chen et al, Phys. Plasmas 7 3129 (2000) [2] F. Zonca et al, Theory of Fusion Plasmas (Bologna: SIF) 17 (2000) [3] L. Chen, Phys. Plasmas 1, 1519 (1994).[4] F. Zonca et al, Nucl. Fusion 45 477 (2005) [5] F. Zonca et al, Plasma Phys. Contr. Fusion 48 B15 (2006)

Isotherm-Based Thermodynamic Model for Solute Activities of Asymmetric Electrolyte Aqueous Solutions.

PubMed

Nandy, Lucy; Dutcher, Cari S

2017-09-21

Adsorption isotherm-based statistical thermodynamic models can be used to determine solute concentration and solute and solvent activities in aqueous solutions. Recently, the number of adjustable parameters in the isotherm model of Dutcher et al. J. Phys. Chem. A/C 2011, 2012, 2013 were reduced for neutral solutes as well as symmetric 1:1 electrolytes by using a Coulombic model to describe the solute-solvent energy interactions (Ohm et al. J. Phys. Chem. A 2015, Nandy et al. J. Phys. Chem. A 2016). Here, the Coulombic treatment for symmetric electrolytes is extended to establish improved isotherm model equations for asymmetric 1-2 and 1-3 electrolyte systems. The Coulombic model developed here results in prediction of activities and other thermodynamic properties in multicomponent systems containing ions of arbitrary charge. The model is found to accurately calculate the osmotic coefficient over the entire solute concentration range with two model parameters, related to intermolecular solute-solute and solute-solvent spacing. The inorganic salts and acids treated here are generally considered to be fully dissociated. However, there are certain weak acids that do not dissociate completely, such as the bisulfate ion. In this work, partial dissociation of the bisulfate ion from sulfuric acid is treated as a mixture, with an additional model parameter that accounts for the dissociation ratio of the dissociated ions to nondissociated ions.

Extended Lindhard-Scharf-Schiott Theory for Ion Implantation Profiles Expressed with Pearson Function

NASA Astrophysics Data System (ADS)

Suzuki, Kunihiro

2009-04-01

Ion implantation profiles are expressed by the Pearson function with first, second, third, and fourth moment parameters of Rp, ΔRp, γ, and β. We derived an analytical model for these profile moments by solving a Lindhard-Scharf-Schiott (LSS) integration equation using perturbation approximation. This analytical model reproduces Monte Carlo data that were well calibrated to reproduce a vast experimental database. The extended LSS theory is vital for instantaneously predicting ion implantation profiles with any combination of incident ions and substrate atoms including their energy dependence.

Unmagnetized diffusion for azimuthally symmetric wave and particle distributions

NASA Technical Reports Server (NTRS)

Dusenbery, P. B.; Lyons, L. R.

1988-01-01

The quasi-linear diffusion of particles from resonant interactions with a spectrum of electrostatic waves is investigated theoretically, extending results obtained for no magnetic field and for strong magnetic fields to cases where the ambient magnetic field which organizes azimuthally symmetric wave and particle distributions does not have to be taken into consideration in evaluating the local interaction. The derivation of the governing equations is explained, and numerical results are presented in extensive graphs and characterized in detail. Slow-mode ion-acoustic waves are shown to be unstable under the plasma conditions studied, and the dependence of resonant-ion diffusion rates with pitch angle, speed, and the distribution of wave energy in wavenumber space is explored. The implications of the present findings for theoretical models of the earth bow shock and plasma-sheet boundary layer are indicated.

Investigating EMIC Wave Dynamics with RAM-SCB-E

NASA Astrophysics Data System (ADS)

Jordanova, V. K.; Fu, X.; Henderson, M. G.; Morley, S.; Welling, D. T.; Yu, Y.

2017-12-01

The distribution of ring current ions and electrons in the inner magnetosphere depends strongly on their transport in realistic electric (E) and magnetic (B) fields and concurrent energization or loss. To investigate the high variability of energetic particle (H+, He+, O+, and electron) fluxes during storms selected by the GEM Surface Charging Challenge, we use our kinetic ring current model (RAM) two-way coupled with a 3-D magnetic field code (SCB). This model was just extended to include electric field calculations, making it a unique, fully self-consistent, anisotropic ring current-atmosphere interactions model, RAM-SCB-E. Recently we investigated electromagnetic ion cyclotron (EMIC) instability in a local plasma using both linear theory and nonlinear hybrid simulations and derived a scaling formula that relates the saturation EMIC wave amplitude to initial plasma conditions. Global dynamic EMIC wave maps obtained with our RAM-SCB-E model using this scaling will be presented and compared with statistical models. These plasma waves can affect significantly both ion and electron precipitation into the atmosphere and the subsequent patterns of ionospheric conductance, as well as the global ring current dynamics.

Computational extended magneto-hydrodynamical study of shock structure generated by flows past an obstacle

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

Zhao, Xuan, E-mail: xzhao@cylance.com; Seyler, C. E., E-mail: ces7@cornell.edu

2015-07-15

The magnetized shock problem is studied in the context where supersonic plasma flows past a solid obstacle. This problem exhibits interesting and important phenomena such as a bow shock, magnetotail formation, reconnection, and plasmoid formation. This study is carried out using a discontinuous Galerkin method to solve an extended magneto-hydrodynamic model (XMHD). The main goals of this paper are to present a reasonably complete picture of the properties of this interaction using the MHD model and then to compare the results to the XMHD model. The inflow parameters, such as the magnetosonic Mach number M{sub f} and the ratio ofmore » thermal pressure to magnetic pressure β, can significantly affect the physical structures of the flow-obstacle interaction. The Hall effect can also significantly influence the results in the regime in which the ion inertial length is numerically resolved. Most of the results presented are for the two-dimensional case; however, two three-dimensional simulations are presented to make a connection to the important case in which the solar wind interacts with a solid body and to explore the possibility of performing scaled laboratory experiments.« less

Magnetic susceptibility of alkali-tetracyanoquinodimethane salts and extended Hubbard models with bond order and charge density wave phases

NASA Astrophysics Data System (ADS)

Kumar, Manoranjan; Topham, Benjamin J.; Yu, RuiHui; Ha, Quoc Binh Dang; Soos, Zoltán G.

2011-06-01

The molar spin susceptibilities χ(T) of Na-tetracyanoquinodimethane (TCNQ), K-TCNQ, and Rb-TCNQ(II) are fit quantitatively to 450 K in terms of half-filled bands of three one-dimensional Hubbard models with extended interactions using exact results for finite systems. All three models have bond order wave (BOW) and charge density wave (CDW) phases with boundary V = Vc(U) for nearest-neighbor interaction V and on-site repulsion U. At high T, all three salts have regular stacks of TCNQ^- anion radicals. The χ(T) fits place Na and K in the CDW phase and Rb(II) in the BOW phase with V ≈ Vc. The Na and K salts have dimerized stacks at T < Td while Rb(II) has regular stacks at 100 K. The χ(T) analysis extends to dimerized stacks and to dimerization fluctuations in Rb(II). The three models yield consistent values of U, V, and transfer integrals t for closely related TCNQ^- stacks. Model parameters based on χ(T) are smaller than those from optical data that in turn are considerably reduced by electronic polarization from quantum chemical calculation of U, V, and t of adjacent TCNQ^- ions. The χ(T) analysis shows that fully relaxed states have reduced model parameters compared to optical or vibration spectra of dimerized or regular TCNQ^- stacks.

Self-consistent Simulation of Microparticle and Ion Wakefield Configuration

NASA Astrophysics Data System (ADS)

Sanford, Dustin; Brooks, Beau; Ellis, Naoki; Matthews, Lorin; Hyde, Truell

2017-10-01

In a complex plasma, positively charged ions often have a directed flow with respect to the negatively charged dust grains. The resulting interaction between the dust and the flowing plasma creates an ion wakefield downstream from the dust particles, with the resulting positive space region modifying the interaction between the grains and contributing to the observed dynamics and equilibrium structure of the system. Here we present a proof of concept method that uses a molecular dynamics simulation to model the ion wakefield allowing the dynamics of the dust particles to be determined self-consistently. The trajectory of each ion is calculated including the forces from all other ions, which are treated as ``Yukawa particles'' and shielded from thermal electrons and the forces of the charged dust particles. Both the dust grain charge and the wakefield structure are also self-consistently determined for various particle configurations. The resultant wakefield potentials are then used to provide dynamic simulations of dust particle pairs. These results will be employed to analyze the formation and dynamics of field-aligned chains in CASPER's PK4 experiment onboard the International Space Station, allowing examination of extended dust chains without the masking force of gravity. This work was supported by the National Science Foundation under Grants PHY-1414523 and PHY-1740203.

A computer program incorporating Pitzer's equations for calculation of geochemical reactions in brines

USGS Publications Warehouse

Plummer, Niel; Parkhurst, D.L.; Fleming, G.W.; Dunkle, S.A.

1988-01-01

The program named PHRQPITZ is a computer code capable of making geochemical calculations in brines and other electrolyte solutions to high concentrations using the Pitzer virial-coefficient approach for activity-coefficient corrections. Reaction-modeling capabilities include calculation of (1) aqueous speciation and mineral-saturation index, (2) mineral solubility, (3) mixing and titration of aqueous solutions, (4) irreversible reactions and mineral water mass transfer, and (5) reaction path. The computed results for each aqueous solution include the osmotic coefficient, water activity , mineral saturation indices, mean activity coefficients, total activity coefficients, and scale-dependent values of pH, individual-ion activities and individual-ion activity coeffients , and scale-dependent values of pH, individual-ion activities and individual-ion activity coefficients. A data base of Pitzer interaction parameters is provided at 25 C for the system: Na-K-Mg-Ca-H-Cl-SO4-OH-HCO3-CO3-CO2-H2O, and extended to include largely untested literature data for Fe(II), Mn(II), Sr, Ba, Li, and Br with provision for calculations at temperatures other than 25C. An extensive literature review of published Pitzer interaction parameters for many inorganic salts is given. Also described is an interactive input code for PHRQPITZ called PITZINPT. (USGS)

Orbital Dimer Model for the Spin-Glass State in Y 2 Mo 2 O 7

DOE PAGES

Thygesen, Peter M. M.; Paddison, Joseph A. M.; Zhang, Ronghuan; ...

2017-02-08

The formation of a spin glass generally requires that magnetic exchange interactions are both frustrated and disordered. Consequently, the origin of spin-glass behavior in Y 2Mo 2O 7-in which magnetic Mo 4+ ions occupy a frustrated pyrochlore lattice with minimal compositional disorder-has been a longstanding question. Here, we use neutron and x-ray pair-distribution function (PDF) analysis to develop a disorder model that resolves apparent incompatibilities between previously reported PDF, extended x-rayabsorption fine structure spectroscopy, and NMR studies, and provides a new and physical explanation of the exchange disorder responsible for spin-glass formation. We show that Mo 4+ ions displace accordingmore » to a local "two-in-two-out" rule on each Mo 4 tetrahedron, driven by orbital dimerization of Jahn-Teller active Mo 4+ ions. Long-range orbital order is prevented by the macroscopic degeneracy of dimer coverings permitted by the pyrochlore lattice. Cooperative O 2- displacements yield a distribution of Mo-O-Mo angles, which in turn introduces disorder into magnetic interactions. In conclusion, our study demonstrates experimentally how frustration of atomic displacements can assume the role of compositional disorder in driving a spin-glass transition.« less

Orbital Dimer Model for the Spin-Glass State in Y_{2}Mo_{2}O_{7}.

PubMed

Thygesen, Peter M M; Paddison, Joseph A M; Zhang, Ronghuan; Beyer, Kevin A; Chapman, Karena W; Playford, Helen Y; Tucker, Matthew G; Keen, David A; Hayward, Michael A; Goodwin, Andrew L

2017-02-10

The formation of a spin glass generally requires that magnetic exchange interactions are both frustrated and disordered. Consequently, the origin of spin-glass behavior in Y_{2}Mo_{2}O_{7}-in which magnetic Mo^{4+} ions occupy a frustrated pyrochlore lattice with minimal compositional disorder-has been a longstanding question. Here, we use neutron and x-ray pair-distribution function (PDF) analysis to develop a disorder model that resolves apparent incompatibilities between previously reported PDF, extended x-ray-absorption fine structure spectroscopy, and NMR studies, and provides a new and physical explanation of the exchange disorder responsible for spin-glass formation. We show that Mo^{4+} ions displace according to a local "two-in-two-out" rule on each Mo_{4} tetrahedron, driven by orbital dimerization of Jahn-Teller active Mo^{4+} ions. Long-range orbital order is prevented by the macroscopic degeneracy of dimer coverings permitted by the pyrochlore lattice. Cooperative O^{2-} displacements yield a distribution of Mo-O-Mo angles, which in turn introduces disorder into magnetic interactions. Our study demonstrates experimentally how frustration of atomic displacements can assume the role of compositional disorder in driving a spin-glass transition.

Influence of nonelectrostatic ion-ion interactions on double-layer capacitance

NASA Astrophysics Data System (ADS)

Zhao, Hui

2012-11-01

Recently a Poisson-Helmholtz-Boltzmann (PHB) model [Bohinc , Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.85.031130 85, 031130 (2012)] was developed by accounting for solvent-mediated nonelectrostatic ion-ion interactions. Nonelectrostatic interactions are described by a Yukawa-like pair potential. In the present work, we modify the PHB model by adding steric effects (finite ion size) into the free energy to derive governing equations. The modified PHB model is capable of capturing both ion specificity and ion crowding. This modified model is then employed to study the capacitance of the double layer. More specifically, we focus on the influence of nonelectrostatic ion-ion interactions on charging a double layer near a flat surface in the presence of steric effects. We numerically compute the differential capacitance as a function of the voltage under various conditions. At small voltages and low salt concentrations (dilute solution), we find out that the predictions from the modified PHB model are the same as those from the classical Poisson-Boltzmann theory, indicating that nonelectrostatic ion-ion interactions and steric effects are negligible. At moderate voltages, nonelectrostatic ion-ion interactions play an important role in determining the differential capacitance. Generally speaking, nonelectrostatic interactions decrease the capacitance because of additional nonelectrostatic repulsion among excess counterions inside the double layer. However, increasing the voltage gradually favors steric effects, which induce a condensed layer with crowding of counterions near the electrode. Accordingly, the predictions from the modified PHB model collapse onto those computed by the modified Poisson-Boltzmann theory considering steric effects alone. Finally, theoretical predictions are compared and favorably agree with experimental data, in particular, in concentrated solutions, leading one to conclude that the modified PHB model adequately predicts the diffuse-charge dynamics of the double layer with ion specificity and steric effects.

Water flow in carbon-based nanoporous membranes impacted by interactions between hydrated ions and aromatic rings.

PubMed

Liu, Jian; Shi, Guosheng; Fang, Haiping

2017-02-24

Carbon-based nanoporous membranes, such as carbon nanotubes (CNTs), graphene/graphene oxide and graphyne, have shown great potential in water desalination and purification, gas and ion separation, biosensors, and lithium-based batteries, etc. A deep understanding of the interaction between hydrated ions in an aqueous solution and the graphitic surface in systems composed of water, ions and a graphitic surface is essential for applications with carbon-based nanoporous membrane platforms. In this review, we describe the recent progress of the interaction between hydrated ions and aromatic ring structures on the carbon-based surface and its applications in the water flow in a carbon nanotube. We expect that these works can be extended to the understanding of water flow in other nanoporous membranes, such as nanoporous graphene, graphyne and stacked sheets of graphene oxide.

Extended wave-packet model to calculate energy-loss moments of protons in matter

NASA Astrophysics Data System (ADS)

Archubi, C. D.; Arista, N. R.

2017-12-01

In this work we introduce modifications to the wave-packet method proposed by Kaneko to calculate the energy-loss moments of a projectile traversing a target which is represented in terms of Gaussian functions for the momentum distributions of electrons in the atomic shells. These modifications are introduced using the Levine and Louie technique to take into account the energy gaps corresponding to the different atomic levels of the target. We use the extended wave-packet model to evaluate the stopping power, the energy straggling, the inverse mean free path, and the ionization cross sections for protons in several targets, obtaining good agreements for all these quantities on an extensive energy range that covers low-, intermediate-, and high-energy regions. The extended wave-packet model proposed here provides a method to calculate in a very straightforward way all the significant terms of the inelastic interaction of light ions with any element of the periodic table.

A Lagrangian model for laser-induced fluorescence and its application to measurements of plasma ion temperature and electrostatic waves

NASA Astrophysics Data System (ADS)

Chu, F.; Skiff, F.

2018-01-01

Extensive information can be obtained on wave-particle interactions and wave fields by a direct measurement of perturbed ion distribution functions using laser-induced fluorescence (LIF). For practical purposes, LIF is frequently performed on metastable states that are produced from neutral gas particles and ions in other electronic states. If the laser intensity is increased to obtain a better LIF signal, then optical pumping can produce systematic effects depending on the collision rates which control metastable population and lifetime. We numerically simulate the ion velocity distribution measurement and wave-detection process using a Lagrangian model for the LIF signal for the case where metastables are produced directly from neutrals. This case requires more strict precautions and is important for discharges with energetic primary electrons and a high density of neutrals. Some of the results also apply to metastables produced from pre-existing ions. The simulations show that optical pumping broadening affects the ion velocity distribution function f0(v) and its first-order perturbation f1(v,t) when the laser intensity is increased above a certain level. The results also suggest that ion temperature measurements are only accurate when the metastable ions can live longer than the ion-ion collision mean free time. For the purposes of wave detection, the wave period has to be significantly shorter than the lifetime of metastable ions for a direct interpretation. It is more generally true that metastable ions may be viewed as test-particles. As long as an appropriate model is available, LIF can be extended to a range of environments.

Ion specific effects: decoupling ion-ion and ion-water interactions

PubMed Central

Song, Jinsuk; Kang, Tae Hui; Kim, Mahn Won; Han, Songi

2015-01-01

Ion-specific effects in aqueous solution, known as the Hofmeister effect is prevalent in diverse systems ranging from pure ionic to complex protein solutions. The objective of this paper is to explicitly demonstrate how complex ion-ion and ion-water interactions manifest themselves in the Hofmeister effects, based on a series of recent experimental observation. These effects are not considered in the classical description of ion effects, such as the Deryaguin-Landau-Verwey-Overbeek (DLVO) theory that, likely for that reason, fail to describe the origin of the phenomenological Hofmeister effect. However, given that models considering the basic forces of electrostatic and van der Waals interactions can offer rationalization for the core experimental observations, a universal interaction model stands a chance to be developed. In this perspective, we separately derive the contribution from ion-ion electrostatic interaction and ion-water interaction from second harmonic generation (SHG) data at the air-ion solution interface, which yields an estimate of ion-water interactions in solution. Hofmeister ion effects observed on biological solutes in solution should be similarly influenced by contributions from ion-ion and ion-water interactions, where the same ion-water interaction parameters derived from SHG data at the air-ion solution interface could be applicable. A key experimental data set available from solution systems to probe ion-water interaction is the modulation of water diffusion dynamics near ions in bulk ion solution, as well as near biological liposome surfaces. It is obtained from Overhauser dynamic nuclear polarization (ODNP), a nuclear magnetic resonance (NMR) relaxometry technique. The surface water diffusivity is influenced by the contribution from ion-water interactions, both from localized surface charges and adsorbed ions, although the relative contribution of the former is larger on liposome surfaces. In this perspective, ion-water interaction energy values derived from experimental data for various ions are compared with theoretical values in the literature. Ultimately, quantifying ion-induced changes in surface energy for the purpose of developing valid theoretical models for ion-water interaction, will be critical to rationalizing the Hofmeister effect. PMID:25761273

Densities and abundances of hot cometary ions in the coma of P/Halley

NASA Technical Reports Server (NTRS)

Neugebauer, M.; Goldstein, R.; Goldstein, B. E.; Fuselier, S. A.; Balsiger, H.; Ip, W.-H.

1991-01-01

On its flight by P/Halley, the Giotto spacecraft carried a High Energy Range Spectrometer (HERS) for measuring the properties of cometary ions picked up by the solar wind in the nearly collisionless regions of the coma. Preliminary estimates of the ion densities observed by HERS were reevaluated and extended; density profiles along the Giotto trajectory are presented for 13 values of ion mass/charge. Comparison with the physical-chemical model of the interaction of sunlight and the solar wind with the comet by other researchers reveals that, with the exception of protons and H2(+), all ion densities were at least an order of magnitude higher than predicted. The high ion densities cannot be explained on the basis of compression of the plasma, but require additional or stronger ionization mechanisms. Ratios of the densities of different ion species reveal an overabundance of carbonaceous material and an underabundance of H2(+) compared to the predictions of the Schmidt. While the densities of solar wind ions (H(+) and He(++)) changed sharply across a magnetic discontinuity located 1.35(10)(exp 5) km from the comet, this feature, which has been called both the 'cometopause' and the 'magnetic pileup boundary' was barely distinguishable in the density profiles of hot cometary ions. This result is consistent with the interpretation that the magnetic pileup boundary detected by Giotto was caused by a discontinuity in the solar wind and is not an intrinsic feature of the interaction of the solar wind with an active comet.

Outer satellite atmospheres: Their nature and planetary interactions. [atmospheric models for Amalthea, Ganymede, Callisto, and Titan are presented

NASA Technical Reports Server (NTRS)

Smyth, W. H.

1978-01-01

Results show that Amalthea is likely to form a tightly-bound partial toroidal-shaped hydrogen cloud about its planet, while Ganymede, Callisto and Titan may have rather large, complete and nearly symmetric toroidal-shaped clouds. The toroidal cloud for Amalthea compares favorably with spacecraft data of Pioneer 10 for a satellite escape flux of order 10 to the 11th power atoms/sq cm/sec. Model results for Ganymede, Callisto and Titan suggest that these extended hydrogen atmospheres are likely to be detected by the Voyager spacecrafts and that Titan's cloud might also be detected by the Pioneer 11 spacecraft. Ions created because of atoms lost through ionization processes from these four extended hydrogen atmospheres and from the sodium cloud of Io are discussed.

Electron-phonon interaction within classical molecular dynamics

DOE PAGES

Tamm, A.; Samolyuk, G.; Correa, A. A.; ...

2016-07-14

Here, we present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e-ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computermore » simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.« less

Jovian Plasmas Torus Interaction with Europa. Plasma Wake Structure and Effect of Inductive Magnetic Field: 3D Hybrid Kinetic Simulation

NASA Technical Reports Server (NTRS)

Lipatov, A. S.; Cooper, J F.; Paterson, W. R.; Sittler, E. C., Jr.; Hartle, R. E.; Simpson, David G.

2013-01-01

The hybrid kinetic model supports comprehensive simulation of the interaction between different spatial and energetic elements of the Europa moon-magnetosphere system with respect to a variable upstream magnetic field and flux or density distributions of plasma and energetic ions, electrons, and neutral atoms. This capability is critical for improving the interpretation of the existing Europa flyby measurements from the Galileo Orbiter mission, and for planning flyby and orbital measurements (including the surface and atmospheric compositions) for future missions. The simulations are based on recent models of the atmosphere of Europa (Cassidy et al., 2007; Shematovich et al., 2005). In contrast to previous approaches with MHD simulations, the hybrid model allows us to fully take into account the finite gyroradius effect and electron pressure, and to correctly estimate the ion velocity distribution and the fluxes along the magnetic field (assuming an initial Maxwellian velocity distribution for upstream background ions). Photoionization, electron-impact ionization, charge exchange and collisions between the ions and neutrals are also included in our model. We consider the models with Oþ þ and Sþ þ background plasma, and various betas for background ions and electrons, and pickup electrons. The majority of O2 atmosphere is thermal with an extended non-thermal population (Cassidy et al., 2007). In this paper, we discuss two tasks: (1) the plasma wake structure dependence on the parameters of the upstream plasma and Europa's atmosphere (model I, cases (a) and (b) with a homogeneous Jovian magnetosphere field, an inductive magnetic dipole and high oceanic shell conductivity); and (2) estimation of the possible effect of an induced magnetic field arising from oceanic shell conductivity. This effect was estimated based on the difference between the observed and modeled magnetic fields (model II, case (c) with an inhomogeneous Jovian magnetosphere field, an inductive magnetic dipole and low oceanic shell conductivity).

Hot electrons and radial transport in Saturn's inner magetosphere: Modeling the effects on ion chemistry

NASA Astrophysics Data System (ADS)

Fleshman, Bobby L.

The E-ring of Saturn, located just beyond the main rings at four Saturn radii, was known to be made mostly of water and its by-products before the Cassini spacecraft arrived at Saturn in 2005. Since then, Cassini has observed water geysers on the tiny moon of Enceladus ejecting ≈ 100 kg of water per second into orbit around Saturn, which most agree is the chief contributor to neutrals in the E-ring. Following several key reactions, many of these neutrals go on to populate large, tenuous structures, known as neutral clouds, extending 10s of Saturn radii. The other side of the story are the ions, which are largely created by the ionization of same neutrals sourced from Enceladus. A key distinction between the neutrals and ions is that ions are carried along by Saturn's magnetic field, and revolve around Saturn at the rotation rate of the planet, while neutrals generally have much slower Keplerian speeds. It is the study of the chemical interaction of these separate, but related populations that is the subject of this thesis. We have developed a series of models to study how the coupling of these systems affect details of the other, such as composition. The first step (Chapter 2) was the development of a water-group physical chemistry model, which includes suprathermal electrons and the effect of radial ion transport. With this "one-box" model, we are able to reproduce observed water and hydrogen ion densities in Enceladus's orbit, but only when the hot electron density is ≈ 0.5% of the total plasma density. Radial transport is found to be slow, requiring 26 days to remove ions from the orbit of Enceladus. Moving toward the development of a radial model of ion chemistry, in Chapter 4 we present a model of Saturn's neutral clouds, which are made of material outgassing from Enceladus. The effects of dissociation and charge exchange are considered, where the details of the latter prove to be of great consequence on neutral cloud morphology. The oxygen cloud is found to the most extended, followed by H2O, and finally OH. The above efforts are combined in Chapter 5, where a neutral cloud model is used to construct a radial model of ion chemistry. It is shown that neutral H2O requires more spreading than yet modeled in order to recover observed water and hydrogen ion abundances near Enceladus. The relative abundance of water-group ion species presented will be useful for analyses of CAPS-IMS data, while loss rates derived from the model can be used to improve neutral cloud models. The case is made that ion chemistry models and neutral cloud models must be developed alongside one another in order to improve understanding of these interrelated populations at Saturn.

Clues From Pluto's Ions

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2016-05-01

Nearly a year ago, in July 2015, the New Horizons spacecraft passed by the Pluto system. The wealth of data amassed from that flyby is still being analyzed including data from the Solar Wind Around Pluto (SWAP) instrument. Recent examination of this data has revealedinteresting new information about Plutos atmosphere and how the solar wind interacts with it.A Heavy Ion TailThe solar wind is a constant stream of charged particles released by the Sun at speeds of around 400 km/s (thats 1 million mph!). This wind travels out to the far reaches of the solar system, interacting with the bodies it encounters along the way.By modeling the SWAP detections, the authors determine the directions of the IMF that could produce the heavy ions detected. Red pixels represent IMF directions permitted. No possible IMF could reproduce the detections if the ions are nitrogen (bottom panels), and only retrograde IMF directions can produce the detections if the ions are methane. [Adapted from Zirnstein et al. 2016]New Horizons data has revealed that Plutos atmosphere leaks neutral nitrogen, methane, and carbon monoxide molecules that sometimes escape its weak gravitational pull. These molecules become ionized and are subsequently picked up by the passing solar wind, forming a tail of heavy ions behind Pluto. The details of the geometry and composition of this tail, however, had not yet been determined.Escaping MethaneIn a recent study led by Eric Zirnstein (Southwest Research Institute), the latest analysis of data from the SWAP instrument on board New Horizons is reported. The team used SWAPs ion detections from just after New Horizons closest approach to Pluto to better understand how the heavy ions around Pluto behave, and how the solar wind interacts with Plutos atmosphere.In the process of analyzing the SWAP data, Zirnstein and collaborators first establish what the majority of the heavy ions picked up by the solar wind are. Models of the SWAP detections indicate they are unlikely to be nitrogen ions, despite nitrogen being the most abundant molecule in Plutos atmosphere. Instead, the detections are likely of methane ions possibly present because methane molecules are lighter, allowing them to more efficiently escape Plutos atmosphere.Reconstructed origins of heavy ions detected by SWAP shortly after New Horizons closest approach to Pluto. Color represents the energy at the time of detection. [Adapted from Zirnstein et al. 2016]Magnetic DirectionNew Horizons does not have a magnetometer on board, which prevented it from making direct measurements of the interplanetary magnetic field (IMF; the solar magnetic field extended throughout the solar system) during the Pluto encounter. In spite of this, Zirnstein and collaborators are able to determine the IMF direction using some clever calculations about SWAPs field of view and the energies of heavy ions it detected.They demonstrate that the IMF was likely oriented roughly parallel to the ecliptic plane, and in the opposite direction of Plutos orbital motion, during New Horizons Pluto encounter. This would cause the solar wind to deflect southward around Pluto, resulting in a north-south asymmetry in the heavy ion tail behind Pluto.The new knowledge gained from SWAP about the geometry and the composition of Plutos extended atmosphere will help us to interpret further data from New Horizons. Ultimately, this provides us with a better understanding both of Plutos atmosphere and how the solar wind interacts with bodies in our solar system.CitationE. J. Zirnstein et al 2016 ApJ 823 L30. doi:10.3847/2041-8205/823/2/L30

A 3D Multi-fluid MHD Study of the Interaction of the Solar Wind with the Ionosphere/Atmosphere System of Venus.

NASA Astrophysics Data System (ADS)

Najib, D.; Nagy, A.; Toth, G.; Ma, Y.-J.

2011-10-01

We use the latest version of our four species multifluid model to study the interaction of the solar wind with Venus. The model solves simultaneously the continuity, momentum and energy equations of the different ions. The lower boundary of our model is at 100 km, below the main ionospheric peak, and the radial resolution is about 10 km in the ionosphere, thus the model does a very good job in reproducing the ionosphere and the associated processes. We carry out calculations for high and low solar activity conditions and establish the importance of mass loading by the extended exosphere of Venus. We demonstrate the importance of using the multi-fluid rather than a single fluid model. We also calculate the atmospheric escape of the ionospheric species and compare our model results with the observed parameters from Pioneer Venus and Venus Express.

Heavy and light flavor jet quenching at RHIC and LHC energies

NASA Astrophysics Data System (ADS)

Cao, Shanshan; Luo, Tan; Qin, Guang-You; Wang, Xin-Nian

2018-02-01

The Linear Boltzmann Transport (LBT) model coupled to hydrodynamical background is extended to include transport of both light partons and heavy quarks through the quark-gluon plasma (QGP) in high-energy heavy-ion collisions. The LBT model includes both elastic and inelastic medium-interaction of both primary jet shower partons and thermal recoil partons within perturbative QCD (pQCD). It is shown to simultaneously describe the experimental data on heavy and light flavor hadron suppression in high-energy heavy-ion collisions for different centralities at RHIC and LHC energies. More detailed investigations within the LBT model illustrate the importance of both initial parton spectra and the shapes of fragmentation functions on the difference between the nuclear modifications of light and heavy flavor hadrons. The dependence of the jet quenching parameter q ˆ on medium temperature and jet flavor is quantitatively extracted.

Heavy and light flavor jet quenching at RHIC and LHC energies

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

Cao, Shanshan; Luo, Tan; Qin, Guang-You

The Linear Boltzmann Transport (LBT) model coupled to hydrodynamical background is extended to include transport of both light partons and heavy quarks through the quark–gluon plasma (QGP) in high-energy heavy-ion collisions. The LBT model includes both elastic and inelastic medium-interaction of both primary jet shower partons and thermal recoil partons within perturbative QCD (pQCD). It is shown to simultaneously describe the experimental data on heavy and light flavor hadron suppression in high-energy heavy-ion collisions for different centralities at RHIC and LHC energies. More detailed investigations within the LBT model illustrate the importance of both initial parton spectra and the shapes of fragmentation functions on the difference between the nuclear modifications of light and heavy flavor hadrons. Finally, the dependence of the jet quenching parametermore » $$\\hat{q}$$ on medium temperature and jet flavor is quantitatively extracted.« less

Heavy and light flavor jet quenching at RHIC and LHC energies

DOE PAGES

Cao, Shanshan; Luo, Tan; Qin, Guang-You; ...

2017-12-14

The Linear Boltzmann Transport (LBT) model coupled to hydrodynamical background is extended to include transport of both light partons and heavy quarks through the quark–gluon plasma (QGP) in high-energy heavy-ion collisions. The LBT model includes both elastic and inelastic medium-interaction of both primary jet shower partons and thermal recoil partons within perturbative QCD (pQCD). It is shown to simultaneously describe the experimental data on heavy and light flavor hadron suppression in high-energy heavy-ion collisions for different centralities at RHIC and LHC energies. More detailed investigations within the LBT model illustrate the importance of both initial parton spectra and the shapes of fragmentation functions on the difference between the nuclear modifications of light and heavy flavor hadrons. Finally, the dependence of the jet quenching parametermore » $$\\hat{q}$$ on medium temperature and jet flavor is quantitatively extracted.« less

Kinetic Framework for the Magnetosphere-Ionosphere-Plasmasphere-Polar Wind System: Modeling Ion Outflow

NASA Astrophysics Data System (ADS)

Schunk, R. W.; Barakat, A. R.; Eccles, V.; Karimabadi, H.; Omelchenko, Y.; Khazanov, G. V.; Glocer, A.; Kistler, L. M.

2014-12-01

A Kinetic Framework for the Magnetosphere-Ionosphere-Plasmasphere-Polar Wind System is being developed in order to provide a rigorous approach to modeling the interaction of hot and cold particle interactions. The framework will include ion and electron kinetic species in the ionosphere, plasmasphere and polar wind, and kinetic ion, super-thermal electron and fluid electron species in the magnetosphere. The framework is ideally suited to modeling ion outflow from the ionosphere and plasmasphere, where a wide range for fluid and kinetic processes are important. These include escaping ion interactions with (1) photoelectrons, (2) cusp/auroral waves, double layers, and field-aligned currents, (3) double layers in the polar cap due to the interaction of cold ionospheric and hot magnetospheric electrons, (4) counter-streaming ions, and (5) electromagnetic wave turbulence. The kinetic ion interactions are particularly strong during geomagnetic storms and substorms. The presentation will provide a brief description of the models involved and discuss the effect that kinetic processes have on the ion outflow.

On the Voyager 1 Zero Radial Velocity Measurements in the Inner Heliosheath

NASA Astrophysics Data System (ADS)

Pogorelov, N. V.; Borovikov, S. N.; Kryukov, I.; Zank, G. P.

2011-12-01

Theoretical analysis of the Voyager 1 data revealed a very small, or even negative, value of the solar wind (SW) radial velocity component. This should not be surprising if we take into account time-dependent processes that take place in the inner heliosheath (IHS). We analyze solar cycle modeling of the SW interaction with the local interstellar medium (LISM) and demonstrate the existence of small and negative values of the SW radial velocity. It shown that, in reality, a similar picture can be observed in the outer heliosheath (OHS), where on the contrary, extended regions of the positive radial velocity are observed. Another scenario discussed in this talk is related to effects of transients, such as global merged interaction regions and corotating interacting regions. Numerical results are obtained with the SW-LISM interaction model developed in the UAHuntsville and implemented in the Multi-Scale Fluid-Kinetic Simulation Suite. This model treats ions magnetohydrodynamically while the transport of neutral atoms is performed kinetically by solving the Boltzmann equation with a Monte Carlo approach or using a multi-fluid approach developed in mid-90's by G. P. Zank. Pickup ions (PUIs) can be treated as a separate fluid. The evolution of the PUI-generated turbulence is addressed on the differential level by adding three additional equations, which are solved self-consistently with the MHD-kinetic system of equations.

Measurements of ion energies from the explosion of large hydrogen iodide clusters irradiated by intense femtosecond laser pulses

NASA Astrophysics Data System (ADS)

Tisch, J. W. G.; Hay, N.; Springate, E.; Gumbrell, E. T.; Hutchinson, M. H. R.; Marangos, J. P.

1999-10-01

We present measurements of ion energies from the interaction of intense, femtosecond laser pulses with large mixed-species clusters. Multi-keV protons and ~100-keV iodine ions are observed from the explosion of HI clusters produced in a gas jet operated at room temperature. Clusters formed from molecular gases such as HI are thus seen to extend the advantages of the laser-cluster interaction to elements that do not readily form single-species clusters. In the light of recently reported nuclear fusion in laser-heated clusters, we also examine the possibility of boosting the explosion energies of low-Z ions through the use of mixed species clusters.

Ion optical design of a collinear laser-negative ion beam apparatus.

PubMed

Diehl, C; Wendt, K; Lindahl, A O; Andersson, P; Hanstorp, D

2011-05-01

An apparatus for photodetachment studies on atomic and molecular negative ions of medium up to heavy mass (M ≃ 500) has been designed and constructed. Laser and ion beams are merged in the apparatus in a collinear geometry and atoms, neutral molecules and negative ions are detected in the forward direction. The ion optical design and the components used to optimize the mass resolution and the transmission through the extended field-free interaction region are described. A 90° sector field magnet with 50 cm bending radius in combination with two slits is used for mass dispersion providing a resolution of M∕ΔM≅800 for molecular ions and M∕ΔM≅400 for atomic ions. The difference in mass resolution for atomic and molecular ions is attributed to different energy distributions of the sputtered ions. With 1 mm slits, transmission from the source through the interaction region to the final ion detector was determined to be about 0.14%.

Explicit ions/implicit water generalized Born model for nucleic acids

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

Tolokh, Igor S.; Thomas, Dennis G.; Onufriev, Alexey V.

Ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model, and utilizes a non-standard approach to defining the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes – disconnected dielectric boundary around the solute-ion or ion-ion pairs. Fully analytical description of all energymore » components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force (PMF) for Na+-Cl− ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. The monovalent (Na+) and trivalent (CoHex3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within kBT. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. These features include preferential CoHex binding inside the major groove of RNA duplex, in contrast to CoHex biding at the "external" surface of the sugar-phosphate backbone of DNA duplex; these differences in the counterion binding patters were shown earlier to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. MC simulations of CoHex ions interacting with homopolymeric poly(dA·dT) DNA duplex with modified (de-methylated) and native Thymine bases are used to explore the physics behind CoHex-Thymine interactions. The simulations suggest that the ion desolvation penalty due to proximity to the low dielectric volume of the methyl group can contribute significantly to CoHex-Thymine interactions. Compared to the steric repulsion between the ion and the methyl group, the desolvation penalty interaction has a longer range, and may be important to consider in the context of methylation effects on DNA condensation.« less

Explicit ions/implicit water generalized Born model for nucleic acids

NASA Astrophysics Data System (ADS)

Tolokh, Igor S.; Thomas, Dennis G.; Onufriev, Alexey V.

2018-05-01

The ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure, and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model and utilizes a non-standard approach to define the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes—disconnected dielectric boundary around the solute-ion or ion-ion pairs. A fully analytical description of all energy components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force for Na+-Cl- ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. The monovalent (Na+) and trivalent (CoHex3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within kBT. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. These features include preferential CoHex binding inside the major groove of the RNA duplex, in contrast to CoHex biding at the "external" surface of the sugar-phosphate backbone of the DNA duplex; these differences in the counterion binding patters were earlier shown to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. MC simulations of CoHex ions interacting with the homopolymeric poly(dA.dT) DNA duplex with modified (de-methylated) and native thymine bases are used to explore the physics behind CoHex-thymine interactions. The simulations suggest that the ion desolvation penalty due to proximity to the low dielectric volume of the methyl group can contribute significantly to CoHex-thymine interactions. Compared to the steric repulsion between the ion and the methyl group, the desolvation penalty interaction has a longer range and may be important to consider in the context of methylation effects on DNA condensation.

The DrugAge database of aging-related drugs.

PubMed

Barardo, Diogo; Thornton, Daniel; Thoppil, Harikrishnan; Walsh, Michael; Sharifi, Samim; Ferreira, Susana; Anžič, Andreja; Fernandes, Maria; Monteiro, Patrick; Grum, Tjaša; Cordeiro, Rui; De-Souza, Evandro Araújo; Budovsky, Arie; Araujo, Natali; Gruber, Jan; Petrascheck, Michael; Fraifeld, Vadim E; Zhavoronkov, Alexander; Moskalev, Alexey; de Magalhães, João Pedro

2017-06-01

Aging is a major worldwide medical challenge. Not surprisingly, identifying drugs and compounds that extend lifespan in model organisms is a growing research area. Here, we present DrugAge (http://genomics.senescence.info/drugs/), a curated database of lifespan-extending drugs and compounds. At the time of writing, DrugAge contains 1316 entries featuring 418 different compounds from studies across 27 model organisms, including worms, flies, yeast and mice. Data were manually curated from 324 publications. Using drug-gene interaction data, we also performed a functional enrichment analysis of targets of lifespan-extending drugs. Enriched terms include various functional categories related to glutathione and antioxidant activity, ion transport and metabolic processes. In addition, we found a modest but significant overlap between targets of lifespan-extending drugs and known aging-related genes, suggesting that some but not most aging-related pathways have been targeted pharmacologically in longevity studies. DrugAge is freely available online for the scientific community and will be an important resource for biogerontologists. © 2017 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

Comparison of kinetic and extended magnetohydrodynamics computational models for the linear ion temperature gradient instability in slab geometry

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

Schnack, D. D.; Department of Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706; Cheng, J.

We perform linear stability studies of the ion temperature gradient (ITG) instability in unsheared slab geometry using kinetic and extended magnetohydrodynamics (MHD) models, in the regime k{sub ∥}/k{sub ⊥}≪1. The ITG is a parallel (to B) sound wave that may be destabilized by finite ion Larmor radius (FLR) effects in the presence of a gradient in the equilibrium ion temperature. The ITG is stable in both ideal and resistive MHD; for a given temperature scale length L{sub Ti0}, instability requires that either k{sub ⊥}ρ{sub i} or ρ{sub i}/L{sub Ti0} be sufficiently large. Kinetic models capture FLR effects to all ordersmore » in either parameter. In the extended MHD model, these effects are captured only to lowest order by means of the Braginskii ion gyro-viscous stress tensor and the ion diamagnetic heat flux. We present the linear electrostatic dispersion relations for the ITG for both kinetic Vlasov and extended MHD (two-fluid) models in the local approximation. In the low frequency fluid regime, these reduce to the same cubic equation for the complex eigenvalue ω=ω{sub r}+iγ. An explicit solution is derived for the growth rate and real frequency in this regime. These are found to depend on a single non-dimensional parameter. We also compute the eigenvalues and the eigenfunctions with the extended MHD code NIMROD, and a hybrid kinetic δf code that assumes six-dimensional Vlasov ions and isothermal fluid electrons, as functions of k{sub ⊥}ρ{sub i} and ρ{sub i}/L{sub Ti0} using a spatially dependent equilibrium. These solutions are compared with each other, and with the predictions of the local kinetic and fluid dispersion relations. Kinetic and fluid calculations agree well at and near the marginal stability point, but diverge as k{sub ⊥}ρ{sub i} or ρ{sub i}/L{sub Ti0} increases. There is good qualitative agreement between the models for the shape of the unstable global eigenfunction for L{sub Ti0}/ρ{sub i}=30 and 20. The results quantify how far fluid calculations can be extended accurately into the kinetic regime. We conclude that for the linear ITG problem in slab geometry with unsheared magnetic field when k{sub ∥}/k{sub ⊥}≪1, the extended MHD model may be a reliable physical model for this problem when ρ{sub i}/L{sub Ti0}<10{sup −2} and k{sub ⊥}ρ{sub i}<0.2.« less

Development of a lifetime prediction model for lithium-ion batteries based on extended accelerated aging test data

NASA Astrophysics Data System (ADS)

Ecker, Madeleine; Gerschler, Jochen B.; Vogel, Jan; Käbitz, Stefan; Hust, Friedrich; Dechent, Philipp; Sauer, Dirk Uwe

2012-10-01

Battery lifetime prognosis is a key requirement for successful market introduction of electric and hybrid vehicles. This work aims at the development of a lifetime prediction approach based on an aging model for lithium-ion batteries. A multivariable analysis of a detailed series of accelerated lifetime experiments representing typical operating conditions in hybrid electric vehicle is presented. The impact of temperature and state of charge on impedance rise and capacity loss is quantified. The investigations are based on a high-power NMC/graphite lithium-ion battery with good cycle lifetime. The resulting mathematical functions are physically motivated by the occurring aging effects and are used for the parameterization of a semi-empirical aging model. An impedance-based electric-thermal model is coupled to the aging model to simulate the dynamic interaction between aging of the battery and the thermal as well as electric behavior. Based on these models different drive cycles and management strategies can be analyzed with regard to their impact on lifetime. It is an important tool for vehicle designers and for the implementation of business models. A key contribution of the paper is the parameterization of the aging model by experimental data, while aging simulation in the literature usually lacks a robust empirical foundation.

Global ICME-Mars Interaction and Induced Atmospheric Loss

NASA Astrophysics Data System (ADS)

Fang, X.; Ma, Y.; Manchester, W.

2013-12-01

Without the shielding of a strong intrinsic magnetic field, the present-day Mars atmosphere is more vulnerable to external solar wind forcing than the Earth's atmosphere. Therefore interplanetary coronal mass ejections (ICMEs) are expected to drive disturbances in the Mars environment in a profoundly different way, which, however, is poorly understood due to the lack of coordinated solar wind and Mars observations. In this study, three sophisticated models work in concert to simulate the physical domain extending from the solar corona to near-Mars space for the 13 May 2005 ICME event. The Space Weather Modeling Framework (SWMF) will be used to investigate the interaction of the ICME with the ambient solar wind and monitor its propagation from the Sun to the planet. A 3-D MHD model for Mars will be applied to assess the planetary atmospheric/ionospheric responses during the ICME passage of Mars. In the Mars weak magnetic field environment, the ion kinetic effects are important and will be included through the use of a 3-D Monte Carlo pickup ion transport model. These physics-based modeling efforts enable us to provide a global and time series view of the Mars response to transient solar wind disturbances and induced atmospheric loss, which is currently not possible due to the limitation of observations.

Ionosphere of venus: first observations of the effects of dynamics on the dayside ion composition.

PubMed

Taylor, H A; Brinton, H C; Bauer, S J; Hartle, R E; Cloutier, P A; Michel, F C; Daniell, R E; Donahue, T M; Maehl, R C

1979-02-23

Bennett radio-frequency ion mass spectrometers have returned the first in situ measurements of the Venus dayside ion composition, including evidence of pronounced structural variability resulting from a dynamic interaction with the solar wind. The ionospheric envelope, dominated above 200 kilometers by O(+), responds dramatically to variations in the solar wind pressure, Which is observed to compress the thermal ion distributions from heights as great as 1800 kilometers inward to 280 kilometers. At the thermal ion boundary, or ionopause, the ambient ions are swept away by the solar wind, such that a zone of accelerated suprathermnal plasma is encountered. At higher altitudes, extending outward on some orbits for thousands of kilometers to the bows shock, energetic ion currents are detected, apparently originating from the shocked solar wind plasma. Within the ionosphere, observations of pass-to-pass differences in the ion scale heights are indicative of the effects of ion convection stimlulated by the solar wind interaction.

Center for Extended Magnetohydrodynamics Modeling - Final Technical Report

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

Parker, Scott

This project funding supported approximately 74 percent of a Ph.D. graduate student, not including costs of travel and supplies. We had a highly successful research project including the development of a second-order implicit electromagnetic kinetic ion hybrid model [Cheng 2013, Sturdevant 2016], direct comparisons with the extended MHD NIMROD code and kinetic simulation [Schnack 2013], modeling of slab tearing modes using the fully kinetic ion hybrid model and finally, modeling global tearing modes in cylindrical geometry using gyrokinetic simulation [Chen 2015, Chen 2016]. We developed an electromagnetic second-order implicit kinetic ion fluid electron hybrid model [Cheng 2013]. As a firstmore » step, we assumed isothermal electrons, but have included drift-kinetic electrons in similar models [Chen 2011]. We used this simulation to study the nonlinear evolution of the tearing mode in slab geometry, including nonlinear evolution and saturation [Cheng 2013]. Later, we compared this model directly to extended MHD calculations using the NIMROD code [Schnack 2013]. In this study, we investigated the ion-temperature-gradient instability with an extended MHD code for the first time and got reasonable agreement with the kinetic calculation in terms of linear frequency, growth rate and mode structure. We then extended this model to include orbit averaging and sub-cycling of the ions and compared directly to gyrokinetic theory [Sturdevant 2016]. This work was highlighted in an Invited Talk at the International Conference on the Numerical Simulation of Plasmas in 2015. The orbit averaging sub-cycling multi-scale algorithm is amenable to hybrid architectures with GPUS or math co-processors. Additionally, our participation in the Center for Extend Magnetohydrodynamics motivated our research on developing the capability for gyrokinetic simulation to model a global tearing mode. We did this in cylindrical geometry where the results could be benchmarked with existing eigenmode calculations. First, we developed a gyrokinetic code capable of simulating long wavelengths using a fluid electron model [Chen 2015]. We benchmarked this code with an eigenmode calculation. Besides having to rewrite the field solver due to the breakdown in the gyrokinetic ordering for long wavelengths, very high radial resolution was required. We developed a technique where we used the solution from the eigenmode solver to specify radial boundary conditions allowing for a very high radial resolution of the inner solution. Using this technique enabled us to use our direct algorithm with gyrokinetic ions and drift kinetic electrons [Chen 2016]. This work was highlighted in an Invited Talk at the American Physical Society - Division of Plasma Physics in 2015.« less

Boosting laser-ion acceleration with multi-picosecond pulses

PubMed Central

Yogo, A.; Mima, K.; Iwata, N.; Tosaki, S.; Morace, A.; Arikawa, Y.; Fujioka, S.; Johzaki, T.; Sentoku, Y.; Nishimura, H.; Sagisaka, A.; Matsuo, K.; Kamitsukasa, N.; Kojima, S.; Nagatomo, H.; Nakai, M.; Shiraga, H.; Murakami, M.; Tokita, S.; Kawanaka, J.; Miyanaga, N.; Yamanoi, K.; Norimatsu, T.; Sakagami, H.; Bulanov, S. V.; Kondo, K.; Azechi, H.

2017-01-01

Using one of the world most powerful laser facility, we demonstrate for the first time that high-contrast multi-picosecond pulses are advantageous for proton acceleration. By extending the pulse duration from 1.5 to 6 ps with fixed laser intensity of 1018 W cm−2, the maximum proton energy is improved more than twice (from 13 to 33 MeV). At the same time, laser-energy conversion efficiency into the MeV protons is enhanced with an order of magnitude, achieving 5% for protons above 6 MeV with the 6 ps pulse duration. The proton energies observed are discussed using a plasma expansion model newly developed that takes the electron temperature evolution beyond the ponderomotive energy in the over picoseconds interaction into account. The present results are quite encouraging for realizing ion-driven fast ignition and novel ion beamlines. PMID:28211913

Ion Larmor radius effects near a reconnection X line at the magnetopause: THEMIS observations and simulation comparison

NASA Astrophysics Data System (ADS)

Phan, T. D.; Shay, M. A.; Haggerty, C. C.; Gosling, J. T.; Eastwood, J. P.; Fujimoto, M.; Malakit, K.; Mozer, F. S.; Cassak, P. A.; Oieroset, M.; Angelopoulos, V.

2016-09-01

We report a Time History of Events and Macroscale Interactions during Substorms (THEMIS-D) spacecraft crossing of a magnetopause reconnection exhaust ~9 ion skin depths (di) downstream of an X line. The crossing was characterized by ion jetting at speeds substantially below the predicted reconnection outflow speed. In the magnetospheric inflow region THEMIS detected (a) penetration of magnetosheath ions and the resulting flows perpendicular to the reconnection plane, (b) ion outflow extending into the magnetosphere, and (c) enhanced electron parallel temperature. Comparison with a simulation suggests that these signatures are associated with the gyration of magnetosheath ions onto magnetospheric field lines due to the shift of the flow stagnation point toward the low-density magnetosphere. Our observations indicate that these effects, ~2-3 di in width, extend at least 9 di downstream of the X line. The detection of these signatures could indicate large-scale proximity of the X line but do not imply that the spacecraft was upstream of the electron diffusion region.

Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes.

PubMed

Havrila, Marek; Stadlbauer, Petr; Islam, Barira; Otyepka, Michal; Šponer, Jiří

2017-08-08

G-quadruplexes (GQs) are key noncanonical DNA and RNA architectures stabilized by desolvated monovalent cations present in their central channels. We analyze extended atomistic molecular dynamics simulations (∼580 μs in total) of GQs with 11 monovalent cation parametrizations, assessing GQ overall structural stability, dynamics of internal cations, and distortions of the G-tetrad geometries. Majority of simulations were executed with the SPC/E water model; however, test simulations with TIP3P and OPC water models are also reported. The identity and parametrization of ions strongly affect behavior of a tetramolecular d[GGG] 4 GQ, which is unstable with several ion parametrizations. The remaining studied RNA and DNA GQs are structurally stable, though the G-tetrad geometries are always deformed by bifurcated H-bonding in a parametrization-specific manner. Thus, basic 10-μs-scale simulations of fully folded GQs can be safely done with a number of cation parametrizations. However, there are parametrization-specific differences and basic force-field errors affecting the quantitative description of ion-tetrad interactions, which may significantly affect studies of the ion-binding processes and description of the GQ folding landscape. Our d[GGG] 4 simulations indirectly suggest that such studies will also be sensitive to the water models. During exchanges with bulk water, the Na + ions move inside the GQs in a concerted manner, while larger relocations of the K + ions are typically separated. We suggest that the Joung-Cheatham SPC/E K + parameters represent a safe choice in simulation studies of GQs, though variation of ion parameters can be used for specific simulation goals.

The aerodynamics of bodies in a rarefied ionized gas with applications to spacecraft environmental dynamics

NASA Technical Reports Server (NTRS)

Stone, N. H.

1981-01-01

The objectives are to provide a parametric description of the electrostatic interaction of a mesosonic, collisionless plasma with conducting bodies on the order of 1 to 10 Debye lengths in size, and to extend this description to the satellite-ionospheric interaction, where possible. Experimental findings include: the wake of the geometrically complex body appears to be a linear superposition of the wakes of its simple geometric components; and vector ion flux measurements show converging ion streams at the wake axis and direct evidence of ion streams deflected from the wake axis by the positive space charge potential associated with the axial ion peak. The extension to the satellite-ionospheric interaction utilizes qualitative scaling and indicates that similar, but smaller amplitude, wake structures may be expected for small or highly charged bodies. However, for large bodies at small potentials, the structure may be diffused by the thermal ion motion and the dispersion resulting for space charge potentials.

State of Charge estimation of lithium ion battery based on extended Kalman filtering algorithm

NASA Astrophysics Data System (ADS)

Yang, Fan; Feng, Yiming; Pan, Binbiao; Wan, Renzhuo; Wang, Jun

2017-08-01

Accurate estimation of state-of-charge (SOC) for lithium ion battery is crucial for real-time diagnosis and prognosis in green energy vehicles. In this paper, a state space model of the battery based on Thevenin model is adopted. The strategy of estimating state of charge (SOC) based on extended Kalman fil-ter is presented, as well as to combine with ampere-hour counting (AH) and open circuit voltage (OCV) methods. The comparison between simulation and experiments indicates that the model’s performance matches well with that of lithium ion battery. The algorithm of extended Kalman filter keeps a good accura-cy precision and less dependent on its initial value in full range of SOC, which is proved to be suitable for online SOC estimation.

Brownian Dynamics simulations of model colloids in channel geometries and external fields

NASA Astrophysics Data System (ADS)

Siems, Ullrich; Nielaba, Peter

2018-04-01

We review the results of Brownian Dynamics simulations of colloidal particles in external fields confined in channels. Super-paramagnetic Brownian particles are well suited two- dimensional model systems for a variety of problems on different length scales, ranging from pedestrian walking through a bottleneck to ions passing ion-channels in living cells. In such systems confinement into channels can have a great influence on the diffusion and transport properties. Especially we will discuss the crossover from single file diffusion in a narrow channel to the diffusion in the extended two-dimensional system. Therefore a new algorithm for computing the mean square displacement (MSD) on logarithmic time scales is presented. In a different study interacting colloidal particles were dragged over a washboard potential and are additionally confined in a two-dimensional micro-channel. In this system kink and anti-kink solitons determine the depinning process of the particles from the periodic potential.

Role of ion hydration for the differential capacitance of an electric double layer.

PubMed

Caetano, Daniel L Z; Bossa, Guilherme V; de Oliveira, Vinicius M; Brown, Matthew A; de Carvalho, Sidney J; May, Sylvio

2016-10-12

The influence of soft, hydration-mediated ion-ion and ion-surface interactions on the differential capacitance of an electric double layer is investigated using Monte Carlo simulations and compared to various mean-field models. We focus on a planar electrode surface at physiological concentration of monovalent ions in a uniform dielectric background. Hydration-mediated interactions are modeled on the basis of Yukawa potentials that add to the Coulomb and excluded volume interactions between ions. We present a mean-field model that includes hydration-mediated anion-anion, anion-cation, and cation-cation interactions of arbitrary strengths. In addition, finite ion sizes are accounted for through excluded volume interactions, described either on the basis of the Carnahan-Starling equation of state or using a lattice gas model. Both our Monte Carlo simulations and mean-field approaches predict a characteristic double-peak (the so-called camel shape) of the differential capacitance; its decrease reflects the packing of the counterions near the electrode surface. The presence of hydration-mediated ion-surface repulsion causes a thin charge-depleted region close to the surface, which is reminiscent of a Stern layer. We analyze the interplay between excluded volume and hydration-mediated interactions on the differential capacitance and demonstrate that for small surface charge density our mean-field model based on the Carnahan-Starling equation is able to capture the Monte Carlo simulation results. In contrast, for large surface charge density the mean-field approach based on the lattice gas model is preferable.

Multi-physics simulations of space weather

NASA Astrophysics Data System (ADS)

Gombosi, Tamas; Toth, Gabor; Sokolov, Igor; de Zeeuw, Darren; van der Holst, Bart; Cohen, Ofer; Glocer, Alex; Manchester, Ward, IV; Ridley, Aaron

Presently magnetohydrodynamic (MHD) models represent the "workhorse" technology for simulating the space environment from the solar corona to the ionosphere. While these models are very successful in describing many important phenomena, they are based on a low-order moment approximation of the phase-space distribution function. In the last decade our group at the Center for Space Environment Modeling (CSEM) has developed the Space Weather Modeling Framework (SWMF) that efficiently couples together different models describing the interacting regions of the space environment. Many of these domain models (such as the global solar corona, the inner heliosphere or the global magnetosphere) are based on MHD and are represented by our multiphysics code, BATS-R-US. BATS-R-US can solve the equations of "standard" ideal MHD, but it can also go beyond this first approximation. It can solve resistive MHD, Hall MHD, semi-relativistic MHD (that keeps the displacement current), multispecies (different ion species have different continuity equations) and multifluid (all ion species have separate continuity, momentum and energy equations) MHD. Recently we added two-fluid Hall MHD (solving the electron and ion energy equations separately) and are working on extended magnetohydrodynamics with anisotropic pressures. This talk will show the effects of added physics and compare space weather simulation results to "standard" ideal MHD.

Particle Energization via Tearing Instability with Global Self-Organization Constraints

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

Sarff, John; Guo, Fan

The presentation reviews how tearing magnetic reconnection leads to powerful ion energization in reversed field pinch (RFP) plasmas. A mature MHD model for tearing instability has been developed that captures key nonlinear dynamics from the global to intermediate spatial scales. A turbulent cascade is also present that extends to at least the ion gyroradius scale, within which important particle energization mechanisms are anticipated. In summary, Ion heating and acceleration associated with magnetic reconnection from tearing instability is a powerful process in the RFP laboratory plasma (gyro-resonant and stochastic processes are likely candidates to support the observed rapid heating and othermore » features, reconnection-driven electron heating appears weaker or even absent, energetic tail formation for ions and electrons). Global self-organization strongly impacts particle energization (tearing interactions that span to core to edge, global magnetic flux change produces a larger electric field and runaway, correlations in electric and magnetic field fluctuations needed for dynamo feedback, impact of transport processes (which can be quite different for ions and electrons), inhomogeneity on the system scale, e.g., strong edge gradients).« less

A VARIABLE REACTIVITY MODEL FOR ION BINDING TO ENVIRONMENTAL SORBENTS

EPA Science Inventory

The conceptual and mathematical basis for a new general-composite modeling approach for ion binding to environmental sorbents is presented. The work extends the Simple Metal Sorption (SiMS) model previously presented for metal and proton binding to humic substances. A surface com...

Additional extensions to the NASCAP computer code, volume 1

NASA Technical Reports Server (NTRS)

Mandell, M. J.; Katz, I.; Stannard, P. R.

1981-01-01

Extensions and revisions to a computer code that comprehensively analyzes problems of spacecraft charging (NASCAP) are documented. Using a fully three dimensional approach, it can accurately predict spacecraft potentials under a variety of conditions. Among the extensions are a multiple electron/ion gun test tank capability, and the ability to model anisotropic and time dependent space environments. Also documented are a greatly extended MATCHG program and the preliminary version of NASCAP/LEO. The interactive MATCHG code was developed into an extremely powerful tool for the study of material-environment interactions. The NASCAP/LEO, a three dimensional code to study current collection under conditions of high voltages and short Debye lengths, was distributed for preliminary testing.

Electrostatic interactions between diffuse soft multi-layered (bio)particles: beyond Debye-Hückel approximation and Deryagin formulation.

PubMed

Duval, Jérôme F L; Merlin, Jenny; Narayana, Puranam A L

2011-01-21

We report a steady-state theory for the evaluation of electrostatic interactions between identical or dissimilar spherical soft multi-layered (bio)particles, e.g. microgels or microorganisms. These generally consist of a rigid core surrounded by concentric ion-permeable layers that may differ in thickness, soft material density, chemical composition and degree of dissociation for the ionogenic groups. The formalism allows the account of diffuse interphases where distributions of ionogenic groups from one layer to the other are position-dependent. The model is valid for any number of ion-permeable layers around the core of the interacting soft particles and covers all limiting situations in terms of nature of interacting particles, i.e. homo- and hetero-interactions between hard, soft or entirely porous colloids. The theory is based on a rigorous numerical solution of the non-linearized Poisson-Boltzmann equation including radial and angular distortions of the electric field distribution within and outside the interacting soft particles in approach. The Gibbs energy of electrostatic interaction is obtained from a general expression derived following the method by Verwey and Overbeek based on appropriate electric double layer charging mechanisms. Original analytical solutions are provided here for cases where interaction takes place between soft multi-layered particles whose size and charge density are in line with Deryagin treatment and Debye-Hückel approximation. These situations include interactions between hard and soft particles, hard plate and soft particle or soft plate and soft particle. The flexibility of the formalism is highlighted by the discussion of few situations which clearly illustrate that electrostatic interaction between multi-layered particles may be partly or predominantly governed by potential distribution within the most internal layers. A major consequence is that both amplitude and sign of Gibbs electrostatic interaction energy may dramatically change depending on the interplay between characteristic Debye length, thickness of ion-permeable layers and their respective protolytic features (e.g. location, magnitude and sign of charge density). This formalism extends a recent model by Ohshima which is strictly limited to interaction between soft mono-shell particles within Deryagin and Debye-Hückel approximations under conditions where ionizable sites are completely dissociated.

Thermodynamics of alternate Ising chains of spins 1 and 3/2 with dipolar, biquadratic, and single ion interactions

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

Fireman, E.C.; dos Santos, R.J.

1997-04-01

Within a recently developed extended decoration-transformation formalism we study the thermodynamic properties of a linear chain of alternate Ising {sigma}=1 and S=3/2 spins. We allow for different anisotropy fields on each subchain of different spins. For some range of the parameter space we show the existence of a crossover from a ferromagnetic to an antiferromagnetic-like behavior of the model, as explicitly captured in the susceptibility results. {copyright} {ital 1997 American Institute of Physics.}

Characterization of xenon ion and neutral interactions in a well-characterized experiment

NASA Astrophysics Data System (ADS)

Patino, Marlene I.; Wirz, Richard E.

2018-06-01

Interactions between fast ions and slow neutral atoms are commonly dominated by charge-exchange and momentum-exchange collisions, which are important to understanding and simulating the performance and behavior of many plasma devices. To investigate these interactions, this work developed a simple, well-characterized experiment that accurately measures the behavior of high energy xenon ions incident on a background of xenon neutral atoms. By using well-defined operating conditions and a simple geometry, these results serve as canonical data for the development and validation of plasma models and models of neutral beam sources that need to ensure accurate treatment of angular scattering distributions of charge-exchange and momentum-exchange ions and neutrals. The energies used in this study are relevant for electric propulsion devices ˜1.5 keV and can be used to improve models of ion-neutral interactions in the plume. By comparing these results to both analytical and computational models of ion-neutral interactions, we discovered the importance of (1) accurately treating the differential cross-sections for momentum-exchange and charge-exchange collisions over a large range of neutral background pressures and (2) properly considering commonly overlooked interactions, such as ion-induced electron emission from nearby surfaces and neutral-neutral ionization collisions.

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

Thygesen, Peter M. M.; Paddison, Joseph A. M.; Zhang, Ronghuan

The formation of a spin glass generally requires that magnetic exchange interactions are both frustrated and disordered. Consequently, the origin of spin-glass behavior in Y 2Mo 2O 7-in which magnetic Mo 4+ ions occupy a frustrated pyrochlore lattice with minimal compositional disorder-has been a longstanding question. Here, we use neutron and x-ray pair-distribution function (PDF) analysis to develop a disorder model that resolves apparent incompatibilities between previously reported PDF, extended x-rayabsorption fine structure spectroscopy, and NMR studies, and provides a new and physical explanation of the exchange disorder responsible for spin-glass formation. We show that Mo 4+ ions displace accordingmore » to a local "two-in-two-out" rule on each Mo 4 tetrahedron, driven by orbital dimerization of Jahn-Teller active Mo 4+ ions. Long-range orbital order is prevented by the macroscopic degeneracy of dimer coverings permitted by the pyrochlore lattice. Cooperative O 2- displacements yield a distribution of Mo-O-Mo angles, which in turn introduces disorder into magnetic interactions. In conclusion, our study demonstrates experimentally how frustration of atomic displacements can assume the role of compositional disorder in driving a spin-glass transition.« less

Ion permeation and glutamate residues linked by Poisson-Nernst-Planck theory in L-type calcium channels.

PubMed Central

Nonner, W; Eisenberg, B

1998-01-01

L-type Ca channels contain a cluster of four charged glutamate residues (EEEE locus), which seem essential for high Ca specificity. To understand how this highly charged structure might produce the currents and selectivity observed in this channel, a theory is needed that relates charge to current. We use an extended Poisson-Nernst-Planck (PNP2) theory to compute (mean) Coulombic interactions and thus to examine the role of the mean field electrostatic interactions in producing current and selectivity. The pore was modeled as a central cylinder with tapered atria; the cylinder (i.e., "pore proper") contained a uniform volume density of fixed charge equivalent to that of one to four carboxyl groups. The pore proper was assigned ion-specific, but spatially uniform, diffusion coefficients and excess chemical potentials. Thus electrostatic selection by valency was computed self-consistently, and selection by other features was also allowed. The five external parameters needed for a system of four ionic species (Na, Ca, Cl, and H) were determined analytically from published measurements of thre limiting conductances and two critical ion concentrations, while treating the pore as a macroscopic ion-exchange system in equilibrium with a uniform bath solution. The extended PNP equations were solved with these parameters, and the predictions were compared to currents measured in a variety of solutions over a range of transmembrane voltages. The extended PNP theory accurately predicted current-voltage relations, anomalous mole fraction effects in the observed current, saturation effects of varied Ca and Na concentrations, and block by protons. Pore geometry, dielectric permittivity, and the number of carboxyl groups had only weak effects. The successful prediction of Ca fluxes in this paper demonstrates that ad hoc electrostatic parameters, multiple discrete binding sites, and logistic assumptions of single-file movement are all unnecessary for the prediction of permeation in Ca channels over a wide range of conditions. Further work is needed, however, to understand the atomic origin of the fixed charge, excess chemical potentials, and diffusion coefficients of the channel. The Appendix uses PNP2 theory to predict ionic currents for published "barrier-and-well" energy profiles of this channel. PMID:9726931

Ion transport controlled by nanoparticle-functionalized membranes.

PubMed

Barry, Edward; McBride, Sean P; Jaeger, Heinrich M; Lin, Xiao-Min

2014-12-17

From proton exchange membranes in fuel cells to ion channels in biological membranes, the well-specified control of ionic interactions in confined geometries profoundly influences the transport and selectivity of porous materials. Here we outline a versatile new approach to control a membrane's electrostatic interactions with ions by depositing ligand-coated nanoparticles around the pore entrances. Leveraging the flexibility and control by which ligated nanoparticles can be synthesized, we demonstrate how ligand terminal groups such as methyl, carboxyl and amine can be used to tune the membrane charge density and control ion transport. Further functionality, exploiting the ligands as binding sites, is demonstrated for sulfonate groups resulting in an enhancement of the membrane charge density. We then extend these results to smaller dimensions by systematically varying the underlying pore diameter. As a whole, these results outline a previously unexplored method for the nanoparticle functionalization of membranes using ligated nanoparticles to control ion transport.

Ion transport controlled by nanoparticle-functionalized membranes

NASA Astrophysics Data System (ADS)

Barry, Edward; McBride, Sean P.; Jaeger, Heinrich M.; Lin, Xiao-Min

2014-12-01

From proton exchange membranes in fuel cells to ion channels in biological membranes, the well-specified control of ionic interactions in confined geometries profoundly influences the transport and selectivity of porous materials. Here we outline a versatile new approach to control a membrane’s electrostatic interactions with ions by depositing ligand-coated nanoparticles around the pore entrances. Leveraging the flexibility and control by which ligated nanoparticles can be synthesized, we demonstrate how ligand terminal groups such as methyl, carboxyl and amine can be used to tune the membrane charge density and control ion transport. Further functionality, exploiting the ligands as binding sites, is demonstrated for sulfonate groups resulting in an enhancement of the membrane charge density. We then extend these results to smaller dimensions by systematically varying the underlying pore diameter. As a whole, these results outline a previously unexplored method for the nanoparticle functionalization of membranes using ligated nanoparticles to control ion transport.

Phase transition studies of BiMnO3: Mean field theory approximations

NASA Astrophysics Data System (ADS)

Priya K. B, Lakshmi; Natesan, Baskaran

2015-06-01

We studied the phase transition and magneto-electric coupling effect of BiMnO3 by employing mean field theory approximations. To capture the ferromagnetic and ferroelectric transitions of BiMnO3, we construct an extended Ising model in a 2D square lattice, wherein, the magnetic (electric) interactions are described in terms of the direct interactions between the localized magnetic (electric dipole) moments of Mn ions with their nearest neighbors. To evaluate our model, we obtain magnetization, magnetic susceptibility and electric polarization using mean field approximation calculations. Our results reproduce both the ferromagnetic and the ferroelectric transitions, matching very well with the experimental reports. Furthermore, consistent with experimental observations, our mean field results suggest that there is indeed a coupling between the magnetic and electric ordering in BiMnO3.

Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations

PubMed Central

McDowell, S. Elizabeth; Jun, Jesse M.; Walter, Nils G.

2010-01-01

Enzymes generally are thought to derive their functional activity from conformational motions. The limited chemical variation in RNA suggests that such structural dynamics may play a particularly important role in RNA function. Minimal hammerhead ribozymes are known to cleave efficiently only in ∼10-fold higher than physiologic concentrations of Mg2+ ions. Extended versions containing native loop–loop interactions, however, show greatly enhanced catalytic activity at physiologically relevant Mg2+ concentrations, for reasons that are still ill-understood. Here, we use Mg2+ titrations, activity assays, ensemble, and single molecule fluorescence resonance energy transfer (FRET) approaches, combined with molecular dynamics (MD) simulations, to ask what influence the spatially distant tertiary loop–loop interactions of an extended hammerhead ribozyme have on its structural dynamics. By comparing hammerhead variants with wild-type, partially disrupted, and fully disrupted loop–loop interaction sequences we find that the tertiary interactions lead to a dynamic motional sampling that increasingly populates catalytically active conformations. At the global level the wild-type tertiary interactions lead to more frequent, if transient, encounters of the loop-carrying stems, whereas at the local level they lead to an enrichment in favorable in-line attack angles at the cleavage site. These results invoke a linkage between RNA structural dynamics and function and suggest that loop–loop interactions in extended hammerhead ribozymes—and Mg2+ ions that bind to minimal ribozymes—may generally allow more frequent access to a catalytically relevant conformation(s), rather than simply locking the ribozyme into a single active state. PMID:20921269

How ions affect the structure of water.

PubMed

Hribar, Barbara; Southall, Noel T; Vlachy, Vojko; Dill, Ken A

2002-10-16

We model ion solvation in water. We use the MB model of water, a simple two-dimensional statistical mechanical model in which waters are represented as Lennard-Jones disks having Gaussian hydrogen-bonding arms. We introduce a charge dipole into MB waters. We perform (NPT) Monte Carlo simulations to explore how water molecules are organized around ions and around nonpolar solutes in salt solutions. The model gives good qualitative agreement with experiments, including Jones-Dole viscosity B coefficients, Samoilov and Hirata ion hydration activation energies, ion solvation thermodynamics, and Setschenow coefficients for Hofmeister series ions, which describe the salt concentration dependence of the solubilities of hydrophobic solutes. The two main ideas captured here are (1) that charge densities govern the interactions of ions with water, and (2) that a balance of forces determines water structure: electrostatics (water's dipole interacting with ions) and hydrogen bonding (water interacting with neighboring waters). Small ions (kosmotropes) have high charge densities so they cause strong electrostatic ordering of nearby waters, breaking hydrogen bonds. In contrast, large ions (chaotropes) have low charge densities, and surrounding water molecules are largely hydrogen bonded.

Molecular simulation of aqueous electrolyte solubility. 2. Osmotic ensemble Monte Carlo methodology for free energy and solubility calculations and application to NaCl.

PubMed

Moučka, Filip; Lísal, Martin; Škvor, Jiří; Jirsák, Jan; Nezbeda, Ivo; Smith, William R

2011-06-23

We present a new and computationally efficient methodology using osmotic ensemble Monte Carlo (OEMC) simulation to calculate chemical potential-concentration curves and the solubility of aqueous electrolytes. The method avoids calculations for the solid phase, incorporating readily available data from thermochemical tables that are based on well-defined reference states. It performs simulations of the aqueous solution at a fixed number of water molecules, pressure, temperature, and specified overall electrolyte chemical potential. Insertion/deletion of ions to/from the system is implemented using fractional ions, which are coupled to the system via a coupling parameter λ that varies between 0 (no interaction between the fractional ions and the other particles in the system) and 1 (full interaction between the fractional ions and the other particles of the system). Transitions between λ-states are accepted with a probability following from the osmotic ensemble partition function. Biasing weights associated with the λ-states are used in order to efficiently realize transitions between them; these are determined by means of the Wang-Landau method. We also propose a novel scaling procedure for λ, which can be used for both nonpolarizable and polarizable models of aqueous electrolyte systems. The approach is readily extended to involve other solvents, multiple electrolytes, and species complexation reactions. The method is illustrated for NaCl, using SPC/E water and several force field models for NaCl from the literature, and the results are compared with experiment at ambient conditions. Good agreement is obtained for the chemical potential-concentration curve and the solubility prediction is reasonable. Future improvements to the predictions will require improved force field models.

State-of-charge inconsistency estimation of lithium-ion battery pack using mean-difference model and extended Kalman filter

NASA Astrophysics Data System (ADS)

Zheng, Yuejiu; Gao, Wenkai; Ouyang, Minggao; Lu, Languang; Zhou, Long; Han, Xuebing

2018-04-01

State-of-charge (SOC) inconsistency impacts the power, durability and safety of the battery pack. Therefore, it is necessary to measure the SOC inconsistency of the battery pack with good accuracy. We explore a novel method for modeling and estimating the SOC inconsistency of lithium-ion (Li-ion) battery pack with low computation effort. In this method, a second-order RC model is selected as the cell mean model (CMM) to represent the overall performance of the battery pack. A hypothetical Rint model is employed as the cell difference model (CDM) to evaluate the SOC difference. The parameters of mean-difference model (MDM) are identified with particle swarm optimization (PSO). Subsequently, the mean SOC and the cell SOC differences are estimated by using extended Kalman filter (EKF). Finally, we conduct an experiment on a small Li-ion battery pack with twelve cells connected in series. The results show that the evaluated SOC difference is capable of tracking the changing of actual value after a quick convergence.

Modeling and simulation of protein elution in linear pH and salt gradients on weak, strong and mixed cation exchange resins applying an extended Donnan ion exchange model.

PubMed

Wittkopp, Felix; Peeck, Lars; Hafner, Mathias; Frech, Christian

2018-04-13

Process development and characterization based on mathematic modeling provides several advantages and has been applied more frequently over the last few years. In this work, a Donnan equilibrium ion exchange (DIX) model is applied for modelling and simulation of ion exchange chromatography of a monoclonal antibody in linear chromatography. Four different cation exchange resin prototypes consisting of weak, strong and mixed ligands are characterized using pH and salt gradient elution experiments applying the extended DIX model. The modelling results are compared with the results using a classic stoichiometric displacement model. The Donnan equilibrium model is able to describe all four prototype resins while the stoichiometric displacement model fails for the weak and mixed weak/strong ligands. Finally, in silico chromatogram simulations of pH and pH/salt dual gradients are performed to verify the results and to show the consistency of the developed model. Copyright © 2018 Elsevier B.V. All rights reserved.

Positive and negative ion outflow at Rhea as observed by Cassini

NASA Astrophysics Data System (ADS)

Desai, Ravindra; Jones, Geraint; Regoli, Leonardo; Cowee, Misa; Coates, Andrew; Kataria, Dhiren

2017-04-01

Rhea is Saturn's largest icy moon and hosts an ethereal oxygen and carbon-dioxide atmosphere as was detected when Cassini observed positive and negative pickup ions outflowing from the moon and an extended neutral exosphere. These pickup ions can form current systems which, with the resulting jxB force, act to slow-down the incident magneto-plasma and cause field-line draping. As well as impacting the plasma interaction, the composition and density of picked up ions provide key diagnostics of the moon's sputter-induced atmosphere and surface. During the first Cassini-Rhea encounter (R1), the Cassini Plasma Spectrometer (CAPS) observed positively and negatively charged pickup ions before and after passing through the moon's plasma wake respectively, in agreement with their anticipated cycloidal trajectories. On the subsequent more distant wake encounter (R1.5) however, only positively charged pickup ions were observed, indicating high loss rates of the negative ions in Saturn's magnetosphere. Here, using an updated model of Cassini's Electron Spectrometer response function, we are able to estimate the outward flux of negatively charged pickup ions, the first time such a plasma population has been constrained. Using test-particle simulations we trace both the positive and negative particles back to Rhea's exobase to better understand their production and loss processes and the implications for Rhea's sputter-induced exosphere. We also look to examine whether the calculated ion densities could generate ion cyclotron wave activity.

Solar wind interaction with Venus and Mars in a parallel hybrid code

NASA Astrophysics Data System (ADS)

Jarvinen, Riku; Sandroos, Arto

2013-04-01

We discuss the development and applications of a new parallel hybrid simulation, where ions are treated as particles and electrons as a charge-neutralizing fluid, for the interaction between the solar wind and Venus and Mars. The new simulation code under construction is based on the algorithm of the sequential global planetary hybrid model developed at the Finnish Meteorological Institute (FMI) and on the Corsair parallel simulation platform also developed at the FMI. The FMI's sequential hybrid model has been used for studies of plasma interactions of several unmagnetized and weakly magnetized celestial bodies for more than a decade. Especially, the model has been used to interpret in situ particle and magnetic field observations from plasma environments of Mars, Venus and Titan. Further, Corsair is an open source MPI (Message Passing Interface) particle and mesh simulation platform, mainly aimed for simulations of diffusive shock acceleration in solar corona and interplanetary space, but which is now also being extended for global planetary hybrid simulations. In this presentation we discuss challenges and strategies of parallelizing a legacy simulation code as well as possible applications and prospects of a scalable parallel hybrid model for the solar wind interactions of Venus and Mars.

Multi-Fluid Simulations of a Coupled Ionosphere-Magnetosphere System

NASA Astrophysics Data System (ADS)

Gombosi, T. I.; Glocer, A.; Toth, G.; Ridley, A. J.; Sokolov, I. V.; de Zeeuw, D. L.

2008-05-01

In the last decade we have developed the Space Weather Modeling Framework (SWMF) that efficiently couples together different models describing the interacting regions of the space environment. Many of these domain models (such as the global solar corona, the inner heliosphere or the global magnetosphere) are based on MHD and are represented by our multiphysics code, BATS-R-US. BATS-R-US can solve the equations of "standard" ideal MHD, but it can also go beyond this first approximation. It can solve resistive MHD, Hall MHD, semi-relativistic MHD (that keeps the displacement current), multispecies (different ion species have different continuity equations) and multifluid (all ion species have separate continuity, momentum and energy equations) MHD. Recently we added two-fluid Hall MHD (solving the electron and ion energy equations separately) and are working on an extended magnetohydrodynamics model with anisotropic pressures. Ionosheric outflow can be a significant contributor to the plasma population of the magnetosphere during active geomagnetic conditions. This talk will present preliminary results of our simulations when we couple a new field- aligned multi-fluid polar wind code to the Ionosphere Electrodynamics (IE), and Global Magnetosphere (GM) components of the SWMF. We use multi-species and multi-fluid MHD to track the resulting plasma composition in the magnetosphere.

Ongoing cosmic ray acceleration in the supernova remnant W51C revealed with the MAGIC telescopes

NASA Astrophysics Data System (ADS)

Krause, J.; Reichardt, I.; Carmona, E.; Gozzini, S. R.; Jankowski, F.; MAGIC Collaboration

2012-12-01

The supernova remnant (SNR) W51C interacts with the molecular clouds of the star-forming region W51B, making the W51 complex one of the most promising targets to study cosmic ray acceleration. Gamma-ray emission from this region was discovered by Fermi/LAT and H.E.S.S., although its location was compatible with the SNR shell, the molecular cloud (MC) and a pulsar wind nebula (PWN) candidate. The modeling of the spectral energy distribution presented by the Fermi/LAT collaboration suggests a hadronic emission mechanism. Furthermore indications of an enhanced flux of low energy cosmic rays in the interaction region between SNR and MC have been reported based on ionization measurements in the mm regime. MAGIC conducted deep observations of W51, yielding a detection of an extended emission with more than 11 standard deviations. We extend the spectrum from the highest Fermi/LAT energies to ~5 TeV and find that it follows a single power law with an index of 2.58+/-0.07stat+/-0.22syst. We restrict the main part of the emission region to the zone where the SNR interacts with the molecular clouds. We also find a tail extending towards the PWN candidate CXO J192318.5+140305, possibly contributing up to 20% of the total flux. The broad band spectral energy distribution can be explained with a hadronic model that implies proton acceleration at least up to 50 TeV. This result, together with the morphology of the source, suggests that we observe ongoing acceleration of ions in the interaction zone between the SNR and the cloud.

Collapse and revival of entanglement between qubits coupled to a spin coherent state

NASA Astrophysics Data System (ADS)

Bahari, Iskandar; Spiller, Timothy P.; Dooley, Shane; Hayes, Anthony; McCrossan, Francis

We extend the study of the Jayne-Cummings (JC) model involving a pair of identical two-level atoms (or qubits) interacting with a single mode quantized field. We investigate the effects of replacing the radiation field mode with a composite spin, comprising N qubits, or spin-1/2 particles. This model is relevant for physical implementations in superconducting circuit QED, ion trap and molecular systems. For the case of the composite spin prepared in a spin coherent state, we demonstrate the similarities of this set-up to the qubits-field model in terms of the time evolution, attractor states and in particular the collapse and revival of the entanglement between the two qubits. We extend our analysis by taking into account an effect due to qubit imperfections. We consider a difference (or “mismatch”) in the dipole interaction strengths of the two qubits, for both the field mode and composite spin cases. To address decoherence due to this mismatch, we then average over this coupling strength difference with distributions of varying width. We demonstrate in both the field mode and the composite spin scenarios that increasing the width of the “error” distribution increases suppression of the coherent dynamics of the coupled system, including the collapse and revival of the entanglement between the qubits.

Cation specific binding with protein surface charges

PubMed Central

Hess, Berk; van der Vegt, Nico F. A.

2009-01-01

Biological organization depends on a sensitive balance of noncovalent interactions, in particular also those involving interactions between ions. Ion-pairing is qualitatively described by the law of “matching water affinities.” This law predicts that cations and anions (with equal valence) form stable contact ion pairs if their sizes match. We show that this simple physical model fails to describe the interaction of cations with (molecular) anions of weak carboxylic acids, which are present on the surfaces of many intra- and extracellular proteins. We performed molecular simulations with quantitatively accurate models and observed that the order K+ < Na+ < Li+ of increasing binding affinity with carboxylate ions is caused by a stronger preference for forming weak solvent-shared ion pairs. The relative insignificance of contact pair interactions with protein surfaces indicates that thermodynamic stability and interactions between proteins in alkali salt solutions is governed by interactions mediated through hydration water molecules. PMID:19666545

Measurements of H(+), He(2+), and He(+), in Corotating Interaction Regions at 1 AU

NASA Astrophysics Data System (ADS)

Chotoo, Kancham

Using the Supra-Thermal Ion Composition Spectrometer (STICS) from the SMS experiment on the WIND spacecraft, measurements of H+, He2+, and He+ were made during two corotating interacting regions (CIRs) at 1 AU. The unique energy range of STICS (6-198 keV/e) allowed simultaneous observation of the pre- and post-accelerated ions. These observations gave important clues about the source population, injection, acceleration mechanism, and ion transport in CIRs. The abundance of He2+ relative to H+ in the velocity range 2.5-6.0 times the solar wind velocity, VSW, (5-90 keV/amu) was between 0.11-0.18, which is more than double the solar wind values. However, the same ratio was observed in the suprathermal tail above 1.4 VSW in the spacecraft frame or above ~0.4 VSW in the solar wind frame. This suggests that the H+ and He2+ ions are injected equally into the CIR acceleration process from the suprathermal tail of the solar wind. At 1 AU the H+ and He2+ ions are primarily from the solar wind, but the He+ ions are interstellar pickup ions. The He+/He2+ ratio at 1 AU was ~0.15 for the same velocity range as above. However, this ratio was greater than 1.0 at 4.5 AU as measured previously (Gloeckler et al., 1994). This shows that the relative contribution of the pickup He+ ions to the seed population increases with radial distance away from the Sun. By combining data from three separate sensors on WIND (SMS-MASS, SMS-STICS, and EPACT-STEP), the extended helium distribution was presented for solar wind ions (~1 keV/amu) through energetic particles up to ~1 MeV/amu. The distribution covered 14 orders of magnitude in phase space density. This is the first time such an extended helium distribution is being reported at any radial distance. Using the Fisk and Lee (1980) model to fit the data between ~10-1000 keV/amu, the energetic particles were found to originate from 1.0-1.2 AU and not from beyond 2 AU, as is conventional believed. Anisotropy measurements were made using STICS for both the H+ and He2+ ions in the solar wind frame, and the results were compared to those made by EPACT-STEP. For both time intervals, the anisotropy directions showed significant deviations away from the average magnetic field direction in agreement with the STEP observations of Dwyer et al. (1997).

Determining the solar-flare photospheric scale height from SMM gamma-ray measurements

NASA Technical Reports Server (NTRS)

Lingenfelter, Richard E.

1991-01-01

A connected series of Monte Carlo programs was developed to make systematic calculations of the energy, temporal and angular dependences of the gamma-ray line and neutron emission resulting from such accelerated ion interactions. Comparing the results of these calculations with the Solar Maximum Mission/Gamma Ray Spectrometer (SMM/GRS) measurements of gamma-ray line and neutron fluxes, the total number and energy spectrum of the flare-accelerated ions trapped on magnetic loops at the Sun were determined and the angular distribution, pitch angle scattering, and mirroring of the ions on loop fields were constrained. Comparing the calculations with measurements of the time dependence of the neutron capture line emission, a determination of the He-3/H ratio in the photosphere was also made. The diagnostic capabilities of the SMM/GRS measurements were extended by developing a new technique to directly determine the effective photospheric scale height in solar flares from the neutron capture gamma-ray line measurements, and critically test current atmospheric models in the flare region.

Characterization of the ITER model negative ion source during long pulse operation

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

Hemsworth, R.S.; Boilson, D.; Crowley, B.

2006-03-15

It is foreseen to operate the neutral beam system of the International Thermonuclear Experimental Reactor (ITER) for pulse lengths extending up to 1 h. The performance of the KAMABOKO III negative ion source, which is a model of the source designed for ITER, is being studied on the MANTIS test bed at Cadarache. This article reports the latest results from the characterization of the ion source, in particular electron energy distribution measurements and the comparison between positive ion and negative ion extraction from the source.

A DIM model for sodium cluster-ions interacting with a charged conducting sphere

NASA Astrophysics Data System (ADS)

Kuntz, P. J.

A diatomics-in-molecules (DIM) model for the energy, shape and charge distribution of metal cluster ions in the presence of a charged insulated conducting sphere is presented. The electrostatic interaction between the sphere and the cluster-ion is introduced in a self-consistent manner which allows the sphere to be polarized by the ion and the ion by the sphere. This interaction appears in the diagonal elements of the model Hamiltonian matrix in such a way that the lowest eigenvalue includes the correct electrostatic energy for the charge distribution in the ground state. The model is applied to the calculation of fusion barriers for Na+2 and Na+3 ions. When both the charge distribution and the geometric configuration of the cluster-ion are allowed to relax freely, the energy as a function of distance from the sphere is nearly the same as that calculated from the electrostatic energy alone, which implies that details of the molecular structure of the cluster-ion can be neglected in calculating fusion barriers from charge polarization alone. That the fusion barriers lie sufficiently far away from the sphere so that the molecule does not dissociate under the influence of the Coulomb interaction confirms that it is meaningful to speak of two separate entities at the barrier position.

Phase transition studies of BiMnO{sub 3}: Mean field theory approximations

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

Lakshmi Priya, K. B.; Natesan, Baskaran, E-mail: nbaski@nitt.edu

We studied the phase transition and magneto-electric coupling effect of BiMnO{sub 3} by employing mean field theory approximations. To capture the ferromagnetic and ferroelectric transitions of BiMnO{sub 3}, we construct an extended Ising model in a 2D square lattice, wherein, the magnetic (electric) interactions are described in terms of the direct interactions between the localized magnetic (electric dipole) moments of Mn ions with their nearest neighbors. To evaluate our model, we obtain magnetization, magnetic susceptibility and electric polarization using mean field approximation calculations. Our results reproduce both the ferromagnetic and the ferroelectric transitions, matching very well with the experimental reports.more » Furthermore, consistent with experimental observations, our mean field results suggest that there is indeed a coupling between the magnetic and electric ordering in BiMnO{sub 3}.« less

Cluster approach to the prediction of thermodynamic and transport properties of ionic liquids

NASA Astrophysics Data System (ADS)

Seeger, Zoe L.; Kobayashi, Rika; Izgorodina, Ekaterina I.

2018-05-01

The prediction of physicochemical properties of ionic liquids such as conductivity and melting point would substantially aid the targeted design of ionic liquids for specific applications ranging from solvents for extraction of valuable chemicals to biowaste to electrolytes in alternative energy devices. The previously published study connecting the interaction energies of single ion pairs (1 IP) of ionic liquids to their thermodynamic and transport properties has been extended to larger systems consisting of two ion pairs (2 IPs), in which many-body and same-ion interactions are included. Routinely used cations, of the imidazolium and pyrrolidinium families, were selected in the study coupled with chloride, tetrafluoroborate, and dicyanamide. Their two ion pair clusters were subjected to extensive configuration screening to establish most stable structures. Interaction energies of these clusters were calculated at the spin-ratio scaled MP2 (SRS-MP2) level for the correlation interaction energy, and a newly developed scaled Hartree-Fock method for the rest of energetic contributions to interaction energy. A full geometry screening for each cation-anion combination resulted in 192 unique structures, whose stability was assessed using two criteria—widely used interaction energy and total electronic energy. Furthermore, the ratio of interaction energy to its dispersion component was correlated with experimentally observed melting points in 64 energetically favourable structures. These systems were also used to test the correlation of the dispersion contribution to interaction energy with measured conductivity.

Damage growth in Si during self-ion irradiation: A study of ion effects over an extended energy range

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

Holland, O.W.; El-Ghor, M.K.; White, C.W.

1989-01-01

Damage nucleation/growth in single-crystal Si during ion irradiation is discussed. For MeV ions, the rate of growth as well as the damage morphology are shown to vary widely along the track of the ion. This is attributed to a change in the dominant, defect-related reactions as the ion penetrates the crystal. The nature of these reactions were elucidated by studying the interaction of MeV ions with different types of defects. The defects were introduced into the Si crystal prior to high-energy irradiation by self-ion implantation at a medium energy (100 keV). Varied damage morphologies were produced by implanting different ionmore » fluences. Electron microscopy and ion-channeling measurements, in conjunction with annealing studies, were used to characterize the damage. Subtle changes in the predamage morphology are shown to result in markedly different responses to the high-energy irradiation, ranging from complete annealing of the damage to rapid growth. These divergent responses occur over a narrow range of dose (2--3 /times/ 10/sup 14/ cm/sup /minus/2/) of the medium-energy ions; this range also marks a transition in the growth behavior of the damage during the predamage implantation. A model is proposed which accounts for these observations and provides insight into ion-induced growth of amorphous layers in Si and the role of the amorphous/crystalline interface in this process. 15 refs, 9 figs.« less

Dynamic ion-ion and water-ion interactions in ion channels.

PubMed Central

Wu, J V

1992-01-01

The dynamic interactions among ions and water molecules in ion channels are treated based on an assumption that ions at binding sites can be knocked off by both transient entering ions and local water molecules. The theory, when applied to a single-site model K+ channel, provides solutions for super- and subsaturations, flux-ratio exponent (n') greater than 1, osmotic streaming current, activity-dependent reversal potentials, and anomalous mole-fraction behavior. The analysis predicts that: (a) the saturation may but, in general, does not follow the Michaelis-Menten relation; (b) streaming current results from imbalanced water-ion knock-off interactions; (c) n' greater than 1 even for single-site channels, but it is unlikely to exceed 1.4 unless the pore is occupied by one or more ion(s); (d) in the calculation involving two permeant ion species with similar radii, the heavier ions show higher affinity; the ion-ion knock-off dissociation from the site is more effective when two interacting ions are identical. Therefore, the "multi-ion behaviors" found in most ion channels are the consequences of dynamic ion-ion and water-ion interactions. The presence of these interactions does not require two or more binding sites in channels. PMID:1376158

Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping

NASA Astrophysics Data System (ADS)

Henke, Paul S.; Mak, Chi H.

2014-08-01

The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg2+ that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.

Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping.

PubMed

Henke, Paul S; Mak, Chi H

2014-08-14

The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg(2+) that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.

Ion flow at comet Halley

NASA Technical Reports Server (NTRS)

Johnstone, A.; Coates, A.; Kellock, S.; Wilken, B.; Jockers, K.

1986-01-01

The three-dimensional positive ion analyzer aboard the Giotto spacecraft has been used to study the interaction between protons and alpha-particles in the solar wind and positive ions from comet Halley. Although the first impression of the overall structure is that the plasma flow evolves smoothly as the nucleus is approached, three sharp transitions of relatively small amplitude can be identified on both the inbound and outbound legs of the trajectory. The outermost one, at about one million km from the nucleus, appears to be a multiple crossing of a weak bow shock. The innermost one, at 80,000 km, is the boundary where the flowing plasma becomes depleted. On a microscopic scale, the turbulence created by the interaction between the two ion populations extends to a distance of several million km from the nucleus. At Giotto's closest approach to the nucleus, the plasma produced around the spacecraft by dust and gas impacts was much more energetic than had been expected.

Long pulse operation of the Kamaboko negative ion source on the MANTIS test bed

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

Tramham, R.; Jacquot, C.; Riz, D.

1998-08-20

Advanced Tokamak concepts and steady state plasma scenarios require external plasma heating and current drive for extended time periods. This poses several problems for the neutral beam injection systems that are currently in use. The power loading of the ion source and accelerator are especially problematic. The Kamaboko negative ion source, a small scale model of the ITER arc source, is being prepared for extended operation of deuterium beams for up to 1000 seconds. The operating conditions of the plasma grid prove to be important for reducing electron power loading of the accelerator. Operation of deuterium beams for extended periodsmore » also poses radiation safety risks which must be addressed.« less

Potentiometric and spectroscopic study of the interaction of 3d transition metal ions with inositol hexakisphosphate

NASA Astrophysics Data System (ADS)

Veiga, Nicolás; Macho, Israel; Gómez, Kerman; González, Gabriel; Kremer, Carlos; Torres, Julia

2015-10-01

Among myo-inositol phosphates, the most abundant in nature is the myo-inositol hexakisphosphate, InsP6. Although it is known to be vital to cell functioning, the biochemical research into its metabolism needs chemical and structural analysis of all the protonation, complexation and precipitation processes that it undergoes in the biological media. In view of its high negative charge at physiological level, our group has been leading a thorough research into the InsP6 chemical and structural behavior in the presence of the alkali and alkaline earth metal ions essential for life. The aim of this article is to extend these studies, dealing with the chemical and structural features of the InsP6 interaction with biologically relevant 3d transition metal ions (Fe(II), Fe(III), Mn(II), Co(II), Ni(II), Cu(II) and Zn(II)), in a non-interacting medium and under simulated physiological conditions. The metal-complex stability constants were determined by potentiometry, showing under ligand-excess conditions the formation of mononuclear species in different protonation states. Under metal ion excess, polymetallic species were detected for Fe(II), Fe(III), Zn(II) and Cu(II). Additionally, the 31P NMR and UV-vis spectroscopic studies provided interesting structural aspects of the strong metal ion-InsP6 interaction.

Multi-ion, multi-event test of ion cyclotron resonance heating

NASA Technical Reports Server (NTRS)

Persoon, Ann M.

1993-01-01

The multi-ion, multi-event study of ion cyclotron resonance heating has been funded to study ion energization through ion cyclotron resonance with low frequency broadband electromagnetic turbulence. The modeling algorithm for the ion cyclotron resonance heating (ICRH) of oxygen ions was presented in Crew et al. (1990). Crew and his co-authors developed a two-parameter representation of selected oxygen conic distributions and modelled the conic formation in terms of resonance heating. The first year of this study seeks to extend the work of Crew and his co-authors by testing the applicability of the ICRH mechanism to helium ion conic distributions, using data obtained from the Energetic Ion Composition Spectrometer and the Plasma Wave Instrument on Dynamics Explorer 1.

A Self-Consistent Model of the Interacting Ring Current Ions and Electromagnetic Ion Cyclotron Waves, Initial Results: Waves and Precipitating Fluxes

NASA Technical Reports Server (NTRS)

Khazanov, G. V.; Gamayunov, K. V.; Jordanova, V. K.; Krivorutsky, E. N.

2002-01-01

Initial results from a newly developed model of the interacting ring current ions and ion cyclotron waves are presented. The model is based on the system of two kinetic equations: one equation describes the ring current ion dynamics, and another equation describes wave evolution. The system gives a self-consistent description of the ring current ions and ion cyclotron waves in a quasilinear approach. These equations for the ion phase space distribution function and for the wave power spectral density were solved on aglobal magnetospheric scale undernonsteady state conditions during the 2-5 May 1998 storm. The structure and dynamics of the ring current proton precipitating flux regions and the ion cyclotron wave-active zones during extreme geomagnetic disturbances on 4 May 1998 are presented and discussed in detail.

Outer satellite atmospheres: Their extended nature and planetary interactions

NASA Technical Reports Server (NTRS)

Smyth, W. H.; Combi, M. R.

1984-01-01

Model calculations for the brightness of the sodium cloud in Region A were performed to clarify the role played by the plasma torus sink in producing the east-west intensity asymmetry observed in the sodium D-lines. It was determined that the east-west electric field, proposed by Barbosa and Kievelson (1983) and Ip and Goertz (1983) to explain the dawn-dusk asymmetry in the torus ion emissions measured by the Voyager UVS instrument, could also produce the east-west sodium intensity asymmetry discovered earlier by Bergstralh et al. (1975, 1977). Model results for the directional features of the sodium cloud are also reported. The completion of the development of the Io potassium cloud model, progress in improving the Titan hydrogen torus model, and efforts in developing our model for hydrogen cometary atmospheres are also discussed.

Mechanisms of plasma-assisted catalyzed growth of carbon nanofibres: a theoretical modeling

NASA Astrophysics Data System (ADS)

Gupta, R.; Sharma, S. C.; Sharma, R.

2017-02-01

A theoretical model is developed to study the nucleation and catalytic growth of carbon nanofibers (CNFs) in a plasma environment. The model includes the charging of CNFs, the kinetics of the plasma species (neutrals, ions and electrons), plasma pretreatment of the catalyst film, and various processes unique to a plasma-exposed catalyst surface such as adsorption of neutrals, thermal dissociation of neutrals, ion induced dissociation, interaction between neutral species, stress exerted by the growing graphene layers and the growth of CNFs. Numerical calculations are carried out for typical glow discharge plasma parameters. It is found that the growth rate of CNFs decreases with the catalyst nanoparticle size. In addition, the effect of hydrogen on the catalyst nanoparticle size, CNF tip diameter, CNF growth rate, and the tilt angle of the graphene layers to the fiber axis are investigated. Moreover, it is also found that the length of CNFs increases with hydrocarbon number density. Our theoretical findings are in good agreement with experimental observations and can be extended to enhance the field emission characteristics of CNFs.

Characterization of the Cu(Π) and Zn(Π) binding to the Amyloid-β short peptides by both the Extended X-ray Absorption Fine Structure and the Synchrotron Radiation Circular Dichroism spectroscopy

NASA Astrophysics Data System (ADS)

Zhang, Zhiyin; Sun, Shuaishuai; Xu, Jianhua; Zhang, Jing; Huang, Yan; Zhang, Bingbing; Tao, Ye

2013-04-01

Alzheimer's disease (AD) is a progressive and devastating neurodegenerative pathology, clinically characterized by dementia, cognitive impairment, personality disorders and memory loss. It is generally accepted that, misfolding of Aβ peptides is the key element in pathogenesis and the secondary structure of Aβ can be changed to major β-strand with reasons unknown yet. Many studies have shown that the misfolding may be linked with some biometals, mainly copper and zinc ions. To characterize interactions of Aβ and metal ions, we utilized both the extended X-ray fine structure spectroscopy (EXAFS) and the synchrotron radiation circular dichroism spectroscopy (SRCD). Aβ (13-22), Aβ (13-21), Aβ (E22G) and Aβ(HH-AA) were selected to study the mechanism of copper and zinc binding to Aβ. We found that Cu interaction with H13 and H14 residues led to the disappearance of the PPΠ, while the Cu binding E22 residue caused a remarkable conformation change to β-sheet enrichment. The Zn ion, in contrast, made little effect on the conformation and it coordinated to only one histidine (H residue) or not.

Density-functional formulation of the generalized pseudopotential theory. III. Transition-metal interatomic potentials

NASA Astrophysics Data System (ADS)

Moriarty, John A.

1988-08-01

The first-principles, density-functional version of the generalized pseudopotential theory (GPT) developed in papers I and II of this series [Phys. Rev. B 16, 2537 (1977); 26, 1754 (1982)] for empty- and filled-d-band metals is here extended to pure transition metals with partially filled d bands. The present focus is on a rigorous, real-space expansion of the bulk total energy in terms of widely transferable, structure-independent interatomic potentials, including both central-force pair interactions and angular-force triplet and quadruplet interactions. To accomplish this expansion, a specialized set of starting equations is derived from the basic local-density formalism for a pure metal, including refined expansions for the exchange-correlation terms and a simplified yet accurate representation of the cohesive energy. The parent pseudo-Green's-function formalism of the GPT is then used to develop these equations in a plane-wave, localized-d-state basis. In this basis, the cohesive energy divides quite naturally into a large volume component and a smaller structural component. The volume component,which includes all one-ion intra-atomic energy contributions, already gives a good description of the cohesion in lowest order. The structural component is expanded in terms of weak interatomic matrix elements and gives rise to a multi-ion series which establishes the interatomic potentials. Special attention is focused on the dominant d-electron contributions to this series and complete formal results for the two-ion, three-ion, and four-ion d-state potentials (vd2, vd3, and vd4) are derived. In addition, a simplified model is used to demonstrate that while vd3 can be of comparable importance to vd2, vd4 is inherently small and the series is rapidly convergent beyond three-ion interactions. Analytic model forms are also derived for vd2 and vd3 in the case of canonical d bands. In this limit, vd2 is purely attractive and varies with interatomic distance as r-10, while vd3 is weak and attractive for almost empty or filled d bands and maximum in strength and repulsive for half-filled d bands. Full first-principles expressions are then developed for the total two-ion and three-ion potentials and implemented for all 20 3d and 4d transition metals. The first-principles potentials qualitatively display all of the trends predicted by the model results, but they also reflect additional effects, including long-range hybridization tails which must be suitably screened in real-space calculations. Finally, illustrative application of the first-principles potentials is made to the calculation of the [100] phonon spectrum for V and Cr, where the importance of three-ion angular forces is explicitly demonstrated.

Plasma IMS Composition Measurements for Europa, Ganymede, and the Jovian System

NASA Technical Reports Server (NTRS)

Sittler, E. C., Jr.; Cooper, J. F.; Hartle, R. E.; Paterson, W. R.; Christian, E. R.; Lipatov, A. S.; Mahaffy, P R.; Paschalidis, N.; Sarantos, M.; Coplan, M. A.;

Plasma IMS Composition Measurements for Europa, Ganymede, and the Jovian Systems

NASA Technical Reports Server (NTRS)

Sittler, E.; Cooper, J.; Hartle, R.; Paterson ,W.; Christian, E.; Mahaffy, P.; Paschalidis, N.; Lipatov, A.; Sarantos, M.; Coplan, M.;

Kinetics and Equilibrium of Fe3+ Ions Adsorption on Carbon Nanofibers

NASA Astrophysics Data System (ADS)

Alimin; Agusu, La; Ahmad, L. O.; Kadidae, L. O.; Ramadhan, L.; Nurdin, M.; Isdayanti, N.; Asria; Aprilia M, P.; Hasrudin

2018-05-01

Generally, the interaction between metal ions and adsorbent is governed by many factors including; concentration of metal ions, interaction time and solution pH. In this work, we applied liquid phase adsorption for studying the interaction between Fe3+ ions and Carbon Nanofibers (CNFs) irradiated by ultrasonic waves. Kinetics and isotherms model of the Fe3+ ion adsorption was investigated by varying contact time and pH. We found that the Fe3+ ions were efficiently adsorbed on CNFs for 0.5 h in acidic pH of around 5. In order to obtain the best-fitted isotherms model, Langmuir and Freundlich’s isotherms were used in this work. The adsorption equilibrium Fe3+ metal ions on CNFs tend to follow Langmuir. Adsorption kinetics of Fe3+ ions on CNFs were investigated by using both pseudo-first and pseudo-second orders. The adsorption kinetics coincided well with the pseudo-second-order.

Protons from carbon ion fragmentation at 0.3–2.0 GeV/nucleon: Comparison with models of ion-ion interactions

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

Abramov, B. M.; Alekseev, P. N.; Borodin, Yu. A.

2015-05-15

Yields of protons at 3.5° from carbon ion fragmentation at energies of T{sub 0} = 0.3, 0.6, 0.95, and 2.0 GeV/nucleon on a Be target were measured in the FRAGM experiment at TWA-ITEP heavy-ion facility. Proton momentum spectra cover both the region of the fragmentation maximum and the cumulative region. The differential cross sections span six orders of its magnitude. The spectra are compared with the predictions of four models of ion-ion interactions: LAQGSM03.03, SHIELD-HIT, QMD, and BC.

Deconvolution of Raman spectroscopic signals for electrostatic, H-bonding, and inner-sphere interactions between ions and dimethyl phosphate in solution

PubMed Central

Christian, Eric L; Anderson, Vernon E.; Harris, Michael E

2011-01-01

Quantitative analysis of metal ion-phosphodiester interactions is a significant experimental challenge due to the complexities introduced by inner-sphere, outer-sphere (H-bonding with coordinated water), and electrostatic interactions that are difficult to isolate in solution studies. Here, we provide evidence that inner-sphere, H-bonding and electrostatic interactions between ions and dimethyl phosphate can be deconvoluted through peak fitting in the region of the Raman spectrum for the symmetric stretch of non-bridging phosphate oxygens (νsPO 2-). An approximation of the change in vibrational spectra due to different interaction modes is achieved using ions capable of all or a subset of the three forms of metal ion interaction. Contribution of electrostatic interactions to ion-induced changes to the Raman νsPO2- signal could be modeled by monitoring attenuation of νsPO2- in the presence of tetramethylammonium, while contribution of H-bonding and inner-sphere coordination could be approximated from the intensities of altered νsPO2- vibrational modes created by an interaction with ammonia, monovalent or divalent ions. A model is proposed in which discrete spectroscopic signals for inner-sphere, H-bonding, and electrostatic interactions are sufficient to account for the total observed change in νsPO2- signal due to interaction with a specific ion capable of all three modes of interaction. Importantly, the quantitative results are consistent with relative levels of coordination predicted from absolute electronegativity and absolute hardness of alkali and alkaline earth metals. PMID:21334281

Influence of the inter-ion interaction on the phase diagrams of the 1D Falicov-Kimball system

NASA Astrophysics Data System (ADS)

Gajek, Z.; Lemański, R.

2004-05-01

A model of itinerant, spinless electrons interacting with ions via the on-site Coulomb potential U, modified by the inter-ionic nearest-neighbour interaction V, is studied on the one-dimensional infinite lattice. Only periodical configurations of the ions with a limited number of lattice sites in a unit cell and their mixtures are taken into account. Phases whose energies reach minimum values for given electron and ion chemical potentials are selected and depicted for a set of model parameters. Then the results are translated into the ion density-electron density canonical phase diagrams and summarized in the electrondensity-U plane. The diagrams clearly show how various kinds of charge ordering evolve with V, starting from V=0 case, that represents the standard Falicov-Kimball model discussed previously.

Molecular simulations of self-assembly processes in metal-organic frameworks: Model dependence

NASA Astrophysics Data System (ADS)

Biswal, Debasmita; Kusalik, Peter G.

2017-07-01

Molecular simulation is a powerful tool for investigating microscopic behavior in various chemical systems, where the use of suitable models is critical to successfully reproduce the structural and dynamic properties of the real systems of interest. In this context, molecular dynamics simulation studies of self-assembly processes in metal-organic frameworks (MOFs), a well-known class of porous materials with interesting chemical and physical properties, are relatively challenging, where a reasonably accurate representation of metal-ligand interactions is anticipated to play an important role. In the current study, we both investigate the performance of some existing models and introduce and test new models to help explore the self-assembly in an archetypal Zn-carboxylate MOF system. To this end, the behavior of six different Zn-ion models, three solvent models, and two ligand models was examined and validated against key experimental structural parameters. To explore longer time scale ordering events during MOF self-assembly via explicit solvent simulations, it is necessary to identify a suitable combination of simplified model components representing metal ions, organic ligands, and solvent molecules. It was observed that an extended cationic dummy atom (ECDA) Zn-ion model combined with an all-atom carboxylate ligand model and a simple dipolar solvent model can reproduce characteristic experimental structures for the archetypal MOF system. The successful use of these models in extensive sets of molecular simulations, which provide key insights into the self-assembly mechanism of this archetypal MOF system occurring during the early stages of this process, has been very recently reported.

A novel model for studies of blood-mediated long-term responses to cellular transplants

PubMed Central

Lindblom, Susanne; Hong, Jaan; Nilsson, Bo; Korsgren, Olle; Ronquist, Gunnar

2015-01-01

Aims Interaction between blood and bio-surfaces is important in many medical fields. With the aim of studying blood-mediated reactions to cellular transplants, we developed a whole-blood model for incubation of small volumes for up to 48 h. Methods Heparinized polyvinyl chloride tubing was cut in suitable lengths and sealed to create small bags. Multiple bags, with fresh venous blood, were incubated attached to a rotating wheel at 37°C. Physiological variables in blood were monitored: glucose, blood gases, mono- and divalent cations and chloride ions, osmolality, coagulation (platelet consumption, thrombin-antithrombin complexes (TAT)), and complement activation (C3a and SC5b-9), haemolysis, and leukocyte viability. Results Basic glucose consumption was high. Glucose depletion resulted in successive elevation of extracellular potassium, while sodium and calcium ions decreased due to inhibition of energy-requiring ion pumps. Addition of glucose improved ion balance but led to metabolic acidosis. To maintain a balanced physiological environment beyond 6 h, glucose and sodium hydrogen carbonate were added regularly based on analyses of glucose, pH, ions, and osmotic pressure. With these additives haemolysis was prevented for up to 72 h and leukocyte viability better preserved. Despite using non-heparinized blood, coagulation and complement activation were lower during long-term incubations compared with addition of thromboplastin and collagen. Conclusion A novel whole-blood model for studies of blood-mediated responses to a cellular transplant is presented allowing extended observations for up to 48 h and highlights the importance of stringent evaluations and adjustment of physiological conditions. PMID:25322825

Simulating the dynamics of complex plasmas.

PubMed

Schwabe, M; Graves, D B

2013-08-01

Complex plasmas are low-temperature plasmas that contain micrometer-size particles in addition to the neutral gas particles and the ions and electrons that make up the plasma. The microparticles interact strongly and display a wealth of collective effects. Here we report on linked numerical simulations that reproduce many of the experimental results of complex plasmas. We model a capacitively coupled plasma with a fluid code written for the commercial package comsol. The output of this model is used to calculate forces on microparticles. The microparticles are modeled using the molecular dynamics package lammps, which we extended to include the forces from the plasma. Using this method, we are able to reproduce void formation, the separation of particles of different sizes into layers, lane formation, vortex formation, and other effects.

Multispacecraft study of shock-flux rope interaction

NASA Astrophysics Data System (ADS)

Blanco-Cano, Xochitl; Burgess, David; Sundberg, Torbjorn; Kajdic, Primoz

2017-04-01

Interplanetary (IP) shocks can be driven in the solar wind by fast coronal mass ejections. These shocks can accelerate particles near the Sun and through the heliosphere, being associated to solar energetic particle (SEP) and energetic storm particle (ESP) events. IP shocks can interact with structures in the solar wind, and with planetary magnetospheres. In this study we show how the properties of an IP shock change when it interacts with a medium scale flux rope (FR) like structure. We use data measurements from CLUSTER, WIND and ACE. These three spacecraft observed the shock-FR interaction at different stages of its evolution. We find that the shock-FR interaction locally changes the shock geometry, affecting ion injection processes, and the upstream and downstream regions. While WIND and ACE observed a quasi-perpendicular shock, CLUSTER crossed a quasi-parallel shock and a foreshock with a variety of ion distributions. The complexity of the ion foreshock can be explained by the dynamics of the shock transitioning from quasi-perpendicular to quasi-parallel, and the geometry of the magnetic field around the flux rope. Interactions such as the one we discuss can occur often along the extended IP shock fronts, and hence their importance towards a better understanding of shock acceleration.

Quantum information processing between different atomic ions

NASA Astrophysics Data System (ADS)

Zhang, Xiang; Zheng, Bo; Zhang, Junhua; Um, Mark; An, Shuoming; Zhao, Tianji; Duan, Luming; Kim, Kihwan

2012-06-01

There is increasing interest in utilizing and combining the advantages of different quantum systems. Here, we discuss the experimental generation of entanglement between the quantum states of different atomic ions through the Coulomb interaction at the same linear radio-frequency trap. This scheme would be extended to implement the teleportation of quantum information from one kind of atom to the other. Moreover, the hybrid system of trapped ions is expected to play an essential role in the realization of a large quantum system, where a quantum state of one species is used for quantum operation and that of the other is for the cooling and stabilization of the whole ion chain. Finally, we will report the experimental progress on building the hybrid trapped ion system.

Alternative modeling methods for plasma-based Rf ion sources

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

Veitzer, Seth A., E-mail: veitzer@txcorp.com; Kundrapu, Madhusudhan, E-mail: madhusnk@txcorp.com; Stoltz, Peter H., E-mail: phstoltz@txcorp.com

Rf-driven ion sources for accelerators and many industrial applications benefit from detailed numerical modeling and simulation of plasma characteristics. For instance, modeling of the Spallation Neutron Source (SNS) internal antenna H{sup −} source has indicated that a large plasma velocity is induced near bends in the antenna where structural failures are often observed. This could lead to improved designs and ion source performance based on simulation and modeling. However, there are significant separations of time and spatial scales inherent to Rf-driven plasma ion sources, which makes it difficult to model ion sources with explicit, kinetic Particle-In-Cell (PIC) simulation codes. Inmore » particular, if both electron and ion motions are to be explicitly modeled, then the simulation time step must be very small, and total simulation times must be large enough to capture the evolution of the plasma ions, as well as extending over many Rf periods. Additional physics processes such as plasma chemistry and surface effects such as secondary electron emission increase the computational requirements in such a way that even fully parallel explicit PIC models cannot be used. One alternative method is to develop fluid-based codes coupled with electromagnetics in order to model ion sources. Time-domain fluid models can simulate plasma evolution, plasma chemistry, and surface physics models with reasonable computational resources by not explicitly resolving electron motions, which thereby leads to an increase in the time step. This is achieved by solving fluid motions coupled with electromagnetics using reduced-physics models, such as single-temperature magnetohydrodynamics (MHD), extended, gas dynamic, and Hall MHD, and two-fluid MHD models. We show recent results on modeling the internal antenna H{sup −} ion source for the SNS at Oak Ridge National Laboratory using the fluid plasma modeling code USim. We compare demonstrate plasma temperature equilibration in two-temperature MHD models for the SNS source and present simulation results demonstrating plasma evolution over many Rf periods for different plasma temperatures. We perform the calculations in parallel, on unstructured meshes, using finite-volume solvers in order to obtain results in reasonable time.« less

Alternative modeling methods for plasma-based Rf ion sources.

PubMed

Veitzer, Seth A; Kundrapu, Madhusudhan; Stoltz, Peter H; Beckwith, Kristian R C

2016-02-01

Rf-driven ion sources for accelerators and many industrial applications benefit from detailed numerical modeling and simulation of plasma characteristics. For instance, modeling of the Spallation Neutron Source (SNS) internal antenna H(-) source has indicated that a large plasma velocity is induced near bends in the antenna where structural failures are often observed. This could lead to improved designs and ion source performance based on simulation and modeling. However, there are significant separations of time and spatial scales inherent to Rf-driven plasma ion sources, which makes it difficult to model ion sources with explicit, kinetic Particle-In-Cell (PIC) simulation codes. In particular, if both electron and ion motions are to be explicitly modeled, then the simulation time step must be very small, and total simulation times must be large enough to capture the evolution of the plasma ions, as well as extending over many Rf periods. Additional physics processes such as plasma chemistry and surface effects such as secondary electron emission increase the computational requirements in such a way that even fully parallel explicit PIC models cannot be used. One alternative method is to develop fluid-based codes coupled with electromagnetics in order to model ion sources. Time-domain fluid models can simulate plasma evolution, plasma chemistry, and surface physics models with reasonable computational resources by not explicitly resolving electron motions, which thereby leads to an increase in the time step. This is achieved by solving fluid motions coupled with electromagnetics using reduced-physics models, such as single-temperature magnetohydrodynamics (MHD), extended, gas dynamic, and Hall MHD, and two-fluid MHD models. We show recent results on modeling the internal antenna H(-) ion source for the SNS at Oak Ridge National Laboratory using the fluid plasma modeling code USim. We compare demonstrate plasma temperature equilibration in two-temperature MHD models for the SNS source and present simulation results demonstrating plasma evolution over many Rf periods for different plasma temperatures. We perform the calculations in parallel, on unstructured meshes, using finite-volume solvers in order to obtain results in reasonable time.

Coherent and incoherent J /ψ photonuclear production in an energy-dependent hot-spot model

NASA Astrophysics Data System (ADS)

Cepila, J.; Contreras, J. G.; Krelina, M.

2018-02-01

In a previous publication, we have presented a model for the photoproduction of J /ψ vector mesons off protons, where the proton structure in the impact-parameter plane is described by an energy-dependent hot-spot profile. Here we extend this model to study the photonuclear production of J /ψ vector mesons in coherent and incoherent interactions of heavy nuclei. We study two methods to extend the model to the nuclear case: using the standard Glauber-Gribov formalism and using geometric scaling to obtain the nuclear saturation scale. We find that the incoherent cross section changes sizably with the inclusion of subnucleonic hot spots and that this change is energy dependent. We propose to search for this behavior by measuring the ratio of the incoherent to coherent cross sections at different energies. We compare the results of our model to results from the Relativistic Heavy-Ion Collider (RHIC) and from run 1 at the Large Hadron Collider (LHC), finding satisfactory agreement. We also present predictions for the LHC at the new energies reached in run 2. The predictions include J /ψ production in ultraperipheral collisions, as well as the recently observed photonuclear production in peripheral collisions.

A Self-Consistent Model of the Interacting Ring Current Ions with Electromagnetic ICWs

NASA Technical Reports Server (NTRS)

Khazanov, G. V.; Gamayunov, K. V.; Jordanova, V. K.; Krivorutsky, E. N.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Initial results from a newly developed model of the interacting ring current ions and ion cyclotron waves are presented. The model is based on the system of two bound kinetic equations: one equation describes the ring current ion dynamics, and another equation describes wave evolution. The system gives a self-consistent description of ring current ions and ion cyclotron waves in a quasilinear approach. These two equations were solved on a global scale under non steady-state conditions during the May 2-5, 1998 storm. The structure and dynamics of the ring current proton precipitating flux regions and the wave active zones at three time cuts around initial, main, and late recovery phases of the May 4, 1998 storm phase are presented and discussed in detail. Comparisons of the model wave-ion data with the Polar/HYDRA and Polar/MFE instruments results are presented..

Ion energy distributions and densities in the plume of Enceladus

NASA Astrophysics Data System (ADS)

Sakai, Shotaro; Cravens, Thomas E.; Omidi, Nojan; Perry, Mark E.; Waite, J. Hunter

2016-10-01

Enceladus has a dynamic plume that is emitting gas, including water vapor, and dust. The gas is ionized by solar EUV radiation, charge exchange, and electron impact and extends throughout the inner magnetosphere of Saturn. The charge exchange collisions alter the plasma composition. Ice grains (dust) escape from the vicinity of Enceladus and form the E ring, including a portion that is negatively charged by the local plasma. The inner magnetosphere within 10 RS (Saturn radii) contains a complex mixture of plasma, neutral gas, and dust that links back to Enceladus. In this paper we investigate the energy distributions, ion species and densities of water group ions in the plume of Enceladus using test particle and Monte Carlo methods that include collisional processes such as charge exchange and ion-neutral chemical reactions. Ion observations from the Cassini Ion and Neutral Mass Spectrometer (INMS) for E07 are presented for the first time. We use the modeling results to interpret observations made by the Cassini Plasma Spectrometer (CAPS) and the INMS. The low energy ions, as observed by CAPS, appear to be affected by a vertical electric field (EZ=-10 μV/m) in the plume. The EZ field may be associated with the charged dust and/or the pressure gradient of plasma. The model results, along with the results of earlier models, show that H3O+ ions created by chemistry are predominant in the plume, which agrees with INMS and CAPS data, but the INMS count rate in the plume for the model is several times greater than the data, which we do not fully understand. This composition and the total ion count found in the plume agree with INMS and CAPS data. On the other hand, the Cassini Langmuir Probe measured a maximum plume ion density more than 30,000 cm-3, which is far larger than the maximum ion density from our model, 900 cm-3. The model results also demonstrate that most of the ions in the plume are from the external magnetospheric flow and are not generated by local ionization. The origin of the ions in the plume was investigated using two different velocity models. Most ions were created by the interaction with background magnetospheric plasma and by photoionization. INMS and CAPS also detected water cluster ions. We will interpret these observations as a result of ion collisions with neutral water clusters, (H2O)n, originating in the tiger stripe vents as suggested by Tokar et al. (2009). We also estimated the process of generating cluster ions based on the INMS observations. We suggest that the most likely source is reaction of H3O+ with neutral water clusters or dimers such as (H2O)2 formed in the plume vents.

A preliminary study of extended magnetic field structures in the ionosphere

NASA Technical Reports Server (NTRS)

Sullivan, James D.; Lane, Barton G.; Post, Richard S.

1987-01-01

Several plasma phenomena which are to be expected around a magnet in LEO were identified and analyzed qualitatively. The ASTROMAG cusp magnet will create an extended field whose strength drops to the ambient level over a scale length of approx. 15 m; the combined field has a complex topology with ring nulls and open and closed field lines. The entire configuration is moving through the partially ionized F-layer of the ionosphere at a speed slow compared to the local Alfven speed but fast compared to the ion sound speed. The ambient plasma crosses the extended field structure in a time short compared to the ion Larmor period yet long relative to the electron Larmor period. Thus, electrons behave as a magnetized fluid while ions move ballistically until reflected from higher fields near the cusp. Since the Debye length is short compared to the field scale length, an electrostatic shock-like structure forms to equilibrate the flows and achieve quasi-neutrality. The ambient plasma will be excluded from a cavity near the magnet. The size and nature of the strong interaction region in which the magnet significantly perturbs the ambient flow were determined by studying ion orbits numerically. Lecture viewgraphs summarizing these results are presented.

Competitive Binding to Cuprous Ions of Protein and BCA in the Bicinchoninic Acid Protein Assay

PubMed Central

Huang, Tao; Long, Mian; Huo, Bo

2010-01-01

Although Bicinchoninic acid (BCA) has been widely used to determine protein concentration, the mechanism of interaction between protein, copper ion and BCA in this assay is still not well known. Using the Micro BCA protein assay kit (Pierce Company), we measured the absorbance at 562 nm of BSA solutions with different concentrations of protein, and also varied the BCA concentration. When the concentration of protein was increased, the absorbance exhibited the known linear and nonlinear increase, and then reached an unexpected plateau followed by a gradual decrease. We introduced a model in which peptide chains competed with BCA for binding to cuprous ions. Formation of the well-known chromogenic complex of BCA-Cu1+-BCA was competed with the binding of two peptide bonds (NTPB) to cuprous ion, and there is the possibility of the existence of two new complexes. A simple equilibrium equation was established to describe the correlations between the substances in solution at equilibrium, and an empirical exponential function was introduced to describe the reduction reaction. Theoretical predictions of absorbance from the model were in good agreement with the measurements, which not only validated the competitive binding model, but also predicted a new complex of BCA-Cu1+-NTPB that might exist in the final solution. This work provides a new insight into understanding the chemical bases of the BCA protein assay and might extend the assay to higher protein concentration. PMID:21625379

Fission product ion exchange between zeolite and a molten salt

NASA Astrophysics Data System (ADS)

Gougar, Mary Lou D.

The electrometallurgical treatment of spent nuclear fuel (SNF) has been developed at Argonne National Laboratory (ANL) and has been demonstrated through processing the sodium-bonded SNF from the Experimental Breeder Reactor-II in Idaho. In this process, components of the SNF, including U and species more chemically active than U, are oxidized into a bath of lithium-potassium chloride (LiCl-KCl) eutectic molten salt. Uranium is removed from the salt solution by electrochemical reduction. The noble metals and inactive fission products from the SNF remain as solids and are melted into a metal waste form after removal from the molten salt bath. The remaining salt solution contains most of the fission products and transuranic elements from the SNF. One technique that has been identified for removing these fission products and extending the usable life of the molten salt is ion exchange with zeolite A. A model has been developed and tested for its ability to describe the ion exchange of fission product species between zeolite A and a molten salt bath used for pyroprocessing of spent nuclear fuel. The model assumes (1) a system at equilibrium, (2) immobilization of species from the process salt solution via both ion exchange and occlusion in the zeolite cage structure, and (3) chemical independence of the process salt species. The first assumption simplifies the description of this physical system by eliminating the complications of including time-dependent variables. An equilibrium state between species concentrations in the two exchange phases is a common basis for ion exchange models found in the literature. Assumption two is non-simplifying with respect to the mathematical expression of the model. Two Langmuir-like fractional terms (one for each mode of immobilization) compose each equation describing each salt species. The third assumption offers great simplification over more traditional ion exchange modeling, in which interaction of solvent species with each other is considered. (Abstract shortened by UMI.)

The search for active Europa plumes in Galileo plasma particle detector data: the E12 flyby

NASA Astrophysics Data System (ADS)

Huybrighs, H.; Roussos, E.; Krupp, N.; Fraenz, M.; Futaana, Y.; Barabash, S. V.; Glassmeier, K. H.

2017-12-01

Hubble Space Telescope observations of Europa's auroral emissions and transits in front of Jupiter suggest that recurring water vapour plumes originating from Europa's surface might exist. If conclusively proven, the discovery of these plumes would be significant, because Europa's potentially habitable ocean could be studied remotely by taking in-situ samples of these plumes from a flyby mission. The first opportunity to collect in-situ evidence of the plumes will not arise before the early 2030's when ESA's JUICE mission or NASA's Europa Clipper are set to arrive. However, it may be possible that NASA's Galileo mission has already encountered the plumes when it was active in the Jupiter system from 1995 to 2003. It has been suggested that the high plasma densities and anomalous magnetic fields measured during one of the Galileo flybys of Europa (flyby E12) could be connected to plume activity. In the context of the search for Europa plume signatures in Galileo particle data we present an overview of the in-situ plasma particle data obtained by the Galileo spacecraft during the E12 flyby. Focus is in particular on the data obtained with the plasma particle instruments PLS (low energy ions and electrons) and EPD (high energy ions and electrons). We search for signs of an extended exosphere/ionosphere that could be consistent with ongoing plume activity. The PLS data obtained during the E12 flyby show an extended interaction region between Europa and the plasma from Jupiter's magnetosphere, hinting at the existence of an extended ionosphere and exosphere. Furthermore we show how the EPD data are analyzed and modelled in order to evaluate whether a series of energetic ion depletions can be attributed to losses on the moon's surface or its neutral exosphere.

Propagation and head-on collisions of ion-acoustic solitons in a Thomas-Fermi magnetoplasma: Relativistic degeneracy effects

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

Akbari-Moghanjoughi, M.

Small amplitude propagation and quasielastic head-on collision of ion-acoustic solitary waves (IASWs) are investigated in a degenerate Thomas-Fermi electron-positron-ion magnetized plasma using extended Poincare-Lighthill-Kuo reductive perturbation method for both ultrarelativistic and nonrelativistic electron/positron degeneracy cases. It is observed that both bright- and dark-type solitary shapes can exist in such plasma, depending on two critical values. The shape of ion-acoustic solitary structures as well as sign of their collision phase shifts are both determined by the same critical values. It is further revealed that relativistic degeneracy of electrons/positrons has significant effect on the propagation as well as interaction of IASWs.

Kinetic and spectral descriptions of autoionization phenomena associated with atomic processes in plasmas

NASA Astrophysics Data System (ADS)

Jacobs, Verne L.

2017-06-01

This investigation has been devoted to the theoretical description and computer modeling of atomic processes giving rise to radiative emission in energetic electron and ion beam interactions and in laboratory plasmas. We are also interested in the effects of directed electron and ion collisions and of anisotropic electric and magnetic fields. In the kinetic-theory description, we treat excitation, de-excitation, ionization, and recombination in electron and ion encounters with partially ionized atomic systems, including the indirect contributions from processes involving autoionizing resonances. These fundamental collisional and electromagnetic interactions also provide particle and photon transport mechanisms. From the spectral perspective, the analysis of atomic radiative emission can reveal detailed information on the physical properties in the plasma environment, such as non-equilibrium electron and charge-state distributions as well as electric and magnetic field distributions. In this investigation, a reduced-density-matrix formulation is developed for the microscopic description of atomic electromagnetic interactions in the presence of environmental (collisional and radiative) relaxation and decoherence processes. Our central objective is a fundamental microscopic description of atomic electromagnetic processes, in which both bound-state and autoionization-resonance phenomena can be treated in a unified and self-consistent manner. The time-domain (equation-of-motion) and frequency-domain (resolvent-operator) formulations of the reduced-density-matrix approach are developed in a unified and self-consistent manner. This is necessary for our ultimate goal of a systematic and self-consistent treatment of non-equilibrium (possibly coherent) atomic-state kinetics and high-resolution (possibly overlapping) spectral-line shapes. We thereby propose the introduction of a generalized collisional-radiative atomic-state kinetics model based on a reduced-density-matrix formulation. It will become apparent that the full atomic data needs for the precise modeling of extreme non-equilibrium plasma environments extend beyond the conventional radiative-transition-probability and collisional-cross-section data sets.

The role of turbulence-flow interactions in L- to H-mode transition dynamics: recent progress

NASA Astrophysics Data System (ADS)

Schmitz, L.

2017-02-01

Recent experimental and simulation work has substantially advanced the understanding of L-mode plasma edge turbulence and plasma flows and their mutual interaction across the L-H transition. Flow acceleration and E   ×   B shear flow amplification via the turbulent Reynolds stress have been directly observed in multiple devices, using multi-tip probe arrays, Doppler backscattering, beam emission spectroscopy, and gas puff imaging diagnostics. L-H transitions characterized by limit-cycle oscillations (LCO) allow probing of the trigger dynamics and the synergy of turbulence-driven and pressure-gradient-driven flows with high spatio-temporal resolution. L-mode turbulent structures exhibit characteristic changes in topology (tilting) and temporal and radial correlation preceding the L-H transition. Long-range toroidal flow correlations increase preceding edge-transport-barrier formation. The energy transfer from the turbulence spectrum to large-scale axisymmetric flows has been quantified in L-LCO and fast L-H transitions in several devices. After formation of a transient barrier, the increasing ion pressure gradient (via the E   ×   B flow shear associated with diamagnetic flow) sustains fluctuation suppression and secures the transition to H-mode. Heuristic models of the L-H trigger dynamics have progressed from 0D predator-prey models to 1D extended models, including neoclassical ion flow-damping and pressure-gradient evolution. Initial results from 2D and 3D reduced fluid models have been obtained for high-collisionality regimes.

Dynamics from Seconds to Hours in Hodgkin-Huxley Model with Time-Dependent Ion Concentrations and Buffer Reservoirs

PubMed Central

Hübel, Niklas; Dahlem, Markus A.

2014-01-01

The classical Hodgkin-Huxley (HH) model neglects the time-dependence of ion concentrations in spiking dynamics. The dynamics is therefore limited to a time scale of milliseconds, which is determined by the membrane capacitance multiplied by the resistance of the ion channels, and by the gating time constants. We study slow dynamics in an extended HH framework that includes time-dependent ion concentrations, pumps, and buffers. Fluxes across the neuronal membrane change intra- and extracellular ion concentrations, whereby the latter can also change through contact to reservoirs in the surroundings. Ion gain and loss of the system is identified as a bifurcation parameter whose essential importance was not realized in earlier studies. Our systematic study of the bifurcation structure and thus the phase space structure helps to understand activation and inhibition of a new excitability in ion homeostasis which emerges in such extended models. Also modulatory mechanisms that regulate the spiking rate can be explained by bifurcations. The dynamics on three distinct slow times scales is determined by the cell volume-to-surface-area ratio and the membrane permeability (seconds), the buffer time constants (tens of seconds), and the slower backward buffering (minutes to hours). The modulatory dynamics and the newly emerging excitable dynamics corresponds to pathological conditions observed in epileptiform burst activity, and spreading depression in migraine aura and stroke, respectively. PMID:25474648

Ionic Structure at Dielectric Interfaces

NASA Astrophysics Data System (ADS)

Jing, Yufei

The behavior of ions in liquids confined between macromolecules determines the outcome of many nanoscale assembly processes in synthetic and biological materials such as colloidal dispersions, emulsions, hydrogels, DNA, cell membranes, and proteins. Theoretically, the macromolecule-liquid boundary is often modeled as a dielectric interface and an important quantity of interest is the ionic structure in a liquid confined between two such interfaces. The knowledge gleaned from the study of ionic structure in such models can be useful in several industrial applications, such as biosensors, lithium-ion batteries double-layer supercapacitors for energy storage and seawater desalination. Electrostatics plays a critical role in the development of such functional materials. Many of the functions of these materials, result from charge and composition heterogeneities. There are great challenges in solving electrostatics problems in heterogeneous media with arbitrary shapes because electrostatic interactions remains unknown but depend on the particular density of charge distributions. Charged molecules in heterogeneous media affect the media's dielectric response and hence the interaction between the charges is unknown since it depends on the media and on the geometrical properties of the interfaces. To determine the properties of heterogeneous systems including crucial effects neglected in classical mean field models such as the hard core of the ions, the dielectric mismatch and interfaces with arbitrary shapes. The effect of hard core interactions accounts properly for short range interactions and the effect of local dielectric heterogeneities in the presence of ions and/or charged molecules for long-range interactions are both analyzed via an energy variational principle that enables to update charges and the medium's response in the same simulation time step. In particular, we compute the ionic structure in a model system of electrolyte confined by two planar dielectric interfaces using molecular dynamics(MD) simulations and compared it with liquid state theory result. We explore the effects of high electrolyte concentrations, multivalent ions, and dielectric contrasts on the ionic distributions. We observe the presence of non-monotonous ionic density profiles leading to structure deformation in the fluid which is attributed to the competition between electrostatic and steric (entropic) interactions. We find that thermal forces that arise from symmetry breaking at the interfaces can have a profound effect on the ionic structure and can oftentimes overwhelm the influence of dielectric discontinuity. The combined effect of ionic correlations and inhomogeneous dielectric permittivity significantly changes the character of effective interaction between two interfaces. We show that, in concentrated electrolytes with confinement, it is imperative to take into account the finite-size of the ions as well as proper description of electrostatic interactions in heterogeneous media, which is not fully fulfilled by Poisson-Boltzmann based approaches. The effect of electric field at interface between two immiscible electrolyte solutions is studied as well. The classical Poisson-Boltzmann theory has been widely used to describe the corresponding ionic distribution, even though it neglects the polarization and ion correlations typical of these charged systems. Using Monte Carlo simulations, we provide an enhanced description of an oil-water interface in the presence of an electric field without needing any adjustable parameter, including realistic ionic sizes, ion correlations, and image charges. Our data agree with experimental measurements of excess surface tension for a wide range of electrolyte concentrations of LiCl and TBATPB (tetrabutylammonium-tetraphenylborate), contrasting with the result of the classical non-linear Poisson-Boltzmann theory. More importantly, we show that the size-asymmetry between small Li+ and large Cl- ions can significantly increase the electric field near the liquid interface, or can even reverse it locally, at high salt concentrations in the aqueous phase. These observations suggest a novel trapping/release mechanism of charged nanoparticles at oil-water interfaces in the vicinity of the point of zero charge. In addition, we study the effects of size asymmetry and charge asymmetry on ion distribution at a dielectric interface using coarse-grained MD based on an energy variational principle. The goal is to explore charge amplification with exact consideration of surface polarization. We find that both size asymmetry and charge asymmetry lead to charge separation at the interfaces. In addition, charge separation is enhanced by interface polarization. We are currently extending the research to charged interfaces that has broad applications such as batteries and supercapacitors for energy storage.

Wave-Particle Interactions As a Driving Mechanism for the Solar Wind

NASA Technical Reports Server (NTRS)

Wagner, William J.

2004-01-01

Our research has been focusing on a highly experimentally relevant issue: intermittency of the fluctuating fields in outflowing plasmas. We have contributed to both the theoretical and experimental research of the topic. In particular, we have developed a theoretical model and data analyzing programs to examine the issue of intermittency in space plasma outflows, including the solar wind. As fluctuating electric fields in the solar wind are likely to provide a heating and acceleration mechanism for the ions, our studies of the intermittency in turbulence in space plasma outflows help us toward achieving the goal of comparing major physical mechanisms that contribute to the driving of the fast solar wind. Our new theoretical model extends the utilities of our global hybrid model, which has allowed us to follow the kinetic evolution of the particle distributions along an inhomogeneous field line while the particles are subjected to various physical mechanisms. The physical effects that were considered in the global hybrid model included wave-particle interactions, an ambipolar electric field that was consistent with the particle distributions themselves, and Coulomb collisions. With an earlier version of the global hybrid model, we examined the overall impact on the solar wind flow due to the combination of these physical effects. In particular, we studied the combined effects of two major mechanisms that had been proposed as the drivers of the fast solar wind: (1) velocity filtration effect due to suprathermal electrons; (2) ion cyclotron resonance. Since the approval of this research grant, we have updated the model such that the effects due to these two driving mechanisms can be examined separately, thereby allowing us to compare their contributions to the acceleration of the solar wind. In the next section, we shall demonstrate that the velocity filtration effect is rather insignificant in comparison with that due to ion cyclotron resonance.

A Self-Consistent Model of the Interacting Ring Current Ions and Electromagnetic ICWs. Initial Results: Waves and Precipitation Fluxes

NASA Technical Reports Server (NTRS)

Khazanov, G. V.; Gamayunov, K. V.; Jordanova, V. K.; Krivorutsky, E. N.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Initial results from the new developed model of the interacting ring current ions and ion cyclotron waves are presented. The model described by the system of two bound kinetic equations: one equation describes the ring current ion dynamics, and another one gives wave evolution. Such system gives a self-consistent description of the ring current ions and ion cyclotron waves in a quasilinear approach. Calculating ion-wave relationships, on a global scale under non steady-state conditions during May 2-5, 1998 storm, we presented the data at three time cuts around initial, main, and late recovery phases of May 4, 1998 storm phase. The structure and dynamics of the ring current proton precipitating flux regions and the wave active ones are discussed in detail.

A parametric study of the drift-tearing mode using an extended-magnetohydrodynamic model

DOE PAGES

King, Jacob R.; Kruger, S. E.

2014-10-24

The linear, collisional, constant-ψ drift-tearing mode is analyzed for different regimes of the plasma-β, ion-skin-depth parameter space with an unreduced, extended-magnetohydrodynamic model. Here, new dispersion relations are found at moderate plasma β and previous drift-tearing results are classified as applicable at small plasma β.

Two-dimensional Radiative Magnetohydrodynamic Simulations of Partial Ionization in the Chromosphere. II. Dynamics and Energetics of the Low Solar Atmosphere

NASA Astrophysics Data System (ADS)

Martínez-Sykora, Juan; De Pontieu, Bart; Carlsson, Mats; Hansteen, Viggo H.; Nóbrega-Siverio, Daniel; Gudiksen, Boris V.

2017-09-01

We investigate the effects of interactions between ions and neutrals on the chromosphere and overlying corona using 2.5D radiative MHD simulations with the Bifrost code. We have extended the code capabilities implementing ion-neutral interaction effects using the generalized Ohm’s law, I.e., we include the Hall term and the ambipolar diffusion (Pedersen dissipation) in the induction equation. Our models span from the upper convection zone to the corona, with the photosphere, chromosphere, and transition region partially ionized. Our simulations reveal that the interactions between ionized particles and neutral particles have important consequences for the magnetothermodynamics of these modeled layers: (1) ambipolar diffusion increases the temperature in the chromosphere; (2) sporadically the horizontal magnetic field in the photosphere is diffused into the chromosphere, due to the large ambipolar diffusion; (3) ambipolar diffusion concentrates electrical currents, leading to more violent jets and reconnection processes, resulting in (3a) the formation of longer and faster spicules, (3b) heating of plasma during the spicule evolution, and (3c) decoupling of the plasma and magnetic field in spicules. Our results indicate that ambipolar diffusion is a critical ingredient for understanding the magnetothermodynamic properties in the chromosphere and transition region. The numerical simulations have been made publicly available, similar to previous Bifrost simulations. This will allow the community to study realistic numerical simulations with a wider range of magnetic field configurations and physics modules than previously possible.

Interactions between Hofmeister anions and the binding pocket of a protein.

PubMed

Fox, Jerome M; Kang, Kyungtae; Sherman, Woody; Héroux, Annie; Sastry, G Madhavi; Baghbanzadeh, Mostafa; Lockett, Matthew R; Whitesides, George M

2015-03-25

This paper uses the binding pocket of human carbonic anhydrase II (HCAII, EC 4.2.1.1) as a tool to examine the properties of Hofmeister anions that determine (i) where, and how strongly, they associate with concavities on the surfaces of proteins and (ii) how, upon binding, they alter the structure of water within those concavities. Results from X-ray crystallography and isothermal titration calorimetry show that most anions associate with the binding pocket of HCAII by forming inner-sphere ion pairs with the Zn(2+) cofactor. In these ion pairs, the free energy of anion-Zn(2+) association is inversely proportional to the free energetic cost of anion dehydration; this relationship is consistent with the mechanism of ion pair formation suggested by the "law of matching water affinities". Iodide and bromide anions also associate with a hydrophobic declivity in the wall of the binding pocket. Molecular dynamics simulations suggest that anions, upon associating with Zn(2+), trigger rearrangements of water that extend up to 8 Å away from their surfaces. These findings expand the range of interactions previously thought to occur between ions and proteins by suggesting that (i) weakly hydrated anions can bind complementarily shaped hydrophobic declivities, and that (ii) ion-induced rearrangements of water within protein concavities can (in contrast with similar rearrangements in bulk water) extend well beyond the first hydration shells of the ions that trigger them. This study paints a picture of Hofmeister anions as a set of structurally varied ligands that differ in size, shape, and affinity for water and, thus, in their ability to bind to—and to alter the charge and hydration structure of—polar, nonpolar, and topographically complex concavities on the surfaces of proteins.

Saturn's Magnetosphere Interaction with Titan for T9 Encounter: 3D Hybrid Modeling and Comparison with CAPS Observations

NASA Technical Reports Server (NTRS)

Lipatov, A. S.; Sittler, E. C., Jr.; Hartle, R. E.; Cooper, J. F.; Simpson, D. G.

2011-01-01

Global dynamics of ionized and neutral gases in the environment of Titan plays an important role in the interaction of Saturn s magnetosphere with Titan. Several hybrid simulations of this problem have already been done (Brecht et al., 2000; Kallio et al., 2004; Modolo et al., 2007a; Simon et al., 2007a, 2007b; Modolo and Chanteur, 2008). Observational data from CAPS for the T9 encounter (Sittler et al., 2009) indicates an absence of O(+) heavy ions in the upstream that change the models of interaction which were discussed in current publications (Kallio et al., 2004; Modolo et al., 2007a; Simon et al., 2007a, 2007b; Ma et al., 2007; Szego et al., 2007). Further analysis of the CAPS data shows very low density or even an absence of H(+) ions in upstream. In this paper we discuss two models of the interaction of Saturn s magnetosphere with Titan: (A) high density of H(+) ions in the upstream flow (0.1/cu cm), and (B) low density of H(+) ions in the upstream flow (0.02/cu cm). The hybrid model employs a fluid description for electrons and neutrals, whereas a particle approach is used for ions. We also take into account charge-exchange and photoionization processes and solve self-consistently for electric and magnetic fields. The model atmosphere includes exospheric H(+), H(2+), N(2+)and CH(4+) pickup ion production as well as an immobile background ionosphere and a shell distribution for active ionospheric ions (M(sub i)=28 amu). The hybrid model allows us to account for the realistic anisotropic ion velocity distribution that cannot be done in fluid simulations with isotropic temperatures. Our simulation shows an asymmetry of the ion density distribution and the magnetic field, including the formation of Alfven wing-like structures. The results of the ion dynamics in Titan s environment are compared with Cassini T9 encounter data (CAPS).

Aqueous alkali halide solutions: can osmotic coefficients be explained on the basis of the ionic sizes alone?

PubMed

Kalyuzhnyi, Yu V; Vlachy, Vojko; Dill, Ken A

2010-06-21

We use the AMSA, associative mean spherical theory of associative fluids, to study ion-ion interactions in explicit water. We model water molecules as hard spheres with four off-center square-well sites and ions as charged hard spheres with sticky sites that bind to water molecules or other ions. We consider alkali halide salts. The choice of model parameters is based on two premises: (i) The strength of the interaction between a monovalent ion and a water molecule is inversely proportional to the ionic (crystal) diameter sigma(i). Smaller ions bind to water more strongly than larger ions do, taking into account the asymmetry of the cation-water and anion-water interactions. (ii) The number of contacts an ion can make is proportional to sigma2(i). In short, small ions bind waters strongly, but only a few of them. Large ions bind waters weakly, but many of them. When both a monovalent cation and anion are large, it yields a small osmotic coefficient of the salt, since the water molecules avoid the space in between large ions. On the other hand, salts formed from one small and one large ion remain hydrated and their osmotic coefficient is high. The osmotic coefficients, calculated using this model in combination with the integral equation theory developed for associative fluids, follow the experimental trends, including the unusual behavior of caesium salts.

Molecular mobility, morphology, and ion conduction in ionomers for electroactive devices

NASA Astrophysics Data System (ADS)

Tudryn, Gregory J.

A sequential study of ion-containing polymers capable of ion solvation with varied ion content, dielectric constant, and counterions is presented in this dissertation in order to compare ion transport properties in ionomers with various ionic interactions. Structure-property relationships in these ion containing polymers are defined using x-ray scattering, rheology and dielectric spectroscopy, enabling the quantification of ion transport dynamics. Poly(ethylene oxide), (PEO) based ionomers are investigated in order to probe the relation between ion conduction and segmental relaxation, and copolymers of PEO and Poly(tetramethylene oxide), (PTMO) further develop an understanding of the trade-off between ion solvation and segmental dynamics. Ionomers with ionic liquid counterions probe diffuse charge interactions and steric effects on ion transport, and incorporation of ionic liquids into ionomer membranes such as Nafion provides desirable thermal and ion conducting properties which extend the use of such membranes for electroactive devices. PEO ionomers exhibit a strong relation between ionic conductivity and segmental dynamics, providing insight that the glass transition temperature, Tg, dominates the ion conduction mechanism. Increasing temperature induces aggregation of ionic groups as evidenced by the static dielectric constant and X-ray scattering as a function of temperature, revealing the contribution of ionic dipoles in the measured dielectric constant. The trade-off between ion solvation and fast polymer segmental dynamics are quantified in copolymer ionomers of PEO and lower Tg PTMO. While conducting ion content remains nearly unchanged, conductivity is lowered upon incorporation of PTMO, because the vast majority of the PTMO microphase separates from the PEO-rich microdomain that remains continuous and contributes most of the ion conduction. Dielectric constants and X-ray scattering show consistent changes with temperature that suggest a cascading aggregation process in Na ionomers as ionic dipoles thermally randomize and lower the measured dielectric constant of the medium, leading to further aggregation. We observe amplified microphase-separation through ionic groups preferentially solvated by PEO chains, as seen in block copolymers with added salt. Even at 25%PEO / 75%PTMO the ionomers have VFT temperature dependence of conducting ion mobility, meaning that the 25% PEO/ion microphase is still continuous A model is developed to describe the frequency dependent storage and loss modulus and the delay in Rouse motion due to ion association lifetime, as functions of ion content and molecular weight for our low molecular weight ionomers. The ion rearrangement relaxation in dielectric spectroscopy is clearly the ion association lifetime that controls terminal dynamics in linear viscoelasticity, allowing a simple sticky Rouse model, using the most-probable distribution based on NMR Mn, to fully describe master curves of the frequency dependent storage and loss modulus. Using insight from ionic interaction strength, ionic liquids are used as counterions, effectively plasticizing the ionomers without added solvent. Ionic interactions were weakened with increasing counterion size, and with modification of cations using ether-oxygen, promoting self-solvation, which increases conducting ion density by an order of magnitude. Room temperature ionic liquids were subsequently used in combination with NafionRTM membranes as electroactive substrates to correlate ion transport to morphology as a function of volume fraction of ionic liquid. This study illuminated the critical volume uptake of ionic liquid in Nafion, identifying percolation of ionic pathways and a significant increase in dielectric constant at low frequencies, indicating an increase in the number density of ions capable of polarizing at the electrode surface. Consequently, the fundamental information obtained about the structure-property relations of ionomers can be used to predict and design advanced ion-containing polymers to be used in battery membranes and a variety of electroactive devices, including actuators and electromechanical sensors.

Multi-timescale power and energy assessment of lithium-ion battery and supercapacitor hybrid system using extended Kalman filter

NASA Astrophysics Data System (ADS)

Wang, Yujie; Zhang, Xu; Liu, Chang; Pan, Rui; Chen, Zonghai

2018-06-01

The power capability and maximum charge and discharge energy are key indicators for energy management systems, which can help the energy storage devices work in a suitable area and prevent them from over-charging and over-discharging. In this work, a model based power and energy assessment approach is proposed for the lithium-ion battery and supercapacitor hybrid system. The model framework of the lithium-ion battery and supercapacitor hybrid system is developed based on the equivalent circuit model, and the model parameters are identified by regression method. Explicit analyses of the power capability and maximum charge and discharge energy prediction with multiple constraints are elaborated. Subsequently, the extended Kalman filter is employed for on-board power capability and maximum charge and discharge energy prediction to overcome estimation error caused by system disturbance and sensor noise. The charge and discharge power capability, and the maximum charge and discharge energy are quantitatively assessed under both the dynamic stress test and the urban dynamometer driving schedule. The maximum charge and discharge energy prediction of the lithium-ion battery and supercapacitor hybrid system with different time scales are explored and discussed.

Energy distributions of an ion in a radio-frequency trap immersed in a buffer gas under the influence of additional external forces

NASA Astrophysics Data System (ADS)

Rouse, I.; Willitsch, S.

2018-04-01

An ion held in a radio-frequency trap interacting with a uniform buffer gas of neutral atoms develops a steady-state energy distribution characterized by a power-law tail at high energies instead of the exponential decay characteristic of thermal equilibrium. We have previously shown that the Tsallis statistics frequently used as an empirical model for this distribution is a good approximation when the ion is heated due to a combination of micromotion interruption and exchange of kinetic energy with the buffer gas [Rouse and Willitsch, Phys. Rev. Lett. 118, 143401 (2017), 10.1103/PhysRevLett.118.143401]. Here, we extend our treatment to include the heating due to additional motion of the ion caused by external forces, including the "excess micromotion" induced by uniform electric fields and rf phase offsets. We show that this also leads to a Tsallis distribution with a potentially different power-law exponent from that observed in the absence of this additional forced motion, with the difference increasing as the ratio of the mass of the neutral atoms to that of the ion decreases. Our results indicate that unless the excess micromotion is minimized to a very high degree, then even a system with very light neutrals and a heavy ion does not exhibit a thermal distribution.

Site Selective Binding of Zn(ll) ot Metallo-b-Lactamase L1 from Stenotrophomonas Maltophilia

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

Costello,A.; Periyannan, G.; Yang, K.

2006-01-01

Extended X-ray absorption fine structure studies of the metallo-{beta}-lactamase L1 from Stenotrophomonas maltophilia containing 1 and 2 equiv of Zn(II) and containing 2 equiv of Zn(II) plus hydrolyzed nitrocefin are presented. The data indicate that the first, catalytically dominant metal ion is bound by L1 at the consensus Zn1 site. The data further suggest that binding of the first metal helps preorganize the ligands for binding of the second metal ion. The di-Zn enzyme displays a well-defined metal-metal interaction at 3.42 Angstroms. Reaction with the {beta}-lactam antibiotic nitrocefin results in a product-bound species, in which the ring-opened lactam rotates inmore » the active site to present the S1 sulfur atom of nitrocefin to one of the metal ions for coordination. The product bridges the two metal ions, with a concomitant lengthening of the Zn-Zn interaction to 3.62 Angstroms.« less

Three-dimensional modeling of the neutral gas depletion effect in a helicon discharge plasma

NASA Astrophysics Data System (ADS)

Kollasch, Jeffrey; Schmitz, Oliver; Norval, Ryan; Reiter, Detlev; Sovinec, Carl

2016-10-01

Helicon discharges provide an attractive radio-frequency driven regime for plasma, but neutral-particle dynamics present a challenge to extending performance. A neutral gas depletion effect occurs when neutrals in the plasma core are not replenished at a sufficient rate to sustain a higher plasma density. The Monte Carlo neutral particle tracking code EIRENE was setup for the MARIA helicon experiment at UW Madison to study its neutral particle dynamics. Prescribed plasma temperature and density profiles similar to those in the MARIA device are used in EIRENE to investigate the main causes of the neutral gas depletion effect. The most dominant plasma-neutral interactions are included so far, namely electron impact ionization of neutrals, charge exchange interactions of neutrals with plasma ions, and recycling at the wall. Parameter scans show how the neutral depletion effect depends on parameters such as Knudsen number, plasma density and temperature, and gas-surface interaction accommodation coefficients. Results are compared to similar analytic studies in the low Knudsen number limit. Plans to incorporate a similar Monte Carlo neutral model into a larger helicon modeling framework are discussed. This work is funded by the NSF CAREER Award PHY-1455210.

Interaction of a sodium ion with the water liquid-vapor interface

NASA Technical Reports Server (NTRS)

Wilson, M. A.; Pohorille, A.; Pratt, L. R.; MacElroy, R. D. (Principal Investigator)

1989-01-01

Molecular dynamics results are presented for the density profile of a sodium ion near the water liquid-vapor interface at 320 K. These results are compared with the predictions of a simple dielectric model for the interaction of a monovalent ion with this interface. The interfacial region described by the model profile is too narrow and the profile decreases too abruptly near the solution interface. Thus, the simple model does not provide a satisfactory description of the molecular dynamics results for ion positions within two molecular diameters from the solution interface where appreciable ion concentrations are observed. These results suggest that surfaces associated with dielectric models of ionic processes at aqueous solution interfaces should be located at least two molecular diameters inside the liquid phase. A free energy expense of about 2 kcal/mol is required to move the ion within two molecular layers of the free water liquid-vapor interface.

Course 1: Physics of Protein-DNA Interaction

NASA Astrophysics Data System (ADS)

Bruinsma, R. F.

1 Introduction 1.1 The central dogma and bacterial gene expression 1.2 Molecular structure 2 Thermodynamics and kinetics of repressor-DNA interaction 2.1 Thermodynamics and the lac repressor 2.2 Kinetics of repressor-DNA interaction 3 DNA deformability and protein-DNA interaction 3.1 Introduction 3.2 The worm-like chain 3.3 The RST model 4 Electrostatics in water and protein-DNA interaction 4.1 Macro-ions and aqueous electrostatics 4.2 The primitive model 4.3 Manning condensation 4.4 Counter-ion release and non-specific protein-DNA interaction

Electronic Structure and Magnetic Interactions in the Radical Salt [BEDT-TTF]2[CuCl4].

PubMed

Calzado, Carmen J; Rodríguez-García, Bárbara; Galán Mascarós, José Ramón; Hernández, Norge Cruz

2018-06-07

The magnetic behavior and electric properties of the hybrid radical salt [BEDT-TTF] 2 [CuCl 4 ] have been revisited through extended experimental analyses and DDCI and periodic DFT plane waves calculations. Single crystal X-ray diffraction data have been collected at different temperatures, discovering a phase transition occurring in the 250-300 K range. The calculations indicate the presence of intradimer, interdimer, and organic-inorganic π-d interactions in the crystal, a magnetic pattern much more complex than the Bleaney-Bowers model initially assigned to this material. Although this simple model was good enough to reproduce the magnetic susceptibility data, our calculations demonstrate that the actual magnetic structure is significantly more intricate, with alternating antiferromagnetic 1D chains of the organic BEDT-TTF + radical, connected through weak antiferromagnetic interactions with the CuCl 4 2- ions. Combination of experiment and theory allowed us to unambiguously determine and quantify the leading magnetic interactions in the system. The density-of-states curves confirm the semiconductor nature of the system and the dominant organic contribution of the valence and conduction band edges. This general and combined approach appears to be fundamental in order to properly understand the magnetic structure of these complex materials, where experimental data can actually be fitted from a variety of models and parameters.

Coupled bipolarons and optical phonons as a model for high-Tc superconductors

NASA Technical Reports Server (NTRS)

Kasperczyk, J.

1991-01-01

The coherence length of the new high-temperature superconductors reaches a small value which is comparable to the dimensions of the unit cell of the compound. This means that a pair consists of two holes occupying the same site or two adjacent sites. Such a situation is described by a model of the local-pairs (bipolarons). The origin of local-pairs may come not only from strong enough electron or hole-phonon interaction but also from other interactions. Independent of the specific nature of such local-pairs, they can undergo a Bose-like condensation to the superconducting state at a critical temperature which is usually much lower than the temperature of the pair formation. An interplay of ferroelectric and superconducting properties is considered within the model of hole-like local-pairs interacting with optical phonons. Therefore, researchers extend the usual local-pair Hamiltonian by including a direct interaction between the local-pairs and the optical phonons. These optical phonons are known to play an important role in the ferroelectric transition and they transform into an additional pseudo-acoustic branch at the ferroelectric critical temperature. (This is associated with nonzero electric polarization due to the existence of two separate lattices composed of negative and positive ions, respectively.)

Introductory lecture: interpreting and predicting Hofmeister salt ion and solute effects on biopolymer and model processes using the solute partitioning model.

PubMed

Record, M Thomas; Guinn, Emily; Pegram, Laurel; Capp, Michael

2013-01-01

Understanding how Hofmeister salt ions and other solutes interact with proteins, nucleic acids, other biopolymers and water and thereby affect protein and nucleic acid processes as well as model processes (e.g. solubility of model compounds) in aqueous solution is a longstanding goal of biophysical research. Empirical Hofmeister salt and solute "m-values" (derivatives of the observed standard free energy change for a model or biopolymer process with respect to solute or salt concentration m3) are equal to differences in chemical potential derivatives: m-value = delta(dmu2/dm3) = delta mu23, which quantify the preferential interactions of the solute or salt with the surface of the biopolymer or model system (component 2) exposed or buried in the process. Using the solute partitioning model (SPM), we dissect mu23 values for interactions of a solute or Hofmeister salt with a set of model compounds displaying the key functional groups of biopolymers to obtain interaction potentials (called alpha-values) that quantify the interaction of the solute or salt per unit area of each functional group or type of surface. Interpreted using the SPM, these alpha-values provide quantitative information about both the hydration of functional groups and the competitive interaction of water and the solute or salt with functional groups. The analysis corroborates and quantifies previous proposals that the Hofmeister anion and cation series for biopolymer processes are determined by ion-specific, mostly unfavorable interactions with hydrocarbon surfaces; the balance between these unfavorable nonpolar interactions and often-favorable interactions of ions with polar functional groups determine the series null points. The placement of urea and glycine betaine (GB) at opposite ends of the corresponding series of nonelectrolytes results from the favorable interactions of urea, and unfavorable interactions of GB, with many (but not all) biopolymer functional groups. Interaction potentials and local-bulk partition coefficients quantifying the distribution of solutes (e.g. urea, glycine betaine) and Hofmeister salt ions in the vicinity of each functional group make good chemical sense when interpreted in terms of competitive noncovalent interactions. These interaction potentials allow solute and Hofmeister (noncoulombic) salt effects on protein and nucleic acid processes to be interpreted or predicted, and allow the use of solutes and salts as probes of

Understanding Nucleic Acid–Ion Interactions

PubMed Central

Lipfert, Jan; Doniach, Sebastian; Das, Rhiju; Herschlag, Daniel

2015-01-01

Ions surround nucleic acids in what is referred to as an ion atmosphere. As a result, the folding and dynamics of RNA and DNA and their complexes with proteins and with each other cannot be understood without a reasonably sophisticated appreciation of these ions’ electrostatic interactions. However, the underlying behavior of the ion atmosphere follows physical rules that are distinct from the rules of site binding that biochemists are most familiar and comfortable with. The main goal of this review is to familiarize nucleic acid experimentalists with the physical concepts that underlie nucleic acid–ion interactions. Throughout, we provide practical strategies for interpreting and analyzing nucleic acid experiments that avoid pitfalls from oversimplified or incorrect models. We briefly review the status of theories that predict or simulate nucleic acid–ion interactions and experiments that test these theories. Finally, we describe opportunities for going beyond phenomenological fits to a next-generation, truly predictive understanding of nucleic acid–ion interactions. PMID:24606136

Novel kinetic model of the removal of divalent heavy metal ions from aqueous solutions by natural clinoptilolite.

PubMed

Jovanovic, Mina; Rajic, Nevenka; Obradovic, Bojana

2012-09-30

Removal of heavy metal ions from aqueous solutions using zeolites is widely described by pseudo-second order kinetics although this model may not be valid under all conditions. In this work, we have extended approaches used for derivation of this model in order to develop a novel kinetic model that is related to the ion exchange mechanism underlying sorption of metal ions in zeolites. The novel model assumed two reversible steps, i.e. release of sodium ions from the zeolite lattice followed by bonding of the metal ion. The model was applied to experimental results of Cu(II) sorption by natural clinoptilolite-rich zeolitic tuff at different initial concentrations and temperatures and then validated by predictions of ion exchange kinetics of other divalent heavy metal ions (i.e. Mn(II), Zn(II) and Pb(II)). Model predictions were in excellent agreements with experimental data for all investigated systems. In regard to the proposed mechanism, modeling results implied that the sodium ion release rate was constant for all investigated metals while the overall rate was mainly determined by the rate of heavy metal ion bonding to the lattice. In addition, prediction capabilities of the novel model were demonstrated requiring one experimentally determined parameter, only. Copyright © 2012 Elsevier B.V. All rights reserved.

The PARTRAC code: Status and recent developments

NASA Astrophysics Data System (ADS)

Friedland, Werner; Kundrat, Pavel

Biophysical modeling is of particular value for predictions of radiation effects due to manned space missions. PARTRAC is an established tool for Monte Carlo-based simulations of radiation track structures, damage induction in cellular DNA and its repair [1]. Dedicated modules describe interactions of ionizing particles with the traversed medium, the production and reactions of reactive species, and score DNA damage determined by overlapping track structures with multi-scale chromatin models. The DNA repair module describes the repair of DNA double-strand breaks (DSB) via the non-homologous end-joining pathway; the code explicitly simulates the spatial mobility of individual DNA ends in parallel with their processing by major repair enzymes [2]. To simulate the yields and kinetics of radiation-induced chromosome aberrations, the repair module has been extended by tracking the information on the chromosome origin of ligated fragments as well as the presence of centromeres [3]. PARTRAC calculations have been benchmarked against experimental data on various biological endpoints induced by photon and ion irradiation. The calculated DNA fragment distributions after photon and ion irradiation reproduce corresponding experimental data and their dose- and LET-dependence. However, in particular for high-LET radiation many short DNA fragments are predicted below the detection limits of the measurements, so that the experiments significantly underestimate DSB yields by high-LET radiation [4]. The DNA repair module correctly describes the LET-dependent repair kinetics after (60) Co gamma-rays and different N-ion radiation qualities [2]. First calculations on the induction of chromosome aberrations have overestimated the absolute yields of dicentrics, but correctly reproduced their relative dose-dependence and the difference between gamma- and alpha particle irradiation [3]. Recent developments of the PARTRAC code include a model of hetero- vs euchromatin structures to enable accounting for variations in DNA damage yields, complexity and repair between these regions. Second, the applicability of the code to low-energy ions has been extended to full stopping by using a modified Barkas scaling of proton cross sections for ions heavier than helium. Third, ongoing studies aim at hitherto unprecedented benchmarking of the code against experiments with sub-muµm focused bunches of low-LET ions mimicking single high-LET ion tracks [5] which separate effects of damage clustering on a sub-mum scale from DNA damage complexity on a nanometer scale. Fourth, motivated by implications for the involvement of mitochondria in intercellular signaling and radiation-induced bystander effects, ongoing work extends the range of PARTRAC DNA models to radiation effects on mitochondrial DNA. The contribution will discuss the PARTRAC modules, benchmarks to experimental data, recent and ongoing developments of the code, with special attention to its implications and potential applications in radiation protection and space research. Acknowledgement. This work was partially funded by the EU (Contract FP7-249689 ‘DoReMi’). References 1. Friedland et al., Mutat. Res. 711, 28 (2011) 2. Friedland et al., Int. J. Radiat. Biol. 88, 129 (2012) 3. Friedland et al., Mutat. Res. 756, 213 (2013) 4. Alloni et al., Radiat. Res. 179, 690 (2013) 5. Schmid et al., Phys. Med. Biol. 57, 5889 (2012)

Plasmon-photon conversion to near-infrared emission from Yb(3+): (Au/Ag-nanoparticles) in tungsten-tellurite glasses.

PubMed

Rivera, V A G; Ledemi, Yannick; Pereira-da-Silva, Marcelo A; Messaddeq, Younes; Marega, Euclydes

2016-01-04

This manuscript reports on the interaction between (2)F5/2→(2)F7/2 radiative transition from Yb(3+) ions and localized surface plasmon resonance (from gold/silver nanoparticles) in a tungsten-tellurite glass. Such an interaction, similar to the down-conversion process, results in the Yb(3+) emission in the near-infrared region via resonant and non-resonant energy transfers. We associated such effects with the dynamic coupling described by the variations generated by the Hamiltonian HDC in either the oscillator strength, or the local crystal field, i.e. the line shape changes in the emission band. Here, the Yb(3+) ions emission is achieved through plasmon-photon coupling, observable as an enhancement or quenching in the luminescence spectra. Metallic nanoparticles have light-collecting capability in the visible spectrum and can accumulate almost all the photon energy on a nanoscale, which enable the excitation and emission of the Yb(3+) ions in the near-infrared region. This plasmon-photon conversion was evaluated from the cavity's quality factor (Q) and the coupling (g) between the nanoparticles and the Yb(3+) ions. We have found samples of low-quality cavities and strong coupling between the nanoparticles and the Yb(3+) ions. Our research can be extended towards the understanding of new plasmon-photon converters obtained from interactions between rare-earth ions and localized surface plasmon resonance.

Plasmon-photon conversion to near-infrared emission from Yb3+: (Au/Ag-nanoparticles) in tungsten-tellurite glasses

PubMed Central

Rivera, V. A. G.; Ledemi, Yannick; Pereira-da-Silva, Marcelo A.; Messaddeq, Younes; Marega Jr, Euclydes

2016-01-01

This manuscript reports on the interaction between 2F5/2→2F7/2 radiative transition from Yb3+ ions and localized surface plasmon resonance (from gold/silver nanoparticles) in a tungsten-tellurite glass. Such an interaction, similar to the down-conversion process, results in the Yb3+ emission in the near-infrared region via resonant and non-resonant energy transfers. We associated such effects with the dynamic coupling described by the variations generated by the Hamiltonian HDC in either the oscillator strength, or the local crystal field, i.e. the line shape changes in the emission band. Here, the Yb3+ ions emission is achieved through plasmon-photon coupling, observable as an enhancement or quenching in the luminescence spectra. Metallic nanoparticles have light-collecting capability in the visible spectrum and can accumulate almost all the photon energy on a nanoscale, which enable the excitation and emission of the Yb3+ ions in the near-infrared region. This plasmon-photon conversion was evaluated from the cavity’s quality factor (Q) and the coupling (g) between the nanoparticles and the Yb3+ ions. We have found samples of low-quality cavities and strong coupling between the nanoparticles and the Yb3+ ions. Our research can be extended towards the understanding of new plasmon-photon converters obtained from interactions between rare-earth ions and localized surface plasmon resonance. PMID:26725938

Magma transport and metasomatism in the mantle: a critical review of current geochemical models

USGS Publications Warehouse

Nielson, J.E.; Wilshire, H.G.

1993-01-01

Conflicting geochemical models of metasomatic interactions between mantle peridotite and melt all assume that mantle reactions reflect chromatographic processes. Examination of field, petrological, and compositional data suggests that the hypothesis of chromatographic fractionation based on the supposition of large-scale percolative processes needs review and revision. Well-constrained rock and mineral data from xenoliths indicate that many elements that behave incompatibly in equilibrium crystallization processes are absorbed immediately when melts emerge from conduits into depleted peridotite. After reacting to equilibrium with the peridotite, melt that percolates away from the conduit is largely depleted of incompatible elements. Continued addition of melts extends the zone of equilibrium farther from the conduit. Such a process resembles ion-exchange chromatography for H2O purification, rather than the model of chromatographic species separation. -from Authors

Theory of anisotropic hybridization-broadened magnetic response in cerium and actinide systems

NASA Astrophysics Data System (ADS)

Hu, Gong-Jia; Cooper, Bernard R.

1993-11-01

Inelastic-neutron-scattering measurements on cerium and plutonium monopnictides, thought to have moderately delocalized f electrons, yield magnetic-excitation spectra with anisotropic dispersion; while reasonably sharp excitations have been observed only for USb and UTe among presumably more-delocalized uranium monopnictides and monochalcogenides. For UTe the broadening as well as the dispersion is quite anisotropic. We have now extended our previous theory for the magnetic behavior of hybridizing partially delocalized f-electron systems to include hybridization-induced relaxation effects in the magnetic response, and this work and results are reported in the present paper. Each partially delocalized f-electron ion is coupled by hybridization to the band sea; and this both leads to a hybridization-mediated anisotropic two-ion interaction giving magnetic ordering and also gives a damping mechanism, via the coupling to the band sea, for the excitations of the magnetically ordered lattice. This coupling also provides a strong renormalization of the magnetic-excitation energies obtained for the ionic lattice coupled by the two-ion interaction. To treat these effects on the magnetic response we have developed a formalism for calculating the dynamic susceptibility based on the projection-operator method developed by Mori and others. We have applied our model and theory to the behavior of CeSb, CeBi, PuSb, UP, UAs, and UTe; and excellent overall agreement with the wide range of unusual experimentally observed anisotropic magnetic-excitation behavior is obtained.

Designing heteropolymers to fold into unique structures via water-mediated interactions.

PubMed

Jamadagni, Sumanth N; Bosoy, Christian; Garde, Shekhar

2010-10-28

Hydrophobic homopolymers collapse into globular structures in water driven by hydrophobic interactions. Here we employ extensive molecular dynamics simulations to study the collapse of heteropolymers containing one or two pairs of oppositely charged monomers. We show that charging a pair of monomers can dramatically alter the most stable conformations from compact globular to more open hairpin-like. We systematically explore a subset of the sequence space of one- and two-charge-pair polymers, focusing on the locations of the charge pairs. Conformational stability is governed by a balance of hydrophobic interactions, hydration and interactions of charge groups, water-mediated charged-hydrophobic monomer repulsions, and other factors. As a result, placing charge pairs in the middle, away from the hairpin ends, leads to stable hairpin-like structures. Turning off the monomer-water attractions enhances hydrophobic interactions significantly leading to a collapse into compact globular structures even for two-charge-pair heteropolymers. In contrast, the addition of salt leads to open and extended structures, suggesting that solvation of charged monomer sites by salt ions dominates the salt-induced enhancement of hydrophobic interactions. We also test the ability of a predictive scheme based on the additivity of free energy of contact formation. The success of the scheme for symmetric two-charge-pair sequences and the failure for their flipped versions highlight the complexity of the heteropolymer conformation space and of the design problem. Collectively, our results underscore the ability of tuning water-mediated interactions to design stable nonglobular structures in water and present model heteropolymers for further studies in the extended thermodynamic space and in inhomogeneous environments.

A model of ion transport processes along and across the neuronal membrane.

PubMed

Xiang, Z X; Liu, G Z; Tang, C X; Yan, L X

2017-01-01

In this study, we provide a foundational model of ion transport processes in the intracellular and extracellular compartments of neurons at the nanoscale. There are two different kinds of ionic transport processes: (i) ionic transport across the neuronal membrane (trans-membrane), and (ii) ionic transport along both the intracellular and extracellular surfaces of the membrane. Brownian dynamics simulations are used to give a description of ionic trans-membrane transport. Electro-diffusion is used to model ion transport along the membrane surface, and the two transport processes can be linked analytically. In our model, we found that the interactions between ions and ion channels result in high-frequency ionic oscillations during trans-membrane transport. In ion transport along the membrane, high-frequency ionic oscillations may be evoked on both the intracellular and extracellular surfaces of the plasma membrane. The electric field caused by Coulomb interactions between the ions is found to be the most likely origin of those ionic oscillations.

Insulator Surface Charge as a Function of Pressure: Theory and Simulation

NASA Technical Reports Server (NTRS)

Hogue, Michael D.; Calle, Carlos I.; Mucciolo, Eduardo; Hintze, Paul

2005-01-01

A two-phase equilibrium model was developed to explain the discontinuous surface charge decay versus atmospheric pressure of insulators that had been charged triboelectrically. The two-phase model is an electrostatic form of the Langmuir Isotherm for ions adsorbed on a surface in equilibrium with ions in the gas phase. In this paper, the model was extended to account for vibrational states of the adsorbed surface ions via the vibrational partition function. An analysis is performed that rules out Paschen discharge as the cause of the discharge observed. Also, a numerical simulation is performed using NWChem to calculate the adsorption energies of ions on insulator surfaces for comparison to curve fit adsorption energies developed from the model and experimental data.

Experimental and simulation-based investigation of He, Ne and Ar irradiation of polymers for ion microscopy

PubMed Central

Rzeznik, Lukasz; Fleming, Yves; Wirtz, Tom

2016-01-01

Summary Secondary ion mass spectrometry (SIMS) on the helium ion microscope (HIM) promises higher lateral resolution than on classical SIMS instruments. However, full advantage of this new technique can only be obtained when the interaction of He+ or Ne+ primary ions with the sample is fully controlled. In this work we investigate how He+ and Ne+ bombardment influences roughness formation and preferential sputtering for polymer samples and how they compare to Ar+ primary ions used in classical SIMS by combining experimental techniques with Molecular Dynamics (MD) simulations and SD_TRIM_SP modelling. The results show that diffusion coefficients for He, Ne and Ar in polymers are sufficiently high to prevent any accumulation of rare gas atoms in the polymers which could lead to some swelling and bubble formation. Roughness formation was also not observed. Preferential sputtering is more of a problem, with enrichment of carbon up to surface concentrations above 80%. In general, the preferential sputtering is largely depending on the primary ion species and the impact energies. For He+ bombardment, it is more of an issue for low keV impact energies and for the heavier primary ion species the preferential sputtering is sample dependent. For He+ steady state conditions are reached for fluences much higher than 1018 ions/cm2. For Ne+ and Ar+, the transient regime extends up to fluences of 1017–1018 ions/cm2. Hence, preferential sputtering needs to be taken into account when interpreting images recorded under He+ or Ne+ bombardment on the HIM. PMID:27547629

Ab Initio Molecular Dynamics Study on the Interactions between Carboxylate Ions and Metal Ions in Water.

PubMed

Mehandzhiyski, Aleksandar Y; Riccardi, Enrico; van Erp, Titus S; Trinh, Thuat T; Grimes, Brian A

2015-08-20

The interaction between a carboxylate anion (deprotonated propanoic acid) and the divalent Mg(2+), Ca(2+), Sr(2+), Ba(2+) metal ions is studied via ab initio molecular dynamics. The main focus of the study is the selectivity of the carboxylate-metal ion interaction in aqueous solution. The interaction is modeled by explicitly accounting for the solvent molecules on a DFT level. The hydration energies of the metal ions along with their diffusion and mobility coefficients are determined and a trend correlated with their ionic radius is found. Subsequently, a series of 16 constrained molecular dynamics simulations for every ion is performed, and the interaction free energy is obtained from thermodynamic integration of the forces between the metal ion and the carboxylate ion. The results indicate that the magnesium ion interacts most strongly with the carboxylate, followed by calcium, strontium, and barium. Because the interaction free energy is not enough to explain the selectivity of the reaction observed experimentally, more detailed analysis is performed on the simulation trajectories to understand the steric changes in the reaction complex during dissociation. The solvent dynamics appear to play an important role during the dissociation of the complex and also in the observed selectivity behavior of the divalent ions.

Gaussian polarizable-ion tight binding.

PubMed

Boleininger, Max; Guilbert, Anne Ay; Horsfield, Andrew P

2016-10-14

To interpret ultrafast dynamics experiments on large molecules, computer simulation is required due to the complex response to the laser field. We present a method capable of efficiently computing the static electronic response of large systems to external electric fields. This is achieved by extending the density-functional tight binding method to include larger basis sets and by multipole expansion of the charge density into electrostatically interacting Gaussian distributions. Polarizabilities for a range of hydrocarbon molecules are computed for a multipole expansion up to quadrupole order, giving excellent agreement with experimental values, with average errors similar to those from density functional theory, but at a small fraction of the cost. We apply the model in conjunction with the polarizable-point-dipoles model to estimate the internal fields in amorphous poly(3-hexylthiophene-2,5-diyl).

Gaussian polarizable-ion tight binding

NASA Astrophysics Data System (ADS)

Boleininger, Max; Guilbert, Anne AY; Horsfield, Andrew P.

2016-10-01

To interpret ultrafast dynamics experiments on large molecules, computer simulation is required due to the complex response to the laser field. We present a method capable of efficiently computing the static electronic response of large systems to external electric fields. This is achieved by extending the density-functional tight binding method to include larger basis sets and by multipole expansion of the charge density into electrostatically interacting Gaussian distributions. Polarizabilities for a range of hydrocarbon molecules are computed for a multipole expansion up to quadrupole order, giving excellent agreement with experimental values, with average errors similar to those from density functional theory, but at a small fraction of the cost. We apply the model in conjunction with the polarizable-point-dipoles model to estimate the internal fields in amorphous poly(3-hexylthiophene-2,5-diyl).

Xenon and Other Volatile Anesthetics Change Domain Structure in Model Lipid Raft Membranes

PubMed Central

Weinrich, Michael; Worcester, David L.

2014-01-01

Inhalation anesthetics have been in clinical use for over 160 years, but the molecular mechanisms of action continue to be investigated. Direct interactions with ion channels received much attention after it was found that anesthetics do not change the structure of homogeneous model membranes. However, it was recently found that halothane, a prototypical anesthetic, changes domain structure of a binary lipid membrane. The noble gas xenon is an excellent anesthetic and provides a pivotal test of the generality of this finding, extended to ternary lipid raft mixtures. We report that xenon and conventional anesthetics change the domain equilibrium in two canonical ternary lipid raft mixtures. These findings demonstrate a membrane-mediated mechanism whereby inhalation anesthetics can affect the lipid environment of trans-membrane proteins. PMID:24299622

Functionalized Fullerene Targeting Human Voltage-Gated Sodium Channel, hNav1.7.

PubMed

Hilder, Tamsyn A; Robinson, Anna; Chung, Shin-Ho

2017-08-16

Mutations of hNa v 1.7 that cause its activities to be enhanced contribute to severe neuropathic pain. Only a small number of hNa v 1.7 specific inhibitors have been identified, most of which interact with the voltage-sensing domain of the voltage-activated sodium ion channel. In our previous computational study, we demonstrated that a [Lys 6 ]-C 84 fullerene binds tightly (affinity of 46 nM) to Na v Ab, the voltage-gated sodium channel from the bacterium Arcobacter butzleri. Here, we extend this work and, using molecular dynamics simulations, demonstrate that the same [Lys 6 ]-C 84 fullerene binds strongly (2.7 nM) to the pore of a modeled human sodium ion channel hNa v 1.7. In contrast, the fullerene binds only weakly to a mutated model of hNa v 1.7 (I1399D) (14.5 mM) and a model of the skeletal muscle hNa v 1.4 (3.7 mM). Comparison of one representative sequence from each of the nine human sodium channel isoforms shows that only hNa v 1.7 possesses residues that are critical for binding the fullerene derivative and blocking the channel pore.

Transportation behavior of alkali ions through a cell membrane ion channel. A quantum chemical description of a simplified isolated model.

PubMed

Billes, Ferenc; Mohammed-Ziegler, Ildikó; Mikosch, Hans

2012-08-01

Quantum chemical model calculations were carried out for modeling the ion transport through an isolated ion channel of a cell membrane. An isolated part of a natural ion channel was modeled. The model channel was a calixarene derivative, hydrated sodium and potassium ions were the models of the transported ion. The electrostatic potential of the channel and the energy of the channel-ion system were calculated as a function of the alkali ion position. Both attractive and repulsive ion-channel interactions were found. The calculations - namely the dependence of the system energy and the atomic charges of the water molecules with respect to the position of the alkali ion in the channel - revealed the molecular-structural background of the potassium selectivity of this artificial ion channel. It was concluded that the studied ion channel mimics real biological ion channel quite well.

Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation

NASA Astrophysics Data System (ADS)

Kekenes-Huskey, P. M.; Gillette, A. K.; McCammon, J. A.

2014-05-01

The macroscopic diffusion constant for a charged diffuser is in part dependent on (1) the volume excluded by solute "obstacles" and (2) long-range interactions between those obstacles and the diffuser. Increasing excluded volume reduces transport of the diffuser, while long-range interactions can either increase or decrease diffusivity, depending on the nature of the potential. We previously demonstrated [P. M. Kekenes-Huskey et al., Biophys. J. 105, 2130 (2013)] using homogenization theory that the configuration of molecular-scale obstacles can both hinder diffusion and induce diffusional anisotropy for small ions. As the density of molecular obstacles increases, van der Waals (vdW) and electrostatic interactions between obstacle and a diffuser become significant and can strongly influence the latter's diffusivity, which was neglected in our original model. Here, we extend this methodology to include a fixed (time-independent) potential of mean force, through homogenization of the Smoluchowski equation. We consider the diffusion of ions in crowded, hydrophilic environments at physiological ionic strengths and find that electrostatic and vdW interactions can enhance or depress effective diffusion rates for attractive or repulsive forces, respectively. Additionally, we show that the observed diffusion rate may be reduced independent of non-specific electrostatic and vdW interactions by treating obstacles that exhibit specific binding interactions as "buffers" that absorb free diffusers. Finally, we demonstrate that effective diffusion rates are sensitive to distribution of surface charge on a globular protein, Troponin C, suggesting that the use of molecular structures with atomistic-scale resolution can account for electrostatic influences on substrate transport. This approach offers new insight into the influence of molecular-scale, long-range interactions on transport of charged species, particularly for diffusion-influenced signaling events occurring in crowded cellular environments.

Strategies for generating peptide radical cations via ion/ion reactions.

PubMed

Gilbert, Joshua D; Fisher, Christine M; Bu, Jiexun; Prentice, Boone M; Redwine, James G; McLuckey, Scott A

2015-02-01

Several approaches for the generation of peptide radical cations using ion/ion reactions coupled with either collision induced dissociation (CID) or ultraviolet photo dissociation (UVPD) are described here. Ion/ion reactions are used to generate electrostatic or covalent complexes comprised of a peptide and a radical reagent. The radical site of the reagent can be generated multiple ways. Reagents containing a carbon-iodine (C-I) bond are subjected to UVPD with 266-nm photons, which selectively cleaves the C-I bond homolytically. Alternatively, reagents containing azo functionalities are collisionally activated to yield radical sites on either side of the azo group. Both of these methods generate an initial radical site on the reagent, which then abstracts a hydrogen from the peptide while the peptide and reagent are held together by either electrostatic interactions or a covalent linkage. These methods are demonstrated via ion/ion reactions between the model peptide RARARAA (doubly protonated) and various distonic anionic radical reagents. The radical site abstracts a hydrogen atom from the peptide, while the charge site abstracts a proton. The net result is the conversion of a doubly protonated peptide to a peptide radical cation. The peptide radical cations have been fragmented via CID and the resulting product ion mass spectra are compared to the control CID spectrum of the singly protonated, even-electron species. This work is then extended to bradykinin, a more broadly studied peptide, for comparison with other radical peptide generation methods. The work presented here provides novel methods for generating peptide radical cations in the gas phase through ion/ion reaction complexes that do not require modification of the peptide in solution or generation of non-covalent complexes in the electrospray process. Copyright © 2015 John Wiley & Sons, Ltd.

Extended Hubbard model for mesoscopic transport in donor arrays in silicon

NASA Astrophysics Data System (ADS)

Le, Nguyen H.; Fisher, Andrew J.; Ginossar, Eran

2017-12-01

Arrays of dopants in silicon are promising platforms for the quantum simulation of the Fermi-Hubbard model. We show that the simplest model with only on-site interaction is insufficient to describe the physics of an array of phosphorous donors in silicon due to the strong intersite interaction in the system. We also study the resonant tunneling transport in the array at low temperature as a mean of probing the features of the Hubbard physics, such as the Hubbard bands and the Mott gap. Two mechanisms of localization which suppresses transport in the array are investigated: The first arises from the electron-ion core attraction and is significant at low filling; the second is due to the sharp oscillation in the tunnel coupling caused by the intervalley interference of the donor electron's wave function. This disorder in the tunnel coupling leads to a steep exponential decay of conductance with channel length in one-dimensional arrays, but its effect is less prominent in two-dimensional ones. Hence, it is possible to observe resonant tunneling transport in a relatively large array in two dimensions.

Neutron imaging with the short-pulse laser driven neutron source at the TRIDENT Laser Facility

DOE PAGES

Guler, Nevzat; Volegov, Petr Lvovich; Favalli, Andrea; ...

2016-10-17

Emerging approaches to short-pulse laser-driven neutron production offer a possible gateway to compact, low cost, and intense broad spectrum sources for a wide variety of applications. They are based on energetic ions, driven by an intense short-pulse laser, interacting with a converter material to produce neutrons via breakup and nuclear reactions. Recent experiments performed with the high-contrast laser at the Trident laser facility of Los Alamos National Laboratory have demonstrated a laser-driven ion acceleration mechanism operating in the regime of relativistic transparency, featuring a volumetric laser-plasma interaction. This mechanism is distinct from previously studied ones that accelerate ions at themore » laser-target surface. The Trident experiments produced an intense beam of deuterons with an energy distribution extending above 100 MeV. This deuteron beam, when directed at a beryllium converter, produces a forward-directed neutron beam with ~5x10 9 n/sr, in a single laser shot, primarily due to deuteron breakup. The neutron beam has a pulse duration on the order of a few nanoseconds with an energy distribution extending from a few hundreds of keV to almost 80 MeV. For the experiments on neutron-source spot-size measurements, our gated neutron imager was setup to select neutrons in the energy range of 2.5 to 35 MeV. The spot size of neutron emission at the converter was measured by two different imaging techniques, using a knife-edge and a penumbral aperture, in two different experimental campaigns. The neutron-source spot size is measured ~1 mm for both experiments. The measurements and analysis reported here give a spatial characterization for this type of neutron source for the first time. In addition, the forward modeling performed provides an empirical estimate of the spatial characteristics of the deuteron ion-beam. Finally, these experimental observations, taken together, provide essential yet unique data to benchmark and verify theoretical work into the basic acceleration mechanism, which remains an ongoing challenge.« less

Neutron imaging with the short-pulse laser driven neutron source at the TRIDENT Laser Facility

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

Guler, Nevzat; Volegov, Petr Lvovich; Favalli, Andrea

Emerging approaches to short-pulse laser-driven neutron production offer a possible gateway to compact, low cost, and intense broad spectrum sources for a wide variety of applications. They are based on energetic ions, driven by an intense short-pulse laser, interacting with a converter material to produce neutrons via breakup and nuclear reactions. Recent experiments performed with the high-contrast laser at the Trident laser facility of Los Alamos National Laboratory have demonstrated a laser-driven ion acceleration mechanism operating in the regime of relativistic transparency, featuring a volumetric laser-plasma interaction. This mechanism is distinct from previously studied ones that accelerate ions at themore » laser-target surface. The Trident experiments produced an intense beam of deuterons with an energy distribution extending above 100 MeV. This deuteron beam, when directed at a beryllium converter, produces a forward-directed neutron beam with ~5x10 9 n/sr, in a single laser shot, primarily due to deuteron breakup. The neutron beam has a pulse duration on the order of a few nanoseconds with an energy distribution extending from a few hundreds of keV to almost 80 MeV. For the experiments on neutron-source spot-size measurements, our gated neutron imager was setup to select neutrons in the energy range of 2.5 to 35 MeV. The spot size of neutron emission at the converter was measured by two different imaging techniques, using a knife-edge and a penumbral aperture, in two different experimental campaigns. The neutron-source spot size is measured ~1 mm for both experiments. The measurements and analysis reported here give a spatial characterization for this type of neutron source for the first time. In addition, the forward modeling performed provides an empirical estimate of the spatial characteristics of the deuteron ion-beam. Finally, these experimental observations, taken together, provide essential yet unique data to benchmark and verify theoretical work into the basic acceleration mechanism, which remains an ongoing challenge.« less

A comparison of experimental and computer model results on the charge-exchange plasma flow from a 30 cm mercury ion thruster

NASA Technical Reports Server (NTRS)

Gabriel, S. B.; Kaufman, H. R.

1982-01-01

Ion thrusters can be used in a variety of primary and auxiliary space-propulsion applications. A thruster produces a charge-exchange plasma which can interact with various systems on the spacecraft. The propagation of the charge-exchange plasma is crucial in determining the interaction of that plasma with the spacecraft. This paper compares experimental measurements with computer model predictions of the propagation of the charge-exchange plasma from a 30 cm mercury ion thruster. The plasma potentials, and ion densities, and directed energies are discussed. Good agreement is found in a region upstream of, and close to, the ion thruster optics. Outside of this region the agreement is reasonable in view of the modeling difficulties.

MARS15

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

Mokhov, Nikolai

MARS is a Monte Carlo code for inclusive and exclusive simulation of three-dimensional hadronic and electromagnetic cascades, muon, heavy-ion and low-energy neutron transport in accelerator, detector, spacecraft and shielding components in the energy range from a fraction of an electronvolt up to 100 TeV. Recent developments in the MARS15 physical models of hadron, heavy-ion and lepton interactions with nuclei and atoms include a new nuclear cross section library, a model for soft pion production, the cascade-exciton model, the quark gluon string models, deuteron-nucleus and neutrino-nucleus interaction models, detailed description of negative hadron and muon absorption and a unified treatment ofmore » muon, charged hadron and heavy-ion electromagnetic interactions with matter. New algorithms are implemented into the code and thoroughly benchmarked against experimental data. The code capabilities to simulate cascades and generate a variety of results in complex media have been also enhanced. Other changes in the current version concern the improved photo- and electro-production of hadrons and muons, improved algorithms for the 3-body decays, particle tracking in magnetic fields, synchrotron radiation by electrons and muons, significantly extended histograming capabilities and material description, and improved computational performance. In addition to direct energy deposition calculations, a new set of fluence-to-dose conversion factors for all particles including neutrino are built into the code. The code includes new modules for calculation of Displacement-per-Atom and nuclide inventory. The powerful ROOT geometry and visualization model implemented in MARS15 provides a large set of geometrical elements with a possibility of producing composite shapes and assemblies and their 3D visualization along with a possible import/export of geometry descriptions created by other codes (via the GDML format) and CAD systems (via the STEP format). The built-in MARS-MAD Beamline Builder (MMBLB) was redesigned for use with the ROOT geometry package that allows a very efficient and highly-accurate description, modeling and visualization of beam loss induced effects in arbitrary beamlines and accelerator lattices. The MARS15 code includes links to the MCNP-family codes for neutron and photon production and transport below 20 MeV, to the ANSYS code for thermal and stress analyses and to the STRUCT code for multi-turn particle tracking in large synchrotrons and collider rings.« less

Event Generators for Simulating Heavy Ion Interactions of Interest in Evaluating Risks in Human Spaceflight

NASA Technical Reports Server (NTRS)

Wilson, Thomas L.; Pinsky, Lawrence; Andersen, Victor; Empl, Anton; Lee, Kerry; Smirmov, Georgi; Zapp, Neal; Ferrari, Alfredo; Tsoulou, Katerina; Roesler, Stefan;

Understanding the Role of Metal Ions in RNA Folding and Function: Lessons from RNase P, a Ribonucleoprotein Enzyme

NASA Astrophysics Data System (ADS)

Harris, Michael E.; Christian, Eric L.

There is a large and rapidly growing literature relating RNA function to metal ion identity and concentration; however, due to the complexity and large number of interactions it remains a significant experimental challenge to tie the interactions of individual ions to specific aspects of RNA function. Investigation of the ribonculeopro-tein enzyme RNase P function has assisted in defining characteristics of RNA—metal ion interactions and provided a useful model system for understanding RNA catalysis and ribonucleoprotein assembly. The goal of this chapter is to review progress in understanding the physical basis of functional metal ion interactions with P RNA and relate this progress to the development of our understanding of RNA metal ion interactions in general. The research results reviewed here encompass: (1) Determination of the contribution of divalent metal ion binding to specific aspects of enzyme function, (2) Identification of individual metal ion binding sites in P RNA and their contribution to function, and (3) The effect of protein binding on RNA—metal ion affinity.

Angular spectra of rainbow scattering at glancing keV He + bombardment of NiAl(1 0 0) surface with transverse energies in the range 1-10 eV

NASA Astrophysics Data System (ADS)

Danailov, Daniel M.

2007-11-01

Previous simulations of glancing incidence ion-surface interaction have demonstrated that classical dynamics using the row-model have successfully reproduced multimodal azimuthal and polar spectra. These studies have also shown considerable sensitivity to the form of the interatomic potential thus making it a strong test of the validity of such potentials and even allow deduction of the ion-surface potentials. In these simulations the individual pairwise interactions between the projectile and the target atoms have been replaced by cylindrical potentials. Comparison to numerous experimental studies have confirmed the existence of rainbow scattering phenomena and successfully tested the validity of the cylindrical potential used in these simulations. The use of cylindrical potentials avoids stochastic effects due to thermal displacements and allows faster computer simulations leading to reliable angular distributions. In the present work we extend the row-model to consider scattering from binary alloys. Using He+ scattered at glancing incidence from NiAl surfaces, Al or Ni terminated, a faster method has been developed to easily and accurately quantize not only the maximum deflection azimuthal angle but all the singular points in the angular distribution. It has been shown that the influence of the surface termination on the rainbow angle and the inelastic losses is small.

KINETIC EVOLUTION OF CORONAL HOLE PROTONS BY IMBALANCED ION-CYCLOTRON WAVES: IMPLICATIONS FOR MEASUREMENTS BY SOLAR PROBE PLUS

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

Isenberg, Philip A.; Vasquez, Bernard J.

We extend the kinetic guiding-center model of collisionless coronal hole protons presented in Isenberg and Vasquez to consider driving by imbalanced spectra of obliquely propagating ion-cyclotron waves. These waves are assumed to be a small by-product of the imbalanced turbulent cascade to high perpendicular wavenumber, and their total intensity is taken to be 1% of the total fluctuation energy. We also extend the kinetic solutions for the proton distribution function in the resulting fast solar wind to heliocentric distances of 20 solar radii, which will be attainable by the Solar Probe Plus spacecraft. We consider three ratios of outward-propagating tomore » inward-propagating resonant intensities: 1, 4, and 9. The self-consistent bulk flow speed reaches fast solar wind values in all cases, and these speeds are basically independent of the intensity ratio. The steady-state proton distribution is highly organized into nested constant-density shells by the resonant wave-particle interaction. The radial evolution of this kinetic distribution as the coronal hole plasma flows outward is understood as a competition between the inward- and outward-directed large-scale forces, causing an effective circulation of particles through the (v{sub ∥}, v{sub ⊥}) phase space and a characteristic asymmetric shape to the distribution. These asymmetries are substantial and persist to the outer limit of the model computation, where they should be observable by the Solar Probe Plus instruments.« less

Control Of Screening Of A Charged Particle In Electrolytic Aqueous Paul Trap

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

Park, Jae Hyun; Krstic, Predrag S.

2011-06-01

Individual charged particles could be trapped and confined by the combined radio-frequency and DC quadrupole electric field of an aqueous Paul trap. Viscosity of water improves confinement and extends the range of the trap parameters which characterize the stability of the trap. Electrolyte, if present in aqueous solution, may screen the charged particle and thus partially or fully suppress electrophoretic interaction with the applied filed, possibly reducing it to a generally much weaker dielectrophoretic interaction with an induced dipole. Applying molecular dynamics simulation we show that the quadrupole field has a different effect at the electrolyte ions and at muchmore » heavier charged particle, effectively eliminating the screening by electrolyte ions and reinstating the electrophoretic confinement.« less

Estimation method of state-of-charge for lithium-ion battery used in hybrid electric vehicles based on variable structure extended kalman filter

NASA Astrophysics Data System (ADS)

Sun, Yong; Ma, Zilin; Tang, Gongyou; Chen, Zheng; Zhang, Nong

2016-07-01

Since the main power source of hybrid electric vehicle(HEV) is supplied by the power battery, the predicted performance of power battery, especially the state-of-charge(SOC) estimation has attracted great attention in the area of HEV. However, the value of SOC estimation could not be greatly precise so that the running performance of HEV is greatly affected. A variable structure extended kalman filter(VSEKF)-based estimation method, which could be used to analyze the SOC of lithium-ion battery in the fixed driving condition, is presented. First, the general lower-order battery equivalent circuit model(GLM), which includes column accumulation model, open circuit voltage model and the SOC output model, is established, and the off-line and online model parameters are calculated with hybrid pulse power characteristics(HPPC) test data. Next, a VSEKF estimation method of SOC, which integrates the ampere-hour(Ah) integration method and the extended Kalman filter(EKF) method, is executed with different adaptive weighting coefficients, which are determined according to the different values of open-circuit voltage obtained in the corresponding charging or discharging processes. According to the experimental analysis, the faster convergence speed and more accurate simulating results could be obtained using the VSEKF method in the running performance of HEV. The error rate of SOC estimation with the VSEKF method is focused in the range of 5% to 10% comparing with the range of 20% to 30% using the EKF method and the Ah integration method. In Summary, the accuracy of the SOC estimation in the lithium-ion battery cell and the pack of lithium-ion battery system, which is obtained utilizing the VSEKF method has been significantly improved comparing with the Ah integration method and the EKF method. The VSEKF method utilizing in the SOC estimation in the lithium-ion pack of HEV can be widely used in practical driving conditions.

Anomalous Protein-Protein Interactions in Multivalent Salt Solution.

PubMed

Pasquier, Coralie; Vazdar, Mario; Forsman, Jan; Jungwirth, Pavel; Lund, Mikael

2017-04-13

The stability of aqueous protein solutions is strongly affected by multivalent ions, which induce ion-ion correlations beyond the scope of classical mean-field theory. Using all-atom molecular dynamics (MD) and coarse grained Monte Carlo (MC) simulations, we investigate the interaction between a pair of protein molecules in 3:1 electrolyte solution. In agreement with available experimental findings of "reentrant protein condensation", we observe an anomalous trend in the protein-protein potential of mean force with increasing electrolyte concentration in the order: (i) double-layer repulsion, (ii) ion-ion correlation attraction, (iii) overcharge repulsion, and in excess of 1:1 salt, (iv) non Coulombic attraction. To efficiently sample configurational space we explore hybrid continuum solvent models, applicable to many-protein systems, where weakly coupled ions are treated implicitly, while strongly coupled ones are treated explicitly. Good agreement is found with the primitive model of electrolytes, as well as with atomic models of protein and solvent.

Heavy ion beam-ionosphere interactions - Charging and neutralizing the payload

NASA Technical Reports Server (NTRS)

Kaufmann, R. L.; Arnoldy, R. L.; Walker, D. N.; Holmes, J. C.; Pollock, C. J.

1989-01-01

Three different electrical charging and neutralization processes were experienced during gun operation in the Argon Release Controlled Studies rocket flights, which carried ion generators to 400-500 km in the nighttime auroral ionosphere: DC charging of the vehicle, brief charging at gun turn-on, and extended oscillatory sequences. The present analysis of these phenomena has determined that, during oscillatory events, the entire environment of a payload could alternate between hot electron and cold electron configurations at rates which may have been in excess of 10 kHz.

Novel computational approach for studying ph effects, excluded volume and ion-ion correlations in electrical double layers around polyelectrolytes and nanoparticles

NASA Astrophysics Data System (ADS)

Ovanesyan, Zaven

Highly charged cylindrical and spherical objects (macroions) are probably the simplest structures for modeling nucleic acids, proteins and nanoparticles. Their ubiquitous presence within biophysical systems ensures that Coulomb forces are among the most important interactions that regulate the behavior of these systems. In these systems, ions position themselves in a strongly correlated manner near the surface of a macroion and form electrical double layers (EDLs). These EDLs play an important role in many biophysical and biochemical processes. For instance, the macroion's net charge can change due to the binding of many multivalent ions to its surface. Thus, proper description of EDLs near the surface of a macroion may reveal a counter-intuitive charge inversion behavior, which can generate attraction between like-charged objects. This is relevant for the variety of fields such as self-assembly of DNA and RNA folding, as well as for protein aggregation and neurodegenerative diseases. Certainly, the key factors that contribute to these phenomena cannot be properly understood without an accurate solvation model. With recent advancements in computer technologies, the possibility to use computational tools for fundamental understanding of the role of EDLs around biomolecules and nanoparticles on their physical and chemical properties is becoming more feasible. Establishing the impact of the excluded volume and ion-ion correlations, ionic strength and pH of the electrolyte on the EDL around biomolecules and nanoparticles, and how changes in these properties consequently affect the Zeta potential and surface charge density are still not well understood. Thus, modeling and understanding the role of these properties on EDLs will provide more insights on the stability, adsorption, binding and function of biomolecules and nanoparticles. Existing mean-field theories such as Poisson Boltzmann (PB) often neglect the ion-ion correlations, solvent and ion excluded volume effects, which are important details for proper description of EDL properties. In this thesis, we implement an efficient and accurate classical solvation density functional theory (CDSFT) for EDLs of spherical macroions and cylindrical polyelectrolytes embedded in aqueous electrolytes. This approach extends the capabilities of mean field approximations by taking into account electrostatic ion-ion correlations, size asymmetry and excluded volume effects without compromising the computational cost. We apply the computational tool to study the structural and thermodynamic properties of the ionic atmosphere around B-DNA and spherical nanoparticles. We demonstrate that the presence of solvent molecules at experimental concentration and size values has a significant impact on the layering of ions. This layering directly influences the integrated charge and mean electrostatic potential in the diffuse region of the spherical electrical double layer (SEDL) and have a noticeable impact on the behavior of zeta potential (ZP). Recently, we have extended the aforementioned CSDFT to account for the charge-regulated mechanisms of the macroion surface on the structural and thermodynamic properties of spherical EDLs. In the approach, the CSDFT is combined with a surface complexation model to account for ion correlation and excluded volume effects on the surface titration of spherical macroions. We apply the proposed computational approach to describe the role that the ion size and solvent excluded volume play on the surface titration properties of silica nanoparticles. We analyze the effects of the nanoparticle size, pH and salt concentration of the aqueous solution on the nanoparticle's surface charge and zeta potential. The results reveal that surface charge density and zeta potential significantly depend on excluded volume and ion-ion correlation effects as well as on pH for monovalent ion species at high salt concentrations. Overall, our results are in good agreement with Monte Carlo simulations and available experimental data. We discuss future directions of this work, which includes extension of the solvation model for studying the flexibility properties of rigid peptides and globular proteins, and describes benefits that this research can potentially bring to scientific and non scientific communities.

Ion Temperature Control of the Io Plasma Torus

NASA Technical Reports Server (NTRS)

Delamere, P. A.; Schneider, N. M.; Steffl, A. J.; Robbins, S. J.

2005-01-01

We report on observational and theoretical studies of ion temperature in the Io plasma torus. Ion temperature is a critical factor for two reasons. First, ions are a major supplier of energy to the torus electrons which power the intense EUV emissions. Second, ion temperature determines the vertical extent of plasma along field lines. Higher temperatures spread plasma out, lowers the density and slows reaction rates. The combined effects can play a controlling role in torus energetics and chemistry. An unexpected tool for the study of ion temperature is the longitudinal structure in the plasma torus which often manifests itself as periodic brightness variations. Opposite sides of the torus (especially magnetic longitudes 20 and 200 degrees) have been observed on numerous occasions to have dramatically different brightness, density, composition, ionization state, electron temperature and ion temperature. These asymmetries must ultimately be driven by different energy flows on the opposite sides, presenting an opportunity to observe key torus processes operating under different conditions. The most comprehensive dataset for the study of longitudinal variations was obtained by the Cassini UVIS instrument during its Jupiter flyby. Steffl (Ph.D. thesis, 2005) identified longitudinal variations in all the quantities listed above wit the exception of ion temperature. We extend his work by undertaking the first search for such variation in the UVIS dataset. We also report on a 'square centimeter' model of the torus which extend the traditional 'cubic centimeter' models by including the controlling effects of ion temperature more completely.

Self-Consistent Model of Magnetospheric Ring Current and Electromagnetic Ion Cyclotron Waves: The May 2-7, 1998, Storm

NASA Technical Reports Server (NTRS)

Khazanov, G. V.; Gamayunov, K. V.; Jordanova, V. K.

2003-01-01

Complete description of a self-consistent model for magnetospheric ring current interacting with electromagnetic ion cyclotron waves is presented. The model is based on the system of two kinetic equations; one equation describes the ring current ion dynamics, and another equation describes the wave evolution. The effects on ring current ions interacting with electromagnetic ion cyclotron waves, and back on waves, are considered self-consistently by solving both equations on a global magnetospheric scale under non steady-state conditions. In the paper by Khazanov et al. [2002] this self-consistent model has only been shortly outlined, and discussions of many the model related details have been omitted. For example, in present study for the first time a new algorithm for numerical finding of the resonant numbers for quasilinear wave-particle interaction is described, or it is demonstrated that in order to describe quasilinear interaction in a multi-ion thermal plasma correctly, both e and He(+) modes of electromagnetic ion cyclotron waves should be employed. The developed model is used to simulate the entire May 2-7, 1998 storm period. Trapped number fluxes of the ring current protons are calculated and presented along with their comparison with the data measured by the 3D hot plasma instrument Polar/HYDRA. Examining of the wave (MLT, L shell) distributions produced during the storm progress reveals an essential intensification of the wave emissions in about two days after main phase of storm. This result is well consistent with the earlier ground-based observations. Also the theoretical shapes and the occurrence rates for power spectral densities of electromagnetic ion cyclotron waves are studied. It is found that in about 2 days after the storm main phase on May 4, mainly non Gaussian shapes of power spectral densities are produced.

Effect of salt entropy on protein solubility and Hofmeister series

NASA Astrophysics Data System (ADS)

Dahal, Yuba; Schmit, Jeremy

We present a theory of salt effects on protein solubility that accounts for salting-in, salting-out, and the Hofmeister series. We represent protein charge by the first order multipole expansion to include attractive and repulsive electrostatic interactions in the model. Our model also includes non-electrostatic protein-ion interactions, and ion-solvent interactions via an effective solvated ion radius. We find that the finite size of the ions has significant effects on the translational entropy of the salt, which accounts for the changes in the protein solubility. At low salt the dominant effect comes from the entropic cost of confining ions within the aggregate. At high concentrations the salt drives a depletion attraction that favors aggregation. Our theory explains the reversal in the Hofmeister series observed in lysozyme cloud point measurements and semi-quantitatively describes the solubility of lysozyme and chymosin crystals.

A Stochastic Model of Space Radiation Transport as a Tool in the Development of Time-Dependent Risk Assessment

NASA Technical Reports Server (NTRS)

Kim, Myung-Hee Y.; Nounu, Hatem N.; Ponomarev, Artem L.; Cucinotta, Francis A.

2011-01-01

A new computer model, the GCR Event-based Risk Model code (GERMcode), was developed to describe biophysical events from high-energy protons and heavy ions that have been studied at the NASA Space Radiation Laboratory (NSRL) [1] for the purpose of simulating space radiation biological effects. In the GERMcode, the biophysical description of the passage of heavy ions in tissue and shielding materials is made with a stochastic approach that includes both ion track structure and nuclear interactions. The GERMcode accounts for the major nuclear interaction processes of importance for describing heavy ion beams, including nuclear fragmentation, elastic scattering, and knockout-cascade processes by using the quantum multiple scattering fragmentation (QMSFRG) model [2]. The QMSFRG model has been shown to be in excellent agreement with available experimental data for nuclear fragmentation cross sections

Extended dynamic model for ion diffusion in all-vanadium redox flow battery including the effects of temperature and bulk electrolyte transfer

NASA Astrophysics Data System (ADS)

Badrinarayanan, Rajagopalan; Zhao, Jiyun; Tseng, K. J.; Skyllas-Kazacos, Maria

2014-12-01

As with all redox flow batteries, the Vanadium Redox flow Battery (VRB) can suffer from capacity loss as the vanadium ions diffuse at different rates leading to a build-up on one half-cell and dilution on the other. In this paper an extended dynamic model of the vanadium ion transfer is developed including the effect of temperature and bulk electrolyte transfer. The model is used to simulate capacity decay for a range of different ion exchange membranes that are being used in the VRB. The simulations show that Selemion CMV and Nafion 115 membranes have similar behavior where the impact of temperature on capacity loss is highest within the first 100 cycles. The results for Selemion AMV membrane however are seen to be very different where the capacity loss at different temperatures observed to increase linearly with increasing charging/discharging cycles. The model is made more comprehensive by including the effect of bulk electrolyte transfer. A volume change of 19% is observed in each half-cell for Nafion 115 membrane based on the simulation parameters. The effect of this change in volume directly affects concentration, and the characteristics are analyzed for each vanadium species as well as the overall concentration in the half-cells.

Continuum Approaches to Understanding Ion and Peptide Interactions with the Membrane

PubMed Central

Latorraca, Naomi R.; Callenberg, Keith M.; Boyle, Jon P.; Grabe, Michael

2014-01-01

Experimental and computational studies have shown that cellular membranes deform to stabilize the inclusion of transmembrane (TM) proteins harboring charge. Recent analysis suggests that membrane bending helps to expose charged and polar residues to the aqueous environment and polar head groups. We previously used elasticity theory to identify membrane distortions that minimize the insertion of charged TM peptides into the membrane. Here, we extend our work by showing that it also provides a novel, computationally efficient method for exploring the energetics of ion and small peptide penetration into membranes. First, we show that the continuum method accurately reproduces energy profiles and membrane shapes generated from molecular simulations of bare ion permeation at a fraction of the computational cost. Next, we demonstrate that the dependence of the ion insertion energy on the membrane thickness arises primarily from the elastic properties of the membrane. Moreover, the continuum model readily provides a free energy decomposition into components not easily determined from molecular dynamics. Finally, we show that the energetics of membrane deformation strongly depend on membrane patch size both for ions and peptides. This dependence is particularly strong for peptides based on simulations of a known amphipathic, membrane binding peptide from the human pathogen Toxoplasma gondii. In total, we address shortcomings and advantages that arise from using a variety of computational methods in distinct biological contexts. PMID:24652510

Effects of air-sea interaction on extended-range prediction of geopotential height at 500 hPa over the northern extratropical region

NASA Astrophysics Data System (ADS)

Wang, Xujia; Zheng, Zhihai; Feng, Guolin

2018-04-01

The contribution of air-sea interaction on the extended-range prediction of geopotential height at 500 hPa in the northern extratropical region has been analyzed with a coupled model form Beijing Climate Center and its atmospheric components. Under the assumption of the perfect model, the extended-range prediction skill was evaluated by anomaly correlation coefficient (ACC), root mean square error (RMSE), and signal-to-noise ratio (SNR). The coupled model has a better prediction skill than its atmospheric model, especially, the air-sea interaction in July made a greater contribution for the improvement of prediction skill than other months. The prediction skill of the extratropical region in the coupled model reaches 16-18 days in all months, while the atmospheric model reaches 10-11 days in January, April, and July and only 7-8 days in October, indicating that the air-sea interaction can extend the prediction skill of the atmospheric model by about 1 week. The errors of both the coupled model and the atmospheric model reach saturation in about 20 days, suggesting that the predictable range is less than 3 weeks.

Ion Mass Spectroscopy for the Outer Solar System

NASA Astrophysics Data System (ADS)

Reisenfeld, D. B.; Elphic, R. C.; McComas, D. J.; Nordholt, J. E.; Steinberg, J. T.; Wiens, R. C.

2001-01-01

A proven method for determination of the exospheric and surface composition of moons and comets is ion mass spectroscopy. Ions are produced via sputtering of surface constituents by the ambient plasma (solar wind or planetary magnetospheres), and via photo- and electron impact ionization of neutral exospheric/atmospheric constituents. A promising emergent technology in the field of space-based ion mass spectrometry is the low-cost, miniaturized but high-performance ion mass spectrometer (IMS) as exhibited by the Plasma Experiment for Planetary Exploration (PEPE) on Deep Space 1 (DS-1). A technology demonstration instrument, the PEPE IMS realized a mass resolution (M/delta(M)) of approximately 10. Its energy range extends from 5 eV to 9 keV at this mass resolution, and up to 33.5 keV in a lower mass resolution mode. With minimal development, these capabilities can be greatly extended. Already, we have produced a fully functional engineering model having a M/delta(M) = 20 and an energy range extending to 18 keV in the high-mass resolution mode. Further design modifications anticipate extending the mass resolution to 30-40 while still maintaining a miniaturized design. This makes possible many more isotopic and molecular differentiations than achievable with the original PEPE design. A PEPE-class spectrometer can address a significant number of the OPP key strategic objectives. In particular, in situ cometary nucleus analysis, studies of Triton's atmospheric and surface composition, and Europa surface composition analysis, can all be performed through IMS measurements. Additional information is contained in the original extended abstract.

Thermophysical properties of simple liquid metals: A brief review of theory

NASA Technical Reports Server (NTRS)

Stroud, David

1993-01-01

In this paper, we review the current theory of the thermophysical properties of simple liquid metals. The emphasis is on thermodynamic properties, but we also briefly discuss the nonequilibrium properties of liquid metals. We begin by defining a 'simple liquid metal' as one in which the valence electrons interact only weakly with the ionic cores, so that the interaction can be treated by perturbation theory. We then write down the equilibrium Hamiltonian of a liquid metal as a sum of five terms: the bare ion-ion interaction, the electron-electron interaction, the bare electron-ion interaction, and the kinetic energies of electrons and ions. Since the electron-ion interaction can be treated by perturbation, the electronic part contributes in two ways to the Helmholtz free energy: it gives a density-dependent term which is independent of the arrangement of ions, and it acts to screen the ion-ion interaction, giving rise to effective ion-ion pair potentials which are density-dependent, in general. After sketching the form of a typical pair potential, we briefly enumerate some methods for calculating the ionic distribution function and hence the Helmholtz free energy of the liquid: monte Carlo simulations, molecular dynamics simulations, and thermodynamic perturbation theory. The final result is a general expression for the Helmholtz free energy of the liquid metal. It can be used to calculate a wide range of thermodynamic properties of simple metal liquids, which we enumerate. They include not only a range of thermodynamic coefficients of both metals and alloys, but also many aspects of the phase diagram, including freezing curves of pure elements and phase diagrams of liquid alloys (including liquidus and solidus curves). We briefly mention some key discoveries resulting from previous applications of this method, and point out that the same methods work for other materials not normally considered to be liquid metals (such as colloidal suspensions, in which the suspended microspheres behave like ions screened by the salt solution in which they are suspended). We conclude with a brief discussion of some non-equilibrium (i.e., transport) properties which can be treated by an extension of these methods. These include electrical resistivity, thermal conductivity, viscosity, atomic self-diffusion coefficients, concentration diffusion coefficients in alloys, surface tension and thermal emissivity. Finally, we briefly mention two methods by which the theory might be extended to non-simple liquid metals: these are empirical techniques (i.e., empirical two- and three-body potentials), and numerical many-body approaches. Both may be potentially applicable to extremely complex systems, such as nonstoichiometric liquid semiconductor alloys.

Beyond the continuum: how molecular solvent structure affects electrostatics and hydrodynamics at solid-electrolyte interfaces.

PubMed

Bonthuis, Douwe Jan; Netz, Roland R

2013-10-03

Standard continuum theory fails to predict several key experimental results of electrostatic and electrokinetic measurements at aqueous electrolyte interfaces. In order to extend the continuum theory to include the effects of molecular solvent structure, we generalize the equations for electrokinetic transport to incorporate a space dependent dielectric profile, viscosity profile, and non-electrostatic interaction potential. All necessary profiles are extracted from atomistic molecular dynamics (MD) simulations. We show that the MD results for the ion-specific distribution of counterions at charged hydrophilic and hydrophobic interfaces are accurately reproduced using the dielectric profile of pure water and a non-electrostatic repulsion in an extended Poisson-Boltzmann equation. The distributions of Na(+) at both surface types and Cl(-) at hydrophilic surfaces can be modeled using linear dielectric response theory, whereas for Cl(-) at hydrophobic surfaces it is necessary to apply nonlinear response theory. The extended Poisson-Boltzmann equation reproduces the experimental values of the double-layer capacitance for many different carbon-based surfaces. In conjunction with a generalized hydrodynamic theory that accounts for a space dependent viscosity, the model captures the experimentally observed saturation of the electrokinetic mobility as a function of the bare surface charge density and the so-called anomalous double-layer conductivity. The two-scale approach employed here-MD simulations and continuum theory-constitutes a successful modeling scheme, providing basic insight into the molecular origins of the static and kinetic properties of charged surfaces, and allowing quantitative modeling at low computational cost.

Numerical implementation of a cold-ion, Boltzmann-electron model for nonplanar plasma-surface interactions

NASA Astrophysics Data System (ADS)

Holgate, J. T.; Coppins, M.

2018-04-01

Plasma-surface interactions are ubiquitous in the field of plasma science and technology. Much of the physics of these interactions can be captured with a simple model comprising a cold ion fluid and electrons which satisfy the Boltzmann relation. However, this model permits analytical solutions in a very limited number of cases. This paper presents a versatile and robust numerical implementation of the model for arbitrary surface geometries in cartesian and axisymmetric cylindrical coordinates. Specific examples of surfaces with sinusoidal corrugations, trenches, and hemi-ellipsoidal protrusions verify this numerical implementation. The application of the code to problems involving plasma-liquid interactions, plasma etching, and electron emission from the surface is discussed.

Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg(2+) ion models commonly used in biomolecular simulations.

PubMed

Panteva, Maria T; Giambaşu, George M; York, Darrin M

2015-05-15

The prevalence of Mg(2+) ions in biology and their essential role in nucleic acid structure and function has motivated the development of various Mg(2+) ion models for use in molecular simulations. Currently, the most widely used models in biomolecular simulations represent a nonbonded metal ion as an ion-centered point charge surrounded by a nonelectrostatic pairwise potential that takes into account dispersion interactions and exchange effects that give rise to the ion's excluded volume. One strategy toward developing improved models for biomolecular simulations is to first identify a Mg(2+) model that is consistent with the simulation force fields that closely reproduces a range of properties in aqueous solution, and then, in a second step, balance the ion-water and ion-solute interactions by tuning parameters in a pairwise fashion where necessary. The present work addresses the first step in which we compare 17 different nonbonded single-site Mg(2+) ion models with respect to their ability to simultaneously reproduce structural, thermodynamic, kinetic and mass transport properties in aqueous solution. None of the models based on a 12-6 nonelectrostatic nonbonded potential was able to reproduce the experimental radial distribution function, solvation free energy, exchange barrier and diffusion constant. The models based on a 12-6-4 potential offered improvement, and one model in particular, in conjunction with the SPC/E water model, performed exceptionally well for all properties. The results reported here establish useful benchmark calculations for Mg(2+) ion models that provide insight into the origin of the behavior in aqueous solution, and may aid in the development of next-generation models that target specific binding sites in biomolecules. © 2015 Wiley Periodicals, Inc.

Alternative Fuels Data Center: Electricity Related Links

Science.gov Websites

-performance safe lithium-ion (Li-ion) batteries for hybrid electric vehicles (HEVs), plug-in HEVs (PHEVs) and ) manufacturers alternative energy vehicles, specializing in battery electric vehicles (BEV) and range extended (NREL) Energy Storage Project is leading the charge on battery thermal management, modeling, and systems

Final Technical Report: Targeting DOE-Relevant Ions with Supramolecular Strategies, DE-SC0010555

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

Bowman-James, Kristin

The effectiveness of three popular supramolecular strategies to selectively target negatively charged ions (anions) was evaluated. Ions of interest included oxo anions, particularly sulfate, that hamper nuclear waste remediation. Three objectives were pursued using a simple building block strategies and by strategically placing anion-binding sites at appropriate positions on organic host molecules. The goal of the first objective was to assess the influence of secondary, tertiary and quaternized amines on binding tetrahedral anions using mixed amide/amine macrocyclic and urea/amine hosts containing aromatic or heteroaromatic spacers. Objective 2 focused on the design of ion pair hosts, using mixed macrocyclic anion hostsmore » joined through polyether linkages. Objective 3 was to explore the synthesis of new metal-linked extended macrocyclic frameworks to leverage anion binding. Key findings were that smaller 24-membered macrocycles provided the most complementary binding for sulfate ion and mixed urea/amine chelates showed enhanced binding over amide corollaries in addition to being highly selective for SO 4 2- in the presence of small quantities of water. In addition to obtaining prototype metal-linked macrocyclic anion hosts, a new dipincer ligand was designed that can be used to link macrocyclic or other supramolecular hosts in extended frameworks. When the tetraamide-based pincers are bound to two metal ions, an interesting phenomenon occurs. Upon deprotonation of the amides, two new protons appear between adjacent carbonyl pairs on the ligand, which may modify the chemistry, and metal-metal interactions in the complexes. Gel formation occurred for some of these extended hosts, and the physical properties are currently under investigation. The new tetracarboxamide-based pincers can also provide basic frameworks for double macrocycles capable of binding ion pairs as well as for binding metal ions and exploring intermetallic interactions through the pyrazine π system. Additionally appendages capable of influencing solvation effects can be introduced, and a number of other potential applications can be realized in areas such as soft materials chemistry, catalysis, sensing, and proton switches, the latter for binding and release of targeted guests. These findings provide a better foundation for understanding the selective binding of anions by targeted placement of hydrogen binding sites, and the strengths and weaknesses of various functional groups, that will allow for more the design of more effective anion sequestering agents. Our design strategy also used simple, cost-effective building blocks for host synthesis to allow for scale-up should real-world applications be forthcoming.« less

New insights on the voltage dependence of the KCa3.1 channel block by internal TBA.

PubMed

Banderali, Umberto; Klein, Hélène; Garneau, Line; Simoes, Manuel; Parent, Lucie; Sauvé, Rémy

2004-10-01

We present in this work a structural model of the open IKCa (KCa3.1) channel derived by homology modeling from the MthK channel structure, and used this model to compute the transmembrane potential profile along the channel pore. This analysis showed that the selectivity filter and the region extending from the channel inner cavity to the internal medium should respectively account for 81% and 16% of the transmembrane potential difference. We found however that the voltage dependence of the IKCa block by the quaternary ammonium ion TBA applied internally is compatible with an apparent electrical distance delta of 0.49 +/- 0.02 (n = 6) for negative potentials. To reconcile this observation with the electrostatic potential profile predicted for the channel pore, we modeled the IKCa block by TBA assuming that the voltage dependence of the block is governed by both the difference in potential between the channel cavity and the internal medium, and the potential profile along the selectivity filter region through an effect on the filter ion occupancy states. The resulting model predicts that delta should be voltage dependent, being larger at negative than positive potentials. The model also indicates that raising the internal K+ concentration should decrease the value of delta measured at negative potentials independently of the external K+ concentration, whereas raising the external K+ concentration should minimally affect delta for concentrations >50 mM. All these predictions are born out by our current experimental results. Finally, we found that the substitutions V275C and V275A increased the voltage sensitivity of the TBA block, suggesting that TBA could move further into the pore, thus leading to stronger interactions between TBA and the ions in the selectivity filter. Globally, these results support a model whereby the voltage dependence of the TBA block in IKCa is mainly governed by the voltage dependence of the ion occupancy states of the selectivity filter.

α-K2AgF4: Ferromagnetism induced by the weak superexchange of different eg orbitals from the nearest neighbor Ag ions

NASA Astrophysics Data System (ADS)

Zhang, Xiaoli; Zhang, Guoren; Jia, Ting; Zeng, Zhi; Lin, H. Q.

2016-05-01

We study the abnormal ferromagnetism in α-K2AgF4, which is very similar to high-TC parent material La2CuO4 in structure. We find out that the electron correlation is very important in determining the insulating property of α-K2AgF4. The Ag(II) 4d9 in the octahedron crystal field has the t2 g 6 eg 3 electron occupation with eg x2-y2 orbital fully occupied and 3z2-r2 orbital partially occupied. The two eg orbitals are very extended indicating both of them are active in superexchange. Using the Hubbard model combined with Nth-order muffin-tin orbital (NMTO) downfolding technique, it is concluded that the exchange interaction between eg 3z2-r2 and x2-y2 from the first nearest neighbor Ag ions leads to the anomalous ferromagnetism in α-K2AgF4.

γ -soft Ba 146 and the role of nonaxial shapes at N ≈ 90

DOE PAGES

Mitchell, A. J.; Lister, C. J.; McCutchan, E. A.; ...

2016-01-12

Low-spin states in the neutron-rich, N = 90 nuclide 146Ba were populated following β decay of 146Cs , with the goal of clarifying the development of deformation in barium isotopes through delineation of their nonyrast structures. Fission fragments of 146Cs were extracted from a 1.7-Ci 252Cf source and mass selected using the CAlifornium Rare Ion Breeder Upgrade (CARIBU) facility. Low-energy ions were deposited at the center of a box of thin β detectors, surrounded by a highly efficient high-purity Ge array. The new 146Ba decay scheme now contains 31 excited levels extending up to ~2.5 MeV excitation energy, double whatmore » was previously known. These data are compared to predictions from the interacting boson approximation (IBA) model. It appears that the abrupt shape change found at N = 90 in Sm and Gd is much more gradual in Ba and Ce, due to an enhanced role of the γ degree of freedom.« less

Rydberg Molecules for Ion-Atom Scattering in the Ultracold Regime

NASA Astrophysics Data System (ADS)

Schmid, T.; Veit, C.; Zuber, N.; Löw, R.; Pfau, T.; Tarana, M.; Tomza, M.

2018-04-01

We propose a novel experimental method to extend the investigation of ion-atom collisions from the so far studied cold, essentially classical regime to the ultracold, quantum regime. The key aspect of this method is the use of Rydberg molecules to initialize the ultracold ion-atom scattering event. We exemplify the proposed method with the lithium ion-atom system, for which we present simulations of how the initial Rydberg molecule wave function, freed by photoionization, evolves in the presence of the ion-atom scattering potential. We predict bounds for the ion-atom scattering length from ab initio calculations of the interaction potential. We demonstrate that, in the predicted bounds, the scattering length can be experimentally determined from the velocity of the scattered wave packet in the case of 6Li+ = 6Li and from the molecular ion fraction in the case of 7Li+ - 7Li. The proposed method to utilize Rydberg molecules for ultracold ion-atom scattering, here particularized for the lithium ion-atom system, is readily applicable to other ion-atom systems as well.

Rydberg Molecules for Ion-Atom Scattering in the Ultracold Regime.

PubMed

Schmid, T; Veit, C; Zuber, N; Löw, R; Pfau, T; Tarana, M; Tomza, M

2018-04-13

We propose a novel experimental method to extend the investigation of ion-atom collisions from the so far studied cold, essentially classical regime to the ultracold, quantum regime. The key aspect of this method is the use of Rydberg molecules to initialize the ultracold ion-atom scattering event. We exemplify the proposed method with the lithium ion-atom system, for which we present simulations of how the initial Rydberg molecule wave function, freed by photoionization, evolves in the presence of the ion-atom scattering potential. We predict bounds for the ion-atom scattering length from ab initio calculations of the interaction potential. We demonstrate that, in the predicted bounds, the scattering length can be experimentally determined from the velocity of the scattered wave packet in the case of ^{6}Li^{+}-^{6}Li and from the molecular ion fraction in the case of ^{7}Li^{+}-^{7}Li. The proposed method to utilize Rydberg molecules for ultracold ion-atom scattering, here particularized for the lithium ion-atom system, is readily applicable to other ion-atom systems as well.

Harnessing the relativistic Buneman instability for laser-ion acceleration in the transparency regime

NASA Astrophysics Data System (ADS)

Stark, D. J.; Yin, L.; Albright, B. J.

2018-06-01

We examine the relativistic Buneman instability in systems relevant to high-intensity laser-plasma interactions under conditions of relativistically-induced transparency, as this instability can generate large-amplitude electrostatic waves at low frequencies that are pertinent to ion dynamics in these systems. Ion flows are shown to significantly alter the range of unstable wave numbers and to increase the phase velocities of the unstable modes; we particularly highlight the relativistic effects from both the ion and electron (with transverse motion) populations. These findings are related to the mode structure seen in particle-in-cell simulation results of a short-pulse laser breaking through an initially opaque target with the onset of relativistic transparency. Additionally, driving mechanisms from free energy present in density and velocity gradients are shown to be capable of significantly enhancing the growth rates, and these instabilities furthermore extend the breadth of the unstable wave number range. Lastly, we discuss how the transverse self-generated magnetic fields characteristic of short-pulse interactions can potentially constrain the unstable wave numbers in a non-trivial manner.

Unraveling halide hydration: A high dilution approach.

PubMed

Migliorati, Valentina; Sessa, Francesco; Aquilanti, Giuliana; D'Angelo, Paola

2014-07-28

The hydration properties of halide aqua ions have been investigated combining classical Molecular Dynamics (MD) with Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy. Three halide-water interaction potentials recently developed [M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144104 (2011)], along with three plausible choices for the value of the absolute hydration free energy of the proton (ΔG [minus sign in circle symbol]hyd[H+]), have been checked for their capability to properly describe the structural properties of halide aqueous solutions, by comparing the MD structural results with EXAFS experimental data. A very good agreement between theory and experiment has been obtained with one parameter set, namely LE, thus strengthening preliminary evidences for a ΔG [minus sign in circle symbol]hyd[H] value of -1100 kJ mol(-1) [M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144104 (2011)]. The Cl(-), Br(-), and I(-) ions have been found to form an unstructured and disordered first hydration shell in aqueous solution, with a broad distribution of instantaneous coordination numbers. Conversely, the F(-) ion shows more ordered and defined first solvation shell, with only two statistically relevant coordination geometries (six and sevenfold complexes). Our thorough investigation on the effect of halide ions on the microscopic structure of water highlights that the perturbation induced by the Cl(-), Br(-), and I(-) ions does not extend beyond the ion first hydration shell, and the structure of water in the F(-) second shell is also substantially unaffected by the ion.

Faraday Discussion 160 Introductory Lecture: Interpreting and Predicting Hofmeister Salt Ion and Solute Effects on Biopolymer and Model Processes Using the Solute Partitioning Model

PubMed Central

Record, M. Thomas; Guinn, Emily; Pegram, Laurel; Capp, Michael

2013-01-01

Understanding how Hofmeister salt ions and other solutes interact with proteins, nucleic acids, other biopolymers and water and thereby affect protein and nucleic acid processes as well as model processes (e.g solubility of model compounds) in aqueous solution is a longstanding goal of biophysical research. Empirical Hofmeister salt and solute “m-values” (derivatives of the observed standard free energy change for a model or biopolymer process with respect to solute or salt concentration m3) are equal to differences in chemical potential derivatives: m-value = Δ(dμ2/dm3) = Δμ23 which quantify the preferential interactions of the solute or salt with the surface of the biopolymer or model system (component 2) exposed or buried in the process. Using the SPM, we dissect μ23 values for interactions of a solute or Hofmeister salt with a set of model compounds displaying the key functional groups of biopolymers to obtain interaction potentials (called α-values) that quantify the interaction of the solute or salt per unit area of each functional group or type of surface. Interpreted using the SPM, these α-values provide quantitative information about both the hydration of functional groups and the competitive interaction of water and the solute or salt with functional groups. The analysis corroborates and quantifies previous proposals that the Hofmeister anion and cation series for biopolymer processes are determined by ion-specific, mostly unfavorable interactions with hydrocarbon surfaces; the balance between these unfavorable nonpolar interactions and often-favorable interactions of ions with polar functional groups determine the series null points. The placement of urea and glycine betaine (GB) at opposite ends of the corresponding series of nonelectrolytes results from the favorable interactions of urea, and unfavorable interactions of GB, with many (but not all) biopolymer functional groups. Interaction potentials and local-bulk partition coefficients quantifying the distribution of solutes (e.g. urea, glycine betaine) and Hofmeister salt ions in the vicinity of each functional group make good chemical sense when interpreted in terms of competitive noncovalent interactions. These interaction potentials allow solute and Hofmeister (noncoulombic) salt effects on protein and nucleic acid processes to be interpreted or predicted, and allow the use of solutes and salts as probes of interface formation and large-scale conformational changes in the steps of a biopolymer mechanism. PMID:23795491

Self-Assembled Films of Dendrimers and Metallophthalocyanines as FET-Based Glucose Biosensors

PubMed Central

Vieira, Nirton C.S.; Figueiredo, Alessandra; de Queiroz, Alvaro A.A.; Zucolotto, Valtencir; Guimarães, Francisco E.G.

2011-01-01

Separative extended gate field effect transistor (SEGFET) type devices have been used as an ion sensor or biosensor as an alternative to traditional ion sensitive field effect transistors (ISFETs) due to their robustness, ease of fabrication, low cost and possibility of FET isolation from the chemical environment. The layer-by-layer technique allows the combination of different materials with suitable properties for enzyme immobilization on simple platforms such as the extended gate of SEGFET devices enabling the fabrication of biosensors. Here, glucose biosensors based on dendrimers and metallophthalocyanines (MPcs) in the form of layer-by-layer (LbL) films, assembled on indium tin oxide (ITO) as separative extended gate material, has been produced. NH3+ groups in the dendrimer allow electrostatic interactions or covalent bonds with the enzyme (glucose oxidase). Relevant parameters such as optimum pH, buffer concentration and presence of serum bovine albumin (BSA) in the immobilization process were analyzed. The relationship between the output voltage and glucose concentration shows that upon detection of a specific analyte, the sub-products of the enzymatic reaction change the pH locally, affecting the output signal of the FET transducer. In addition, dendritic layers offer a nanoporous environment, which may be permeable to H+ ions, improving the sensibility as modified electrodes for glucose biosensing. PMID:22163704

Update on J /ψ regeneration in a hadron gas

NASA Astrophysics Data System (ADS)

Abreu, L. M.; Khemchandani, K. P.; Torres, A. Martínez; Navarra, F. S.; Nielsen, M.

2018-04-01

In heavy-ion collisions, after the quark-gluon plasma there is a hadronic gas phase. Using effective Lagrangians, we study the interactions of charmed mesons which lead to J /ψ production and absorption in this gas. We update and extend previous calculations introducing strange meson interactions and also including the interactions mediated by the recently measured exotic charmonium resonances Z (3900 ) and Z (4025 ) . These resonances open new reaction channels for the J /ψ , which could potentially lead to changes in its multiplicity. We compute the J /ψ production cross section in processes such as D(s) (*)+D¯(*)→J /ψ +(π ,ρ ,K ,K*) and also the J /ψ absorption cross section in the corresponding inverse processes. Using the obtained cross sections as input to solve the appropriate rate equation, we conclude that the interactions in the hadron gas phase lead to a 20-24% reduction of the J /ψ abundance. Within the uncertainties of the calculation, this reduction is the same at the Relativistic Heavy Ion Collider and the large Hadron Collider.

Millimeter-Wave Time Resolved Studies of the Formation and Decay of CO^+

NASA Astrophysics Data System (ADS)

Oesterling, Lee; Herbst, Eric; de Lucia, Frank

1998-04-01

Since the rate constants for ion-molecule interactions are typically much larger than neutral-neutral interactions, understanding ion-molecule interactions is essential to interpreting radio astronomical spectra from interstellar clouds and modeling the processes which lead to the formation of stars in these regions. We have developed a cell which allows us to study ion-molecule interactions in gases at low temperatures and pressures by using an electron gun technique to create ions. By centering our millimeter-wave source on a rotational resonance and gating the electron beam on and off, we are able to study the time-dependent rotational state distribution of the ion during its formation and decay, and so learn about excitation and relaxation processes as functions of temperature, pressure, electron beam energy, and electron beam current.

Combining Sequential Extractions and X-ray Absorption Spectroscopy for Quantitative and Qualitative Zinc Speciation in Soil

NASA Astrophysics Data System (ADS)

Bauer, Tatiana; Minkina, Tatiana; Batukaev, Abdulmalik; Nevidomskaya, Dina; Burachevskaya, Marina; Tsitsuashvili, Viktoriya; Urazgildieva, Kamilya

2017-04-01

The combined use of X-ray absorption spectrometry and extractive fractionation is an effective approach for studying the interaction of metal ions with soil compounds and identifying the phases-carriers of metals in soil and their stable fixation. These studies were carried out using the technique of X-ray absorption spectroscopy and chemical extractive fractionation. In a model experiment the samples taken in Calcic Chernozem were artificially contaminated with higher portion of Zn(NO3)2 (2000 mg/kg). The metal were incubated in soil samples for 2 year. The samples of soil mineral and organic phases (calcite, kaolinite, bentonite, humic acids) were saturated with Zn2+ from a solution of nitrate salts of metal. The total content of Zn in soil and soil various phases was determined using the X-ray fluorescence method. Extended X-ray absorption fine structure (EXAFS) Zn was measured at the Structural Materials Science beamline of the Kurchatov Center for Synchrotron Radiation. Sequential fractionation of Zn in soil conducted by Tessier method (Tessier et al., 1979) which determining 5 fractions of metals in soil: exchangeable, bound to Fe-Mn oxide, bound to carbonate, bound to the organic matter, and bound to silicate (residual). This methodology has so far more than 4000 citations (Web of Science), which demonstrates the popularity of this approach. Much Zn compounds are contained in uncontaminated soils in stable primary and secondary silicates inherited from the parental rocks (67% of the total concentrations in all fractions), which is a regional trait of soils in the fore-Caucasian plain. Extracted fractionation of metal compounds in soil samples, artificially contaminated with Zn salts, indicates the priority holding of Zn2+ ions by silicates, carbonates and Fe-Mn oxides. The Zn content significantly increases in the exchangeable fraction. Atomic structure study of the soil various phases saturated with Zn2+ ion by using (XANES) X-ray absorption spectroscopy allowed the determination of mechanism of metal ions interaction with soil phases and the resulting types of chemical bonds. Interaction with soil components modifies the electron structure of the metal ions themselves. The soil contamination with Zn is accompanied by decreasing the stable connection between metal and soil components. Interacting with humic acids in chernozem, the Zn2+ ion is coordinated by functional groups and ligands and forms unstable outer-sphere complexes. Zinc included into octahedral structures of layered minerals and hydro(oxides) can be inner-and outer-sphere adsorbed. The Zn2+ ions enable to replace Ca2+ ions in octahedral positions being coordinated with carbonate ions as ligands, thus forming absorbed complexes at the surface of mineral calcite. This work was supported by grant of the Russian Scientific Foundation № 16-14-10217.

3D magnetic nanostructures grown by focused electron and ion beam induced deposition

NASA Astrophysics Data System (ADS)

Fernandez-Pacheco, Amalio

Three-dimensional nanomagnetism is an emerging research area, where magnetic nanostructures extend along the whole space, presenting novel functionalities not limited to the substrate plane. The development of this field could have a revolutionary impact in fields such as electronics, the Internet of Things or bio-applications. In this contribution, I will show our recent work on 3D magnetic nanostructures grown by focused electron and ion beam induced deposition. This 3D nano-printing techniques, based on the local chemical vapor deposition of a gas via the interaction with electrons and ions, makes the fabrication of complex 3D magnetic nanostructures possible. First, I will show how by exploiting different growth regimes, suspended Cobalt nanowires with modulated diameter can be patterned, with potential as domain wall devices. Afterwards, I will show recent results where the synthesis of Iron-Gallium alloys can be exploited in the field of artificial multiferroics. Moreover, we are developing novel methodologies combining physical vapor deposition and 3D nano-printing, creating Permalloy 3D nanostrips with controllable widths and lengths up to a few microns. This approach has been extended to more complex geometries by exploiting advanced simulation growth techniques combining Monte Carlo and continuum model methods. Throughout the talk, I will show the methodology we are following to characterize 3D magnetic nanostructures, by combining magneto-optical Kerr effect, scanning probe microscopy and electron and X-R magnetic imaging, and I will highlight some of the challenges and opportunities when studying these structures. I acknowledge funding from EPSRC and the Winton Foundation.

Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme

PubMed Central

Roychowdhury-Saha, Manami; Burke, Donald H.

2007-01-01

Divalent ion sensitivity of hammerhead ribozymes is significantly reduced when the RNA structure includes appropriate tertiary stabilization. Therefore, we investigated the activity of the tertiary stabilized “RzB” hammerhead ribozyme in several nondivalent ions. Ribozyme RzB is active in spermidine and Na+ alone, although the cleavage rates are reduced by more than 1,000-fold relative to the rates observed in Mg2+ and in transition metal ions. The trivalent cobalt hexammine (CoHex) ion is often used as an exchange-inert analog of hydrated magnesium ion. Trans-cleavage rates exceeded 8 min−1 in 20 mM CoHex, which promoted cleavage through outersphere interactions. The stimulation of catalysis afforded by the tertiary structural interactions within RzB does not require Mg2+, unlike other extended hammerhead ribozymes. Site-specific interaction with at least one Mg2+ ion is suggested by CoHex competition experiments. In the presence of a constant, low concentration of Mg2+, low concentrations of CoHex decreased the rate by two to three orders of magnitude relative to the rate in Mg2+ alone. Cleavage rates increased as CoHex concentrations were raised further, but the final fraction cleaved was lower than what was observed in CoHex or Mg2+ alone. These observations suggest that Mg2+ and CoHex compete for binding and that they cause misfolded structures when they are together. The results of this study support the existence of an alternate catalytic mechanism used by nondivalent ions (especially CoHex) that is distinct from the one promoted by divalent metal ions, and they imply that divalent metals influence catalysis through a specific nonstructural role. PMID:17456566

Recent progress towards a physics-based understanding of the H-mode transition

DOE PAGES

Tynan, G. R.; Cziegler, I.; Diamond, P. H.; ...

2016-01-22

Results from recent experiment and numerical simulation point towards a picture of the L-H transition in which edge shear flows interacting with edge turbulence create the conditions needed to produce a non-zero turbulent Reynolds stress at and just inside the LCFS during L-mode discharges. This stress acts to reinforce the shear flow at this location and the flow drive gets stronger as heating is increased. The L-H transition ensues when the rate of work done by this stress is strong enough to drive the shear flow to large values, which then grows at the expense of the turbulence intensity. Themore » drop in turbulence intensity momentarily reduces the heat flux across the magnetic flux surface, which then allows the edge plasma pressure gradient to build. A sufficiently strong ion pressure gradient then locks in the H-mode state. The results are in general agreement with previously published reduced 0D and 1D predator prey models. An extended predator–prey model including separate ion and electron heat channels yields a non-monotonic power threshold dependence on plasma density provided that the fraction of heat deposited on the ions increases with plasma density. Possible mechanisms to explain other macroscopic transition threshold criteria are identified. A number of open questions and unexplained observations are identified, and must be addressed and resolved in order to build a physics-based model that can yield predictions of the macroscopic conditions needed for accessing H-mode.« less

Purification/annealing of graphene with 100-MeV Ag ion irradiation

PubMed Central

2014-01-01

Studies on interaction of graphene with radiation are important because of nanolithographic processes in graphene-based electronic devices and for space applications. Since the electronic properties of graphene are highly sensitive to the defects and number of layers in graphene sample, it is desirable to develop tools to engineer these two parameters. We report swift heavy ion (SHI) irradiation-induced annealing and purification effects in graphene films, similar to that observed in our studies on fullerenes and carbon nanotubes (CNTs). Raman studies after irradiation with 100-MeV Ag ions (fluences from 3 × 1010 to 1 × 1014 ions/cm2) show that the disorder parameter α, defined by ID/IG ratio, decreases at lower fluences but increases at higher fluences beyond 1 × 1012 ions/cm2. This indicates that SHI induces annealing effects at lower fluences. We also observe that the number of graphene layers is reduced at fluences higher than 1 × 1013 ions/cm2. Using inelastic thermal spike model calculations, we estimate a radius of 2.6 nm for ion track core surrounded by a halo extending up to 11.6 nm. The transient temperature above the melting point in the track core results in damage, whereas lower temperature in the track halo is responsible for annealing. The results suggest that SHI irradiation fluence may be used as one of the tools for defect annealing and manipulation of the number of graphene layers. PACS 60.80.x; 81.05.ue PMID:24636520

Contribution of capillary electrophoresis to an integrated vision of humic substances size and charge characterizations

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

D'Orlye, Fanny; Reiller, Pascal E.

2014-02-15

The physicochemical properties of three different humic substances (HS) are probed using capillary zone electrophoresis in alkaline carbonate buffers, pH 10. Special attention is drawn to the impact of the electrolyte ionic strength and counter-ion nature, chosen within the alkali-metal series, on HS electrophoretic mobility. Taylor-Aris dispersion analysis provides insights into the hydrodynamic radius (R-H) distributions of HS. The smallest characterized entities are of nano-metric dimensions, showing neither ionic strength- nor alkali-metal-induced aggregation. These results are compared with the entities evidenced in dynamic light scattering measurements, the size of which is two order of magnitude higher, ca. 100 nm. Themore » extended Onsager model provides a reasonable description of measured electrophoretic mobilities in the ionic strength range 1-50 mM, thus allowing the estimation of limiting mobilities and ionic charge numbers for the different HS samples. An unexpected HS electrophoretic mobility increase (in absolute value) is observed in the order Li{sup +} ≤ Na{sup +} ≤ K{sup +} ≤ Cs{sup +} and discussed either in terms of retarding forces or in terms of ion-ion interactions. (authors)« less

Modeling the near-Earth interaction between ring current ions and exospheric neutrals: escape through energetic neutral atoms (ENAs)

NASA Astrophysics Data System (ADS)

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

2016-12-01

The two major loss processes for ring current decay are precipitation and energetic neutral atoms (ENAs). Since the exospheric neutral density increases with decreasing altitudes, precipitating ring current ions (reaching down to 200 - 800 km in altitude) also produce low-altitude ENA signatures that can be stronger than the ring current emission at equatorial distances ( 2 - 9 Re). The higher density results in multiple collisions between the ring current ions and exospheric oxygen. The affect on hydrogen ions is the focus of this study. Since the H particle sustains energy loss ( 36 eV) at each neutralizing or re-ionizing interaction, the escaped ENAs do not directly reflect the ring current properties. We model the energy loss due to multiple charge exchange and electron stripping interactions of 1 - 100 keV precipitating ring current ions undergo before emerging as low-altitude ENAs. The H particle is either an ion or an ENA throughout the simulation. Their lifetime is analytically determined by the length of one mean free path. We track the ion state with Lorentz motion while the ENA travels ballistically across the geomagnetic field. Our simulations show the energy loss is greater than 20% for hydrogen ring current ions below 30 keV (60 keV for the simulations that wander equatorward). This is the first quantification of the energy loss associated with the creation of low-altitude ENAs. Our model (currently constrained in the meridional plane) has revealed characteristics on how precipitation is affected by the near-Earth neutral exosphere. This ion-neutral interaction removes particles from the loss cone but promotes loss through ENA generation. These findings should be implemented in models predicting the ring current decay and used as an analysis tool to reconstruct the ring current population from observed low-altitude ENAs.

The structure of ions and zwitterionic lipids regulates the charge of dipolar membranes.

PubMed

Szekely, Or; Steiner, Ariel; Szekely, Pablo; Amit, Einav; Asor, Roi; Tamburu, Carmen; Raviv, Uri

2011-06-21

In pure water, zwitterionic lipids form lamellar phases with an equilibrium water gap on the order of 2 to 3 nm as a result of the dominating van der Waals attraction between dipolar bilayers. Monovalent ions can swell those neutral lamellae by a small amount. Divalent ions can adsorb onto dipolar membranes and charge them. Using solution X-ray scattering, we studied how the structure of ions and zwitterionic lipids regulates the charge of dipolar membranes. We found that unlike monovalent ions that weakly interact with all of the examined dipolar membranes, divalent and trivalent ions adsorb onto membranes containing lipids with saturated tails, with an association constant on the order of ∼10 M(-1). One double bond in the lipid tail is sufficient to prevent divalent ion adsorption. We suggest that this behavior is due to the relatively loose packing of lipids with unsaturated tails that increases the area per lipid headgroup, enabling their free rotation. Divalent ion adsorption links two lipids and limits their free rotation. The ion-dipole interaction gained by the adsorption of the ions onto unsaturated membranes is insufficient to compensate for the loss of headgroup free-rotational entropy. The ion-dipole interaction is stronger for cations with a higher valence. Nevertheless, polyamines behave as monovalent ions near dipolar interfaces in the sense that they interact weakly with the membrane surface, whereas in the bulk their behavior is similar to that of multivalent cations. Advanced data analysis and comparison with theory provide insight into the structure and interactions between ion-induced regulated charged interfaces. This study models biologically relevant interactions between cell membranes and various ions and the manner in which the lipid structure governs those interactions. The ability to monitor these interactions creates a tool for probing systems that are more complex and forms the basis for controlling the interactions between dipolar membranes and charged proteins or biopolymers for encapsulation and delivery applications. © 2011 American Chemical Society

Ion acceleration in shell cylinders irradiated by a short intense laser pulse

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

Andreev, A.; ELI-ALPS, Szeged; Platonov, K.

The interaction of a short high intensity laser pulse with homo and heterogeneous shell cylinders has been analyzed using particle-in-cell simulations and analytical modeling. We show that the shell cylinder is proficient of accelerating and focusing ions in a narrow region. In the case of shell cylinder, the ion energy exceeds the ion energy for a flat target of the same thickness. The constructed model enables the evaluation of the ion energy and the number of ions in the focusing region.

Capturing nonlocal interaction effects in the Hubbard model: Optimal mappings and limits of applicability

NASA Astrophysics Data System (ADS)

van Loon, E. G. C. P.; Schüler, M.; Katsnelson, M. I.; Wehling, T. O.

2016-10-01

We investigate the Peierls-Feynman-Bogoliubov variational principle to map Hubbard models with nonlocal interactions to effective models with only local interactions. We study the renormalization of the local interaction induced by nearest-neighbor interaction and assess the quality of the effective Hubbard models in reproducing observables of the corresponding extended Hubbard models. We compare the renormalization of the local interactions as obtained from numerically exact determinant quantum Monte Carlo to approximate but more generally applicable calculations using dual boson, dynamical mean field theory, and the random phase approximation. These more approximate approaches are crucial for any application with real materials in mind. Furthermore, we use the dual boson method to calculate observables of the extended Hubbard models directly and benchmark these against determinant quantum Monte Carlo simulations of the effective Hubbard model.

Assessment of Simple Models for Molecular Simulation of Ethylene Carbonate and Propylene Carbonate as Solvents for Electrolyte Solutions.

PubMed

Chaudhari, Mangesh I; Muralidharan, Ajay; Pratt, Lawrence R; Rempe, Susan B

2018-02-12

Progress in understanding liquid ethylene carbonate (EC) and propylene carbonate (PC) on the basis of molecular simulation, emphasizing simple models of interatomic forces, is reviewed. Results on the bulk liquids are examined from the perspective of anticipated applications to materials for electrical energy storage devices. Preliminary results on electrochemical double-layer capacitors based on carbon nanotube forests and on model solid-electrolyte interphase (SEI) layers of lithium ion batteries are considered as examples. The basic results discussed suggest that an empirically parameterized, non-polarizable force field can reproduce experimental structural, thermodynamic, and dielectric properties of EC and PC liquids with acceptable accuracy. More sophisticated force fields might include molecular polarizability and Buckingham-model description of inter-atomic overlap repulsions as extensions to Lennard-Jones models of van der Waals interactions. Simple approaches should be similarly successful also for applications to organic molecular ions in EC/PC solutions, but the important case of Li[Formula: see text] deserves special attention because of the particularly strong interactions of that small ion with neighboring solvent molecules. To treat the Li[Formula: see text] ions in liquid EC/PC solutions, we identify interaction models defined by empirically scaled partial charges for ion-solvent interactions. The empirical adjustments use more basic inputs, electronic structure calculations and ab initio molecular dynamics simulations, and also experimental results on Li[Formula: see text] thermodynamics and transport in EC/PC solutions. Application of such models to the mechanism of Li[Formula: see text] transport in glassy SEI models emphasizes the advantage of long time-scale molecular dynamics studies of these non-equilibrium materials.

Precision Tests of the Electroweak Interaction using Trapped Atoms and Ions

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

Melconian, Daniel George

The objective of the proposed research is to study fundamental aspects of the electroweak interaction via precision measurements in beta decay to test our current understanding of fundamental particles and forces as contained in the so-called "Standard Model" of particle physics. By comparing elegant experiments to rigorous theoretical predictions, we will either confirm the Standard Model to a higher degree and rule out models which seek to extend it, or find evidence of new physics and help guide theorists in developing the New Standard Model. The use of ion and neutral atom traps at radioactive ion beam facilities has openedmore » up a new vista in precision low-energy nuclear physics experiments. Traps provide an ideal source of decaying atoms: they can be extremely cold (~1 mK); they are compact (~1 mm^3); and perhaps most importantly, the daughter particles escape with negligible distortions to their momenta in a scattering-free, open environment. The project is taking advantage of these technologies and applying them to precision beta-decay studies at radioactive beam facilities. The program consists of two complementary efforts: 1) Ion traps are an extremely versatile tool for purifying, cooling and bunching low-energy beams of short-lived nuclei. A large-bore (210~mm) superconducting 7-Tesla solenoid is at the heart of a Penning trap system for which there is a dedicated beamline at T-REX, the upgraded radioactive beam facility at the Cyclotron Institute, Texas A&M University. In addition to providing a general-purpose decay station, the flagship program for this system is measuring the ft-values and beta-neutrino correlation parameters from isospin T=2 superallowed beta-delayed proton decays, complimenting and expanding the already strong program in fundamental interactions at the Institute. 2) A magneto-optical trap is being used at the TRIUMF Neutral Atom Trap facility to observe the (un)polarized angular distribution parameters of isotopes of potassium. We are able to highly polarize laser-cooled atoms and observe their decay with unprecedented precision. The correlation of the daughter beta particle with the initial nuclear spin as well as other correlations are sensitive to physics beyond the Standard Model. Both of these cutting-edge and exciting research efforts will test our understanding of the fundamental symmetries underlying our current theory of electroweak interactions. Complementary to high-energy collider experiments, these low-energy nuclear physics "table-top" experiments will search for new particles and interactions which are not already described by the Standard Model of particle physics. The value of this research is recognized to be cross-disciplinary, exciting and potentially revolutionary in our understanding of nature's fundamental interactions. Accordingly, it has been endorsed by the recent (2007) Nuclear Science Advisory Committee's Long Range Plan as part of their recommendation for a "New Standard Model Initiative." In addition to the near-term benefits of scholarly publications and visibility through description of this work at international conferences, an important benefit of this research program is the training of new, young and enthusiastic nuclear physicists. Participants in this demanding and rewarding field develop a very strong background in physics with experience in a range of its subfields since we use atomic techniques and apply them to a nuclear physics experiment which in the end tests the theories of high-energy physics.« less

Femtosecond Dynamics of the Photo-Induced Lattice Rearrangements in Quasi-One Halogen-Bridged Platinum Complexes

NASA Astrophysics Data System (ADS)

Suemoto, Tohru; Tomimoto, Shinichi; Matsuoka, Taira

Recent developments in femtosecond dynamics of the photoexcited state in quasi-one-dimensional platinum complexes [Pt(en)2][Pt(en)2X2] (ClO4)4 with X = Cl, Br and I are reviewed. The experimental results of time-resolved luminescence spectroscopy based on up-conversion technique are presented and analyzed in terms of a theory of wave-packet motion. An attempt to make a movie of wave-packet motion is mentioned. In Sec. 1, a brief introduction to the dynamics of the excited states in quasi-one-dimensional platinum complexes is given. It is stressed that this system can be a good model system for investigating the photo-induced structural phase transition. In order to describe a one-dimensional chain consisting of metal ions and halogen ions, the extended Peierls-Hubbard model is introduced in Sec. 2. The theoretical model of the relaxation dynamics in the excited states with a strong electron-lattice coupling is given in Sec. 3. The model is based on the interaction mode, which is appropriate for understanding the vibrational relaxation of localized centers in solids. Experimental backgrounds with some historical survey are given in Sec. 4. The recent experimental results of time-resolved luminescence for Pt-Cl, Pt-Br and Pt-I systems are presented in Secs. 5 to 8. The main result contains the direct observation of the wave-packet oscillation in the self-trapped excitons. The relaxation process observed in experiments has been successfully interpreted in terms of the model based on the interaction mode and the dynamical aspects are compared with the transient absorption measurements. The lifetime of the STE is shorter in Pt-X with heavier halogen ions. This behavior is discussed in relation with the non-radiative process leading to lattice rearrangements. In Secs. 9 and 10, visualization of the wave-packet form is presented. The basic behavior of the wave-packet is well understood in terms of a harmonic oscillator model. A non-exponential decay profiles are revealed from the center of gravity motion of the wave-packets. The exciton localization process is also discussed in the last section.

Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field

NASA Astrophysics Data System (ADS)

Jing, Zhifeng; Qi, Rui; Liu, Chengwen; Ren, Pengyu

2017-10-01

The interactions between metal ions and proteins are ubiquitous in biology. The selective binding of metal ions has a variety of regulatory functions. Therefore, there is a need to understand the mechanism of protein-ion binding. The interactions involving metal ions are complicated in nature, where short-range charge-penetration, charge transfer, polarization, and many-body effects all contribute significantly, and a quantitative description of all these interactions is lacking. In addition, it is unclear how well current polarizable force fields can capture these energy terms and whether these polarization models are good enough to describe the many-body effects. In this work, two energy decomposition methods, absolutely localized molecular orbitals and symmetry-adapted perturbation theory, were utilized to study the interactions between Mg2+/Ca2+ and model compounds for amino acids. Comparison of individual interaction components revealed that while there are significant charge-penetration and charge-transfer effects in Ca complexes, these effects can be captured by the van der Waals (vdW) term in the AMOEBA force field. The electrostatic interaction in Mg complexes is well described by AMOEBA since the charge penetration is small, but the distance-dependent polarization energy is problematic. Many-body effects were shown to be important for protein-ion binding. In the absence of many-body effects, highly charged binding pockets will be over-stabilized, and the pockets will always favor Mg and thus lose selectivity. Therefore, many-body effects must be incorporated in the force field in order to predict the structure and energetics of metalloproteins. Also, the many-body effects of charge transfer in Ca complexes were found to be non-negligible. The absorption of charge-transfer energy into the additive vdW term was a main source of error for the AMOEBA many-body interaction energies.

Atomistic understanding of cation exchange in PbS nanocrystals using simulations with pseudoligands

PubMed Central

Fan, Zhaochuan; Lin, Li-Chiang; Buijs, Wim; Vlugt, Thijs J. H.; van Huis, Marijn A.

2016-01-01

Cation exchange is a powerful tool for the synthesis of nanostructures such as core–shell nanocrystals, however, the underlying mechanism is poorly understood. Interactions of cations with ligands and solvent molecules are systematically ignored in simulations. Here, we introduce the concept of pseudoligands to incorporate cation-ligand-solvent interactions in molecular dynamics. This leads to excellent agreement with experimental data on cation exchange of PbS nanocrystals, whereby Pb ions are partially replaced by Cd ions from solution. The temperature and the ligand-type control the exchange rate and equilibrium composition of cations in the nanocrystal. Our simulations reveal that Pb ions are kicked out by exchanged Cd interstitials and migrate through interstitial sites, aided by local relaxations at core–shell interfaces and point defects. We also predict that high-pressure conditions facilitate strongly enhanced cation exchange reactions at elevated temperatures. Our approach is easily extendable to other semiconductor compounds and to other families of nanocrystals. PMID:27160371

Building thiol and metal-thiolate functions into coordination nets: Clues from a simple molecule

NASA Astrophysics Data System (ADS)

He, Jun; Yang, Chen; Xu, Zhengtao; Zeller, Matthias; Hunter, Allen D.; Lin, Jianhua

2009-07-01

The simple and easy-to-prepare bifunctional molecule 2,5-dimercapto-1,4-benzenedicarboxylic acid (H 4DMBD) interacts with the increasingly harder metal ions of Cu +, Pb 2+ and Eu 3+ to form the coordination networks of Cu 6(DMBD) 3(en) 4(Hen) 6 ( 1), Pb 2(DMBD)(en) 2 ( 2) and Eu 2(H 2DMBD) 3(DEF) 4 ( 3), where the carboxyl and thiol groups bind with distinct preference to the hard and soft metal ions, respectively. Notably, 1 features uncoordinated carboxylate groups and Cu 3 cluster units integrated via the thiolate groups into an extended network with significant interaction between the metal centers and the organic molecules; 2 features a 2D coordination net based on the mercapto and carboxylic groups all bonded to the Pb 2+ ions; 3 features free-standing thiol groups inside the channels of a metal-carboxylate-based network. This study illustrates the rich solid state structural features and potential functions offered by the carboxyl-thiol combination.

Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field

PubMed Central

2016-01-01

Small metal ions play critical roles in numerous biological processes. Of particular interest is how metalloenzymes are allosterically regulated by the binding of specific ions. Understanding how ion binding affects these biological processes requires atomic models that accurately treat the microscopic interactions with the protein ligands. Theoretical approaches at different levels of sophistication can contribute to a deeper understanding of these systems, although computational models must strike a balance between accuracy and efficiency in order to enable long molecular dynamics simulations. In this study, we present a systematic effort to optimize the parameters of a polarizable force field based on classical Drude oscillators to accurately represent the interactions between ions (K+, Na+, Ca2+, and Cl–) and coordinating amino-acid residues for a set of 30 biologically important proteins. By combining ab initio calculations and experimental thermodynamic data, we derive a polarizable force field that is consistent with a wide range of properties, including the geometries and interaction energies of gas-phase ion/protein-like model compound clusters, and the experimental solvation free-energies of the cations in liquids. The resulting models display significant improvements relative to the fixed-atomic-charge additive CHARMM C36 force field, particularly in their ability to reproduce the many-body electrostatic nonadditivity effects estimated from ab initio calculations. The analysis clarifies the fundamental limitations of the pairwise additivity assumption inherent in classical fixed-charge force fields, and shows its dramatic failures in the case of Ca2+ binding sites. These optimized polarizable models, amenable to computationally efficient large-scale MD simulations, set a firm foundation and offer a powerful avenue to study the roles of the ions in soluble and membrane transport proteins. PMID:25578354

Structure and dynamics of the ionosphere. [Venus atmosphere

NASA Technical Reports Server (NTRS)

Nagy, A. F.; Brace, L. H.

1982-01-01

The structure of the Venus ionosphere and the major processes occurring within it are summarized. The daytime ionosphere is created by solar EUV radiation incident on the thermosphere; it is in photochemical equilibrium near its peak at about 142 km, where O2(+) is the major ion, and near diffusive equilibrium in its upper regions, where the major ion is O(+). The day-to-night plasma pressure gradient across the terminator drives a nightward ion flow which, together with electron precipitation, contributes to the formation of the nighttime ionosphere. Large-scale radial holes or plasma depletions extending downwards to nearly the ionization peak in the antisolar region are also observed which are associated with regions of strong radial magnetic fields. The ionopause is a highly dynamic and complex surface, extending from an average altitude of 290 km at the subsolar point to about 1000 km at the terminator and from 200 to over 3000 km on the nightside. A variety of solar wind interaction products are observed in the mantle, a transition region between the ionospheric plasma and the flowing shocked solar wind.

Helium ions for radiotherapy? Physical and biological verifications of a novel treatment modality

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

Krämer, Michael, E-mail: m.kraemer@gsi.de; Scifoni, Emanuele; Schuy, Christoph

Purpose: Modern facilities for actively scanned ion beam radiotherapy allow in principle the use of helium beams, which could present specific advantages, especially for pediatric tumors. In order to assess the potential use of these beams for radiotherapy, i.e., to create realistic treatment plans, the authors set up a dedicated {sup 4}He beam model, providing base data for their treatment planning system TRiP98, and they have reported that in this work together with its physical and biological validations. Methods: A semiempirical beam model for the physical depth dose deposition and the production of nuclear fragments was developed and introduced inmore » TRiP98. For the biological effect calculations the last version of the local effect model was used. The model predictions were experimentally verified at the HIT facility. The primary beam attenuation and the characteristics of secondary charged particles at various depth in water were investigated using {sup 4}He ion beams of 200 MeV/u. The nuclear charge of secondary fragments was identified using a ΔE/E telescope. 3D absorbed dose distributions were measured with pin point ionization chambers and the biological dosimetry experiments were realized irradiating a Chinese hamster ovary cells stack arranged in an extended target. Results: The few experimental data available on basic physical processes are reproduced by their beam model. The experimental verification of absorbed dose distributions in extended target volumes yields an overall agreement, with a slight underestimation of the lateral spread. Cell survival along a 4 cm extended target is reproduced with remarkable accuracy. Conclusions: The authors presented a simple simulation model for therapeutical {sup 4}He beams which they introduced in TRiP98, and which is validated experimentally by means of physical and biological dosimetries. Thus, it is now possible to perform detailed treatment planning studies with {sup 4}He beams, either exclusively or in combination with other ion modalities.« less

Mapping the function of neuronal ion channels in model and experiment

PubMed Central

Podlaski, William F; Seeholzer, Alexander; Groschner, Lukas N; Miesenböck, Gero; Ranjan, Rajnish; Vogels, Tim P

2017-01-01

Ion channel models are the building blocks of computational neuron models. Their biological fidelity is therefore crucial for the interpretation of simulations. However, the number of published models, and the lack of standardization, make the comparison of ion channel models with one another and with experimental data difficult. Here, we present a framework for the automated large-scale classification of ion channel models. Using annotated metadata and responses to a set of voltage-clamp protocols, we assigned 2378 models of voltage- and calcium-gated ion channels coded in NEURON to 211 clusters. The IonChannelGenealogy (ICGenealogy) web interface provides an interactive resource for the categorization of new and existing models and experimental recordings. It enables quantitative comparisons of simulated and/or measured ion channel kinetics, and facilitates field-wide standardization of experimentally-constrained modeling. DOI: http://dx.doi.org/10.7554/eLife.22152.001 PMID:28267430

Modeling the interaction and toxicity of Cu-Cd mixture to wheat roots affected by humic acids, in terms of cell membrane surface characteristics.

PubMed

Wang, Yi-Min; Zhou, Dong-Mei; Yuan, Xu-Yin; Zhang, Xiao-Hui; Li, Yi

2018-05-01

Responses of wheat (Triticum aestivum L.) seedling roots to the mixtures of copper (Cu), cadmium (Cd) and humic acids (HA) were investigated using the solution culture experiments, focusing on the interaction patterns between multiple metals and their influences on root proton release. A concentration-addition multiplication (CA) model was introduced into the modeling analysis. In comparison with metal ion activities in bulk-phase solutions, the incorporation of ion activities at the root cell membrane surfaces (CMs) (denoted as {Cu 2+ } 0 and {Cd 2+ } 0 ) into the CA model could significantly improve their correlation with RRE (relative root elongation) from 0.819 to 0.927. Modeling analysis indicated that the co-existence of {Cu 2+ } 0 significantly enhanced the rhizotoxicity of {Cd 2+ } 0 , while no significant effect of {Cd 2+ } 0 on the {Cu 2+ } 0 rhizotoxicity. 10 mg/L HA stimulated the root elongation even under metal stress. Although high concentration of metal ions inhibited the root proton release rate (ΔH + ), both the low concentration of metal ions and HA treatments increased the values of ΔH + . In HA-Cu-Cd mixtures, actions of metal ions on ΔH + values were varied intricately among treatments but well modeled by the CA model. We concluded from the CA models that the electrostatic effect is vitally important for explaining the effect of {Cu 2+ } 0 on the rhizotoxicity of {Cd 2+ } 0 , while it plays no unique role in understanding the influence of {Cd 2+ } 0 on the rhizotoxicity of {Cu 2+ } 0. Thus our study provide a novel way for modeling multiple metals behaviors in the environment and understanding the mechanisms of ion interactions. Copyright © 2018 Elsevier Ltd. All rights reserved.

Towards full-Braginskii implicit extended MHD

NASA Astrophysics Data System (ADS)

Chacon, Luis

2009-05-01

Recently, viable algorithms have been proposed for the scalable, fully-implicit temporal integration of 3D resistive MHD and cold-ion extended MHD models. While significant, these achievements must be tempered by the fact that such models lack predictive capabilities in regimes of interest for magnetic fusion. Short of including kinetic closures, a natural evolution path towards predictability starts by considering additional terms as described in Braginskii's fluid closures in the collisional regime. Here, we focus on the inclusion of two fundamental elements of relevance for fusion plasmas: anisotropic parallel electron transport, and warm-ion physics (i.e., ion finite Larmor radius effects, included via gyroviscosity). Both these elements introduce significant numerical difficulties, due to the strong anisotropy in the former, and the presence of dispersive waves in the latter. In this presentation, we will discuss progress in our fully implicit algorithmic formulation towards the inclusion of both these elements. L. Chac'on, Phys. Plasmas, 15, 056103 (2008) L. Chac'on, J. Physics: Conf. Series, 125, 012041 (2008)

Charging and Release Mechanisms of Flexible Macromolecules in Droplets

NASA Astrophysics Data System (ADS)

Oh, Myong In; Consta, Styliani

2017-08-01

We study systematically the charging and release mechanisms of a flexible macromolecule, modeled by poly(ethylene glycol) (PEG), in a droplet by using molecular dynamics simulations. We compare how PEG is solvated and charged by sodium Na+ ions in a droplet of water (H2O), acetonitrile (MeCN), and their mixtures. Initially, we examine the location and the conformation of the macromolecule in a droplet bearing no net charge. It is revealed that the presence of charge carriers do not affect the location of PEG in aqueous and MeCN droplets compared with that in the neutral droplets, but the location of the macromolecule and the droplet size do affect the PEG conformation. PEG is charged on the surface of a sodiated aqueous droplet that is found close to the Rayleigh limit. Its charging is coupled to the extrusion mechanism, where PEG segments leave the droplet once they coordinate a Na+ ion or in a correlated motion with Na+ ions. In contrast, as PEG resides in the interior of a MeCN droplet, it is sodiated inside the droplet. The compact macro-ion transitions through partially unwound states to an extended conformation, a process occurring during the final stage of desolvation and in the presence of only a handful of MeCN molecules. For charged H2O/MeCN droplets, the sodiation of PEG is determined by the H2O component, reflecting its slower evaporation and preference over MeCN for solvating Na+ ions. We use the simulation data to construct an analytical model that suggests that the droplet surface electric field may play a role in the macro-ion-droplet interactions that lead to the extrusion of the macro-ion. This study provides the first evidence of the effect of the surface electric field by using atomistic simulations. [Figure not available: see fulltext.

Extracting p Λ scattering lengths from heavy ion collisions

NASA Astrophysics Data System (ADS)

Shapoval, V. M.; Erazmus, B.; Lednicky, R.; Sinyukov, Yu. M.

2015-09-01

The source radii previously extracted by the STAR Collaboration from the p -Λ ⊕p ¯-Λ ¯ and p ¯-Λ ⊕p -Λ ¯ correlation functions measured in 10% most central Au+Au collisions at top Relativistic Heavy Ion Collider (RHIC) energy, √{sN N}=200 GeV, differ by a factor of 2. The probable reason for this is the neglect of residual correlation effect in the STAR analysis. In the present paper we analyze baryon correlation functions within the Lednický and Lyuboshitz analytical model, extended to effectively account for the residual correlation contribution. Different analytical approximations for such a contribution are considered. We also use the averaged source radii extracted from hydrokinetic model (HKM) simulations to fit the experimental data. In contrast to the STAR experimental study, the calculations in HKM show both p Λ and p Λ ¯ radii to be quite close, as expected from theoretical considerations. Using the effective Gaussian parametrization of residual correlations we obtain a satisfactory fit to the measured baryon-antibaryon correlation function with the HKM source radius value 3.28 fm. The baryon-antibaryon spin-averaged strong interaction scattering length is also extracted from the fit to the experimental correlation function.

Refined potentials for rare gas atom adsorption on rare gas and alkali-halide surfaces

NASA Technical Reports Server (NTRS)

Wilson, J. W.; Heinbockel, J. H.; Outlaw, R. A.

1985-01-01

The utilization of models of interatomic potential for physical interaction to estimate the long range attractive potential for rare gases and ions is discussed. The long range attractive force is calculated in terms of the atomic dispersion properties. A data base of atomic dispersion parameters for rare gas atoms, alkali ion, and halogen ions is applied to the study of the repulsive core; the procedure for evaluating the repulsive core of ion interactions is described. The interaction of rare gas atoms on ideal rare gas solid and alkali-halide surfaces is analyzed; zero coverage absorption potentials are derived.

Mechanism of Interaction between the General Anesthetic Halothane and a Model Ion Channel Protein, II: Fluorescence and Vibrational Spectroscopy Using a Cyanophenylalanine Probe

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

Liu, J.; Strzalka, J; Tronin, A

2009-01-01

We demonstrate that cyano-phenylalanine (PheCN) can be utilized to probe the binding of the inhalational anesthetic halothane to an anesthetic-binding, model ion channel protein hbAP-PheCN. The Trp to PheCN mutation alters neither the a-helical conformation nor the 4-helix bundle structure. The halothane binding properties of this PheCN mutant hbAP-PheCN, based on fluorescence quenching, are consistent with those of the prototype, hbAP1. The dependence of fluorescence lifetime as a function of halothane concentration implies that the diffusion of halothane in the nonpolar core of the protein bundle is one-dimensional. As a consequence, at low halothane concentrations, the quenching of the fluorescencemore » is dynamic, whereas at high concentrations the quenching becomes static. The 4-helix bundle structure present in aqueous detergent solution and at the air-water interface, is preserved in multilayer films of hbAP-PheCN, enabling vibrational spectroscopy of both the protein and its nitrile label (-CN). The nitrile groups' stretching vibration band shifts to higher frequency in the presence of halothane, and this blue-shift is largely reversible. Due to the complexity of this amphiphilic 4-helix bundle model membrane protein, where four PheCN probes are present adjacent to the designed cavity forming the binding site within each bundle, all contributing to the infrared absorption, molecular dynamics (MD) simulation is required to interpret the infrared results. The MD simulations indicate that the blue-shift of -CN stretching vibration induced by halothane arises from an indirect effect, namely an induced change in the electrostatic protein environment averaged over the four probe oscillators, rather than a direct interaction with the oscillators. hbAP-PheCN therefore provides a successful template for extending these investigations of the interactions of halothane with the model membrane protein via vibrational spectroscopy, using cyano-alanine residues to form the anesthetic binding cavity.« less

Electrostatic interactions in soft particle systems: mesoscale simulations of ionic liquids.

PubMed

Wang, Yong-Lei; Zhu, You-Liang; Lu, Zhong-Yuan; Laaksonen, Aatto

2018-05-21

Computer simulations provide a unique insight into the microscopic details, molecular interactions and dynamic behavior responsible for many distinct physicochemical properties of ionic liquids. Due to the sluggish and heterogeneous dynamics and the long-ranged nanostructured nature of ionic liquids, coarse-grained meso-scale simulations provide an indispensable complement to detailed first-principles calculations and atomistic simulations allowing studies over extended length and time scales with a modest computational cost. Here, we present extensive coarse-grained simulations on a series of ionic liquids of the 1-alkyl-3-methylimidazolium (alkyl = butyl, heptyl-, and decyl-) family with Cl, [BF4], and [PF6] counterions. Liquid densities, microstructures, translational diffusion coefficients, and re-orientational motion of these model ionic liquid systems have been systematically studied over a wide temperature range. The addition of neutral beads in cationic models leads to a transition of liquid morphologies from dispersed apolar beads in a polar framework to that characterized by bi-continuous sponge-like interpenetrating networks in liquid matrices. Translational diffusion coefficients of both cations and anions decrease upon lengthening of the neutral chains in the cationic models and by enlarging molecular sizes of the anionic groups. Similar features are observed in re-orientational motion and time scales of different cationic models within the studied temperature range. The comparison of the liquid properties of the ionic systems with their neutral counterparts indicates that the distinctive microstructures and dynamical quantities of the model ionic liquid systems are intrinsically related to Coulombic interactions. Finally, we compared the computational efficiencies of three linearly scaling O(N log N) Ewald summation methods, the particle-particle particle-mesh method, the particle-mesh Ewald summation method, and the Ewald summation method based on a non-uniform fast Fourier transform technique, to calculate electrostatic interactions. Coarse-grained simulations were performed using the GALAMOST and the GROMACS packages and hardware efficiently utilizing graphics processing units on a set of extended [1-decyl-3-methylimidazolium][BF4] ionic liquid systems of up to 131 072 ion pairs.

Hadronic Resonance production in ALICE

NASA Astrophysics Data System (ADS)

Markert, Christina; ALICE Collaboration

2017-07-01

In heavy ion collisions a fireball of hot and dense matter is created. Short lived hadronic resonances are sensitive to the medium properties, in particular to the temperature, density and system size. Resonance yields and momentum distributions are used to gain insight into the hadronic phase, its expansion velocity and time duration. The multiplicity dependent hadronic resonance production in p-p, p-Pb and Pb-Pb collisions will be discussed within the context of the possible extended hadronic and partonic phase. The experimental results will be compared to EPOS+UrQMD model calculations to discuss the system size dependent interactions of the hadronic medium on various resonances. Small systems such as p-p and p-Pb collisions will be discussed with respect to resonance and strange particle measurements.

Effects of van der Waals forces and salt ions on the growth of water films on ice and the detachment of CO2 bubbles

NASA Astrophysics Data System (ADS)

Thiyam, P.; Lima, E. R. A.; Malyi, O. I.; Parsons, D. F.; Buhmann, S. Y.; Persson, C.; Boström, M.

2016-02-01

We study the effect of salts on the thickness of wetting films on melting ice and interactions acting on CO2 bubble near ice-water and vapor-water interfaces. Governing mechanisms are the Lifshitz and the double-layer interactions in the respective three-layer geometries. We demonstrate that the latter depend on the Casimir-Polder interaction of the salt ions dissolved in water with the respective ice, vapor and CO2 interfaces, as calculated using different models for their effective polarizability in water. Significant variation in the predicted thickness of the equilibrium water film is observed for different salt ions and when using different models for the ions' polarizabilities. We find that CO2 bubbles are attracted towards the ice-water interface and repelled from the vapor-water interface.

Electrochemical state and internal variables estimation using a reduced-order physics-based model of a lithium-ion cell and an extended Kalman filter

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

Stetzel, KD; Aldrich, LL; Trimboli, MS

2015-03-15

This paper addresses the problem of estimating the present value of electrochemical internal variables in a lithium-ion cell in real time, using readily available measurements of cell voltage, current, and temperature. The variables that can be estimated include any desired set of reaction flux and solid and electrolyte potentials and concentrations at any set of one-dimensional spatial locations, in addition to more standard quantities such as state of charge. The method uses an extended Kalman filter along with a one-dimensional physics-based reduced-order model of cell dynamics. Simulations show excellent and robust predictions having dependable error bounds for most internal variables.more » (C) 2014 Elsevier B.V. All rights reserved.« less

Self-Consistent Model of Magnetospheric Ring Current and Electromagnetic Ion Cyclotron Waves: The 2-7 May 1998 Storm

NASA Technical Reports Server (NTRS)

Khazanov, G. V.; Gamayunov, K. V.; Jordanova, V. K.

2003-01-01

A complete description of a self-consistent model of magnetospheric ring current interacting with electromagnetic ion cyclotron waves is presented. The model is based on the system of two kinetic equations; one equation describes the ring current ion dynamics, and another equation describes the wave evolution. The effects on ring current ions interacting with electromagnetic ion cyclotron waves and back on waves are considered self-consistently by solving both equations on a global magnetospheric scale under nonsteady state conditions. The developed model is employed to simulate the entire 2-7 May 1998 storm period. First, the trapped number fluxes of the ring current protons are calculated and presented along with comparison with the data measured by the three- dimensional hot plasma instrument Polar/HYDRA. Incorporating in the model the wave-particle interaction leads to much better agreement between the experimental data and the model results. Second, examining of the wave (MLT, L shell) distributions produced by the model during the storm progress reveals an essential intensification of the wave emission about 2 days after the main phase of the storm. This result is well consistent with the earlier ground-based observations. Finally, the theoretical shapes and the occurrence rates of the wave power spectral densities are studied. It is found that about 2 days after the storm s main phase on 4 May, mainly non-Gaussian shapes of power spectral densities are produced.

Molecular Dynamics Simulations of Ion-Doped Microphase Separated Diblock Copolymers

NASA Astrophysics Data System (ADS)

Seo, Youngmi; Brown, Jonathan R.; Hall, Lisa M.

The effects of ion doping on microphase separated block copolymers are crucial to understand for transport applications such as battery electrolytes or fuel cell membranes. Prior experiments and theories have observed interesting trends, e.g. ions generally increase effective χ, broaden the domain interface at high loadings, and significantly change the order-to-disorder transition point. To provide a molecular level understanding of these trends and further information about ion dynamics, in this study, we perform molecular dynamics (MD) simulations using a generic coarse-grained model. We capture the selective ion solvation in one polymer microphase by adding an 1/r4 term to the intermolecular potential to account for the charge induced dipole effect between cations and A monomers. The model was validated by comparing with experimental domain spacing and density profile results. We find that as ions are added, the lamellar interface becomes sharper at first, then broadens with further ion loading, and finally forms a cylindrical morphology. We also observe that the interfacial broadening is retarded as the associative interaction between cations and A monomers or the ion-ion interaction strength is increased. These observations are compared to the results from fluids density functional theory (fDFT) which uses a similar model. We analyze ion dynamics in the model systems and discuss the impacts of ion selectivity and other variables on transport. This material is based upon work supported by the National Science Foundation under Grant 1454343.

Transferability of polarizable models for ion-water electrostatic interaction

NASA Astrophysics Data System (ADS)

Masia, Marco

2009-06-01

Studies of ion-water systems at condensed phase and at interfaces have pointed out that molecular and ionic polarization plays an important role for many phenomena ranging from hydrogen bond dynamics to water interfaces' structure. Classical and ab initio Molecular Dynamics simulations reveal that induced dipole moments at interfaces (e.g. air-water and water-protein) are usually high, hinting that polarizable models to be implemented in classical force fields should be very accurate in reproducing the electrostatic properties of the system. In this paper the electrostatic properties of three classical polarizable models for ion-water interaction are compared with ab initio results both at gas and condensed phase. For Li+- water and Cl--water dimers the reproducibility of total dipole moments obtained with high level quantum chemical calculations is studied; for the same ions in liquid water, Car-Parrinello Molecular Dynamics simulations are used to compute the time evolution of ionic and molecular dipole moments, which are compared with the classical models. The PD2-H2O model developed by the author and coworkers [Masia et al. J. Chem. Phys. 2004, 121, 7362] together with the gaussian intermolecular damping for ion-water interaction [Masia et al. J. Chem. Phys. 2005, 123, 164505] showed to be the fittest in reproducing the ab initio results from gas to condensed phase, allowing for force field transferability.

Neptune's inner magnetosphere and aurora: Energetic particle constraints

NASA Technical Reports Server (NTRS)

Mauk, B. H.; Krimigis, S. M.; Acuna, M. H.

1994-01-01

A dramatic and peculiar dropout of greater than 500-keV ions (but not electrons) was observed within Neptune's inner magnetosphere near 2 R(sub N) as the Voyager 2 spacecraft approached the planet. Unlike a number of other energetic particle features this feature could not be accounted for by known material bodies in the context of the most utilized magnetic field models (neither the offset tilted dipole models nor the spehrical harmonic model 'O8'). However, the configuration of Neptune's inner magnetosphere is highly uncertain. By applying a novel technique, utilizing energetic particle measurements, to constrain the magnetic field configuration of the inner regions, we show that appeals to unobserved materials within Neptune's system are unnecessary, and that the ion dropout feature was, in all likelihood, the result of ion interactions with maximum L excursions of the ring 1989N1R. The constraints also favor the se of the M2 magnetic field model (Selesnick, 1992) over the previous models. An electron feature was probably absent because the electron interactions with the ring occurred substantially before the ion interactions (about 2 hours for the electrons versus a few minutes for the ions). Pitch-angle scattering apparently eliminated the electron signature. Minimum scattering rates determined based on this premise yield enough electron precipitation power to explain the brightest component of Neptune's aurora. We propose that this bright component is analogous to the Earth's diffuse aurora.

Coronal mass ejection (CME) activity of low mass M stars as an important factor for the habitability of terrestrial exoplanets. II. CME-induced ion pick up of Earth-like exoplanets in close-in habitable zones.

PubMed

Lammer, Helmut; Lichtenegger, Herbert I M; Kulikov, Yuri N; Griessmeier, Jean-Mathias; Terada, N; Erkaev, Nikolai V; Biernat, Helfried K; Khodachenko, Maxim L; Ribas, Ignasi; Penz, Thomas; Selsis, Franck

2007-02-01

Atmospheric erosion of CO2-rich Earth-size exoplanets due to coronal mass ejection (CME)-induced ion pick up within close-in habitable zones of active M-type dwarf stars is investigated. Since M stars are active at the X-ray and extreme ultraviolet radiation (XUV) wave-lengths over long periods of time, we have applied a thermal balance model at various XUV flux input values for simulating the thermospheric heating by photodissociation and ionization processes due to exothermic chemical reactions and cooling by the CO2 infrared radiation in the 15 microm band. Our study shows that intense XUV radiation of active M stars results in atmospheric expansion and extended exospheres. Using thermospheric neutral and ion densities calculated for various XUV fluxes, we applied a numerical test particle model for simulation of atmospheric ion pick up loss from an extended exosphere arising from its interaction with expected minimum and maximum CME plasma flows. Our results indicate that the Earth-like exoplanets that have no, or weak, magnetic moments may lose tens to hundreds of bars of atmospheric pressure, or even their whole atmospheres due to the CME-induced O ion pick up at orbital distances

Solubility of KF and NaCl in water by molecular simulation.

PubMed

Sanz, E; Vega, C

2007-01-07

The solubility of two ionic salts, namely, KF and NaCl, in water has been calculated by Monte Carlo molecular simulation. Water has been modeled with the extended simple point charge model (SPC/E), ions with the Tosi-Fumi model and the interaction between water and ions with the Smith-Dang model. The chemical potential of the solute in the solution has been computed as the derivative of the total free energy with respect to the number of solute particles. The chemical potential of the solute in the solid phase has been calculated by thermodynamic integration to an Einstein crystal. The solubility of the salt has been calculated as the concentration at which the chemical potential of the salt in the solution becomes identical to that of the pure solid. The methodology used in this work has been tested by reproducing the results for the solubility of KF determined previously by Ferrario et al. [J. Chem. Phys. 117, 4947 (2002)]. For KF, it was found that the solubility of the model is only in qualitative agreement with experiment. The variation of the solubility with temperature for KF has also been studied. For NaCl, the potential model used predicts a solubility in good agreement with the experimental value. The same is true for the hydration chemical potential at infinite dilution. Given the practical importance of solutions of NaCl in water the model used in this work, whereas simple, can be of interest for future studies.

An advanced model framework for solid electrolyte intercalation batteries.

PubMed

Landstorfer, Manuel; Funken, Stefan; Jacob, Timo

2011-07-28

Recent developments of solid electrolytes, especially lithium ion conductors, led to all solid state batteries for various applications. In addition, mathematical models sprout for different electrode materials and battery types, but are missing for solid electrolyte cells. We present a mathematical model for ion flux in solid electrolytes, based on non-equilibrium thermodynamics and functional derivatives. Intercalated ion diffusion within the electrodes is further considered, allowing the computation of the ion concentration at the electrode/electrolyte interface. A generalized Frumkin-Butler-Volmer equation describes the kinetics of (de-)intercalation reactions and is here extended to non-blocking electrodes. Using this approach, numerical simulations were carried out to investigate the space charge region at the interface. Finally, discharge simulations were performed to study different limitations of an all solid state battery cell. This journal is © the Owner Societies 2011

Wave-Particle Interactions and Particle Acceleration in Turbulent Plasmas: Hybrid Simulations

NASA Astrophysics Data System (ADS)

Kucharek, Harald; Pogorelov, Nikolai; Mueller, Hans; Gamayunov, Konstantin; Farrugia, Charles

2015-04-01

Wave-particle interactions and acceleration processes are present in all key regions inside and outside of the heliosphere. Spacecraft observations measure ion distributions and accelerated ion populations, which are the result of one or several processes. For instance STEREO measures energetic particles associated with interplanetary discontinuities and in the solar wind. Voyager and IBEX provide unique data of energetic particles from the termination shock and the inner and outer heliopause. The range of plasma conditions covered by observations is enormous. However, the physical processes causing particle acceleration and wave-particle interaction and determining the particle distributions are still unknown. Currently two mechanisms, the so-called pumping mechanism (Fisk and Gloeckler, 2010) and merging/contracting island (Fermo, Drake & Swisdak, 2010) are discussed as promising models. In order to determine these individual processes, numerical models or theoretical considerations are needed. Hybrid simulations, which include all kinetic processes self-consistently on the ion level, are a very proven, powerful tool to investigate wave-particle interaction, turbulence, and phase-space evolution of pickup and solar wind ions. In the framework of this study we performed 3D multi-species hybrid simulations for an ion/ion beam instability to study the temporal evolution of ion distributions, their stability, and the influence of self-generated waves. We investigated the energization of ions downstream of interplanetary discontinuities and shocks and downstream of the termination shock, the turbulence, and growth rate of instabilities and compared the results with theoretical predictions. The simulations show that ions can be accelerated downstream of collisionless shocks by trapping of charged particles in coherent wave fronts.

Human Birth Weight and Reproductive Immunology: Testing for Interactions between Maternal and Offspring KIR and HLA-C Genes.

PubMed

Clark, Michelle M; Chazara, Olympe; Sobel, Eric M; Gjessing, Håkon K; Magnus, Per; Moffett, Ashley; Sinsheimer, Janet S

2016-01-01

Maternal and offspring cell contact at the site of placentation presents a plausible setting for maternal-fetal genotype (MFG) interactions affecting fetal growth. We test hypotheses regarding killer cell immunoglobulin-like receptor (KIR) and HLA-C MFG effects on human birth weight by extending the quantitative MFG (QMFG) test. Until recently, association testing for MFG interactions had limited applications. To improve the ability to test for these interactions, we developed the extended QMFG test, a linear mixed-effect model that can use multi-locus genotype data from families. We demonstrate the extended QMFG test's statistical properties. We also show that if an offspring-only model is fit when MFG effects exist, associations can be missed or misattributed. Furthermore, imprecisely modeling the effects of both KIR and HLA-C could result in a failure to replicate if these loci's allele frequencies differ among populations. To further illustrate the extended QMFG test's advantages, we apply the extended QMFG test to a UK cohort study and the Norwegian Mother and Child Cohort (MoBa) study. We find a significant KIR-HLA-C interaction effect on birth weight. More generally, the QMFG test can detect genetic associations that may be missed by standard genome-wide association studies for quantitative traits. © 2017 S. Karger AG, Basel.

Ion Counting from Explicit-Solvent Simulations and 3D-RISM

PubMed Central

Giambaşu, George M.; Luchko, Tyler; Herschlag, Daniel; York, Darrin M.; Case, David A.

2014-01-01

The ionic atmosphere around nucleic acids remains only partially understood at atomic-level detail. Ion counting (IC) experiments provide a quantitative measure of the ionic atmosphere around nucleic acids and, as such, are a natural route for testing quantitative theoretical approaches. In this article, we replicate IC experiments involving duplex DNA in NaCl(aq) using molecular dynamics (MD) simulation, the three-dimensional reference interaction site model (3D-RISM), and nonlinear Poisson-Boltzmann (NLPB) calculations and test against recent buffer-equilibration atomic emission spectroscopy measurements. Further, we outline the statistical mechanical basis for interpreting IC experiments and clarify the use of specific concentration scales. Near physiological concentrations, MD simulation and 3D-RISM estimates are close to experimental results, but at higher concentrations (>0.7 M), both methods underestimate the number of condensed cations and overestimate the number of excluded anions. The effect of DNA charge on ion and water atmosphere extends 20–25 Å from its surface, yielding layered density profiles. Overall, ion distributions from 3D-RISMs are relatively close to those from corresponding MD simulations, but with less Na+ binding in grooves and tighter binding to phosphates. NLPB calculations, on the other hand, systematically underestimate the number of condensed cations at almost all concentrations and yield nearly structureless ion distributions that are qualitatively distinct from those generated by both MD simulation and 3D-RISM. These results suggest that MD simulation and 3D-RISM may be further developed to provide quantitative insight into the characterization of the ion atmosphere around nucleic acids and their effect on structure and stability. PMID:24559991

Ion propulsion cost effectivity

NASA Technical Reports Server (NTRS)

Zafran, S.; Biess, J. J.

1978-01-01

Ion propulsion modules employing 8-cm thrusters and 30-cm thrusters were studied for Multimission Modular Spacecraft (MMS) applications. Recurring and nonrecurring cost elements were generated for these modules. As a result, ion propulsion cost drivers were identified to be Shuttle charges, solar array, power processing, and thruster costs. Cost effective design approaches included short length module configurations, array power sharing, operation at reduced thruster input power, simplified power processing units, and power processor output switching. The MMS mission model employed indicated that nonrecurring costs have to be shared with other programs unless the mission model grows. Extended performance missions exhibited the greatest benefits when compared with monopropellant hydrazine propulsion.

Mechanistic study of plasma damage to porous low-k: Process development and dielectric recovery

NASA Astrophysics Data System (ADS)

Shi, Hualiang

Low-k dielectrics with porosity are being introduced to reduce the RC delay of Cu/low-k interconnect. However, during the O2 plasma ashing process, the porous low-k dielectrics tend to degrade due to methyl depletion, moisture uptake, and densification, increasing the dielectric constant and leakage current. This dissertation presents a study of the mechanisms of plasma damage and dielectric recovery. The kinetics of plasma interaction with low-k dielectrics was investigated both experimentally and theoretically. By using a gap structure, the roles of ion, photon, and radical in producing damage on low-k dielectrics were differentiated. Oxidative plasma induced damage was proportional to the oxygen radical density, enhanced by VUV photon, and increased with substrate temperature. Ion bombardment induced surface densification, blocking radical diffusion. Two analytical models were derived to quantify the plasma damage. Based on the radical diffusion, reaction, and recombination inside porous low-k dielectrics, a plasma altered layer model was derived to interpret the chemical effect in the low ion energy region. It predicted that oxidative plasma induced damage can be reduced by decreasing pore radius, substrate temperature, and oxygen radical density and increasing carbon concentration and surface recombination rate inside low-k dielectrics. The model validity was verified by experiments and Monte-Carlo simulations. This model was also extended to the patterned low-k structure. Based on the ion collision cascade process, a sputtering yield model was introduced to interpret the physical effect in the high ion energy region. The model validity was verified by checking the ion angular and energy dependences of sputtering yield using O2/He/Ar plasma, low-k dielectrics with different k values, and a Faraday cage. Low-k dielectrics and plasma process were optimized to reduce plasma damage, including increasing carbon concentration in low-k dielectrics, switching plasma generator from ICP to RIE, increasing hard mask thickness, replacing O2 by CO2 plasma, increasing CO addition in CO/O 2 plasma, and increasing N2 addition in CO2/N 2 plasma. By combining analytical techniques with the Kramers-Kronig dispersion relation and quantum chemistry calculation, the origin of dielectric loss was ascribed to the physisorbed water molecules. Post-ash CH4 plasma treatment, vapor silylation process, and UV radiation were developed to repair plasma damage.

The Poisson-Helmholtz-Boltzmann model.

PubMed

Bohinc, K; Shrestha, A; May, S

2011-10-01

We present a mean-field model of a one-component electrolyte solution where the mobile ions interact not only via Coulomb interactions but also through a repulsive non-electrostatic Yukawa potential. Our choice of the Yukawa potential represents a simple model for solvent-mediated interactions between ions. We employ a local formulation of the mean-field free energy through the use of two auxiliary potentials, an electrostatic and a non-electrostatic potential. Functional minimization of the mean-field free energy leads to two coupled local differential equations, the Poisson-Boltzmann equation and the Helmholtz-Boltzmann equation. Their boundary conditions account for the sources of both the electrostatic and non-electrostatic interactions on the surface of all macroions that reside in the solution. We analyze a specific example, two like-charged planar surfaces with their mobile counterions forming the electrolyte solution. For this system we calculate the pressure between the two surfaces, and we analyze its dependence on the strength of the Yukawa potential and on the non-electrostatic interactions of the mobile ions with the planar macroion surfaces. In addition, we demonstrate that our mean-field model is consistent with the contact theorem, and we outline its generalization to arbitrary interaction potentials through the use of a Laplace transformation. © EDP Sciences / Società Italiana di Fisica / Springer-Verlag 2011

Energetic Ion Interactions with the Galilean Satellites

NASA Technical Reports Server (NTRS)

Cooper, John F.

2000-01-01

The principal research tasks of this investigation are: (1) specification of the energetic (keV to MeV) ion environments upstream of the four Galilean satellites and (2) data analysis and numerical modeling of observed ion interactions with the satellites. Differential flux spectra are being compiled for the most abundant ions (protons, oxygen, and sulfur) from measurements at 20 keV to 100 MeV total energy by the Energetic Particle Detector (EPD) experiment and at higher ion energies by the Heavy Ion Counter (HIC) experiment. Runge-Kutta and other numerical techniques are used to propagate test particles sampled from the measured upstream spectra to the satellite surface or spacecraft through the local magnetic and corotational electric field environment of each satellite. Modeling of spatial variations in directional flux anisotropies measured during each close flyby provides limits on atomic charge states for heavy (O, S) magnetospheric ions and on internal or induced magnetic fields of the satellites. Validation of models for magnetic and electric field configurations then allows computation of rates for ion implantation, sputtering, and energy deposition into the satellite surfaces for further modeling of observable chemical changes induced by irradiation. Our ongoing work on production of oxidants and other secondary species by ice irradiation on Europa's surface has significant applications, already acknowledged in current literature, to astrobiological evolution. Finally, the work will improve understanding of energetic ion sources and sinks at the satellite orbits for improved modeling of magnetospheric transport processes. The scope of the research effort mainly includes data from the primary Galileo mission (1995-1997) but may also include some later data where directly relevant (e.g., comparison of J0 and I27 data for Io) to the primary mission objectives. Funding for this contract also includes partial support for our related education and public outreach activity, 'Interaction of Magnetospheric Particles Applied to Classroom Teaching (IMPACT).'

Does an electronic continuum correction improve effective short-range ion-ion interactions in aqueous solution?

NASA Astrophysics Data System (ADS)

Bruce, Ellen E.; van der Vegt, Nico F. A.

2018-06-01

Non-polarizable force fields for hydrated ions not always accurately describe short-range ion-ion interactions, frequently leading to artificial ion clustering in bulk aqueous solutions. This can be avoided by adjusting the nonbonded anion-cation or cation-water Lennard-Jones parameters. This approach has been successfully applied to different systems, but the parameterization is demanding owing to the necessity of separate investigations of each ion pair. Alternatively, polarization effects may effectively be accounted for using the electronic continuum correction (ECC) of Leontyev et al. [J. Chem. Phys. 119, 8024 (2003)], which involves scaling the ionic charges with the inverse square-root of the water high-frequency dielectric permittivity. ECC has proven to perform well for monovalent salts as well as for divalent salts in water. Its performance, however, for multivalent salts with higher valency remains unexplored. The present work illustrates the applicability of the ECC model to trivalent K3PO4 and divalent K2HPO4 in water. We demonstrate that the ECC models, without additional tuning of force field parameters, provide an accurate description of water-mediated interactions between salt ions. This results in predictions of the osmotic coefficients of aqueous K3PO4 and K2HPO4 solutions in good agreement with experimental data. Analysis of ion pairing thermodynamics in terms of contact ion pair (CIP), solvent-separated ion pair, and double solvent-separated ion pair contributions shows that potassium-phosphate CIP formation is stronger with trivalent than with divalent phosphate ions.

Electrical double layers and differential capacitance in molten salts from density functional theory

DOE PAGES

Frischknecht, Amalie L.; Halligan, Deaglan O.; Parks, Michael L.

2014-08-05

Classical density functional theory (DFT) is used to calculate the structure of the electrical double layer and the differential capacitance of model molten salts. The DFT is shown to give good qualitative agreement with Monte Carlo simulations in the molten salt regime. The DFT is then applied to three common molten salts, KCl, LiCl, and LiKCl, modeled as charged hard spheres near a planar charged surface. The DFT predicts strong layering of the ions near the surface, with the oscillatory density profiles extending to larger distances for larger electrostatic interactions resulting from either lower temperature or lower dielectric constant. Inmore » conclusion, overall the differential capacitance is found to be bell-shaped, in agreement with recent theories and simulations for ionic liquids and molten salts, but contrary to the results of the classical Gouy-Chapman theory.« less

Current models of the intensely ionizing particle environment in space

NASA Technical Reports Server (NTRS)

Adams, James H., Jr.

1988-01-01

The Cosmic Ray Effects on MicroElectronics (CREME) model that is currently in use to estimate single event effect rates in spacecraft is described. The CREME model provides a description of the radiation environment in interplanetary space near the orbit of the earth that contains no major deficiencies. The accuracy of the galactic cosmic ray model is limited by the uncertainties in solar modulation. The model for solar energetic particles could be improved by making use of all the data that has been collected on solar energetic particle events. There remain major uncertainties about the environment within the earth's magnetosphere, because of the uncertainties over the charge states of the heavy ions in the anomalous component and solar flares, and because of trapped heavy ions. The present CREME model is valid only at 1 AU, but it could be extended to other parts of the heliosphere. There is considerable data on the radiation environment from 0.2 to 35 AU in the ecliptic plane. This data could be used to extend the CREME model.

Conformational Preference of ‘CαNN’ Short Peptide Motif towards Recognition of Anions

PubMed Central

Banerjee, Raja

2013-01-01

Among several ‘anion binding motifs’, the recently described ‘CαNN’ motif occurring in the loop regions preceding a helix, is conserved through evolution both in sequence and its conformation. To establish the significance of the conserved sequence and their intrinsic affinity for anions, a series of peptides containing the naturally occurring ‘CαNN’ motif at the N-terminus of a designed helix, have been modeled and studied in a context free system using computational techniques. Appearance of a single interacting site with negative binding free-energy for both the sulfate and phosphate ions, as evidenced in docking experiments, establishes that the ‘CαNN’ segment has an intrinsic affinity for anions. Molecular Dynamics (MD) simulation studies reveal that interaction with anion triggers a conformational switch from non-helical to helical state at the ‘CαNN’ segment, which extends the length of the anchoring-helix by one turn at the N-terminus. Computational experiments substantiate the significance of sequence/structural context and justify the conserved nature of the ‘CαNN’ sequence for anion recognition through “local” interaction. PMID:23516403

Ion-Neutral Coupling in Solar Prominence

NASA Technical Reports Server (NTRS)

Gilbert, H.; DeVore, C. R.; Karpen, J.; Kucera, T.; Antiochos, S.; Kawashima, R.

2011-01-01

Coupling between ions and neutrals in magnetized plasmas is fundamentally important to many aspects of heliophysics, including our ionosphere, the solar chromosphere, the solar wind interaction with planetary atmospheres, and the interface between the heliosphere and the interstellar medium. Ion-neutral coupling also plays a major role in the physics of solar prominences. By combining theory, modeling, and observations we are working toward a better understanding of the structure and dynamics of partially ionized prominence plasma. Two key questions are addressed in the present work: 1) what physical mechanism(s) sets the cross-field scale of prominence threads? 2) Are ion-neutral interactions responsible for the vertical flows and structure in prominences? We present initial results from a study investigating what role ion-neutral interactions play in prominence dynamics and structure. This research was supported by NASA.

Clusters and holes: Exchange networks in hematite-ilmenite solid solutions

NASA Astrophysics Data System (ADS)

Fabian, K.; McEnroe, S. A.; Robinson, P.

2009-04-01

Holes and clusters of exchange networks dominate the low-temperature, metastable phase diagram of the system (1 - x)Fe2O3 xF eTiO3 (Ilmx ). By our measurements we have probed and extended the phase diagram of Ishikawa et al. (1985) in the light of magnetic influences of the random exchange links, which originate either by replacing random pairs of Fe2+ and Ti4+ ions in the ordered ilmenite lattice by two Fe3+ions (ordered Ilmx phase), or by randomly replacing two Fe3+ ions in the hematite lattice by a pair of Fe2+ and Ti4+ ions (disordered Ilmx phase). Now a large dataset is available from these measurements, and we propose several new ideas to interpret the sometimes unexpected results. By refining a method of Ishikawa (1967), we analyze the PM' region of the phase diagram in terms of a mean field theory of interacting clusters. This allows to determine cluster sizes and interaction field distribution by inverting hysteresis measurements of Ilm92 and Ilm97. To understand the relation between ordered and disordered phases we design a mean field theory to determine Neel and Curie temperatures of both. An especially interesting finding is that the experimentally observed intersection of PM-PM' crossover with the AF phase boundary close to Ilm97 can be explained by analyzing average exchange interaction strengths.

Three Dimensional Explicit Model for Cometary Tail Ions Interactions with Solar Wind

NASA Astrophysics Data System (ADS)

Al Bermani, M. J. F.; Alhamed, S. A.; Khalaf, S. Z.; Ali, H. Sh.; Selman, A. A.

2009-06-01

The different interactions between cometary tail and solar wind ions are studied in the present paper based on three-dimensional Lax explicit method. The model used in this research is based on the continuity equations describing the cometary tail-solar wind interactions. Three dimensional system was considered in this paper. Simulation of the physical system was achieved using computer code written using Matlab 7.0. The parameters studied here assumed Halley comet type and include the particle density rho, the particles velocity v, the magnetic field strength B, dynamic pressure p and internal energy E. The results of the present research showed that the interaction near the cometary nucleus is mainly affected by the new ions added to the plasma of the solar wind, which increases the average molecular weight and result in many unique characteristics of the cometary tail. These characteristics were explained in the presence of the IMF.

Fidelity Study of Superconductivity in Extended Hubbard Models

NASA Astrophysics Data System (ADS)

Plonka, Nachum; Jia, Chunjing; Moritz, Brian; Wang, Yao; Devereaux, Thomas

2015-03-01

The role of strong electronic correlations on unconventional superconductivity remains an important open question. Here, we explore the influence of long-range Coulomb interactions, present in real material systems, through nearest and next-nearest neighbor extended Hubbard interactions in addition to the usual on-site terms. Utilizing large scale, numerical exact diagonalization, we analyze the signatures of superconductivity in the ground states through the fidelity metric of quantum information theory. We find that these extended interactions enhance charge fluctuations with various wave vectors. These suppress superconductivity in general, but in certain parameter regimes superconductivity is sustained. This has implications for tuning extended interactions in real materials.

Polyelectrolyte properties of single stranded DNA measured using SAXS and single molecule FRET: beyond the wormlike chain model

PubMed Central

Meisburger, Steve P.; Sutton, Julie L.; Chen, Huimin; Pabit, Suzette A.; Kirmizialtin, Serdal; Elber, Ron; Pollack, Lois

2013-01-01

Nucleic acids are highly charged polyelectrolytes that interact strongly with salt ions. Rigid, base-paired regions are successfully described with worm like chain models, but non base-paired single stranded regions have fundamentally different polymer properties because of their greater flexibility. Recently, attention has turned to single stranded nucleic acids due to the growing recognition of their biological importance, as well as the availability of sophisticated experimental techniques sensitive to the conformation of individual molecules. We investigate polyelectrolyte properties of poly(dT), an important and widely studied model system for flexible single stranded nucleic acids, in physiologically important mixed mono- and di-valent salt. We report measurements of the form factor and interparticle interactions using SAXS, end to end distances using smFRET, and number of excess ions using ASAXS. We present a coarse-grained model that accounts for flexibility, excluded volume, and electrostatic interactions in these systems. Predictions of the model are validated against experiment. We also discuss the state of all-atom, explicit solvent Molecular Dynamics simulations of poly(dT), the next step in understanding the complexities of ion interactions with these highly charged and flexible polymers. PMID:23606337

Studies on the Ionic Permeability of Muscle Cells and their Models

PubMed Central

Ling, Gilbert N.; Ochsenfeld, Margaret M.

1965-01-01

We studied the effect an alkali-metal ion exercised on the rate of entry of another alkali-metal ion into frog sartorius muscle cells and their models (i.e., ion exchange resin and sheep's wool). In the case of frog muscle, it was shown that the interaction fell into one of four categories; competition, facilitation, and two types of indifference. The observed pK value (4.6 to 4.7) of the surface anionic groups that combine with the alkali-metal ions suggests that they are β- or γ-carboxyl groups of proteins on the cell surface. The results were compared with four theoretical models which included three membrane models (continuous lipoid membrane with carrier; leaky membrane with carrier; membrane with fixed ionic sites) and one bulk-phase model. This comparison led to the conclusion that the only model that is self-consistent and agrees with all of the experimental facts is the one based on the concept that the entire living cell represents a proteinaceous fixed-charge system; this model correctly predicts all four types of interaction observed. PMID:5884012

Noncontact bimolecular photoionization followed by radical-ions separation and their geminate recombination assisted by coherent HFI induced spin-conversion.

PubMed

Dodin, Dmitry V; Ivanov, Anatoly I; Burshtein, Anatoly I

2008-02-07

The Hamiltonian description of the spin-conversion induced by a hyperfine interaction (HFI) in photogenerated radical-ion pairs is substituted for the rate (incoherent) description of the same conversion provided by the widely used earlier elementary spin model. The quantum yields of the free ions as well as the singlet and triplet products of geminate recombination are calculated using distant dependent ionization and recombination rates, instead of their contact analogs. Invoking the simplest models of these rates, we demonstrate with the example of a spin-less system that the diffusional acceleration of radical-ion pair recombination at lower viscosity gives way to its diffusional deceleration (Angulo effect), accomplished with a kinetic plateau inherent with the primitive exponential model. Qualitatively the same behavior is found in real systems, assuming both ionization and recombination is carried out by the Marcus electron-transfer rates. Neglecting the Coulomb interaction between solvated ions, the efficiencies of radical-ion pair recombination to the singlet and triplet products are well fitted to the available experimental data. The magnetic field dependence of these yields is specified.

A multiphase ion-transport analysis of the electrostatic disjoining pressure: implications for binary droplet coalescence

NASA Astrophysics Data System (ADS)

Mason, Lachlan; Gebauer, Felix; Bart, Hans-Jörg; Stevens, Geoffrey; Harvie, Dalton

2016-11-01

Understanding the physics of emulsion coalescence is critical for the robust simulation of industrial solvent extraction processes, in which loaded organic and raffinate phases are separated via the coalescence of dispersed droplets. At the droplet scale, predictive collision-outcome models require an accurate description of the repulsive surface forces arising from electrical-double-layer interactions. The conventional disjoining-pressure treatment of double-layer forces, however, relies on assumptions which do not hold generally for deformable droplet collisions: namely, low interfacial curvature and negligible advection of ion species. This study investigates the validity bounds of the disjoining pressure approximation for low-inertia droplet interactions. A multiphase ion-transport model, based on a coupling of droplet-scale Nernst-Planck and Navier-Stokes equations, predicts ion-concentration fields that are consistent with the equilibrium Boltzmann distribution; indicating that the disjoining-pressure approach is valid for both static and dynamic interactions in low-Reynolds-number settings. The present findings support the development of coalescence kernels for application in macro-scale population balance modelling.

Effect of silver ions and clusters on the luminescence properties of Eu-doped borate glasses

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

Jiao, Qing, E-mail: jiaoqing@nbu.edu.cn; Wang, Xi; Qiu, Jianbei

2015-12-15

Highlights: • Ag{sup +} and Ag clusters are investigated in the borate glasses via ion exchange method. • The aggregation of silver ions to the clusters was controlled by the ion exchange concentration. • Eu{sup 3+}/Eu{sup 2+} ions emission was enhanced with the sensitization of the silver species. • Energy transfer process from Ag ions and Ag clusters to Eu ions is identified by the lifetime measurements. - Abstract: Silver ions and clusters were applied to Eu{sup 3+}-doped borate glasses via the Ag{sup +}–Na{sup +} ion exchange method. Eu{sup 3+}/Eu{sup 2+} ion luminescence enhancement was achieved after silver ion exchange.more » Absorption spectra showed no band at 420 nm, which indicates that silver nanoparticles can be excluded as a silver state in the glass. Silver ion aggregation into clusters during the ion exchange process may be inferred. The effect of silver ions and clusters on rare earth emissions was investigated using spectral information and lifetime measurements. Significant luminescence enhancements were observed from the energy transfer of Ag{sup +} ions and clusters to Eu{sup 3+}/Eu{sup 2+} ions, companied with the silver ions aggregated into the clusters state. The results of this research may extend the current understanding of interactions between rare-earth ions and Ag species.« less

Electron plasma environment at comet Grigg-Skjellerup: General observations and comparison with the environment at comet Halley

NASA Technical Reports Server (NTRS)

Reme, H.; Mazelle, C.; Sauvaud, J. A.; D'Uston, C.; Froment, F.; Lin, R. P.; Anderson, K. A.; Carlson, C. W.; Larson, D. E.; Korth, A.

1993-01-01

The three-dimensional electron spectrometer of the Reme plasma analyzer-complete positive ion, electron and ram negative ion measurements near comet Halley (RPA-COPERNIC) experiment aboard the Giotto spacecraft, although damaged during the comet Halley encounter in March 1986, has provided very new results during the encounter on July 10, 1992, with the weakly active comet Grigg-Skjellerup (G-S). The main characteristic features of the highly structured interaction region extending from approximately 26,500 km inbound to approximately 37,200 km outbound are presented. These results are compared to the results obtained by the same instrument during the Giotto comet Halley fly-by. Despite the large difference in the size of the interaction regions (approximately 60,000 km for G-S, approximately 2000,000 km for Halley) due to 2 orders of magnitude difference in cometary neutral gas production rate, there are striking similarities in the solar wind interactions with the two comets.

Development and flight history of SERT 2 spacecraft

NASA Technical Reports Server (NTRS)

Kerslake, William R.; Ignaczak, Louis R.

1992-01-01

A 25-year historical review of the Space Electric Rocket Test 2 (SERT 2) mission is presented. The Agena launch vehicle; the SERT 2 spacecraft; and mission-peculiar spacecraft hardware, including two ion thruster systems, are described. The 3 1/2-year development period, from 1966 to 1970, that was needed to design, fabricate, and qualify the ion thruster system and the supporting spacecraft components, is documented. Major testing of two ion thruster systems and related auxiliary experiments that were conducted in space after the 3 Feb. 1970, launch are reviewed. Extended ion thruster restarts from 1973 to 1981 are reported, in addition to cross-neutralization tests. Tests of a reflector erosion experiment were continued in 1989 to 1991. The continuing performance of spacecraft subsystems, including the solar arrays, over the 1970-1991 period is summarized. Finally, the knowledge of thruster-spacecraft interactions learned from SERT 2 is listed.

The role of correlation and solvation in ion interactions with B-DNA

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

Sushko, Maria L.; Thomas, Dennis G.; Pabit, Suzette

Ionic atmosphere around nucleic acids plays important roles in biological function. Large-scale explicit solvent simulations coupled to experimental assays such as anomalous small-angle X-ray scattering (ASAXS) can provide important insights into the structure and energetics of the ionic atmosphere but are time- and resource-intensive. In this paper, we demonstrate the use of classical density functional theory to model DNA-ion interactions and explore the balance between ion-DNA, ion-water, and ion-ion interactions. In particular, we compute the distribution of RbCl, SrCl2, and CoHexCl3 (cobalt hexammine chlo- ride) around a B-form DNA molecule. The accuracy of the DFT calculations was assessed by comparisonmore » between simulated and experimental ASAXS curves. As expected, these calculations revealed significant differences between the monovalent, divalent, and trivalent cations. About half of the DNA-bound Rb+ ions penetrate into the minor groove of the DNA and half adsorb on the DNA strands. The fraction of cations in the minor groove decreases for the larger Sr2+ ions and becomes zero for CoHex3+ ions, which all adsorb on the DNA strands. The distribution of CoHex3+ ions is mainly determined by Coulomb interactions, while ion-correlation forces play a central role in the monovalent Rb+ distribution and a combination of ion-correlation and hydration forces affect the Sr2+ distribution around DNA.« less

Counting the ions surrounding nucleic acids

PubMed Central

2017-01-01

Abstract Nucleic acids are strongly negatively charged, and thus electrostatic interactions—screened by ions in solution—play an important role in governing their ability to fold and participate in biomolecular interactions. The negative charge creates a region, known as the ion atmosphere, in which cation and anion concentrations are perturbed from their bulk values. Ion counting experiments quantify the ion atmosphere by measuring the preferential ion interaction coefficient: the net total number of excess ions above, or below, the number expected due to the bulk concentration. The results of such studies provide important constraints on theories, which typically predict the full three-dimensional distribution of the screening cloud. This article reviews the state of nucleic acid ion counting measurements and critically analyzes their ability to test both analytical and simulation-based models. PMID:28034959

Engineered long-range interactions on a 2D array of trapped ions

NASA Astrophysics Data System (ADS)

Britton, Joseph W.; Sawyer, Brian C.; Bollinger, John J.; Freericks, James K.

2014-03-01

Ising interactions are one paradigm used to model quantum magnetism in condensed matter systems. At NIST Boulder we confine and Doppler laser cool hundreds of 9Be+ ions in a Penning trap. The valence electron of each ion behaves as an ideal spin-1/2 particle and, in the limit of weak radial confinement relative to axial confinement, the ions naturally form a two-dimensional triangular lattice. A variable-range anti-ferromagnetic Ising interaction is engineered with a spin-dependent optical dipole force (ODF) through spin-dependent excitation of collective modes of ion motion. We have also exploited this spin-dependent force to perform spectroscopy and thermometry of the normal modes of the trapped ion crystal. The high spin-count and long-range spin-spin couplings achievable in the NIST Penning trap brings within reach simulation of computationally intractable problems in quantum magnetism. Examples include modeling quantum magnetic phase transitions and propagation of spin correlations resulting from a quantum quench. The Penning system may also be amenable to observation of spin-liquid behavior thought to arise in systems where the underlying lattice structure can frustrate long-range ordering. Supported by DARPA OLE and NIST.

Testing the role of metal hydrolysis in the anomalous electrodeposition of Ni-Fe alloys

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

Harris, T.M.; St. Clair, J.

1996-12-01

With the objective of testing several models of the anomalous codeposition (ACD) encountered in the electrodeposition of nickel-iron alloys, the effects of bath pH and complexing agents on the composition of deposits were examined. When the pH of the base line bath was increased from 3.0 to 5.0, the Ni/Fe mass ratio of the deposit increased (i.e., the deposition became less anomalous). The presence of tartrate ion in the bath produced a slight decrease in the Ni/Fe of the deposit. This complexing agent complexes ferric ion and thus prevents its precipitation but has little interaction with ferrous ion or nickelmore » ion under the electrodeposition conditions examined. The addition of ethylenediamine to the bath produced a significant increase in the Ni/Fe mass ratio. This complexing agent does not interact significantly with ferric ion or ferrous ion under the test conditions. None of these observations are consistent with the Dahms and Croll model of ACD. The effects of pH and tartaric acid on the deposit composition are consistent with the predictions of the Grande and Talbot model and the Matlosz model. The effect of ethylenediamine is not consistent with the Grande and Talbot model, but may be interpreted within the framework of the Matlosz model and the Hessami and Tobias model.« less

Continuum theory of lipid bilayer electrostatics.

PubMed

Gerami, R; Bruinsma, R F

2009-10-01

In order to address the concerns about the applicability of the continuum theory of lipid bilayers, we generalize it by including a film with uniaxial dielectric properties representing the polar head groups of the lipid molecules. As a function of the in-plane dielectric constant κ|| of this film, we encounter a sequence of different phases. For low values of κ||, transmembrane pores have aqueous cores, ions are repelled by the bilayer, and the ion permeability of the bilayer is independent of the ion radius as in the existing theory. For increasing κ||, a threshold is reached--of the order of the dielectric constant of water--beyond which ions are attracted to the lipid bilayer by generic polarization attraction, transmembrane pores collapse, and the ion permeability becomes sensitively dependent on the ion radius, results that are more consistent with experimental and numerical studies of the interaction of ions with neutral lipid bilayers. At even higher values of κ||, the ion/pore complexes are predicted to condense in the form of extended arrays. The generalized continuum theory can be tested quantitatively by studies of the ion permeability as a function of salt concentration and co-surfactant concentration.

Test particle simulation study of whistler wave packets observed near Comet Giacobini-Zinner

NASA Astrophysics Data System (ADS)

Kaya, N.; Matsumoto, H.; Tsurutani, B. T.

1989-01-01

Nonlinear interactions of water group ions with large-amplitude whistler wave packets detected at the leading edge of steepened magnetosonic waves observed near Comet Giacobini-Zinner (GZ) are studied using test particle simulations of water-ion interactions with a model wave based on GZ data. Some of the water ions are found to be decelerated in the steepened portion of the magnetosonic wave to the resonance velocity with the whistler wave packets. Through resonance and related nonlinear interaction with the large-amplitude whistler waves, the water ions become trapped by the packet. An energy balance calculation demonstrates that the trapped ions lose their kinetic energy during the trapped motion in the packet. Thus, the nonlinear trapping motion in the wave structure leads to effective energy transfer from the water group ions to the whistler wave packets in the leading edge of the steepened MHD waves.

Molecular Modeling of Thermodynamic and Transport Properties for CO2 and Aqueous Brines.

PubMed

Jiang, Hao; Economou, Ioannis G; Panagiotopoulos, Athanassios Z

2017-04-18

Molecular simulation techniques using classical force-fields occupy the space between ab initio quantum mechanical methods and phenomenological correlations. In particular, Monte Carlo and molecular dynamics algorithms can be used to provide quantitative predictions of thermodynamic and transport properties of fluids relevant for geologic carbon sequestration at conditions for which experimental data are uncertain or not available. These methods can cover time and length scales far exceeding those of quantum chemical methods, while maintaining transferability and predictive power lacking from phenomenological correlations. The accuracy of predictions depends sensitively on the quality of the molecular models used. Many existing fixed-point-charge models for water and aqueous mixtures fail to represent accurately these fluid properties, especially when descriptions covering broad ranges of thermodynamic conditions are needed. Recent work on development of accurate models for water, CO 2 , and dissolved salts, as well as their mixtures, is summarized in this Account. Polarizable models that can respond to the different dielectric environments in aqueous versus nonaqueous phases are necessary for predictions of properties over extended ranges of temperatures and pressures. Phase compositions and densities, activity coefficients of the dissolved salts, interfacial tensions, viscosities and diffusivities can be obtained in near-quantitative agreement to available experimental data, using relatively modest computational resources. In some cases, for example, for the composition of the CO 2 -rich phase in coexistence with an aqueous phase, recent results from molecular simulations have helped discriminate among conflicting experimental data sets. The sensitivity of properties on the quality of the intermolecular interaction model varies significantly. Properties such as the phase compositions or electrolyte activity coefficients are much more sensitive than phase densities, viscosities, or component diffusivities. Strong confinement effects on physical properties in nanoscale media can also be directly obtained from molecular simulations. Future work on molecular modeling for CO 2 and aqueous brines is likely to be focused on more systematic generation of interaction models by utilizing quantum chemical as well as direct experimental measurements. New ion models need to be developed for use with the current generation of polarizable water models, including ion-ion interactions that will allow for accurate description of dense, mixed brines. Methods will need to be devised that go beyond the use of effective potentials for incorporation of quantum effects known to be important for water, and reactive force fields developed that can handle bond creation and breaking in systems with carbonate and silicate minerals. Another area of potential future work is the integration of molecular simulation methods in multiscale models for the chemical reactions leading to mineral dissolution and flow within the porous media in underground formations.

The Colorado Solar Wind Experiment

NASA Astrophysics Data System (ADS)

Munsat, Tobin; Han, Jia; Horanyi, Mihaly; Ulibarri, Zach; Wang, Xu; Yeo, Lihsia

2016-10-01

The Colorado Solar Wind Experiment (CSWE) is a new device developed at the Institute for Modeling Plasma, Atmospheres, and Cosmic Dust (IMPACT) at the University of Colorado. This large ion source is for studies of the interaction of solar wind plasma with planetary surfaces and cosmic dust, and for the investigation of plasma wake physics. With a plasma beam diameter of 12 cm at the source, ion energies of up to 1 keV, and ion flows of up to 1 mA/cm2, a large cross-section Kaufman Ion Source is used to create steady state plasma flow to model the solar wind in an experimental vacuum chamber. Chamber pressure can be reduced to 3e-5 Torr under operating conditions to suppress ion-neutral collisions and create a uniform ion velocity distribution. Diagnostic instruments such as a double Langmuir probe and an ion energy analyzer are mounted on a two-dimensional translation stage that allow the beam to be characterized throughout the chamber. Early experiments include the measurement of dust grain charging from the interaction with flowing plasma, and measurements of the plasma sheath created by the interaction of the flowing plasma impinging on a surface with a dipole magnetic field. This poster will describe the facility and the scientific results obtained to date.

Refined Dummy Atom Model of Mg(2+) by Simple Parameter Screening Strategy with Revised Experimental Solvation Free Energy.

PubMed

Jiang, Yang; Zhang, Haiyang; Feng, Wei; Tan, Tianwei

2015-12-28

Metal ions play an important role in the catalysis of metalloenzymes. To investigate metalloenzymes via molecular modeling, a set of accurate force field parameters for metal ions is highly imperative. To extend its application range and improve the performance, the dummy atom model of metal ions was refined through a simple parameter screening strategy using the Mg(2+) ion as an example. Using the AMBER ff03 force field with the TIP3P model, the refined model accurately reproduced the experimental geometric and thermodynamic properties of Mg(2+). Compared with point charge models and previous dummy atom models, the refined dummy atom model yields an enhanced performance for producing reliable ATP/GTP-Mg(2+)-protein conformations in three metalloenzyme systems with single or double metal centers. Similar to other unbounded models, the refined model failed to reproduce the Mg-Mg distance and favored a monodentate binding of carboxylate groups, and these drawbacks needed to be considered with care. The outperformance of the refined model is mainly attributed to the use of a revised (more accurate) experimental solvation free energy and a suitable free energy correction protocol. This work provides a parameter screening strategy that can be readily applied to refine the dummy atom models for metal ions.

Coarse-graining, Electrostatics and pH effects in phospholipid systems

NASA Astrophysics Data System (ADS)

Travesset, Alex; Vangaveti, Sweta

2010-03-01

We introduce a minimal free energy describing the interaction of charged groups and counterions including both classical electrostatic and specific interactions. The predictions of the model are compared against the standard model for describing ions next to charged interfaces, consisting of Poisson-Boltzmann theory with additional constants describing ion binding, which are specific to the counterion and the interfacial charge (``chemical binding''). It is shown that the ``chemical'' model can be appropriately described by an underlying ``physical'' model over several decades in concentration, but the extracted binding constants are not uniquely defined, as they differ depending on the particular observable quantity being studied. It is also shown that electrostatic correlations for divalent (or higher valence) ions enhance the surface charge by increasing deprotonation, an effect not properly accounted within chemical models. The model is applied to the charged phospholipids phosphatidylserine, Phosphatidc acid and Phosphoinositides and implications for different biological processes are discussed.

Nanoparticles in natural systems II: The natural oxide fraction at interaction with natural organic matter and phosphate

NASA Astrophysics Data System (ADS)

Hiemstra, Tjisse; Antelo, Juan; van Rotterdam, A. M. D.(Debby); van Riemsdijk, Willem H.

2010-01-01

Information on the particle size and reactive surface area of natural samples and its interaction with natural organic matter (NOM) is essential for the understanding bioavailability, toxicity, and transport of elements in the natural environment. In part I of this series ( Hiemstra et al., 2010), a method is presented that allows the determination of the effective reactive surface area ( A, m 2/g soil) of the oxide particles of natural samples which uses a native probe ion (phosphate) and a model oxide (goethite) as proxy. In soils, the natural oxide particles are generally embedded in a matrix of natural organic matter (NOM) and this will affect the ion binding properties of the oxide fraction. A remarkably high variation in the natural phosphate loading of the oxide surfaces ( Γ, μmol/m 2) is observed in our soils and the present paper shows that it is due to surface complexation of NOM, acting as a competitor via site competition and electrostatic interaction. The competitive interaction of NOM can be described with the charge distribution (CD) model by defining a ≡NOM surface species. The interfacial charge distribution of this ≡NOM surface species can be rationalized based on calculations done with an evolved surface complexation model, known as the ligand and charge distribution (LCD) model. An adequate choice is the presence of a charge of -1 v.u. at the 1-plane and -0.5 v.u. at the 2-plane of the electrical double layer used (Extended Stern layer model). The effective interfacial NOM adsorption can be quantified by comparing the experimental phosphate concentration, measured under standardized field conditions (e.g. 0.01 M CaCl 2), with a prediction that uses the experimentally derived surface area ( A) and the reversibly bound phosphate loading ( Γ, μmol/m 2) of the sample (part I) as input in the CD model. Ignoring the competitive action of adsorbed NOM leads to a severe under-prediction of the phosphate concentration by a factor ˜10 to 1000. The calculated effective loading of NOM is low at a high phosphate loading ( Γ) and vice versa, showing the mutual competition of both constituents. Both constituents in combination usually dominate the surface loading of natural oxide fraction of samples and form the backbone in modeling the fate of other (minor) ions in the natural environment. Empirically, the effective NOM adsorption is found to correlate well to the organic carbon content (OC) of the samples. The effective NOM adsorption can also be linked to DOC. For this, a Non-Ideal Competitive adsorption (NICA) model is used. DOC is found to be a major explaining factor for the interfacial loading of NOM as well as phosphate. The empirical NOM-OC relation or the parameterized NICA model can be used as an alternative for estimating the effective NOM adsorption to be implemented in the CD model for calculation of the surface complexation of field samples. The biogeochemical impact of the NOM-PO 4 interaction is discussed.

Local Magnetism in Strongly Correlated Electron Systems with Orbital Degrees of Freedom

NASA Astrophysics Data System (ADS)

Ducatman, Samuel Charles

The central aim of my research is to explain the connection between the macroscopic behavior and the microscopic physics of strongly correlated electron systems with orbital degrees of freedom through the use of effective models. My dissertation focuses on the sub-class of these materials where electrons appear to be localized by interactions, and magnetic ions have well measured magnetic moments. This suggests that we can capture the low-energy physics of the material by employing a minimal model featuring localized spins which interact with each other through exchange couplings. I describe Fe1+y Te and beta-Li2IrO3 with effective models primarily focusing on the spins of the magnetic ions, in this case Fe and Ir, respectively. The goal with both materials is to gain insight and make predictions for experimentalists. In chapter 2, I focus on Fe1+yTe. I describe why we believe the magnetic ground state of this material, with an observed Bragg peak at Q +/- pi/2, pi/2), can be described by a Heisenberg model with 1st, 2nd, and 3rd neighbor interactions. I present two possible ground states of this model in the small J1 limit, the bicollinear and plaquette states. In order to predict which ground state the model prefers, I calculate the spin wave spectrum with 1/S corrections, and I find the model naturally selects the "plaquette state." I give a brief description of the ways this result could be tested using experimental techniques such as polarized neutron scattering. In chapter 3, I extend the model used in chapter 2. This is necessary because the Heisenberg model we employed cannot explain why Fe1+yTe undergoes a phase transition as y is increased. We add an additional elements to our calculation; we assume that electrons in some of the Fe 3D orbitals have selectively localized while others remain itinerant. We write a new Hamiltonian, where localized moments acquire a new long-range RKKY-like interaction from interactions with the itinerant electrons. We are able to reproduce the phase diagram found from experimentalists, and make predictions about how Fe1+y Te could potentially be driven into a "stripe" magnetic ground state. In chapter 4, I examine another strongly correlated material, beta-Li 2IrO3, which exhibits Kitaev physics. I begin with a minimal model employing nearest neighbor isotropic and anisotropic exchange couplings between neighboring Iridium ions. I calculate the phase diagram, and find two states. I characterize both states in terms of spins along the zigzag chains of the hyperhoneycomb lattice, and calculate linear spin waves for both states. I find that, besides for special points in our phase diagram, the excitations are gapped. As the spectrum has many branches, I calculate the dynamic structure factor to find which branches of the spin wave spectrum have the highest intensity. It will be interesting to compare my dynamic structure factor results to single crystal inelastic neutron scattering, which to this point has not been performed for beta-Li2IrO3.

Molecular models of alginic acid: Interactions with calcium ions and calcite surfaces

NASA Astrophysics Data System (ADS)

Perry, Thomas D.; Cygan, Randall T.; Mitchell, Ralph

2006-07-01

Cation binding by polysaccharides is observed in many environments and is important for predictive environmental modeling, and numerous industrial and food technology applications. The complexities of these cation-organic interactions are well suited for predictive molecular modeling and the analysis of conformation and configuration of polysaccharides and their influence on cation binding. In this study, alginic acid was chosen as a model polymer system and representative disaccharide and polysaccharide subunits were developed. Molecular dynamics simulation of the torsion angles of the ether linkage between various monomeric subunits identified local and global energy minima for selected disaccharides. The simulations indicate stable disaccharide configurations and a common global energy minimum for all disaccharide models at Φ = 274 ± 7°, Ψ = 227 ± 5°, where Φ and Ψ are the torsion angles about the ether linkage. The ability of disaccharide subunits to bind calcium ions and to associate with the (101¯4) surface of calcite was also investigated. Molecular models of disaccharide interactions with calcite provide binding energy differences for conformations that are related to the proximity and residence densities of the electron-donating moieties with calcium ions on the calcite surface, which are controlled, in part, by the torsion of the ether linkage between monosaccharide units. Dynamically optimized configurations for polymer alginate models with calcium ions were also derived.

Structural diversity of alkaline-earth 2,5-thiophenedicarboxylates

NASA Astrophysics Data System (ADS)

Balendra; Ramanan, Arunachalam

2017-03-01

Exploration of the structural landscape of the system containing divalent alkaline-earth metal ion (Mg, Ca and Sr) with the rigid 2,5-thiophenedicarboxylic acid (TDC) under varying solvothermal condition (DMF, DMA and DEF) yielded five new crystals: [Mg(TDC) (DEF)2(H2O)1/2] (1), [Ca(TDC) (DMA)] (2), [Ca(TDC) (DMA) (H2O)] (3), [Sr(TDC) (DMA)] (4) and [Sr(TDC) (DMA) (H2O)] (5) and two known solids. Single crystal structures of all the solids are characteristic of extended coordination interaction between metal and carboxylate ions. While the smaller magnesium ion crystallized into a 2D coordination polymer, the larger calcium and strontium compounds resulted into the growth of 3D metal organic frameworks. All the solids show blue emission arising from intra ligand charge transfer.

On the Scattering of the Electron off the Hydrogen Atom and the Helium Ion Below and Above the Ionization Threshold: Temkin-Poet Model

NASA Astrophysics Data System (ADS)

Yarevsky, E.; Yakovlev, S. L.; Elander, N.; Volkov, M. V.

2014-08-01

We generalize here the splitting approach to the long range (Coulomb) interaction for the three body scattering problem. With this approach, the exterior complex rotation technique can be applied for systems with asymptotic Coulomb interaction. We illustrate the method with calculations of the electron scattering on the hydrogen atom and positive helium ion in the frame of the Temkin-Poet model.

Geant4 models for simulation of hadron/ion nuclear interactions at moderate and low energies.

NASA Astrophysics Data System (ADS)

Ivantchenko, Anton; Ivanchenko, Vladimir; Quesada, Jose-Manuel; Wright, Dennis

The Geant4 toolkit is intended for Monte Carlo simulation of particle transport in media. It was initially designed for High Energy Physics purposes such as experiments at the Large Hadron Collider (LHC) at CERN. The toolkit offers a set of models allowing effective simulation of cosmic ray interactions with different materials. For moderate and low energy hadron/ion interactions with nuclei there are a number of competitive models: Binary and Bertini intra-nuclear cascade models, quantum molecular dynamic model (QMD), INCL/ABLA cascade model, and Chiral Invariant Phase Space Decay model (CHIPS). We report the status of these models for the recent version of Geant4 (release 9.3, December 2009). The Bertini cascade in-ternal cross sections were upgraded. The native Geant4 precompound and deexcitation models were used in the Binary cascade and QMD. They were significantly improved including emis-sion of light fragments, the Fermi break-up model, the General Evaporation Model (GEM), the multi-fragmentation model, and the fission model. Comparisons between model predictions and data for thin target experiments for neutron, proton, light ions, and isotope production are presented and discussed. The focus of these validations is concentrated on target materials important for space missions.

Environment spectrum and coherence behaviours in a rare-earth doped crystal for quantum memory.

PubMed

Gong, Bo; Tu, Tao; Zhou, Zhong-Quan; Zhu, Xing-Yu; Li, Chuan-Feng; Guo, Guang-Can

2017-12-21

We theoretically investigate the dynamics of environment and coherence behaviours of the central ion in a quantum memory based on a rare-earth doped crystal. The interactions between the central ion and the bath spins suppress the flip-flop rate of the neighbour bath spins and yield a specific environment spectral density S(ω). Under dynamical decoupling pulses, this spectrum provides a general scaling for the coherence envelope and coherence time, which significantly extend over a range on an hour-long time scale. The characterized environment spectrum with ultra-long coherence time can be used to implement various quantum communication and information processing protocols.

Development of a sensitive setup for laser spectroscopy studies of very exotic calcium isotopes

NASA Astrophysics Data System (ADS)

Garcia Ruiz, R. F.; Gorges, C.; Bissell, M.; Blaum, K.; Gins, W.; Heylen, H.; Koenig, K.; Kaufmann, S.; Kowalska, M.; Krämer, J.; Lievens, P.; Malbrunot-Ettenauer, S.; Neugart, R.; Neyens, G.; Nörtershäuser, W.; Yordanov, D. T.; Yang, X. F.

2017-04-01

An experimental setup for sensitive high-resolution measurements of hyperfine structure spectra of exotic calcium isotopes has been developed and commissioned at the COLLAPS beam line at ISOLDE, CERN. The technique is based on the radioactive detection of decaying isotopes after optical pumping and state selective neutralization (ROC) (Vermeeren et al 1992 Phys. Rev. Lett. 68 1679). The improvements and developments necessary to extend the applicability of the experimental technique to calcium isotopes produced at rates as low as few ions s-1 are discussed. Numerical calculations of laser-ion interaction and ion-beam simulations were explored to obtain the optimum performance of the experimental setup. Among the implemented features are a multi-step optical pumping region for sensitive measurements of isotopes with hyperfine splitting, a high-voltage platform for adequate control of low-energy ion beams and simultaneous β-detection of neutralized and remaining ions. The commissioning of the experimental setup, and the first online results on neutron-rich calcium isotopes are presented.

Interaction of slow highly charged ions with hard dental tissue: studies of fluoride uptake and reminalization efficacy

NASA Astrophysics Data System (ADS)

Daskalova, A.; Kasperski, G.; Rousseau, P.; Domaracka, A.; Lawicki, A.

2014-05-01

TOF-SIMS mass spectroscopy data are presented on ion irradiation of hard dental tissue using a beam of 129Xe20+ (15 kV) ions delivered in the ARIBE facility by an ECR source. The investigation was focused on the mass distribution of the fragment ions. A comparison is made between the mass spectra from hard dental tissue treated by olaflur-(C27H60F2N2O3) and untreated hard dental tissue obtained under irradiation by low-energy highly-charged ions (HCIs). We found significant differences between the mass spectra of enamel after introducing amine fluoride (olaflur) and the mass spectra of pure untreated enamel. Further, we separated out the effects caused by radiation induced in the tooth enamel from those induced in dentin, which has not been performed before. In order to conduct a further detailed analysis, it is necessary to extend the research scope to include the influence of fluorine compounds on enamel and dentin.

Enhanced localized energetic ion losses resulting from first-orbit linear and non-linear interactions with Alfvén eigenmodes in DIII-D

DOE PAGES

Chen, Xi; Heidbrink, William W.; Kramer, Gerrit J.; ...

2014-08-04

Two key insights into interactions between Alfvén eigenmodes (AEs) and energetic particles in the plasma core are gained from measurements and modeling of first-orbit beam-ion loss in DIII-D. First, the neutral beam-ion first-orbit losses are enhanced by AEs and a single AE can cause large fast-ion displacement. The coherent losses are from born trapped full energy beam-ions being non-resonantly scattered by AEs onto loss orbits within their first poloidal transit. The loss amplitudes scale linearly with the mode amplitude but the slope is different for different modes. The radial displacement of fast-ions by individual AEs can be directly inferred frommore » the measurements. Second, oscillations in the beam-ion first-orbit losses are observed at the sum, difference, and harmonic frequencies of two independent AEs. These oscillations are not plasma modes and are absent in magnetic, density, and temperature fluctuations. The origin of the non-linearity as a wave-particle coupling is confirmed through bi-coherence analysis, which is clearly observed because the coherences are preserved by the first-orbit loss mechanism. Finally, an analytic model and full orbit simulations show that the non-linear features seen in the loss signal can be explained by a non-linear interaction between the fast ions and the two independent AEs.« less

Enhanced localized energetic ion losses resulting from first-orbit linear and non-linear interactions with Alfvén eigenmodes in DIII-D

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

Chen, X.; General Atomics, P.O. Box 85608, San Diego, California 92186; Heidbrink, W. W.

2014-08-15

Two key insights into interactions between Alfvén eigenmodes (AEs) and energetic particles in the plasma core are gained from measurements and modeling of first-orbit beam-ion loss in DIII-D. First, the neutral beam-ion first-orbit losses are enhanced by AEs and a single AE can cause large fast-ion displacement. The coherent losses are from born trapped full energy beam-ions being non-resonantly scattered by AEs onto loss orbits within their first poloidal transit. The loss amplitudes scale linearly with the mode amplitude but the slope is different for different modes. The radial displacement of fast-ions by individual AEs can be directly inferred frommore » the measurements. Second, oscillations in the beam-ion first-orbit losses are observed at the sum, difference, and harmonic frequencies of two independent AEs. These oscillations are not plasma modes and are absent in magnetic, density, and temperature fluctuations. The origin of the non-linearity as a wave-particle coupling is confirmed through bi-coherence analysis, which is clearly observed because the coherences are preserved by the first-orbit loss mechanism. An analytic model and full orbit simulations show that the non-linear features seen in the loss signal can be explained by a non-linear interaction between the fast ions and the two independent AEs.« less

Electron Bubbles in Superfluid (3) 3 He-A: Exploring the Quasiparticle-Ion Interaction

NASA Astrophysics Data System (ADS)

Shevtsov, Oleksii; Sauls, J. A.

2017-06-01

When an electron is forced into liquid ^3He, it forms an "electron bubble", a heavy ion with radius, R˜eq 1.5 nm, and mass, M˜eq 100 m_3, where m_3 is the mass of a ^3He atom. These negative ions have proven to be powerful local probes of the physical properties of the host quantum fluid, especially the excitation spectra of the superfluid phases. We recently developed a theory for Bogoliubov quasiparticles scattering off electron bubbles embedded in a chiral superfluid that provides a detailed understanding of the spectrum of Weyl Fermions bound to the negative ion, as well as a theory for the forces on moving electron bubbles in superfluid ^3He-A (Shevtsov and Sauls in Phys Rev B 94:064511, 2016). This theory is shown to provide quantitative agreement with measurements reported by the RIKEN group (Ikegami et al. in Science 341(6141):59, 2013) for the drag force and anomalous Hall effect of moving electron bubbles in superfluid ^3He-A. In this report, we discuss the sensitivity of the forces on the moving ion to the effective interaction between normal-state quasiparticles and the ion. We consider models for the quasiparticle-ion (QP-ion) interaction, including the hard-sphere potential, constrained random-phase-shifts, and interactions with short-range repulsion and intermediate-range attraction. Our results show that the transverse force responsible for the anomalous Hall effect is particularly sensitive to the structure of the QP-ion potential and that strong short-range repulsion, captured by the hard-sphere potential, provides an accurate model for computing the forces acting on the moving electron bubble in superfluid 3He-A.

Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields.

PubMed

Yoo, Jejoong; Wilson, James; Aksimentiev, Aleksei

2016-10-01

Calcium ions (Ca(2+) ) play key roles in various fundamental biological processes such as cell signaling and brain function. Molecular dynamics (MD) simulations have been used to study such interactions, however, the accuracy of the Ca(2+) models provided by the standard MD force fields has not been rigorously tested. Here, we assess the performance of the Ca(2+) models from the most popular classical force fields AMBER and CHARMM by computing the osmotic pressure of model compounds and the free energy of DNA-DNA interactions. In the simulations performed using the two standard models, Ca(2+) ions are seen to form artificial clusters with chloride, acetate, and phosphate species; the osmotic pressure of CaAc2 and CaCl2 solutions is a small fraction of the experimental values for both force fields. Using the standard parameterization of Ca(2+) ions in the simulations of Ca(2+) -mediated DNA-DNA interactions leads to qualitatively wrong outcomes: both AMBER and CHARMM simulations suggest strong inter-DNA attraction whereas, in experiment, DNA molecules repel one another. The artificial attraction of Ca(2+) to DNA phosphate is strong enough to affect the direction of the electric field-driven translocation of DNA through a solid-state nanopore. To address these shortcomings of the standard Ca(2+) model, we introduce a custom model of a hydrated Ca(2+) ion and show that using our model brings the results of the above MD simulations in quantitative agreement with experiment. Our improved model of Ca(2+) can be readily applied to MD simulations of various biomolecular systems, including nucleic acids, proteins and lipid bilayer membranes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 752-763, 2016. © 2016 Wiley Periodicals, Inc.

Ion distribution effects of turbulence on a kinetic auroral arc model

NASA Technical Reports Server (NTRS)

Cornwall, J. M.; Chiu, Y. T.

1982-01-01

An inverted-V auroral arc structure plasma-kinetic model is extended to phenomenologically include the effects of electrostatic turbulence, with k-parallel/k-perpendicular being much less than unity. It is shown that, unless plasma sheet ions are very much more energetic than the electrons, anomalous resistivity is not a large contributor to parallel electrostatic potential drops, since the support of the observed potential drop requires a greater dissipation of energy than can be provided by the plasma sheet. Wave turbulence can, however, be present, with the ion cyclotron turbulence levels suggested by the ion resonance broadening saturation mechanism of Dum and Dupree (1970) being comparable to those observed on auroral field lines. The diffusion coefficient and net growth rate are much smaller than estimates based solely on local plasma properties.

Upstream energetic ions under radial IMF - A critical test of the Fermi model

NASA Technical Reports Server (NTRS)

Sarris, E. T.; Krimigis, S. M.

1988-01-01

Eight years of interplanetary magnetic field (IMF) and energetic particle observations obtained by the IMP-8 spacecraft upstream from the bow shock have been surveyed, and 63 cases when the upstream IMF remained radial for extended periods of time (greater than 1 hour) have been accumulated. Of these, two cases have been selected during which measurable fluxes of ambient solar or corotating energetic particle events were absent. These conditions provide an excellent test to the theories of the origin of upstream energetic ions. It is shown that there are extended periods with radial IMF when no upstream energetic ions were detected. It is further shown that energetic ions in the range E of between 50 keV and 1 MeV, inclusive, are not continuously present but appear in bursts of intensities varying by more than an order of magnitude under persistently radial IMF. These measurements contradict a fundamental prediction of the Fermi mechanism for the origin of the upstream energetic ions, namely that such ions should always be present on radial IMF lines. The observations are consistent with the hypothesis that energetic (greater than about 50 keV) ions leak out from, and appear in the upstream medium sporadically, following the onset of magnetic activity within the magnetosphere.

Improved hydrophilic interaction chromatography LC/MS of heparinoids using a chip with postcolumn makeup flow.

PubMed

Staples, Gregory O; Naimy, Hicham; Yin, Hongfeng; Kileen, Kevin; Kraiczek, Karsten; Costello, Catherine E; Zaia, Joseph

2010-01-15

Heparan sulfate (HS) and heparin are linear, heterogeneous carbohydrates of the glycosaminoglycan (GAG) family that are modified by N-acetylation, N-sulfation, O-sulfation, and uronic acid epimerization. HS interacts with growth factors in the extracellular matrix, thereby modulating signaling pathways that govern cell growth, development, differentiation, proliferation, and adhesion. High-performance liquid chromatography (HPLC)-chip-based hydrophilic interaction liquid chromatography/mass spectrometry has emerged as a method for analyzing the domain structure of GAGs. However, analysis of highly sulfated GAG structures decasaccharide or larger in size has been limited by spray instability in the negative-ion mode. This report demonstrates that addition of postcolumn makeup flow to the amide-HPLC-chip configuration permits robust and reproducible analysis of extended GAG domains (up to degree of polymerization 18) from HS and heparin. This platform provides quantitative information regarding the oligosaccharide profile, degree of sulfation, and nonreducing chain termini. It is expected that this technology will enable quantitative, comparative glycomics profiling of extended GAG oligosaccharide domains of functional interest.

Calculation of Transport Coefficients in Dense Plasma Mixtures

NASA Astrophysics Data System (ADS)

Haxhimali, T.; Cabot, W. H.; Caspersen, K. J.; Greenough, J.; Miller, P. L.; Rudd, R. E.; Schwegler, E. R.

2011-10-01

We use classical molecular dynamics (MD) to estimate species diffusivity and viscosity in mixed dense plasmas. The Yukawa potential is used to describe the screened Coulomb interaction between the ions. This potential has been used widely, providing the basis for models of dense stellar materials, inertial confined plasmas, and colloidal particles in electrolytes. We calculate transport coefficients in equilibrium simulations using the Green- Kubo relation over a range of thermodynamic conditions including the viscosity and the self - diffusivity for each component of the mixture. The interdiffusivity (or mutual diffusivity) can then be related to the self-diffusivities by using a generalization of the Darken equation. We have also employed non-equilibrium MD to estimate interdiffusivity during the broadening of the interface between two regions each with a high concentration of either species. Here we present results for an asymmetric mixture between Ar and H. These can easily be extended to other plasma mixtures. A main motivation for this study is to develop accurate transport models that can be incorporated into the hydrodynamic codes to study hydrodynamic instabilities. We use classical molecular dynamics (MD) to estimate species diffusivity and viscosity in mixed dense plasmas. The Yukawa potential is used to describe the screened Coulomb interaction between the ions. This potential has been used widely, providing the basis for models of dense stellar materials, inertial confined plasmas, and colloidal particles in electrolytes. We calculate transport coefficients in equilibrium simulations using the Green- Kubo relation over a range of thermodynamic conditions including the viscosity and the self - diffusivity for each component of the mixture. The interdiffusivity (or mutual diffusivity) can then be related to the self-diffusivities by using a generalization of the Darken equation. We have also employed non-equilibrium MD to estimate interdiffusivity during the broadening of the interface between two regions each with a high concentration of either species. Here we present results for an asymmetric mixture between Ar and H. These can easily be extended to other plasma mixtures. A main motivation for this study is to develop accurate transport models that can be incorporated into the hydrodynamic codes to study hydrodynamic instabilities. This work was performed under the auspices of the US Dept. of Energy by Lawrence Livermore National Security, LLC under Contract DE-AC52-07NA27344.

Spatiotemporal pH dynamics in concentration polarization near ion-selective membranes.

PubMed

Andersen, Mathias B; Rogers, David M; Mai, Junyu; Schudel, Benjamin; Hatch, Anson V; Rempe, Susan B; Mani, Ali

2014-07-08

We present a detailed analysis of the transient pH dynamics for a weak, buffered electrolyte subject to voltage-driven transport through an ion-selective membrane. We show that pH fronts emanate from the concentration polarization zone next to the membrane and that these propagating fronts change the pH in the system several units from its equilibrium value. The analysis is based on a 1D model using the unsteady Poisson-Nernst-Planck equations with nonequilibrium chemistry and without assumptions of electroneutrality or asymptotically thin electric double layers. Nonequilibrium chemical effects, especially for water splitting, are shown to be important for the dynamical and spatiotemporal evolution of the pH fronts. Nonetheless, the model also shows that at steady state the assumption of chemical equilibrium can still lead to good approximations of the global pH distribution. Moreover, our model shows that the transport of the hydronium ion in the extended space charge region is governed by a balance between electromigration and water self-ionization. On the basis of this observation, we present a simple model showing that the net flux of the hydronium ion is proportional to the length of the extended space charge region and the water self-ionization rate. To demonstrate these effects in practice, we have adopted the experiment of Mai et al. (Mai, J.; Miller, H.; Hatch, A. V. Spatiotemporal Mapping of Concentration Polarization Induced pH Changes at Nanoconstrictions. ACS Nano 2012, 6, 10206) as a model problem, and by including the full chemistry and transport, we show that the present model can capture the experimentally observed pH fronts. Our model can, among other things, be used to predict and engineer pH dynamics, which can be essential to the performance of membrane-based systems for biochemical separation and analysis.

Nonequilibrium Nonideal Nanoplasma Generated by a Fast Single Ion in Condensed Matter

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

Faenov, A. Ya.; Kansai Photon Science Institut, Japan Atomic Energy Agency; Lankin, A. V.

A plasma model of relaxation of a medium in heavy ion tracks in condensed matter is proposed. The model is based on three assumptions: the Maxwell distribution of plasma electrons, localization of plasma inside the track nanochannel and constant values of the plasma electron density and temperature during the X-ray irradiation. It is demonstrated that the plasma relaxation model adequately describes the X-ray spectra observed upon interaction of a fast ion with condensed target. Preassumptions of plasma relaxation model are validated by the molecular dynamics modeling and simulation.

Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions.

PubMed

Kashefolgheta, Sadra; Vila Verde, Ana

2017-08-09

We present a set of Lennard-Jones parameters for classical, all-atom models of acetate and various alkylated and non-alkylated forms of sulfate, sulfonate and phosphate ions, optimized to reproduce their interactions with water and with the physiologically relevant sodium, ammonium and methylammonium cations. The parameters are internally consistent and are fully compatible with the Generalized Amber Force Field (GAFF), the AMBER force field for proteins, the accompanying TIP3P water model and the sodium model of Joung and Cheatham. The parameters were developed primarily relying on experimental information - hydration free energies and solution activity derivatives at 0.5 m concentration - with ab initio, gas phase calculations being used for the cases where experimental information is missing. The ab initio parameterization scheme presented here is distinct from other approaches because it explicitly connects gas phase binding energies to intermolecular interactions in solution. We demonstrate that the original GAFF/AMBER parameters often overestimate anion-cation interactions, leading to an excessive number of contact ion pairs in solutions of carboxylate ions, and to aggregation in solutions of divalent ions. GAFF/AMBER parameters lead to excessive numbers of salt bridges in proteins and of contact ion pairs between sodium and acidic protein groups, issues that are resolved by using the optimized parameters presented here.

CHANDRA OBSERVATIONS OF COMETS C/2012 S1 (ISON) AND C/2011 L4 (PanSTARRS)

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

Snios, Bradford; Kharchenko, Vasili; Lisse, Carey M.

2016-02-20

We present our results on the Chandra X-ray Observatory Advanced CCD Imaging Spectrometer (ACIS) observations of the bright Oort Cloud comets C/2012 S1 (ISON) and C/2011 L4 (PanSTARRS). ISON was observed between 2013 October 31–November 06 during variable speed solar wind (SW), and PanSTARRS was observed between 2013 April 17–23 during fast SW. ISON produced an extended parabolic X-ray morphology consistent with a collisionally thick coma, while PanSTARRS demonstrated only a diffuse X-ray-emitting region. We consider these emissions to be from charge exchange (CX) and model each comet's emission spectrum from first principles accordingly. Our model agrees with the observationalmore » spectra and also generates composition ratios for heavy, highly charged SW ions interacting with the cometary atmosphere. We compare our derived SW ion compositions to observational data and find a strong agreement between them. These results further demonstrate the utility of CX emissions as a remote diagnostics tool of both astrophysical plasma interaction and SW composition. In addition, we observe potential soft X-ray emissions via ACIS around 0.2 keV from both comets that are correlated in intensity to the hard X-ray emissions between 0.4–1.0 keV. We fit our CX model to these emissions, but our lack of a unique solution at low energies makes it impossible to conclude if they are cometary CX in origin. Finally, we discuss probable emission mechanism sources for the soft X-rays and explore new opportunities these findings present in understanding cometary emission processes via Chandra.« less

Comparison of analytical models for zonal flow generation in ion-temperature-gradient mode turbulence

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

Anderson, J.; Miki, K.; Uzawa, K.

2006-11-30

During the past years the understanding of the multi scale interaction problems have increased significantly. However, at present there exists a flora of different analytical models for investigating multi scale interactions and hardly any specific comparisons have been performed among these models. In this work two different models for the generation of zonal flows from ion-temperature-gradient (ITG) background turbulence are discussed and compared. The methods used are the coherent mode coupling model and the wave kinetic equation model (WKE). It is shown that the two models give qualitatively the same results even though the assumption on the spectral difference ismore » used in the (WKE) approach.« less

Using affinity capillary electrophoresis and computational models for binding studies of heparinoids with p-selectin and other proteins.

PubMed

Mozafari, Mona; Balasupramaniam, Shantheya; Preu, Lutz; El Deeb, Sami; Reiter, Christian G; Wätzig, Hermann

2017-06-01

A fast and precise affinity capillary electrophoresis (ACE) method has been developed and applied for the investigation of the binding interactions between P-selectin and heparinoids as potential P-selectin inhibitors in the presence and absence of calcium ions. Furthermore, model proteins and vitronectin were used to appraise the binding behavior of P-selectin. The normalized mobility ratios (∆R/R f ), which provided information about the binding strength and the overall charge of the protein-ligand complex, were used to evaluate the binding affinities. It was found that P-selectin interacts more strongly with heparinoids in the presence of calcium ions. P-selectin was affected by heparinoids at the concentration of 3 mg/L. In addition, the results of the ACE experiments showed that among other investigated proteins, albumins and vitronectin exhibited strong interactions with heparinoids. Especially with P-selectin and vitronectin, the interaction may additionally induce conformational changes. Subsequently, computational models were applied to interpret the ACE experiments. Docking experiments explained that the binding of heparinoids on P-selectin is promoted by calcium ions. These docking models proved to be particularly well suited to investigate the interaction of charged compounds, and are therefore complementary to ACE experiments. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Small-angle fragmentation of carbon ions at 0.6 GeV/n: A comparison with models of ion-ion interactions

DOE PAGES

Krutenkova, A. P.; Abramov, B. M.; Alekseev, P. N.; ...

2015-05-29

Momentum distributions of hydrogen and helium isotopes from ¹²C fragmentation at 3.5° were measured at 0.6 GeV/nucleon in the FRAGM experiment at ITEP TWA heavy ion accelerator. The fragments were selected by correlated time of flight and dE/dx measurements with a magnetic spectrometer with scintillation counters. The main attention was drawn to the high momentum region where the fragment velocity exceeds the velocity of the projectile nucleus. The momentum spectra of fragments span the region of the fragmentation peak as well as the cumulative region. The differential cross sections cover six orders of magnitude. The distributions measured are compared tomore » the predictions of three ion-ion interaction models: BC, QMD and LAQGSM03.03. The kinetic energy spectra of fragments in the projectile rest frame have an exponential shape with two temperatures, being defined by their slope parameters.« less

Small-angle fragmentation of carbon ions at 0.6 GeV/n. A comparison with models of ion-ion interactions

DOE PAGES

Krutenkova, Anna P.; Abramov, B. M.; Alekseev, P. N.; ...

2015-05-29

The momentum distributions of hydrogen and helium isotopes from 12C fragmentation at 3.5° were measured at 0.6 GeV/nucleon in the FRAGM experiment at ITEP TWA heavy ion accelerator. The fragments were selected by correlated time of flight and dE/dx measurements with a magnetic spectrometer with scintillation counters. The main attention was drawn to the high momentum region where the fragment velocity exceeds the velocity of the projectile nucleus. The momentum spectra of fragments span the region of the fragmentation peak as well as the cumulative region. Moreover, the differential cross sections cover six orders of magnitude. The distributions measured aremore » compared to the predictions of three ion-ion interaction models: BC, QMD and LAQGSM03.03. The kinetic energy spectra of fragments in the projectile rest frame have an exponential shape with two temperatures, being defined by their slope parameters.« less

Entangling spin-spin interactions of ions in individually controlled potential wells

NASA Astrophysics Data System (ADS)

Wilson, Andrew; Colombe, Yves; Brown, Kenton; Knill, Emanuel; Leibfried, Dietrich; Wineland, David

2014-03-01

Physical systems that cannot be modeled with classical computers appear in many different branches of science, including condensed-matter physics, statistical mechanics, high-energy physics, atomic physics and quantum chemistry. Despite impressive progress on the control and manipulation of various quantum systems, implementation of scalable devices for quantum simulation remains a formidable challenge. As one approach to scalability in simulation, here we demonstrate an elementary building-block of a configurable quantum simulator based on atomic ions. Two ions are trapped in separate potential wells that can individually be tailored to emulate a number of different spin-spin couplings mediated by the ions' Coulomb interaction together with classical laser and microwave fields. We demonstrate deterministic tuning of this interaction by independent control of the local wells and emulate a particular spin-spin interaction to entangle the internal states of the two ions with 0.81(2) fidelity. Extension of the building-block demonstrated here to a 2D-network, which ion-trap micro-fabrication processes enable, may provide a new quantum simulator architecture with broad flexibility in designing and scaling the arrangement of ions and their mutual interactions. This research was funded by the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA), ONR, and the NIST Quantum Information Program.

Extraction of highly charged ions from the Berlin Electron Beam Ion Trap for interactions with a gas target

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

Allen, F.I.; Biedermann, C.; Radtke, R.

2006-03-15

Highly charged ions are extracted from the Berlin Electron Beam Ion Trap for investigations of charge exchange with a gas target. The classical over-the-barrier model for slow highly charged ions describes this process, whereby one or more electrons are captured from the target into Rydberg states of the ion. The excited state relaxes via a radiative cascade of the electron to ground energy. The cascade spectra are characteristic of the capture state. We investigate x-ray photons emitted as a result of interactions between Ar{sup 17+} ions at energies {<=}5q keV with Ar atoms. Of particular interest is the velocity dependencemore » of the angular momentum capture state l{sub c}.« less

A classical density functional theory for the asymmetric restricted primitive model of ionic liquids

NASA Astrophysics Data System (ADS)

Lu, Hongduo; Nordholm, Sture; Woodward, Clifford E.; Forsman, Jan

2018-05-01

A new three-parameter (valency, ion size, and charge asymmetry) model, the asymmetric restricted primitive model (ARPM) of ionic liquids, has recently been proposed. Given that ionic liquids generally are composed of monovalent species, the ARPM effectively reduces to a two-parameter model. Monte Carlo (MC) simulations have demonstrated that the ARPM is able to reproduce key properties of room temperature ionic liquids (RTILs) in bulk and at charged surfaces. The relatively modest complexity of the model raises the possibility, which is explored here, that a classical density functional theory (DFT) could resolve its properties. This is relevant because it might generate great improvements in terms of both numerical efficiency and understanding in the continued research of RTILs and their applications. In this report, a DFT for rod-like molecules is proposed as an approximate theoretical tool for an ARPM fluid. Borrowing data on the ion pair fraction from a single bulk simulation, the ARPM is modelled as a mixture of dissociated ions and connected ion pairs. We have specifically studied an ARPM where the hard-sphere diameter is 5 Å, with the charge located 1 Å from the hard-sphere centre. We focus on fluid structure and electrochemical behaviour of this ARPM fluid, into which a model electrode is immersed. The latter is modelled as a perfect conductor, and surface polarization is handled by the method of image charges. Approximate methods, which were developed in an earlier study, to take image interactions into account, are also incorporated in the DFT. We make direct numerical comparisons between DFT predictions and corresponding simulation data. The DFT theory is implemented both in the normal mean field form with respect to the electrostatic interactions and in a correlated form based on hole formation by both steric repulsions and ion-ion Coulomb interactions. The results clearly show that ion-ion correlations play a very important role in the screening of the charged surfaces by our ARPM ionic liquid. We have studied electrostatic potentials and ion density profiles as well the differential capacitance. The mean-field DFT fails to reproduce these properties, but the inclusion of ion-ion correlation by a simple approximate treatment yields quite reasonable agreement with the corresponding simulation results. An interesting finding is that there appears to be a surface phase transition at relatively low surface charge which is readily explored by DFT, but seen also in the MC simulations at somewhat higher asymmetry.

Fast trimers in a one-dimensional extended Fermi-Hubbard model

NASA Astrophysics Data System (ADS)

Dhar, A.; Törmä, P.; Kinnunen, J. J.

2018-04-01

We consider a one-dimensional two-component extended Fermi-Hubbard model with nearest-neighbor interactions and mass imbalance between the two species. We study the binding energy of trimers, various observables for detecting them, and expansion dynamics. We generalize the definition of the trimer gap to include the formation of different types of clusters originating from nearest-neighbor interactions. Expansion dynamics reveal rapidly propagating trimers, with speeds exceeding doublon propagation in the strongly interacting regime. We present a simple model for understanding this unique feature of the movement of the trimers, and we discuss the potential for experimental realization.

Lateral Structure Formation in Polyelectrolyte Brushes Induced by Multivalent Ions

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

Brettmann, Blair; Pincus, Philip; Tirrell, Matthew

2017-01-13

We provide a theoretical model for the collapse of polyelectrolyte brushes in the presence of multivalent ions, focusing on the formation of lateral inhomogeneties in the collapsed state. Polyelectrolyte brushes are important in a variety of applications, including stabilizing colloidal particles and lubricating surfaces. Many uses rely on the extension of the densely grafted polymer chains from the surface in the extended brush morphology. In the presence Extended Brush of multivalent ions, brushes are significantly shorter than in monovalent ionic solutions, which greatly affects their properties. We base our theoretical analysis on an analogous collapse of polyelectrolyte brushes in amore » poor solvent, providing an energy balance representation for pinned micelles and cylindrical bundles. The equilibrium brush heights predicted for these structures are of a similar magnitude to those measured experimentally. The formation of lateral structures can open new avenues for stimuli-responsive applications that rely on nanoscale pattern formation on surfaces.« less

Predicting Electrostatic Forces in RNA Folding

PubMed Central

Tan, Zhi-Jie; Chen, Shi-Jie

2016-01-01

Metal ion-mediated electrostatic interactions are critical to RNA folding. Although considerable progress has been made in mechanistic studies, the problem of accurate predictions for the ion effects in RNA folding remains unsolved, mainly due to the complexity of several potentially important issues such as ion correlation and dehydration effects. In this chapter, after giving a brief overview of the experimental findings and theoretical approaches, we focus on a recently developed new model, the tightly bound ion (TBI) model, for ion electrostatics in RNA folding. The model is unique because it can treat ion correlation and fluctuation effects for realistic RNA 3D structures. For monovalent ion (such as Na+) solutions, where ion correlation is weak, TBI and the Poisson–Boltzmann (PB) theory give the same results and the results agree with the experimental data. For multivalent ion (such as Mg2+) solutions, where ion correlation can be strong, however, TBI gives much improved predictions than the PB. Moreover, the model suggests an ion correlation- induced mechanism for the unusual efficiency of Mg2+ ions in the stabilization of RNA tertiary folds. In this chapter, after introducing the theoretical framework of the TBI model, we will describe how to apply the model to predict ion-binding properties and ion-dependent folding stabilities. PMID:20946803

Molecular Dynamics Simulations of Ion Transport and Mechanisms in Polymer Nanocomposites

NASA Astrophysics Data System (ADS)

Mogurampelly, Santosh; Ganesan, Venkat

2015-03-01

Using all atom molecular dynamics and trajectory-extending kinetic Monte Carlo simulations, we study the influence of Al2O3 nanoparticles on the transport properties of Li+ ions in polymer electrolytes consisting of polyethylene oxide (PEO) melt solvated with LiBF4 salt. We observe that the nanoparticles have a strong influence on polymer segmental dynamics which in turn correlates with the mobility of Li+ ions. Explicitly, polymer segmental relaxation times and Li+ ion residence times around polymer were found to increase with the addition of nanoparticles. We also observe that increasing short range repulsive interactions between nanoparticles and polymer membrane leads to increasing polymer dynamics and ion mobility. Overall, our simulation results suggest that nanoparticle induced changes in conformational and dynamic properties of the polymer influences the ion mobilities in polymer electrolytes and suggests possible directions for using such findings to improve the polymer matrix conductivity. The authors acknowledge the Texas Advanced Computing Center (TACC) at The University of Texas at Austin for providing computing resources that have contributed to the research.

Modelling the biologic effect of ions with the Local Effect Model

NASA Astrophysics Data System (ADS)

Friedrich, Thomas; Elsässer, Thilo; Durante, Marco; Scholz, Michael

In many cases in radiobiological experiments as well as in ion beam therapy the Local Effect Model (LEM) has proven to be capable to describe the biologic effect of ion irradiation based on the response to X-rays. During the last years, the LEM has been extended to include important processes such as the diffusion of free radicals or the biologic effect enhancement due to clustered lesions of the DNA in a more mechanistic fashion. In its current status the predictive power of the LEM covers a wide range of ions with good quantitative precision. Hence there is potential to also apply the LEM to problems in radiation protection. In this talk, the development stages of the LEM are illustrated. Emphasis is put on the most recent version of the LEM, where spatial distributions of DNA lesions are considered. Applicability, limits and strategies for an advanced model testing are discussed. Finally, planned extensions and applications of the LEM are presented.

Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na+ Ion Release

PubMed Central

Koldsø, Heidi; Noer, Pernille; Grouleff, Julie; Autzen, Henriette Elisabeth; Sinning, Steffen; Schiøtt, Birgit

2011-01-01

Monoamine transporters are responsible for termination of synaptic signaling and are involved in depression, control of appetite, and anxiety amongst other neurological processes. Despite extensive efforts, the structures of the monoamine transporters and the transport mechanism of ions and substrates are still largely unknown. Structural knowledge of the human serotonin transporter (hSERT) is much awaited for understanding the mechanistic details of substrate translocation and binding of antidepressants and drugs of abuse. The publication of the crystal structure of the homologous leucine transporter has resulted in homology models of the monoamine transporters. Here we present extended molecular dynamics simulations of an experimentally supported homology model of hSERT with and without the natural substrate yielding a total of more than 1.5 µs of simulation of the protein dimer. The simulations reveal a transition of hSERT from an outward-facing occluded conformation to an inward-facing conformation in a one-substrate-bound state. Simulations with a second substrate in the proposed symport effector site did not lead to conformational changes associated with translocation. The central substrate binding site becomes fully exposed to the cytoplasm leaving both the Na+-ion in the Na2-site and the substrate in direct contact with the cytoplasm through water interactions. The simulations reveal how sodium is released and show indications of early events of substrate transport. The notion that ion dissociation from the Na2-site drives translocation is supported by experimental studies of a Na2-site mutant. Transmembrane helices (TMs) 1 and 6 are identified as the helices involved in the largest movements during transport. PMID:22046120

Laboratory Simulations of the Solar Wind's Effect on Surface Interactions and Plasma Wakes

NASA Astrophysics Data System (ADS)

Munsat, T. L.; Ulibarri, Z.; Han, J.; Horanyi, M.; Wang, X.; Yeo, L. H.

2016-12-01

The Colorado Solar Wind Experiment (CSWE) is a new device constructed at the Institute for Modeling Plasma, Atmospheres, and Cosmic Dust (IMPACT) at the University of Colorado. This large ion source is being developed for studies of the interaction of solar wind plasma with planetary surfaces and cosmic dust, and for the investigation of plasma wake physics. With a plasma beam diameter of 12 cm at the source, ion energies of up to 1 keV, and ion flows of up to 1 mA/cm^2, a large cross-section Kaufman Ion Source is used to create steady state plasma flow to model the solar wind in an experimental vacuum chamber. Chamber pressure can be reduced to 3x10^-5 Torr under operating conditions to suppress ion-neutral collisions and create a uniform ion velocity distribution. Diagnostic instruments such as a double Langmuir probe and an ion energy analyzer are mounted on a two-dimensional translation stage that allow the beam to be characterized throughout the chamber. Initial experimental results and technical details of the device will be explained.

A coarse-grained DNA model for the prediction of current signals in DNA translocation experiments

NASA Astrophysics Data System (ADS)

Weik, Florian; Kesselheim, Stefan; Holm, Christian

2016-11-01

We present an implicit solvent coarse-grained double-stranded DNA (dsDNA) model confined to an infinite cylindrical pore that reproduces the experimentally observed current modulations of a KaCl solution at various concentrations. Our model extends previous coarse-grained and mean-field approaches by incorporating a position dependent friction term on the ions, which Kesselheim et al. [Phys. Rev. Lett. 112, 018101 (2014)] identified as an essential ingredient to correctly reproduce the experimental data of Smeets et al. [Nano Lett. 6, 89 (2006)]. Our approach reduces the computational effort by orders of magnitude compared with all-atom simulations and serves as a promising starting point for modeling the entire translocation process of dsDNA. We achieve a consistent description of the system's electrokinetics by using explicitly parameterized ions, a friction term between the DNA beads and the ions, and a lattice-Boltzmann model for the solvent.

Dark matter and color octets beyond the Standard Model

NASA Astrophysics Data System (ADS)

Krnjaic, Gordan Z.

Although the Standard Model (SM) of particles and interactions has survived forty years of experimental tests, it does not provide a complete description of nature. From cosmological and astrophysical observations, it is now clear that the majority of matter in the universe is not baryonic and interacts very weakly (if at all) via non-gravitational forces. The SM does not provide a dark matter candidate, so new particles must be introduced. Furthermore, recent Tevatron results suggest that SM predictions for benchmark collider observables are in tension with experimental observations. In this thesis, we will propose extensions to the SM that address each of these issues. Although there is abundant indirect evidence for the existence of dark matter, terrestrial efforts to observe its interactions have yielded conflicting results. We address this situation with a simple model of dark matter that features hydrogen-like bound states that scatter off SM nuclei by undergoing inelastic hyperfine transitions. We explore the available parameter space that results from demanding that DM self-interactions satisfy experimental bounds and ameliorate the tension between positive and null signals at the DAMA and CDMS experiments respectively. However, this simple model does not explain the cosmological abundance of dark matter and also encounters a Landau pole at a low energy scale. We, therefore, extend the field content and gauge group of the dark sector to resolve these issues with a renormalizable UV completion. We also explore the galactic dynamics of unbound dark matter and find that "dark ions" settle into a diffuse isothermal halo that differs from that of the bound states. This suppresses the local dark-ion density and expands the model's viable parameter space. We also consider the > 3σ excess in W plus dijet events recently observed at the Tevatron collider. We show that decays of a color-octet, electroweak-triplet scalar particle ("octo-triplet") can yield the requisite final state to explain the data. We also find that octotriplets can induce mixing in the B - B¯ system and may give rise to additional CP violation. The model makes concrete predictions for several final states accessible at the LHC, so it can promptly be discovered or falsified. Finally we address the anomalous top forward-backward asymmetry observed the Tevatron. We find that a spin-1 color octet particle with flavor blind axial interactions can explain this anomaly if the mass is in the 50 - 90 GeV range. We explore the multitude of experimental constrains in this mass window and present the viable parameter space as a function of the axigluon mass and coupling constant.

Multisite adsorption of cadmium on goethite

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

Venema, P.; Hiemstra, T.; Riemsdijk, W.H. van

1996-11-10

Recently a new general ion adsorption model has been developed for ion binding to mineral surfaces (Hiemstra and van Riemsdijk, 1996). The model uses the Pauling concept of charge distribution (CD) and is an extension of the multi-site complexation (MUSIC) approach. In the CD-MUSIC model the charge of an adsorbing ion that forms an inner sphere complex is distributed over its ligands, which are present in two different electrostatic planes. In this paper the authors have applied the CD-MUSIC model to the adsorption of metal cations, using an extended data set for cadmium adsorbing on goethite. The adsorption of cadmiummore » and the cadmium-proton exchange ratio were measured as function of metal ion concentration, pH, and ionic strength. The data could be described well, taking into account the surface heterogeneity resulting from the presence of two different crystal planes (the dominant 110 face and the minor 021 face). The surface species used in the model are consistent with recent EXAFS data. In accordance with the EXAFS results, high-affinity complexes at the 021 face were used in the model.« less

The lanthanide contraction beyond coordination chemistry

DOE PAGES

Ferru, Geoffroy; Reinhart, Benjamin; Bera, Mrinal K.; ...

2016-04-06

Lanthanide chemistry is dominated by the ‘lanthanide contraction’, which is conceptualized traditionally through coordination chemistry. Here we break this mold, presenting evidence that the lanthanide contraction manifests outside of the coordination sphere, influencing weak interactions between groups of molecules that drive mesoscale-assembly and emergent behavior in an amphiphile solution. Furthermore, changes in these weak interactions correlate with differences in lanthanide ion transport properties, suggesting new forces to leverage rare earth separation and refining. Our results show that the lanthanide contraction paradigm extends beyond the coordination sphere, influencing structure and properties usually associated with soft matter science.

The lanthanide contraction beyond coordination chemistry

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

Ferru, Geoffroy; Reinhart, Benjamin; Bera, Mrinal K.

Lanthanide chemistry is dominated by the ‘lanthanide contraction’, which is conceptualized traditionally through coordination chemistry. Here we break this mold, presenting evidence that the lanthanide contraction manifests outside of the coordination sphere, influencing weak interactions between groups of molecules that drive mesoscale-assembly and emergent behavior in an amphiphile solution. Furthermore, changes in these weak interactions correlate with differences in lanthanide ion transport properties, suggesting new forces to leverage rare earth separation and refining. Our results show that the lanthanide contraction paradigm extends beyond the coordination sphere, influencing structure and properties usually associated with soft matter science.

Considering ionic state in modeling sorption of pharmaceuticals to sewage sludge.

PubMed

Rybacka, Aleksandra; Andersson, Patrik L

2016-12-01

Information on the partitioning of chemicals between particulate matter and water in sewage treatment plants (STPs) can be used to predict their subsequent environmental fate. However, this information can be challenging to acquire, especially for pharmaceuticals that are frequently present in ionized forms. This study investigated the relationship between the ionization state of active pharmaceutical ingredients (APIs) and their partitioning between water and sludge in STPs. We also investigated the underlying mechanisms of sludge sorption by using chemical descriptors based on ionized structures, and evaluated the usefulness of these descriptors in quantitative structure-property relationship (QSPR) modeling. K D values were collected for 110 APIs, which were classified as neutral, positive, or negative at pH 7. The models with the highest performance had the R 2 Y and Q 2 values of above 0.75 and 0.65, respectively. We found that the dominant intermolecular forces governing the interactions of neutral and positively charged APIs with sludge are hydrophobic, pi-pi, and dipole-dipole interactions, whereas the interactions of negatively charged APIs with sludge were mainly governed by covalent bonding as well as ion-ion, ion-dipole, and dipole-dipole interactions; hydrophobicity-driven interactions were rather unimportant. Including charge-related descriptors improved the models' performance by 5-10%, underlining the importance of electrostatic interactions. The use of descriptors calculated for ionized structures did not improve the model statistics for positive and negative APIs, but slightly increased model performance for neutral APIs. We attribute this to a better description of neutral zwitterions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nuclear fragmentation of GCR-like ions: comparisons between data and PHITS

NASA Astrophysics Data System (ADS)

Zeitlin, Cary; Guetersloh, Stephen; Heilbronn, Lawrence; Miller, Jack; Sihver, Lembit; Mancusi, Davide; Fukumura, Aki; Iwata, Yoshi; Murakami, Takeshi

We present a summary of results from recent work in which we have compared nuclear fragmentation cross section data to predictions of the PHITS Monte Carlo simulation. The studies used beams of 12 C, 35 Cl, 40 Ar, 48 Ti, and 56 Fe at energies ranging from 290 MeV/nucleon to 1000 MeV/nucleon. Some of the data were obtained at the Brookhaven National Laboratory, others at the National Institute of Radiological Sciences in Japan. These energies and ion species are representative of the heavy ion component of the Galactic Cosmic Rays (GCR), which contribute significantly to the dose and dose equivalent that will be received by astronauts on deep-space missions. A critical need for NASA is the ability to accurately model the transport of GCR heavy ions through matter, including spacecraft walls, equipment racks, and other shielding materials, as well as through tissue. Nuclear interaction cross sections are of primary importance in the GCR transport problem. These interactions generally cause the incoming ion to break up (fragment) into one or more lighter ions, which continue approximately along the initial trajectory and with approximately the same velocity the incoming ion had prior to the interaction. Since the radiation dose delivered by a particle is proportional to the square of the quantity (charge/velocity), i.e., to (Z/β)2 , fragmentation reduces the dose (and, typically, dose equivalent) delivered by incident ions. The other mechanism by which dose can be reduced is ionization energy loss, which can lead to some particles stopping in the shielding. This is the conventional notion of shielding, but it is not applicable to human spaceflight, since the particles in the GCR tend to be highly energetic and because shielding must be relatively thin in order to keep overall mass as low as possible, keeping launch costs within reason. To support these goals, our group has systematically measured a large number of nuclear cross sections, intended to be used as either input to, or validation of, NASA transport models. A database containing over 200 charge-changing cross sections, and over 2000 fragment production cross sections, is nearing completion, with most results available online. In the past year, we have been investigating the PHITS (Particle and Heavy Ion Transport System) model of Niita et al. For purposes of modeling nuclear interactions, PHITS combines the Jet AA Microscopic Transport Model (JAM) hadron cascade model, the Jaeri Quantum Molecular Dynamics (JQMD) model, and the Generalized Evaporation Model (GEM). We will present detailed comparisons of our data to the cross sections and fragment angular distributions that arise from this model. The model contains some significant deficiencies, but, as we will show, also represents a significant advance over older, simpler models of fragmentation. 504b030414000600080000002100828abc13fa0000001c020000130000005b436f6e74656e745f54797065735d2e78

Can the vector space model be used to identify biological entity activities?

PubMed Central

2011-01-01

Background Biological systems are commonly described as networks of entity interactions. Some interactions are already known and integrate the current knowledge in life sciences. Others remain unknown for long periods of time and are frequently discovered by chance. In this work we present a model to predict these unknown interactions from a textual collection using the vector space model (VSM), a well known and established information retrieval model. We have extended the VSM ability to retrieve information using a transitive closure approach. Our objective is to use the VSM to identify the known interactions from the literature and construct a network. Based on interactions established in the network our model applies the transitive closure in order to predict and rank new interactions. Results We have tested and validated our model using a collection of patent claims issued from 1976 to 2005. From 266,528 possible interactions in our network, the model identified 1,027 known interactions and predicted 3,195 new interactions. Iterating the model according to patent issue dates, interactions found in a given past year were often confirmed by patent claims not in the collection and issued in more recent years. Most confirmation patent claims were found at the top 100 new interactions obtained from each subnetwork. We have also found papers on the Web which confirm new inferred interactions. For instance, the best new interaction inferred by our model relates the interaction between the adrenaline neurotransmitter and the androgen receptor gene. We have found a paper that reports the partial dependence of the antiapoptotic effect of adrenaline on androgen receptor. Conclusions The VSM extended with a transitive closure approach provides a good way to identify biological interactions from textual collections. Specifically for the context of literature-based discovery, the extended VSM contributes to identify and rank relevant new interactions even if these interactions occcur in only a few documents in the collection. Consequently, we have developed an efficient method for extracting and restricting the best potential results to consider as new advances in life sciences, even when indications of these results are not easily observed from a mass of documents. PMID:22369514

Atmospheric, Ionospheric, and Energetic Radiation Environments of Saturn's Rings

NASA Astrophysics Data System (ADS)

Cooper, J. F.; Kollmann, P.; Sittler, E. C., Jr.; Johnson, R. E.; Sturner, S. J.

2015-12-01

Planetary magnetospheric and high-energy cosmic ray interactions with Saturn's rings were first explored in-situ during the Pioneer 11 flyby in 1979. The following Voyager flybys produced a wealth of new information on ring structure and mass, and on spatial structure of the radiation belts beyond the main rings. Next came the Cassini Orbiter flyover of the rings during Saturn Orbital Insertion in 2004 with the first in-situ measurements of the ring atmosphere and plasma ionosphere. Cassini has since fully explored the radiation belt and magnetospheric plasma region beyond the main rings, discovering how Enceladus acts as a source of water group neutrals and water ions for the ion plasma. But do the main rings also substantially contribute by UV photolysis to water group plasma (H+, O+, OH+, H2O+, H3O+, O2+) and neutrals inwards from Enceladus? More massive rings, than earlier inferred from Pioneer 11 and Voyager observations, would further contribute by bulk ring ice radiolysis from interactions of galactic cosmic ray particles. Products of these interactions include neutron-decay proton and electron injection into the radiation belts beyond the main rings. How does radiolysis from moon and ring sweeping of the radiation belt particles compare with direct gas and plasma sources from the main rings and Enceladus? Can the magnetospheric ion and electron populations reasonably be accounted for by the sum of the ring-neutron-decay and outer magnetospheric inputs? Pioneer 11 made the deepest radial penetration into the C-ring, next followed by Cassini SOI. What might Cassini's higher-inclination proximal orbits reveal about the atmospheric, ionospheric, and energetic radiation environments in the D-ring and the proximal gap region? Recent modeling predicts a lower-intensity innermost radiation belt extending from the gap to the inner D-ring. Other remaining questions include the lifetimes of narrow and diffuse dust rings with respect to plasma and energetic particle irradiation processes, the mass flux of water group ions along planetary magnetic field lines into the Saturn planetary atmosphere, seasonal dust charging dynamics of the now-reappeared Saturn ring spokes, and the exchange of energy via energetic neutral atoms between the outer magnetosphere and the rings.

Charging and Heating Dynamics of Nanoparticles in Nonthermal Plasmas

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

Kortshagen, Uwe R.

2014-08-15

The focus of this award was to understand the interactions of nanometer-sized particles with ionized gases, also called plasmas. Plasmas are widely used in the fabrication of electronic circuits such as microprocessors and memory devices, in plasma display panels, as well as in medical applications. Recently, these ionized gases are finding applications in the synthesis of advanced nanomaterials with novel properties, which are based on nanometer-sized particulate (nanoparticles) building blocks. As these nanoparticles grow in the plasma environment, they interact with the plasmas species such as electrons and ions which critically determines the nanoparticle properties. The University of Minnesota researchersmore » conducting this project performed numerical simulations and developed analytical models that described the interaction of plasma-bound nanoparticles with the plasma ions. The plasma ions bombard the nanoparticle surface with substantial energy, which can result in the rearrangement of the nanoparticles’ atoms, giving them often desirable structures at the atomic scale. Being able to tune the ion energies allows to control the properties of nanoparticles produced in order to tailor their attributes for certain applications. For instance, when used in high efficiency light emitting devices, nanoparticles produced under high fluxes of highly energetic ions may show superior light emission to particles produced under low fluxes of less energetic ions. The analytical models developed by the University of Minnesota researchers enable the research community to easily determine the energy of ions bombarding the nanoparticles. The researchers extensively tested the validity of the analytical models by comparing them to sophisticated computer simulations based on stochastic particle modeling, also called Monte Carlo modeling, which simulated the motion of hundreds of thousands of ions and their interaction with the nanoparticle surfaces. Beyond the scientific intellectual merits, this award had significant broader impacts. Two graduate students received their doctoral degrees and both have joined a U.S. manufacturer of plasma-based semiconductor processing equipment. Four undergraduate students participated in research conducted under this grant and gained valuable hands-on laboratory experience. A middle school science teacher observed research conducted under this grant and developed three new course modules that introduce middle school students to the concepts of nanometer scale, the atomic structure of matter, and the composition of matter of different chemical elements.« less

Long Duration Gamma-Ray Flares & Solar Energetic Particles — Is there a Connection?

NASA Astrophysics Data System (ADS)

de Nolfo, G. A.; Boezio, M.; Bruno, A.; Christian, E. R.; Martucci, M.; Mergè, M.; Munini, R.; Ricci, M.; Ryan, J. M.; Share, G.; Stochaj, S.

2017-12-01

Little is known still about the origin of the high-energy and sustained emission from Long Duration Gamma-Ray Flares (LDGRFs), identified with Compton Gamma-Ray Observatory (CGRO), the Solar Maximum Mission (SMM), and now Fermi. Though Fermi/LAT has identified dozens of flares with LDGRF emission, the nature of this emission has been a challenge to explain both due to the extreme energies and long durations. The highest energy emission has generally been attributed to pion production from the interaction of high-energy protons with the ambient matter, suggesting that particle acceleration occurs over large volumes extending high in the corona, either from stochastic acceleration within large coronal loops or from back precipitation from CME-driven shocks. It is possible to test these models by making direct comparisons between the accelerated ion population at the flare derived from the observations of Fermi/LAT with PAMELA measurements of solar energetic particles in the energy range corresponding to the pion-related emission observed with Fermi. For nearly a dozen SEP events, we compare the two populations (SEPs in space and the interacting population at the Sun) and discuss the implications in terms of particle acceleration and transport models.

Comparison of Global Martian Plasma Models in the Context of MAVEN Observations

NASA Astrophysics Data System (ADS)

Egan, Hilary; Ma, Yingjuan; Dong, Chuanfei; Modolo, Ronan; Jarvinen, Riku; Bougher, Stephen; Halekas, Jasper; Brain, David; Mcfadden, James; Connerney, John; Mitchell, David; Jakosky, Bruce

2018-05-01

Global models of the interaction of the solar wind with the Martian upper atmosphere have proved to be valuable tools for investigating both the escape to space of the Martian atmosphere and the physical processes controlling this complex interaction. The many models currently in use employ different physical assumptions, but it can be difficult to directly compare the effectiveness of the models since they are rarely run for the same input conditions. Here we present the results of a model comparison activity, where five global models (single-fluid MHD, multifluid MHD, multifluid electron pressure MHD, and two hybrid models) were run for identical conditions corresponding to a single orbit of observations from the Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft. We find that low-altitude ion densities are very similar across all models and are comparable to MAVEN ion density measurements from periapsis. Plasma boundaries appear generally symmetric in all models and vary only slightly in extent. Despite these similarities there are clear morphological differences in ion behavior in other regions such as the tail and southern hemisphere. These differences are observable in ion escape loss maps and are necessary to understand in order to accurately use models in aiding our understanding of the Martian plasma environment.

Collisions of energetic particles with atoms, molecules & solids: A theoretical study

NASA Astrophysics Data System (ADS)

Quashie, Edwin Exam

The detailed knowledge of the accurate ion-solid interaction is at the heart of many technological applications such as nuclear safety, applied material science, medical physics and fusion and fission applications. Its accurate evaluation poses an enormous challenge due to the need of incorporating electronic structure, bound states, size effects, basis sets, and the quantum classical aspects of the problem. Most recent approaches relying on the fitting to experimental data or phenomenological model, fail to describe the ion-solid interaction properly (see [S. N. Markin, D. Primetzhofer, M. Spitz, and P. Bauer, Phys. Rev. B 80 (2009)]) for slow ions. A general Time-Dependent Density Functional Theory (TDDFT) is used in this thesis to evaluate electron-dynamics easily. For the first time a unified theory is proposed to describe the ion-solid interaction accurately over several orders of magnitude in the ion velocities, unveiling different regimes that before were only partially seen by separate experiments and rarely by any level of existing theory. We identified an electronic stopping which in the band-regime produces a quantum friction that is nonlinear with a power-law with an exponent ˜1.5. At low velocity this nonlinear effect will provide a new impetus for experimental investigations and an improve microscopic models of electron-ion dissipative dynamics. Our study will potentially impact both the experimental and theoretical research in condensed matter. We have applied our developed theory to study stopping of H+ in Cu. The target Cu comprises complicated band structure and this system will help to understand radiation of matter, both in its experimental understanding and also in the modeling of the process, for example in the context of damped molecular dynamics for the simulation of radiation cascades. At this present stage in the field of ion-solid interactions and quantum dissipative dynamics, our findings remain very significant. The same techniques are used in studying the ion-molecule interactions at lower ion velocities. We reported here H+ + CH4 collision dynamics at E = 30 eV. Different exchange-correlation (XC) approximations were implemented and their important roles are studied systematically. For a single orientation of CH4 our rainbow angle at E = 30 eV agrees well with experimental and other theoretical values.

Dramatic pressure-sensitive ion conduction in conical nanopores.

PubMed

Jubin, Laetitia; Poggioli, Anthony; Siria, Alessandro; Bocquet, Lydéric

2018-04-17

Ion transporters in Nature exhibit a wealth of complex transport properties such as voltage gating, activation, and mechanosensitive behavior. When combined, such processes result in advanced ionic machines achieving active ion transport, high selectivity, or signal processing. On the artificial side, there has been much recent progress in the design and study of transport in ionic channels, but mimicking the advanced functionalities of ion transporters remains as yet out of reach. A prerequisite is the development of ionic responses sensitive to external stimuli. In the present work, we report a counterintuitive and highly nonlinear coupling between electric and pressure-driven transport in a conical nanopore, manifesting as a strong pressure dependence of the ionic conductance. This result is at odds with standard linear response theory and is akin to a mechanical transistor functionality. We fully rationalize this behavior on the basis of the coupled electrohydrodynamics in the conical pore by extending the Poisson-Nernst-Planck-Stokes framework. The model is shown to capture the subtle mechanical balance occurring within an extended spatially charged zone in the nanopore. The pronounced sensitivity to mechanical forcing offers leads in tuning ion transport by mechanical stimuli. The results presented here provide a promising avenue for the design of tailored membrane functionalities.

Transport coefficients of a hot QCD medium and their relative significance in heavy-ion collisions

NASA Astrophysics Data System (ADS)

Mitra, Sukanya; Chandra, Vinod

2017-11-01

The main focus of this article is to obtain various transport coefficients for a hot QCD medium that is likely to be produced while colliding two heavy nuclei ultra-relativistically. The technical approach adopted here is the semiclassical transport theory. The away-from-equilibrium linearized transport equation has been set up by employing the Chapman-Enskog technique from the kinetic theory of a many-particle system with a collision term that includes the binary collisions of quarks/antiquarks and gluons. In order to include the effects of a strongly interacting, thermal medium, a quasi-particle description of a realistic hot QCD equation of state has been employed through the equilibrium modeling of the momentum distributions of gluons and quarks with nontrivial dispersion relations while extending the model for finite but small quark chemical potential. The effective coupling for strong interaction has been redefined following the charge renormalization under the scheme of the quasi-particle model. The consolidated effects on transport coefficients are seen to have a significant impact on their temperature dependence. Finally, the relative significances of momentum and heat transfer, as well as the charge diffusion processes in hot QCD, have been investigated by studying the ratios of the respective transport coefficients indicating different physical laws.

Charge exchange, ENAs and the loss of planetary ions at Mars

NASA Astrophysics Data System (ADS)

Kallio, E.; Janhunen, P.; Säles, T.

Neither Mars nor Venus has a strong global intrinsic magnetic field and therefore the solar wind can flow close to the planets in high neutral density regions. Because of the formed direct interaction between the atmosphere/exosphere and the solar wind, the ionized atmospheric neutrals can be picked up by the solar wind. Charge exchange between solar wind protons and planetary neutrals, instead, produce energetic neutral hydrogen atoms (H-ENA) which are the manifestation of the direct interaction between the solar wind and planetary neutrals. Picked-up planetary O+ ions in turn form energetic neutral oxygen atoms (O-ENA) via charge exchange process. The ion escape, H-ENAs, O-ENAs and electrons will be investigated at Mars and Venus by two identical instruments: ASPERA-3 on MarsExpress (measurements started in Jan. 2004) and ASPERA-4 on VenusExpress (2006). We present a self-consistent, three-dimensional quasi-neutral hybrid (ions are particles, electrons a fluid) simulation to study Mars/Venus-solar wind interaction in general and ASPERA-3/4 measurements in particular. Our model includes three ion species (H+, O+, O2+), and contains charge exchange, ion-neutral and chemical reactions. We show results of quasi-neutral hybrid model runs that we have used to study the escape of planetary ions, the effects of planetary ions on the Martian plasma environment and the production and properties of fast hydrogen(H) and oxygen(O) ENAs near Mars. We also compare these hydrogen ENA images with the hydrogen ENA images that has been derived from an empirical flow model by line-of-sight integration. The advantage of the analytical gas dynamic like flow model is that it is computationally so fast that it provides a possibility to perform an ENA inversion, that is, to derive global plasma parameters from the measured ENA image.

Numerical Solution of the Extended Nernst-Planck Model.

PubMed

Samson; Marchand

1999-07-01

The main features of a numerical model aiming at predicting the drift of ions in an electrolytic solution upon a chemical potential gradient are presented. The mechanisms of ionic diffusion are described by solving the extended Nernst-Planck system of equations. The electrical coupling between the various ionic fluxes is accounted for by the Poisson equation. Furthermore, chemical activity effects are considered in the model. The whole system of nonlinear equations is solved using the finite-element method. Results yielded by the model for simple test cases are compared to those obtained using an analytical solution. Applications of the model to more complex problems are also presented and discussed. Copyright 1999 Academic Press.

Water-mediated ion-ion interactions are enhanced at the water vapor-liquid interface.

PubMed

Venkateshwaran, Vasudevan; Vembanur, Srivathsan; Garde, Shekhar

2014-06-17

There is overwhelming evidence that ions are present near the vapor-liquid interface of aqueous salt solutions. Charged groups can also be driven to interfaces by attaching them to hydrophobic moieties. Despite their importance in many self-assembly phenomena, how ion-ion interactions are affected by interfaces is not understood. We use molecular simulations to show that the effective forces between small ions change character dramatically near the water vapor-liquid interface. Specifically, the water-mediated attraction between oppositely charged ions is enhanced relative to that in bulk water. Further, the repulsion between like-charged ions is weaker than that expected from a continuum dielectric description and can even become attractive as the ions are drawn to the vapor side. We show that thermodynamics of ion association are governed by a delicate balance of ion hydration, interfacial tension, and restriction of capillary fluctuations at the interface, leading to nonintuitive phenomena, such as water-mediated like charge attraction. "Sticky" electrostatic interactions may have important consequences on biomolecular structure, assembly, and aggregation at soft liquid interfaces. We demonstrate this by studying an interfacially active model peptide that changes its structure from α-helical to a hairpin-turn-like one in response to charging of its ends.

Additive effects of electronic and nuclear energy losses in irradiation-induced amorphization of zircon

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

Zarkadoula, Eva; Toulemonde, Marcel; Weber, William J.

2015-12-28

We used a combination of ion cascades and the unified thermal spike model to study the electronic effects from 800 keV Kr and Xe ion irradiation in zircon. We compared the damage production for four cases: (a) due to ion cascades alone, (b) due to ion cascades with the electronic energy loss activated as a friction term, (c) due to the thermal spike from the combined electronic and nuclear energy losses, and (d) due to ion cascades with electronic stopping and the electron-phonon interactions superimposed. We found that taking the electronic energy loss out as a friction term results in reducedmore » damage, while the electronic electron-phonon interactions have additive impact on the final damage created per ion.« less

Additive effects of electronic and nuclear energy loss in irradiation-induced amorphization of zircon

DOE PAGES

Zarkadoula, Eva; Toulemonde, Marcel; Weber, William J.

2015-12-29

We used a combination of ion cascades and the unified thermal spike model to study the electronic effects from 800 keV Kr and Xe ion irradiation in zircon. We compared the damage production for four cases: (a) due to ion cascades alone, (b) due to ion cascades with the electronic energy loss activated as a friction term, (c) due to the thermal spike from the combined electronic and nuclear energy losses, and (d) due to ion cascades with electronic stopping and the electron-phonon interactions superimposed. As a result, we found that taking the electronic energy loss out as a frictionmore » term results in reduced damage, while the electronic electron-phonon interactions have additive impact on the final damage created per ion.« less

Soft Wall Ion Channel in Continuum Representation with Application to Modeling Ion Currents in α-Hemolysin

PubMed Central

Simakov, Nikolay A.

2010-01-01

A soft repulsion (SR) model of short range interactions between mobile ions and protein atoms is introduced in the framework of continuum representation of the protein and solvent. The Poisson-Nernst-Plank (PNP) theory of ion transport through biological channels is modified to incorporate this soft wall protein model. Two sets of SR parameters are introduced: the first is parameterized for all essential amino acid residues using all atom molecular dynamic simulations; the second is a truncated Lennard – Jones potential. We have further designed an energy based algorithm for the determination of the ion accessible volume, which is appropriate for a particular system discretization. The effects of these models of short-range interaction were tested by computing current-voltage characteristics of the α-hemolysin channel. The introduced SR potentials significantly improve prediction of channel selectivity. In addition, we studied the effect of choice of some space-dependent diffusion coefficient distributions on the predicted current-voltage properties. We conclude that the diffusion coefficient distributions largely affect total currents and have little effect on rectifications, selectivity or reversal potential. The PNP-SR algorithm is implemented in a new efficient parallel Poisson, Poisson-Boltzman and PNP equation solver, also incorporated in a graphical molecular modeling package HARLEM. PMID:21028776

Application of retention modelling to the simulation of separation of organic anions in suppressed ion chromatography.

PubMed

Zakaria, Philip; Dicinoski, Greg W; Ng, Boon Khing; Shellie, Robert A; Hanna-Brown, Melissa; Haddad, Paul R

2009-09-18

The ion-exchange separation of organic anions of varying molecular mass has been demonstrated using ion chromatography with isocratic, gradient and multi-step eluent profiles on commercially available columns with UV detection. A retention model derived previously for inorganic ions and based solely on electrostatic interactions between the analytes and the stationary phase was applied. This model was found to accurately describe the observed elution of all the anions under isocratic, gradient and multi-step eluent conditions. Hydrophobic interactions, although likely to be present to varying degrees, did not limit the applicability of the ion-exchange retention model. Various instrumental configurations were investigated to overcome problems associated with the use of organic modifiers in the eluent which caused compatibility issues with the electrolytically derived, and subsequently suppressed, eluent. The preferred configuration allowed the organic modifier stream to bypass the eluent generator, followed by subsequent mixing before entering the injection valve and column. Accurate elution prediction was achieved even when using 5-step eluent profiles with errors in retention time generally being less than 1% relative standard deviation (RSD) and all being less than 5% RSD. Peak widths for linear gradient separations were also modelled and showed good agreement with experimentally determined values.

Ion beam generated modes in the lower hybrid frequency range in a laboratory magnetoplasma

NASA Astrophysics Data System (ADS)

Van Compernolle, B.; Tripathi, S.; Gekelman, W. N.; Colestock, P. L.; Pribyl, P.

2012-12-01

The generation of waves by ion ring distributions is of great importance in many instances in space plasmas. They occur naturally in the magnetosphere through the interaction with substorms, or they can be man-made in ionospheric experiments by photo-ionization of neutral atoms injected perpendicular to the earth's magnetic field. The interaction of a fast ion beam with a low β plasma has been studied in the laboratory. Experiments were performed at the LArge Plasma Device (LAPD) at UCLA. The experiments were done in a Helium plasma (n ≃ 1012 \\ cm-3, B0 = 1000 G - 1800 G, fpe}/f{ce ≃ 1 - 5, Te = 0.25\\ eV, vte ≤ vA). The ion beam \\cite{Tripathi_ionbeam} is a Helium beam with energies ranging from 5 keV to 18 keV. The fast ion velocity is on the order of the Alfvén velocity. The beam is injected from the end of the machine, and spirals down the linear device. Waves were observed below fci in the shear Alfvén wave regime, and in a broad spectrum above fci in the lower hybrid frequency range, the focus of this paper. The wave spectra have distinct peaks close to ion cyclotron harmonics, extending out to the 100th harmonic in some cases. The wave generation was studied for various magnetic fields and background plasma densities, as well as for different beam energies and pitch angles. The waves were measured with 3-axis electric and magnetic probes. Detailed measurements of the perpendicular mode structure will be shown. Langmuir probes were used to measure density and temperature evolution due to the beam-plasma interaction. Retarding field energy analyzers captured the ion beam profiles. The work was performed at the LArge Plasma Device at the Basic Plasma Science Facility (BaPSF) at UCLA, funded by DOE/NSF.

Numerical studies of wall–plasma interactions and ionization phenomena in an ablative pulsed plasma thruster

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

Yang, Lei; School of Astronautics, Beihang University, Beijing 100191; Zeng, Guangshang

2016-07-15

Wall–plasma interactions excited by ablation controlled arcs are very critical physical processes in pulsed plasma thrusters (PPTs). Their effects on the ionization processes of ablated vapor into discharge plasma directly determine PPT performances. To reveal the physics governing the ionization phenomena in PPT discharge, a modified model taking into account the pyrolysis effect of heated polytetrafluoroethylene propellant on the wall–plasma interactions was developed. The feasibility of the modified model was analyzed by creating a one-dimensional simulation of a rectangular ablative PPT. The wall–plasma interaction results based on this modified model were found to be more realistic than for the unmodifiedmore » model; this reflects the dynamic changes of the inflow parameters during discharge in our model. Furthermore, the temporal and spatial variations of the different plasma species in the discharge chamber were numerically studied. The numerical studies showed that polytetrafluoroethylene plasma was mainly composed of monovalent ions; carbon and fluorine ions were concentrated in the upstream and downstream discharge chamber, respectively. The results based on this modified model were in good agreement with the experimental formation times of the various plasma species. A large number of short-lived and highly ionized carbon and fluorine species (divalent and trivalent ions) were created during initial discharge. These highly ionized species reached their peak density earlier than the singly ionized species.« less

A Study of Green's Function Methods Applied to Space Radiation Protection

NASA Technical Reports Server (NTRS)

Heinbockel, John H.

2001-01-01

The purpose of this research was to study the propagation of galactic ions through various materials. Galactic light ions result from the break up of heavy ion particles and their propagation through materials is modeled using the one-dimensional Boltzmann equation. When ions enter materials there can occur (i) the interaction of ions with orbital electrons which causes ionization within the material and (ii) ions collide with atoms causing production of secondary particles which penetrate deeper within the material. These processes are modeled by a continuum model. The basic idea is to place a control volume within the material and examine the change in ion flux across this control volume. In this way on can derive the basic equations for the transport of light and heavy ions in matter. Green's function perturbation methods can then be employed to solve the resulting equations using energy dependent nuclear cross sections.

The structure of mass-loading shocks. [interaction of solar wind with cometary coma or local interstellar medium using two-fluid model

NASA Technical Reports Server (NTRS)

Zank, G. P.; Khabibrakhmanov, I. KH.; Story, T.

1993-01-01

A new two-fluid model which describes mass loading in the solar wind (e.g., the interaction of the solar wind with a cometary coma or the local interstellar medium) is presented. The self-consistent back-reaction of the mass-loaded ions is included through their effective scattering in low-frequency MHD turbulence and the invocation of a diffusive approximation. Such an approximation has the advantage of introducing self-consistent dissipation coefficients into the governing equations, thereby facilitating the investigation of the internal structure of shocks in mass-loading environments. To illustrate the utility of the new model, we consider the structure of cometary shocks in the hypersonic one-dimensional limit, finding that the incoming solar wind is slowed by both mass loading and the development of a large cometary ion pressure gradient. The shock is broadened and smoothed by the cometary ions with a thickness of the order of the cometary ion diffusion scale.

Computer Simulations of Resonant Coherent Excitation of Heavy Hydrogen-Like Ions Under Planar Channeling

NASA Astrophysics Data System (ADS)

Babaev, A. A.; Pivovarov, Yu L.

2010-04-01

Resonant coherent excitation (RCE) of relativistic hydrogen-like ions is investigated by computer simulations methods. The suggested theoretical model is applied to the simulations of recent experiments on RCE of 390 MeV/u Ar17+ ions under (220) planar channeling in a Si crystal performed by T.Azuma et al at HIMAC (Tokyo). Theoretical results are in a good agreement with these experimental data and clearly show the appearance of the doublet structure of RCE peaks. The simulations are also extended to greater ion energies in order to predict the new RCE features at the future accelerator facility FAIR OSI and as an example, RCE of II GeV/u U91+ ions is considered in detail.

2nd-order optical model of the isotopic dependence of heavy ion absorption cross sections for radiation transport studies

NASA Astrophysics Data System (ADS)

Cucinotta, Francis A.; Yan, Congchong; Saganti, Premkumar B.

2018-01-01

Heavy ion absorption cross sections play an important role in radiation transport codes used in risk assessment and for shielding studies of galactic cosmic ray (GCR) exposures. Due to the GCR primary nuclei composition and nuclear fragmentation leading to secondary nuclei heavy ions of charge number, Z with 3 ≤ Z ≥ 28 and mass numbers, A with 6 ≤ A ≥ 60 representing about 190 isotopes occur in GCR transport calculations. In this report we describe methods for developing a data-base of isotopic dependent heavy ion absorption cross sections for interactions. Calculations of a 2nd-order optical model solution to coupled-channel solutions to the Eikonal form of the nucleus-nucleus scattering amplitude are compared to 1st-order optical model solutions. The 2nd-order model takes into account two-body correlations in the projectile and target ground-states, which are ignored in the 1st-order optical model. Parameter free predictions are described using one-body and two-body ground state form factors for the isotopes considered and the free nucleon-nucleon scattering amplitude. Root mean square (RMS) matter radii for protons and neutrons are taken from electron and muon scattering data and nuclear structure models. We report on extensive comparisons to experimental data for energy-dependent absorption cross sections for over 100 isotopes of elements from Li to Fe interacting with carbon and aluminum targets. Agreement between model and experiments are generally within 10% for the 1st-order optical model and improved to less than 5% in the 2nd-order optical model in the majority of comparisons. Overall the 2nd-order optical model leads to a reduction in absorption compared to the 1st-order optical model for heavy ion interactions, which influences estimates of nuclear matter radii.

Recent Results from Phobos

NASA Astrophysics Data System (ADS)

García, Edmundo; Back, B. B.; Baker, M. D.; Ballintijn, M.; Barton, D. S.; Betts, R. R.; Bickley, A. A.; Bindel, R.; Busza, W.; Carroll, A.; Chai, Z.; Decowski, M. P.; García, E.; Gburek, T.; George, N.; Gulbrandsen, K.; Halliwell, C.; Hamblen, J.; Hauer, M.; Henderson, C.; Hofman, D. J.; Hollis, R. S.; Hołyński, R.; Holzman, B.; Iordanova, A.; Johnson, E.; Kane, J. L.; Khan, N.; Kulinich, P.; Kuo, C. M.; Lin, W. T.; Manly, S.; Mignerey, A. C.; Nouicer, R.; Olszewski, A.; Pak, R.; Reed, C.; Roland, C.; Roland, G.; Sagerer, J.; Seals, H.; Sedykh, I.; Smith, C. E.; Stankiewicz, M. A.; Steinberg, P.; Stephans, G. S. F.; Sukhanov, A.; Tonjes, M. B.; Trzupek, A.; Vale, C.; van Nieuwenhuizen, G. J.; Vaurynovich, S. S.; Verdier, R.; Veres, G. I.; Wenger, E.; Wolfs, F. L. H.; Wosiek, B.; Woźniak, K.; Wysłouch, B.

2007-02-01

The PHOBOS detector is one of four heavy ion experiments at the Relativistic Heavy Ion Collider at Brookhaven National Laboratory. In this paper we will review some of the results of PHOBOS from the data collected in p+p, d+Au and Au+Au collisions at nucleon-nucleon center-of-mass energies up to 200 GeV. Evidence is found of the formation of a very high energy density and highly interactive system, which can not be described in terms of hadrons, and has a relatively low baryon density. There is evidence that the system formed is thermalized to a certain degree. Scaling with the number of participants and extended longitudinal scaling behavior are also observed in distributions of produced charged particles.

Laser-driven three-stage heavy-ion acceleration from relativistic laser-plasma interaction.

PubMed

Wang, H Y; Lin, C; Liu, B; Sheng, Z M; Lu, H Y; Ma, W J; Bin, J H; Schreiber, J; He, X T; Chen, J E; Zepf, M; Yan, X Q

2014-01-01

A three-stage heavy ion acceleration scheme for generation of high-energy quasimonoenergetic heavy ion beams is investigated using two-dimensional particle-in-cell simulation and analytical modeling. The scheme is based on the interaction of an intense linearly polarized laser pulse with a compound two-layer target (a front heavy ion layer + a second light ion layer). We identify that, under appropriate conditions, the heavy ions preaccelerated by a two-stage acceleration process in the front layer can be injected into the light ion shock wave in the second layer for a further third-stage acceleration. These injected heavy ions are not influenced by the screening effect from the light ions, and an isolated high-energy heavy ion beam with relatively low-energy spread is thus formed. Two-dimensional particle-in-cell simulations show that ∼100MeV/u quasimonoenergetic Fe24+ beams can be obtained by linearly polarized laser pulses at intensities of 1.1×1021W/cm2.

Rate theory of ion pairing at the water liquid-vapor interface: A case of sodium iodide.

PubMed

Dang, Liem X; Schenter, Gregory K

2018-06-14

Studies on ion pairing at interfaces have been intensified recently because of their importance in many chemical reactive phenomena, such as ion-ion interactions that are affected by interfaces and their influence on kinetic processes. In this study, we performed simulations to examine the thermodynamics and kinetics of small polarizable sodium iodide ions in the bulk and near the water liquid-vapor interface. Using classical transition state theory, we calculated the dissociation rates and corrected them with transmission coefficients obtained from the reactive flux formalism and Grote-Hynes theory. Our results show that in addition to affecting the free energy of ions in solution, the interfacial environments significantly influence the kinetics of ion pairing. The results on the relaxation time obtained using the reactive flux formalism and Grote-Hynes theory present an unequivocal picture that the interface suppresses ion dissociation. The effects of the use of molecular models on the ion interactions as well as the ion-pair configurations at the interface are also quantified and discussed.

Rate theory of ion pairing at the water liquid-vapor interface: A case of sodium iodide

NASA Astrophysics Data System (ADS)

Dang, Liem X.; Schenter, Gregory K.

2018-06-01

Studies on ion pairing at interfaces have been intensified recently because of their importance in many chemical reactive phenomena, such as ion-ion interactions that are affected by interfaces and their influence on kinetic processes. In this study, we performed simulations to examine the thermodynamics and kinetics of small polarizable sodium iodide ions in the bulk and near the water liquid-vapor interface. Using classical transition state theory, we calculated the dissociation rates and corrected them with transmission coefficients obtained from the reactive flux formalism and Grote-Hynes theory. Our results show that in addition to affecting the free energy of ions in solution, the interfacial environments significantly influence the kinetics of ion pairing. The results on the relaxation time obtained using the reactive flux formalism and Grote-Hynes theory present an unequivocal picture that the interface suppresses ion dissociation. The effects of the use of molecular models on the ion interactions as well as the ion-pair configurations at the interface are also quantified and discussed.

Ion exchange of several radionuclides on the hydrous crystalline silicotitanate, UOP IONSIV IE-911

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

Huckman, M.E.; Latheef, I.M.; Anthony, R.G.

1999-04-01

The crystalline silicotitanate, UOP IONSIV IE-911, is a proven material for removing radionuclides from a wide variety of waste streams. It is superior for removing several radionuclides from the highly alkaline solutions typical of DOE wastes. This laboratory previously developed an equilibrium model applicable to complex solutions for IE-910 (the power form of the granular IE-911), and more recently, the authors have developed several single component ion-exchange kinetic models for predicting column breakthrough curves and batch reactor concentration histories. In this paper, the authors model ion-exchange column performance using effective diffusivities determined from batch kinetic experiments. This technique is preferablemore » because the batch experiments are easier, faster, and cheaper to perform than column experiments. They also extend these ideas to multicomponent systems. Finally, they evaluate the ability of the equilibrium model to predict data for IE-911.« less

Charged patchy particle models in explicit salt: Ion distributions, electrostatic potentials, and effective interactions.

PubMed

Yigit, Cemil; Heyda, Jan; Dzubiella, Joachim

2015-08-14

We introduce a set of charged patchy particle models (CPPMs) in order to systematically study the influence of electrostatic charge patchiness and multipolarity on macromolecular interactions by means of implicit-solvent, explicit-ion Langevin dynamics simulations employing the Gromacs software. We consider well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size which are composed of discrete atoms. The studied mono- and multipole moments of the CPPMs are comparable to those of globular proteins with similar size. We first characterize ion distributions and electrostatic potentials around a single CPPM. Although angle-resolved radial distribution functions reveal the expected local accumulation and depletion of counter- and co-ions around the patches, respectively, the orientation-averaged electrostatic potential shows only a small variation among the various CPPMs due to space charge cancellations. Furthermore, we study the orientation-averaged potential of mean force (PMF), the number of accumulated ions on the patches, as well as the CPPM orientations along the center-to-center distance of a pair of CPPMs. We compare the PMFs to the classical Derjaguin-Verwey-Landau-Overbeek theory and previously introduced orientation-averaged Debye-Hückel pair potentials including dipolar interactions. Our simulations confirm the adequacy of the theories in their respective regimes of validity, while low salt concentrations and large multipolar interactions remain a challenge for tractable theoretical descriptions.

Characteristics of Ions Emission from Ultrashort Laser Produced Plasma

PubMed Central

Elsied, Ahmed M.; Termini, Nicholas C.; Diwakar, Prasoon K.; Hassanein, Ahmed

2016-01-01

The dynamic characteristics of the ions emitted from ultrashort laser interaction with materials were studied. A series of successive experiments were conducted for six different elements (C, Al, Cu, Mo, Gd, and W) using 40 fs, 800 nm Ti: Sapphire laser. Time-of-flight (TOF) ion profile was analyzed and charge emission dependencies were investigated. The effects of incident laser interaction with each element were studied over a wide range of laser fluences (0.8 J/cm2 to 24 J/cm2) corresponding to laser intensities (2.0 × 1013 W/cm2 to 6.0 × 1014 W/cm2). The dependencies of the angular resolved ion flux and energy were also investigated. The TOF ion profile exhibits two peaks corresponding to a fast and a slow ion regime. The slow ions emission was the result of thermal vaporization while fast ions emission was due to time dependent ambipolar electric field. A theoretical model is proposed to predict the total ion flux emitted during femtosecond laser interaction that depends on laser parameters, material properties, and plume hydrodynamics. Incident laser fluence directly impacts average charge state and in turn affects the ion flux. Slow ions velocity exhibited different behavior from fast ions velocity. The fast ions energy and flux were found to be more collimated. PMID:27905553

A multiscale model for charge inversion in electric double layers

NASA Astrophysics Data System (ADS)

Mashayak, S. Y.; Aluru, N. R.

2018-06-01

Charge inversion is a widely observed phenomenon. It is a result of the rich statistical mechanics of the molecular interactions between ions, solvent, and charged surfaces near electric double layers (EDLs). Electrostatic correlations between ions and hydration interactions between ions and water molecules play a dominant role in determining the distribution of ions in EDLs. Due to highly polar nature of water, near a surface, an inhomogeneous and anisotropic arrangement of water molecules gives rise to pronounced variations in the electrostatic and hydration energies of ions. Classical continuum theories fail to accurately describe electrostatic correlations and molecular effects of water in EDLs. In this work, we present an empirical potential based quasi-continuum theory (EQT) to accurately predict the molecular-level properties of aqueous electrolytes. In EQT, we employ rigorous statistical mechanics tools to incorporate interatomic interactions, long-range electrostatics, correlations, and orientation polarization effects at a continuum-level. Explicit consideration of atomic interactions of water molecules is both theoretically and numerically challenging. We develop a systematic coarse-graining approach to coarse-grain interactions of water molecules and electrolyte ions from a high-resolution atomistic scale to the continuum scale. To demonstrate the ability of EQT to incorporate the water orientation polarization, ion hydration, and electrostatic correlations effects, we simulate confined KCl aqueous electrolyte and show that EQT can accurately predict the distribution of ions in a thin EDL and also predict the complex phenomenon of charge inversion.

Etude fondamentale des mecanismes de gravure par plasma de materiaux de pointe: Application a la fabrication de dispositifs photoniques

NASA Astrophysics Data System (ADS)

Stafford, Luc

Advances in electronics and photonics critically depend upon plasma-based materials processing either for transferring small lithographic patterns into underlying materials (plasma etching) or for the growth of high-quality films. This thesis deals with the etching mechanisms of materials using high-density plasmas. The general objective of this work is to provide an original framework for the plasma-material interaction involved in the etching of advanced materials by putting the emphasis on complex oxides such as SrTiO3, (Ba,Sr)TiO 3 and SrBi2Ta2O9 films. Based on a synthesis of the descriptions proposed by different authors to explain the etching characteristics of simple materials in noble and halogenated plasma mixtures, we propose comprehensive rate models for physical and chemical plasma etching processes. These models have been successfully validated using experimental data published in literature for Si, Pt, W, SiO2 and ZnO. As an example, we have been able to adequately describe the simultaneous dependence of the etch rate on ion and reactive neutral fluxes and on the ion energy. From an exhaustive experimental investigation of the plasma and etching properties, we have also demonstrated that the validity of the proposed models can be extended to complex oxides such as SrTiO3, (Ba,Sr)TiO 3 and SrBi2Ta2O9 films. We also reported for the first time physical aspects involved in plasma etching such as the influence of the film microstructural properties on the sputter-etch rate and the influence of the positive ion composition on the ion-assisted desorption dynamics. Finally, we have used our deep investigation of the etching mechanisms of STO films and the resulting excellent control of the etch rate to fabricate a ridge waveguide for photonic device applications. Keywords: plasma etching, sputtering, adsorption and desorption dynamics, high-density plasmas, plasma diagnostics, advanced materials, photonic applications.

Existence domains of slow and fast ion-acoustic solitons in two-ion space plasmas

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

Maharaj, S. K., E-mail: smaharaj@sansa.org.za; Bharuthram, R., E-mail: rbharuthram@uwc.ac.za; Singh, S. V., E-mail: satyavir@iigs.iigm.res.in

2015-03-15

A study of large amplitude ion-acoustic solitons is conducted for a model composed of cool and hot ions and cool and hot electrons. Using the Sagdeev pseudo-potential formalism, the scope of earlier studies is extended to consider why upper Mach number limitations arise for slow and fast ion-acoustic solitons. Treating all plasma constituents as adiabatic fluids, slow ion-acoustic solitons are limited in the order of increasing cool ion concentrations by the number densities of the cool, and then the hot ions becoming complex valued, followed by positive and then negative potential double layer regions. Only positive potentials are found formore » fast ion-acoustic solitons which are limited only by the hot ion number density having to remain real valued. The effect of neglecting as opposed to including inertial effects of the hot electrons is found to induce only minor quantitative changes in the existence regions of slow and fast ion-acoustic solitons.« less

Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water

NASA Astrophysics Data System (ADS)

Reif, Maria M.; Hünenberger, Philippe H.

2011-04-01

The raw single-ion solvation free energies computed from atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions and treatment of electrostatic interactions used during these simulations. However, as shown recently [M. A. Kastenholz and P. H. Hünenberger, J. Chem. Phys. 124, 224501 (2006), 10.1529/biophysj.106.083667; M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144103 (2010)], the application of appropriate correction terms permits to obtain methodology-independent results. The corrected values are then exclusively characteristic of the underlying molecular model including in particular the ion-solvent van der Waals interaction parameters, determining the effective ion size and the magnitude of its dispersion interactions. In the present study, the comparison of calculated (corrected) hydration free energies with experimental data (along with the consideration of ionic polarizabilities) is used to calibrate new sets of ion-solvent van der Waals (Lennard-Jones) interaction parameters for the alkali (Li+, Na+, K+, Rb+, Cs+) and halide (F-, Cl-, Br-, I-) ions along with either the SPC or the SPC/E water models. The experimental dataset is defined by conventional single-ion hydration free energies [Tissandier et al., J. Phys. Chem. A 102, 7787 (1998), 10.1021/jp982638r; Fawcett, J. Phys. Chem. B 103, 11181] along with three plausible choices for the (experimentally elusive) value of the absolute (intrinsic) hydration free energy of the proton, namely, Δ G_hyd^{ominus }[H+] = -1100, -1075 or -1050 kJ mol-1, resulting in three sets L, M, and H for the SPC water model and three sets LE, ME, and HE for the SPC/E water model (alternative sets can easily be interpolated to intermediate Δ G_hyd^{ominus }[H+] values). The residual sensitivity of the calculated (corrected) hydration free energies on the volume-pressure boundary conditions and on the effective ionic radius entering into the calculation of the correction terms is also evaluated and found to be very limited. Ultimately, it is expected that comparison with other experimental ionic properties (e.g., derivative single-ion solvation properties, as well as data concerning ionic crystals, melts, solutions at finite concentrations, or nonaqueous solutions) will permit to validate one specific set and thus, the associated Δ G_hyd^{ominus }[H+] value (atomistic consistency assumption). Preliminary results (first-peak positions in the ion-water radial distribution functions, partial molar volumes of ionic salts in water, and structural properties of ionic crystals) support a value of Δ G_hyd^{ominus }[H+] close to -1100 kJ.mol-1.

Measurement-induced operation of two-ion quantum heat machines

NASA Astrophysics Data System (ADS)

Chand, Suman; Biswas, Asoka

2017-03-01

We show how one can implement a quantum heat machine by using two interacting trapped ions, in presence of a thermal bath. The electronic states of the ions act like a working substance, while the vibrational mode is modelled as the cold bath. The heat exchange with the cold bath is mimicked by the projective measurement of the electronic states. We show how such measurement in a suitable basis can lead to either a quantum heat engine or a refrigerator, which undergoes a quantum Otto cycle. The local magnetic field is adiabatically changed during the heat cycle. The performance of the heat machine depends upon the interaction strength between the ions, the magnetic fields, and the measurement cost. In our model, the coupling to the hot and the cold baths is never switched off in an alternative fashion during the heat cycle, unlike other existing proposals of quantum heat engines. This makes our proposal experimentally realizable using current tapped-ion technology.

Measurement-induced operation of two-ion quantum heat machines.

PubMed

Chand, Suman; Biswas, Asoka

2017-03-01

We show how one can implement a quantum heat machine by using two interacting trapped ions, in presence of a thermal bath. The electronic states of the ions act like a working substance, while the vibrational mode is modelled as the cold bath. The heat exchange with the cold bath is mimicked by the projective measurement of the electronic states. We show how such measurement in a suitable basis can lead to either a quantum heat engine or a refrigerator, which undergoes a quantum Otto cycle. The local magnetic field is adiabatically changed during the heat cycle. The performance of the heat machine depends upon the interaction strength between the ions, the magnetic fields, and the measurement cost. In our model, the coupling to the hot and the cold baths is never switched off in an alternative fashion during the heat cycle, unlike other existing proposals of quantum heat engines. This makes our proposal experimentally realizable using current tapped-ion technology.

Light ion components of the galactic cosmic rays: Nuclear interactions and transport theory

NASA Technical Reports Server (NTRS)

Cucinotta, F. A.; Townsend, L. W.; Wilson, J. W.; Shinn, J. L.; Badhwar, G. D.; Dubey, R. R.

1996-01-01

Light nuclei are present in the primary galactic cosmic rays (GCR) and are produced in thick targets due to projectile or target fragmentation from both nucleon and heavy induced reactions. In the primary GCR, He-4 is the most abundant nucleus after H-1. However, there are also a substantial fluxes of H-2 and He-3. In this paper we describe theoretical models based on quantum multiple scattering theory for the description of light ion nuclear interactions. The energy dependence of the light ion fragmentation cross section is considered with comparisons of inclusive yields and secondary momentum distributions to experiments described. We also analyze the importance of a fast component of lights ions from proton and neutron induced target fragementation. These theoretical models have been incorporated into the cosmic ray transport code HZETRN and will be used to analyze the role of shielding materials in modulating the production and the energy spectrum of light ions.

Quenching of fluorescence of phenolic compounds and modified humic acids by cadmium ions.

PubMed

Tchaikovskaya, O N; Nechaev, L V; Yudina, N V; Mal'tseva, E V

2016-08-01

The interaction of a number of phenolic compounds, being 'model fragments' of humic acids, with cadmium ions was investigated. The fluorescence quenching method was used to determine the complexation constants of these compounds with cadmium ions. It was established that bonding of phenolic compounds by cadmium ions at рН 7 is weak and reaches a maximum value of 15% for interaction with resorcinol. It was demonstrated that modification of humic acids by the mechanoactivation method increases by three times bonding of cadmium ions, which is caused by strengthening the acid properties of carboxyl and hydroxyl groups at the aromatic ring. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Electron-beam-ion-source (EBIS) modeling progress at FAR-TECH, Inc

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

Kim, J. S., E-mail: kim@far-tech.com; Zhao, L., E-mail: kim@far-tech.com; Spencer, J. A., E-mail: kim@far-tech.com

FAR-TECH, Inc. has been developing a numerical modeling tool for Electron-Beam-Ion-Sources (EBISs). The tool consists of two codes. One is the Particle-Beam-Gun-Simulation (PBGUNS) code to simulate a steady state electron beam and the other is the EBIS-Particle-In-Cell (EBIS-PIC) code to simulate ion charge breeding with the electron beam. PBGUNS, a 2D (r,z) electron gun and ion source simulation code, has been extended for efficient modeling of EBISs and the work was presented previously. EBIS-PIC is a space charge self-consistent PIC code and is written to simulate charge breeding in an axisymmetric 2D (r,z) device allowing for full three-dimensional ion dynamics.more » This 2D code has been successfully benchmarked with Test-EBIS measurements at Brookhaven National Laboratory. For long timescale (< tens of ms) ion charge breeding, the 2D EBIS-PIC simulations take a long computational time making the simulation less practical. Most of the EBIS charge breeding, however, may be modeled in 1D (r) as the axial dependence of the ion dynamics may be ignored in the trap. Where 1D approximations are valid, simulations of charge breeding in an EBIS over long time scales become possible, using EBIS-PIC together with PBGUNS. Initial 1D results are presented. The significance of the magnetic field to ion dynamics, ion cooling effects due to collisions with neutral gas, and the role of Coulomb collisions are presented.« less

Ions interacting in solution: Moving from intrinsic to collective properties

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

Duignan, Timothy T.; Baer, Marcel D.; Mundy, Christopher J.

A crucial determinant of Hofmeister effects is the direct interaction of ions in solution with the charged groups on the surface of larger particles. Understanding ion–ion interactions in solution is therefore a necessary first step to explaining Hofmeister effects. Here, we advocate an approach to modeling these types of properties where state of the art Ab Initio Molecular Dynamics (AIMD) simulation of ions in solution is used to establish benchmark values for the intrinsic properties of ions in solution such as solvation structures and ion–ion Potentials of Mean Force (PMFs). This information can then be combined with or used to parametrize and improve reduced models, which use approximations such as the continuum solvent model.(CSM) These reduced models can then be used to calculate collective and concentration dependent properties of electrolyte solution and so make accurate predictions about complex systems of relevance for direct applications. We provide an example of this approach using AIMD calculations of the sodium chloride dimer to calculate osmotic coefficients of all 20 alkali halide electrolytes. This research used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. TD and CJM were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MSmore » $$^{3}$$ (Materials Synthesis and Simulation Across Scales) Initiative, a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy.« less

Light fragments from (C + Be) interactions at 0.6 GeV/nucleon

DOE PAGES

Abramov, B. M.; Alekseev, P. N.; Borodin, Yu. A.; ...

2016-05-01

We measured nuclear fragments emitted at 3.5° in 12C fragmentation at 0.6 GeV/nucleon. We also used the spectra obtained to test the predictions of four ion-ion interaction models: INCL++, BC, LAQGSM03.03 and QMD as well as for the comparison with the analytical parametrization in the framework of thermodynamical picture of fragmentation.

Incorporating water-release and lateral protein interactions in modeling equilibrium adsorption for ion-exchange chromatography.

PubMed

Thrash, Marvin E; Pinto, Neville G

2006-09-08

The equilibrium adsorption of two albumin proteins on a commercial ion exchanger has been studied using a colloidal model. The model accounts for electrostatic and van der Waals forces between proteins and the ion exchanger surface, the energy of interaction between adsorbed proteins, and the contribution of entropy from water-release accompanying protein adsorption. Protein-surface interactions were calculated using methods previously reported in the literature. Lateral interactions between adsorbed proteins were experimentally measured with microcalorimetry. Water-release was estimated by applying the preferential interaction approach to chromatographic retention data. The adsorption of ovalbumin and bovine serum albumin on an anion exchanger at solution pH>pI of protein was measured. The experimental isotherms have been modeled from the linear region to saturation, and the influence of three modulating alkali chlorides on capacity has been evaluated. The heat of adsorption is endothermic for all cases studied, despite the fact that the net charge on the protein is opposite that of the adsorbing surface. Strong repulsive forces between adsorbed proteins underlie the endothermic heat of adsorption, and these forces intensify with protein loading. It was found that the driving force for adsorption is the entropy increase due to the release of water from the protein and adsorbent surfaces. It is shown that the colloidal model predicts protein adsorption capacity in both the linear and non-linear isotherm regions, and can account for the effects of modulating salt.

A simulation assessment of the thermodynamics of dense ion-dipole mixtures with polarization

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

Bastea, Sorin, E-mail: sbastea@llnl.gov

Molecular dynamics (MD) simulations are employed to ascertain the relative importance of various electrostatic interaction contributions, including induction interactions, to the thermodynamics of dense, hot ion-dipole mixtures. In the absence of polarization, we find that an MD-constrained free energy term accounting for the ion-dipole interactions, combined with well tested ionic and dipolar contributions, yields a simple, fairly accurate free energy form that may be a better option for describing the thermodynamics of such mixtures than the mean spherical approximation (MSA). Polarization contributions induced by the presence of permanent dipoles and ions are found to be additive to a good approximation,more » simplifying the thermodynamic modeling. We suggest simple free energy corrections that account for these two effects, based in part on standard perturbative treatments and partly on comparisons with MD simulation. Even though the proposed approximations likely need further study, they provide a first quantitative assessment of polarization contributions at high densities and temperatures and may serve as a guide for future modeling efforts.« less

Status of the Space Radiation Monte Carlos Simulation Based on FLUKA and ROOT

NASA Technical Reports Server (NTRS)

Andersen, Victor; Carminati, Federico; Empl, Anton; Ferrari, Alfredo; Pinsky, Lawrence; Sala, Paola; Wilson, Thomas L.

2002-01-01

The NASA-funded project reported on at the first IWSSRR in Arona to develop a Monte-Carlo simulation program for use in simulating the space radiation environment based on the FLUKA and ROOT codes is well into its second year of development, and considerable progress has been made. The general tasks required to achieve the final goals include the addition of heavy-ion interactions into the FLUKA code and the provision of a ROOT-based interface to FLUKA. The most significant progress to date includes the incorporation of the DPMJET event generator code within FLUKA to handle heavy-ion interactions for incident projectile energies greater than 3GeV/A. The ongoing effort intends to extend the treatment of these interactions down to 10 MeV, and at present two alternative approaches are being explored. The ROOT interface is being pursued in conjunction with the CERN LHC ALICE software team through an adaptation of their existing AliROOT software. As a check on the validity of the code, a simulation of the recent data taken by the ATIC experiment is underway.

Interchange mode excited by trapped energetic ions

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

Nishimura, Seiya, E-mail: n-seiya@kobe-kosen.ac.jp

2015-07-15

The kinetic energy principle describing the interaction between ideal magnetohydrodynamic (MHD) modes with trapped energetic ions is revised. A model is proposed on the basis of the reduced ideal MHD equations for background plasmas and the bounce-averaged drift-kinetic equation for trapped energetic ions. The model is applicable to large-aspect-ratio toroidal devices. Specifically, the effect of trapped energetic ions on the interchange mode in helical systems is analyzed. Results show that the interchange mode is excited by trapped energetic ions, even if the equilibrium states are stable to the ideal interchange mode. The energetic-ion-induced branch of the interchange mode might bemore » associated with the fishbone mode in helical systems.« less

Dose-dependent misrejoining of radiation-induced DNA double-strand breaks in human fibroblasts: Experimental and theoretical study for high and low LET radiation

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

Rydberg, Bjorn; Cooper, Brian; Cooper, Priscilla K.

2004-11-18

Misrejoining of DNA double-strand breaks (DSBs) was measured in human primary fibroblasts after exposure to X-rays and high LET particles (He, N and Fe) in the dose range 10-80 Gy. To measure joining of wrong DNA ends, the integrity of a 3.2 Mbp restriction fragment was analyzed directly after exposure and after 16 hr of repair incubation. It was found that the misrejoining frequency for X-rays was non-linearly related to dose, with less probability of misrejoining at low doses than at high doses. The dose dependence for the high LET particles, on the other hand, was closer to being linear,more » with misrejoining frequencies higher than for X-rays particularly at the lower doses. These experimental results were simulated with a Monte-Carlo approach that includes a cell nucleus model with all 46 chromosomes present, combined with realistic track structure simulations to calculate the geometrical positions of all DSBs induced for each dose. The model assumes that the main determinant for misrejoining probability is the distance between two simultaneously present DSBs. With a Gaussian interaction probability function with distance, it was found that both the low and high LET data could be fitted with an interaction distance (sigma of the Gaussian curve) of 0.25 {micro}m. This is half the distance previously found to best fit chromosomal aberration data in human lymphocytes using the same methods (Holley et al. Radiat. Res . 158, 568-580 (2002)). The discrepancy may indicate inadequacies in the chromosome model, for example insufficient chromosomal overlap, but may also partly be due to differences between fibroblasts and lymphocytes. Although the experimental data was obtained at high doses, the Monte Carlo calculations could be extended to lower doses. It was found that a linear component of misrejoining versus dose dominated for doses below 1 Gy for all radiations, including X-rays. The calculated relative biological efficiency (RBE) for misrejoining at this low dose region was 31 for the He-ions, 28 for the N-ions and 19 for Fe-ions.« less

Dendritic growth shapes in kinetic Monte Carlo models

NASA Astrophysics Data System (ADS)

Krumwiede, Tim R.; Schulze, Tim P.

2017-02-01

For the most part, the study of dendritic crystal growth has focused on continuum models featuring surface energies that yield six pointed dendrites. In such models, the growth shape is a function of the surface energy anisotropy, and recent work has shown that considering a broader class of anisotropies yields a correspondingly richer set of growth morphologies. Motivated by this work, we generalize nanoscale models of dendritic growth based on kinetic Monte Carlo simulation. In particular, we examine the effects of extending the truncation radius for atomic interactions in a bond-counting model. This is done by calculating the model’s corresponding surface energy and equilibrium shape, as well as by running KMC simulations to obtain nanodendritic growth shapes. Additionally, we compare the effects of extending the interaction radius in bond-counting models to that of extending the number of terms retained in the cubic harmonic expansion of surface energy anisotropy in the context of continuum models.

Velocity fluctuations of a heavy particle interacting with a hot and cold gas: Applications to molecular ion traps

NASA Astrophysics Data System (ADS)

Vaca, Christian; Bruinsma, Robijn; Levine, Alex J.

2014-03-01

Understanding the stochastic motion of a heavy particle in a gas of lighter ones is a classic problem in statistical mechanics. Alkemade, MacDonald, and Van Kampen (AMvK) analyzed this problem in one dimension, computing the velocity distribution function of the heavy particle in a perturbation expansion using the ratio of mass of the light to the heavy particle as a small parameter. Novel tests of this theory are now being provided by modern molecular ion traps [arXiv:1310.5190]. In such experiments, the heavy molecular ion interacts with a cold gas used for sympathetic cooling and low density hot gasses that leak into the system. Thus, the heavy ion is maintained in a complex nonequilibrium state due to its interactions with the hot and cold gasses. In this talk, we present an extension of the AMvK model appropriate to these experiments. Using new analytic and computational techniques, we explore the time-dependent velocity distribution function of the molecular ion interacting with the gasses including higher order perturbative corrections necessary to discuss the case in which the ion's mass is not significantly larger than that of the other two species. Using this analysis we address the experimental observation of non-Gaussian velocity distributions of the heavy ions.

Tunable spin-spin interactions and entanglement of ions in separate potential wells.

PubMed

Wilson, A C; Colombe, Y; Brown, K R; Knill, E; Leibfried, D; Wineland, D J

2014-08-07

Quantum simulation--the use of one quantum system to simulate a less controllable one--may provide an understanding of the many quantum systems which cannot be modelled using classical computers. Considerable progress in control and manipulation has been achieved for various quantum systems, but one of the remaining challenges is the implementation of scalable devices. In this regard, individual ions trapped in separate tunable potential wells are promising. Here we implement the basic features of this approach and demonstrate deterministic tuning of the Coulomb interaction between two ions, independently controlling their local wells. The scheme is suitable for emulating a range of spin-spin interactions, but to characterize the performance of our set-up we select one that entangles the internal states of the two ions with a fidelity of 0.82(1) (the digit in parentheses shows the standard error of the mean). Extension of this building block to a two-dimensional network, which is possible using ion-trap microfabrication processes, may provide a new quantum simulator architecture with broad flexibility in designing and scaling the arrangement of ions and their mutual interactions. To perform useful quantum simulations, including those of condensed-matter phenomena such as the fractional quantum Hall effect, an array of tens of ions might be sufficient.

Parameterization of Ca+2-protein interactions for molecular dynamics simulations.

PubMed

Project, Elad; Nachliel, Esther; Gutman, Menachem

2008-05-01

Molecular dynamics simulations of Ca+2 ions near protein were performed with three force fields: GROMOS96, OPLS-AA, and CHARMM22. The simulations reveal major, force-field dependent, inconsistencies in the interaction between the Ca+2 ions with the protein. The variations are attributed to the nonbonded parameterizations of the Ca+2-carboxylates interactions. The simulations results were compared to experimental data, using the Ca+2-HCOO- equilibrium as a model. The OPLS-AA force field grossly overestimates the binding affinity of the Ca+2 ions to the carboxylate whereas the GROMOS96 and CHARMM22 force fields underestimate the stability of the complex. Optimization of the Lennard-Jones parameters for the Ca+2-carboxylate interactions were carried out, yielding new parameters which reproduce experimental data. Copyright 2007 Wiley Periodicals, Inc.

Role of lower hybrid waves in ion heating at dipolarization fronts

NASA Astrophysics Data System (ADS)

Greco, A.; Artemyev, A.; Zimbardo, G.; Angelopoulos, V.; Runov, A.

2017-05-01

One of the important sources of hot ions in the magnetotail is the bursty bulk flows propagating away from the reconnection region and heating the ambient plasma. Charged particles interact with nonlinear magnetic field pulses (dipolarization fronts, DFs) embedded into these flows. The convection electric fields associated with DF propagation are known to reflect and accelerate ambient ions. Moreover, a wide range of waves is observed within/near these fronts, the electric field fluctuations being dominated by the lower hybrid drift (LHD) instability. Here we investigate the potential role of these waves in the further acceleration of ambient ions. We use a LHD wave emission profile superimposed on the leading edge of a two-dimensional model profile of a DF and a test particle approach. We show that LHD waves with realistic amplitudes can significantly increase the upper limit of energies gained by ions. Wave-particle interaction near the front is more effective in producing superthermal ions than in increasing the flux of thermal ions. Comparison of test particle simulations and Time History of Events and Macroscale Interactions during Substorms observations show that ion acceleration by LHD waves is more important for slower DFs.

Magnetic interactions in La0.7Sr0.3Mn1-xMexO3 (Me=Ga, Fe, Cr) manganites

NASA Astrophysics Data System (ADS)

Troyanchuk, I. O.; Bushinsky, M. V.; Karpinsky, D. V.; Tereshko, N. V.; Dobryansky, V. M.; Többens, D. M.; Sikolenko, V.; Efimov, V.

2015-11-01

Magnetic properties and crystal structure of La0.7Sr0.3Mn1-xMexO3 (Me=Ga, Fe, Cr; x≤0.3) have been studied by neutron powder diffraction and magnetization measurements. It is shown that substitution of manganese ions by chromium or gallium ions (x=0.3) leads to phase separation into antiferromagnetic and ferromagnetic phases whereas replacement by Fe ions stabilizes spin glass state (x=0.3). Ferromagnetic interactions in Cr-substituted compounds are much more pronounced than in Fe- and Ga-doped ones. Magnetic properties are discussed in the model assuming a dominance of superexchange interactions. It is considered that ferromagnetism in the Cr-substituted compositions is associated with nearly equal contributions from positive and negative components of the superexchange interaction between Mn3+ and Cr3+ ions as well as to mixed valence of chromium ions. The spin glass state observed for the Fe-doped sample (x=0.3) is associated with strong antiferromagnetic superexchange between Fe3+-O-Fe3+ and Fe3+-O-(Mn3+, Mn4+).

Nonlinear resonances in linear segmented Paul trap of short central segment.

PubMed

Kłosowski, Łukasz; Piwiński, Mariusz; Pleskacz, Katarzyna; Wójtewicz, Szymon; Lisak, Daniel

2018-03-23

Linear segmented Paul trap system has been prepared for ion mass spectroscopy experiments. A non-standard approach to stability of trapped ions is applied to explain some effects observed with ensembles of calcium ions. Trap's stability diagram is extended to 3-dimensional one using additional ∆a besides standard q and a stability parameters. Nonlinear resonances in (q,∆a) diagrams are observed and described with a proposed model. The resonance lines have been identified using simple simulations and comparing the numerical and experimental results. The phenomenon can be applied in electron-impact ionization experiments for mass-identification of obtained ions or purification of their ensembles. This article is protected by copyright. All rights reserved.

Are Ring Current Ions Lost in Electromagnetic Ion Cyclotron Wave Dispersion Relation?

NASA Technical Reports Server (NTRS)

Khazanov, G. V.; Gamayunov, K. V.

2006-01-01

Electromagnetic ion cyclotron (EMIC) waves are widely observed in the inner and outer magnetosphere, at geostationary orbit, at high latitudes along the plasmapause, and at the ionospheric altitudes. Interaction of the Ring Current (RC) ions and EMIC waves causes ion scattering into the loss cone and leads to decay of the RC, especially during the main phase of storms when the RC decay times of about one hour or less are observed. The oblique EMIC waves damp due to Landau resonance with the thermal plasmaspheric electrons, and subsequent transport of the dissipating wave energy into the ionosphere below causes an ionosphere temperature enhancement. Induced scattering of these waves by the plasmaspheric thermal ions leads to ion temperature enhancement, and forms a so-called hot zone near the plasmapause where the temperature of core plasma ions can reach tens of thousands of degrees. Relativistic electrons in the outer radiation belt also interact well with the EMIC waves, and during the main and/or recovery phases of the storms these electrons can easily be scattered into the loss cone over a time scale from several hours to a day. The plasma density distribution in the magnetosphere and the ion content play a critical role in EMIC wave generation and propagation, but the wave dispersion relation in the known RC-EMIC wave interaction models is assumed to be determined by the thermal plasma distribution only. In these models, the modification of the EMIC wave dispersion relation caused by the RC ions is not taken into account, and the RC ions are only treated as a source of free energy in order to generate EMIC waves. At the same time, the RC ions can dominate the thermal magnetospheric content in the night MLT sector at great L shells during the main and/or recovery storm phase. In this study, using our self-consistent RC-EMIC wave model [Khazanov et al., 2006], we simulate the May 1998 storm in order to quantify the global EMIC wave redistribution caused by taking into account the RC ions in the EMIC wave dispersion relation. The dramatic wave pattern redistribution is observed in the postdusk-predawn MLT sector (night sector) for L greater than 5. We found the intense EMIC waves (about a few nT) there during the main and early recovery phases of the storm. The observed wave generation in this sector is caused by taking into account the EMIC wave dispersion change due to the RC ions. There are no waves at these locations in our model if the RC ions are taken into account in the wave growth rate only, and the wave dispersion relation is only governed by the thermal plasmaspheric model.

Effect of Ring Current Ions on Electromagnetic Ion Cyclotron Wave Dispersion Relation

NASA Technical Reports Server (NTRS)

Gamayunov, K. V.; Khazanov, G. V.

2006-01-01

Electromagnetic ion cyclotron (EMIC) waves are widely observed in the inner and outer magnetosphere, at geostationary orbit, at high latitudes along the plasmapause, and at the ionospheric altitudes. Interaction of the Ring Current (RC) ions and EMIC waves causes ion scattering into the loss cone and leads to decay of the RC, especially during the main phase of storms when the RC decay times of about one hour or less are observed. The oblique EMIC waves damp due to Landau resonance with the thermal plasmaspheric electrons, and subsequent transport of the dissipating wave energy into the ionosphere below causes an ionosphere temperature enhancement. Induced scattering of these waves by the plasmaspheric thermal ions leads to ion temperature enhancement, and forms a so-called hot zone near the plasmapause where the temperature of core plasma ions can reach tens of thousands of degrees. Relativistic electrons in the outer radiation belt also interact well with the EMIC waves, and during the main and/or recovery phases of the storms these electrons can easily be scattered into the loss cone over a time scale from several hours to a day. The plasma density distribution in the magnetosphere and the ion content play a critical role in EMIC wave generation and propagation, but the wave dispersion relation in the known RC-EMIC wave interaction models is assumed to be determined by the thermal plasma distribution only. In these models, the modification of the EMIC wave dispersion relation caused by the RC ions is not taken into account, and the RC ions are only treated as a source of free energy in order to generate EMIC waves. At the same time, the RC ions can dominate the thermal magnetospheric content in the night MLT sector at great L shells during the main and/or recovery storm phase. In this study, using our self-consistent RC-EMIC wave model [Khazanov et al., 2006], we simulate the May 1998 storm in order to quantify the global EMIC wave redistribution caused by taking into account the RC ions in the EMIC wave dispersion relation. The dramatic wave pattern redistribution is observed in the postdusk-predawn MLT sector (night sector) for L greater than 5. We found the intense EMIC waves (about a few nT) there during the main and early recovery phases of the storm. The observed wave generation in this sector is caused by taking into account the EMIC wave dispersion change due to the RC ions. There are no waves at these locations in our model if the RC ions are taken into account in the wave growth rate only, and the wave dispersion relation is only governed by the thermal plasmaspheric model.

Sensing of heavy metal ions by intrinsic TMV coat protein fluorescence

NASA Astrophysics Data System (ADS)

Bayram, Serene S.; Green, Philippe; Blum, Amy Szuchmacher

2018-04-01

We propose the use of a cysteine mutant of TMV coat protein as a signal transducer for the selective sensing and quantification of the heavy metal ions, Cd2+, Pb2+, Zn2+ and Ni2+ based on intrinsic tryptophan quenching. TMV coat protein is inexpensive, can be mass-produced since it is expressed and extracted from E-coli. It also displays several different functional groups, enabling a wide repertoire of bioconjugation chemistries; thus it can be easily integrated into functional devices. In addition, TMV-ion interactions have been widely reported and utilized for metallization to generate organic-inorganic hybrid composite novel materials. Building on these previous observations, we herein determine, for the first time, the TMV-ion binding constants assuming the static fluorescence quenching model. We also show that by comparing TMV-ion interactions between native and denatured coat protein, we can distinguish between chemically similar heavy metal ions such as cadmium and zinc ions.

Interaction of monovalent ions with the water liquid-vapor interface - A molecular dynamics study

NASA Technical Reports Server (NTRS)

Wilson, Michael A.; Pohorille, Andrew

1991-01-01

Results of molecular dynamics calculations are presented for a series of ions at infinite dilution near the water liquid-vapor interface. The free energies of ion transfer from the bulk to the interface are discussed, as are the accompanying changes of water structure at the surface and ion mobilities as a function of their proximity to the interface. It is shown that simple dielectric models do not provide an accurate description of ions at the water surface. The results of the study should be useful in the development of better models incorporating the shape and molecular structure of the interface.

Solar Wind Deflection by Mass Loading in the Martian Magnetosheath Based on MAVEN Observations

NASA Astrophysics Data System (ADS)

Dubinin, E.; Fraenz, M.; Pätzold, M.; Halekas, J. S.; Mcfadden, J.; Connerney, J. E. P.; Jakosky, B. M.; Vaisberg, O.; Zelenyi, L.

2018-03-01

Mars Atmosphere and Volatile EvolutioN observations at Mars show clear signatures of the shocked solar wind interaction with the extended oxygen atmosphere and hot corona displayed in a lateral deflection of the magnetosheath flow in the direction opposite to the direction of the solar wind motional electric field. The value of the velocity deflection reaches ˜50 km/s. The occurrence of such deflection is caused by the "Lorentz-type" force due to a differential streaming of the solar wind protons and oxygen ions originating from the extended oxygen corona. The value of the total deceleration of the magnetosheath flow due to mass loading is estimated as ˜40 km/s.

Interpretation of Simultaneous Mechanical-Electrical-Thermal Failure in a Lithium-Ion Battery Module: Preprint

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

Zhang, Chao; Santhanagopalan, Shriram; Stock, Mark J.

Lithium-ion batteries are currently the state-of- the-art power sources for electric vehicles, and their safety behavior when subjected to abuse, such as a mechanical impact, is of critical concern. A coupled mechanical-electrical-thermal model for simulating the behavior of a lithium-ion battery under a mechanical crush has been developed. We present a series of production-quality visualizations to illustrate the complex mechanical and electrical interactions in this model.

Thomson scattering from a three-component plasma.

PubMed

Johnson, W R; Nilsen, J

2014-02-01

A model for a three-component plasma consisting of two distinct ionic species and electrons is developed and applied to study x-ray Thomson scattering. Ions of a specific type are assumed to be identical and are treated in the average-atom approximation. Given the plasma temperature and density, the model predicts mass densities, effective ionic charges, and cell volumes for each ionic type, together with the plasma chemical potential and free-electron density. Additionally, the average-atom treatment of individual ions provides a quantum-mechanical description of bound and continuum electrons. The model is used to obtain parameters needed to determine the dynamic structure factors for x-ray Thomson scattering from a three-component plasma. The contribution from inelastic scattering by free electrons is evaluated in the random-phase approximation. The contribution from inelastic scattering by bound electrons is evaluated using the bound-state and scattering wave functions obtained from the average-atom calculations. Finally, the partial static structure factors for elastic scattering by ions are evaluated using a two-component version of the Ornstein-Zernike equations with hypernetted chain closure, in which electron-ion interactions are accounted for using screened ion-ion interaction potentials. The model is used to predict the x-ray Thomson scattering spectrum from a CH plasma and the resulting spectrum is compared with experimental results obtained by Feltcher et al. [Phys. Plasmas 20, 056316 (2013)].

Solvent-mediated nonelectrostatic ion-ion interactions predicting anomalies in electrophoresis.

PubMed

Goswami, Prakash; Dhar, Jayabrata; Ghosh, Uddipta; Chakraborty, Suman

2017-03-01

We study the effects of solvent-mediated nonelectrostatic ion-ion interactions on electrophoretic mobility of a charged spherical particle. To this end, we consider the case of low surface electrostatic potential resulting in the linearization of the governing equations, which enables us to deduce a closed-form analytical solution to the electrophoretic mobility. We subsequently compare our results to the standard model using Henry's approach and report the changes brought about by the nonelectrostatic potential. The classical approach to determine the electrophoretic mobility underpredicts the particle velocity when compared with experiments. We show that this issue can be resolved by taking into account nonelectrostatic interactions. Our analysis further reveals the phenomenon of electrophoretic mobility reversal that has been experimentally observed in numerous previous studies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparison of Nernst-Planck and reaction rate models for multiply occupied channels.

PubMed Central

Levitt, D G

1982-01-01

The Nernst-Planck continuum equation for a channel that can be occupied by at most two ions is solved for two different physical cases. The first case is for the assumption that the water and ion cannot get around each other anywhere in the channel, so that if there are two ions in the channel the distance between them is fixed by the number of water molecules between them. The second case is for the assumption that there are regions at he ends of the channel where the ions and water can get around each other. For these two cases, the validity of the simple two-site reaction-rate approximation when there is a continuously varying central energy barrier was evaluated by comparing it with the exact Nernst-Planck solution. For the first continuum case, the kinetics for the continuum and reaction-rate models are nearly identical. For the second case, the agreement depends on the strength of the ion-ion interaction energy. For a low interaction energy (large channel diameter) a high ion concentrations, there is a large difference in the flux as a function of voltage for the two models-with the continuum flux becoming more than four times larger at 250 mV. Simple analytical expressions are derived for the two-ion continuum channel for the case where the ends are in equilibrium with the bulk solution and for the case where ion mobility becomes zero when there are two ions in the channel. The implications of these results for biological channels are discussed. PMID:6280783

Atomically informed nonlocal semi-discrete variational Peierls-Nabarro model for planar core dislocations

PubMed Central

Liu, Guisen; Cheng, Xi; Wang, Jian; Chen, Kaiguo; Shen, Yao

2017-01-01

Prediction of Peierls stress associated with dislocation glide is of fundamental concern in understanding and designing the plasticity and mechanical properties of crystalline materials. Here, we develop a nonlocal semi-discrete variational Peierls-Nabarro (SVPN) model by incorporating the nonlocal atomic interactions into the semi-discrete variational Peierls framework. The nonlocal kernel is simplified by limiting the nonlocal atomic interaction in the nearest neighbor region, and the nonlocal coefficient is directly computed from the dislocation core structure. Our model is capable of accurately predicting the displacement profile, and the Peierls stress, of planar-extended core dislocations in face-centered cubic structures. Our model could be extended to study more complicated planar-extended core dislocations, such as <110> {111} dislocations in Al-based and Ti-based intermetallic compounds. PMID:28252102

Polarizable Force Fields and Polarizable Continuum Model: A Fluctuating Charges/PCM Approach. 1. Theory and Implementation.

PubMed

Lipparini, Filippo; Barone, Vincenzo

2011-11-08

We present a combined fluctuating charges-polarizable continuum model approach to describe molecules in solution. Both static and dynamic approaches are discussed: analytical first and second derivatives are shown as well as an extended lagrangian for molecular dynamics simluations. In particular, we use the polarizable continuum model to provide nonperiodic boundary conditions for molecular dynamics simulations of aqueous solutions. The extended lagrangian method is extensively discussed, with specific reference to the fluctuating charge model, from a numerical point of view by means of several examples, and a rationalization of the behavior found is presented. Several prototypical applications are shown, especially regarding solvation of ions and polar molecules in water.

Lithium-ion battery cell-level control using constrained model predictive control and equivalent circuit models

NASA Astrophysics Data System (ADS)

Xavier, Marcelo A.; Trimboli, M. Scott

2015-07-01

This paper introduces a novel application of model predictive control (MPC) to cell-level charging of a lithium-ion battery utilizing an equivalent circuit model of battery dynamics. The approach employs a modified form of the MPC algorithm that caters for direct feed-though signals in order to model near-instantaneous battery ohmic resistance. The implementation utilizes a 2nd-order equivalent circuit discrete-time state-space model based on actual cell parameters; the control methodology is used to compute a fast charging profile that respects input, output, and state constraints. Results show that MPC is well-suited to the dynamics of the battery control problem and further suggest significant performance improvements might be achieved by extending the result to electrochemical models.

Outer satellite atmospheres: Their extended nature and planetary interactions. [sodium cloud of Io, hydrogen torus of Titan, and comet atmospheres

NASA Technical Reports Server (NTRS)

Smyth, W. H.

1980-01-01

Highly developed numerical models are applied to interpret extended-atmosphere data for the sodium cloud of Io and the hydrogen torus of Titan. Solar radiation pressure was identified and verified by model calculations as the mechanism to explain two different east-west asymmetries observed in the sodium cloud. Analysis of sodium line profile data, suggesting that a Jupiter magnetospheric wind may be responsible for high speed sodium atoms emitted from Io, and preliminary modeling of the interaction of the Io plasma torus and Io's sodium cloud are also reported. Models presented for Titan's hydrogen torus are consistent both with the recent Pioneer 11 measurements and earlier Earth-orbiting observations by the Copernicus satellite. Progress is reported on developing models for extended gas and dust atmospheres of comets.

Global hybrid simulation of the solar wind interaction with the dayside of Venus

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

Moore, K.R.; Thomas, V.A.; McComas, D.J.

1991-05-01

The authors present a 3-dimensional global hybrid simulation of the interaction of the solar wind with the entire dayside of Venus. The model obstacle is half the size of Venus, and planetary ion mass loading is included self-consistently. Results are compared to observations as well as to results from gasdynamic convected field modeling. Magnetic field magnitudes and bulk flow speeds along the planet-Sun line are comparable in both models, but only the hybrid model reproduces the experimentally observed magnetic barrier proton density depletions. The finite gyroradius of the planetary pickup ions causes a number density asymmetry in the direction ofmore » the convective ({minus}V {times} B) electric field, as predicted and observed. Mass addition consistent with photoionization of the planetary neutral hot oxygen corona has little effect on the geometry of the shock, including the subsolar and terminator shock altitudes. Mass addition rates well in excess of likely values are required to significantly affect the model shock geometry. The hybrid model results imply that oxygen ions originating deep within the dayside Venus magnetic barrier are nearly fluidlike while oxygen ions produced higher on the dayside, at much lower densities, behave more as test particles. Gasdynamic modeling incorporating both fluid and test particle mass addition reproduces the O{sup +} terminator escape flux (a few times 10{sup 24} s{sup {minus}1}) found in the hybrid model and inferred from observations, but underestimates the escape region spatial extent. The hybrid model predictions include a shock asymmetry dependent on the upstream IMF orientation, asymmetries in the magnetic barrier position and field magnitude, an asymmetry in pickup ion speed altitude profiles, and a finite gyroradius effect asymmetry in pickup ion number density caused by field draping.« less

The influence of polarizability and charge transfer on specific ion effects in the dynamics of aqueous salt solutions

NASA Astrophysics Data System (ADS)

Nguyen, Mary; Rick, Steven W.

2018-06-01

The diffusion rates for water molecules in salt solutions depend on the identity of the ions, as well as their concentration. Among the alkali metal ions, cesium and potassium increase and sodium strongly decreases the diffusion constant of water. The origin of the difference can be understood by examining the simulation results using different potential models. In this work, aqueous solutions of salts are simulated with a variety of models. Commonly used non-polarizable models, which otherwise reproduce many experimental properties, do not capture the trend in the diffusion constant, while models which include polarization and/or charge transfer interactions do. For the non-polarizable models, the diffusion constant decreases too strongly with salt concentration. The changes in the water diffusion constant with increasing salt concentration match the diffusion constant of the ion. The ion diffusion constant is dependent on the residence time for water in the ion solvation shell. The non-polarizable models over-estimate the residence time, relative to the translational diffusion constant and so tend to under-estimate the ion and water diffusion constants.

Room temperature ionic liquids: A simple model. Effect of chain length and size of intermolecular potential on critical temperature.

PubMed

Chapela, Gustavo A; Guzmán, Orlando; Díaz-Herrera, Enrique; del Río, Fernando

2015-04-21

A model of a room temperature ionic liquid can be represented as an ion attached to an aliphatic chain mixed with a counter ion. The simple model used in this work is based on a short rigid tangent square well chain with an ion, represented by a hard sphere interacting with a Yukawa potential at the head of the chain, mixed with a counter ion represented as well by a hard sphere interacting with a Yukawa potential of the opposite sign. The length of the chain and the depth of the intermolecular forces are investigated in order to understand which of these factors are responsible for the lowering of the critical temperature. It is the large difference between the ionic and the dispersion potentials which explains this lowering of the critical temperature. Calculation of liquid-vapor equilibrium orthobaric curves is used to estimate the critical points of the model. Vapor pressures are used to obtain an estimate of the triple point of the different models in order to calculate the span of temperatures where they remain a liquid. Surface tensions and interfacial thicknesses are also reported.

Studying ion exchange in solution and at biological membranes by FCS.

PubMed

Widengren, Jerker

2013-01-01

By FCS, a wide range of processes can be studied, covering time ranges from subnanoseconds to seconds. In principle, any process at equilibrium conditions can be measured, which reflects itself by a change in the detected fluorescence intensity. In this review, it is described how FCS and variants thereof can be used to monitor ion exchange, in solution and along biological membranes. Analyzing fluorescence fluctuations of ion-sensitive fluorophores by FCS offers selective advantages over other techniques for measuring local ion concentrations, and, in particular, for studying exchange kinetics of ions on a very local scale. This opens for several areas of application. The FCS approach was used to investigate fundamental aspects of proton exchange at and along biological membranes. The protonation relaxation rate, as measured by FCS for a pH-sensitive dye, can also provide information about local accessibility/interaction of a particular labeling site and conformational states of biomolecules, in a similar fashion as in a fluorescence quenching experiment. The same FCS concept can also be applied to ion exchange studies using other ion-sensitive fluorophores, and by use of dyes sensitive to other ambient conditions the concept can be extended also beyond ion exchange studies. Copyright © 2013 Elsevier Inc. All rights reserved.

IR and TPD studies of the interaction of alkenes with Cu + sites in CuNaY and CuNaX zeolites of various Cu content. The heterogeneity of Cu + sites

NASA Astrophysics Data System (ADS)

Datka, J.; Kukulska-Zajaç, E.; Kozyra, P.

2006-08-01

Cu + ions in zeolites activate organic molecules containing π electrons by π back donation, which results in a distinct weakening of multiple bonds. In this study, we followed the activation of alkenes (ethene and propene) by Cu + ions in CuY and CuX zeolites of various Cu content. We also studied the strength of bonding of alkenes to Cu + ions. IR studies have shown that there are two kinds of Cu + sites of various electron donor properties. We suppose that they could be attributed to the presence of Cu + ions of various number of oxygen atoms surrounding the cation. IR studies have shown that Cu ions introduced into Y and X zeolites in the first-order (at low Cu content) form Cu + ions of stronger electron donor properties (i.e. activate alkenes to larger extend) than Cu ions introduced in the next order (at higher Cu content). IR and TPD studies of alkenes desorption evidenced that Cu + ions of stronger electron donor properties bond alkenes stronger than less electron donor ones. It suggests that π back donation has more important contribution to the strength of bonding alkenes to cation than π donation.

Pseudomonas stutzeri N2O reductase contains CuA-type sites.

PubMed Central

Scott, R A; Zumft, W G; Coyle, C L; Dooley, D M

1989-01-01

N2O reductase (N2O----N2) is the terminal enzyme in the energy-conserving denitrification pathway of soil and marine denitrifying bacteria. The protein is composed of two identical subunits and contains eight copper ions per enzyme molecule. The magnetic circular dichroism spectrum of resting (oxidized) N2O reductase is strikingly similar to the magnetic circular dichroism spectrum of the CuA site in mammalian cytochrome c oxidase [Greenwood, C., Hull, B. C., Barber, D., Eglinton, D. G. & Thomson, A. J. (1983) Biochem. J. 215, 303-316] and is unlike the magnetic circular dichroism spectra of all other biological copper chromophores obtained to date. Sulfur (or chlorine) scatterers are required to fit the copper extended x-ray absorption fine structure data of both the oxidized and reduced forms of N2O reductase. Satisfactory fits require a Cu-N or Cu-O [denoted Cu-(N, O)] interaction at 2.0 A, a Cu-(S, Cl) interaction at 2.3 A and an additional Cu(S, Cl) interaction at approximately 2.6 A (oxidized) or approximately 2.7 A (reduced). Approximately eight sulfur ions (per eight copper ions) at approximately 2.3 A are required to fit the extended x-ray absorption fine structure data for both the oxidized and reduced N2O reductase. The 2.3-A Cu-(S, Cl) distance is nearly identical to that previously determined for the CuA site in cytochrome c oxidase. A 2.6-2.7 A Cu-(S, Cl) interaction is also present in resting and fully reduced cytochrome c oxidase. Comparison of the N2O reductase sequence, determined by translating the structural NosZ gene, with cytochrome c oxidase subunit II sequences from several sources indicates that a Gly-Xaa-Xaa-Xaa-Xaa-Xaa-Cys-Ser-Xaa-Xaa-Cys-Xaa-Xaa-Xaa-His stretch is highly conserved. This sequence contains three of the probable ligands (two cysteines and one histidine) in a CuA-type site. Collectively these data establish that Pseudomonas stutzeri N2O reductase contains CuA-type sites. PMID:2542963

Plasma IMS Composition Measurements for Europa and the Other Galilean Moons

NASA Technical Reports Server (NTRS)

Sittler, Edward; Cooper, John; Hartle, Richard; Lipatov, Alexander; Mahaffy, Paul; Paterson, William; Pachalidis, Nick; Coplan, Mike; Cassidy, Tim

2010-01-01

NASA and ESA are planning the joint Europa Jupiter System Mission (EJSM) to the Jupiter system with specific emphasis to Europa and Ganymede, respectively. The Japanese Space Agency is also planning an orbiter mission to explore Jupiter's magnetosphere and the Galilean satellites. For NASA's Jupiter Europa Orbiter (JEO) we are developing the 3D Ion Mass Spectrometer (IMS) with two main goals which can also be applied to the other Galilean moons, 1) measure the plasma interaction between Europa and Jupiter's magnetosphere and 2) infer the 4 pi surface composition to trace elemental and significant isotopic levels. The first goal supports the magnetometer (MAG) measurements, primarily directed at detection of Europa's sub-surface ocean, while the second gives information about transfer of material between the Galilean moons, and between the moon surfaces and subsurface layers putatively including oceans. The measurement of the interactions for all the Galilean moons can be used to trace the in situ ion measurements of pickup ions back to either Europa's or Ganymede's surface from the respectively orbiting spacecraft. The IMS instrument, being developed under NASA's Astrobiology Instrument Development Program, would maximally achieve plasma measurement requirements for JEO and EJSM while moving forward our knowledge of Jupiter system composition and source processes to far higher levels than previously envisaged. The composition of the global surfaces of Europa and Ganymede can be inferred from the measurement of ejected neutrals and pick-up ions using at minimum an in situ payload including MAG and IMS also fully capable of meeting Level 1 mission requirements for ocean detection and survey. Elemental and isotopic analysis of potentially extruded oceanic materials at the moon surfaces would further support the ocean objectives. These measurements should be made from a polar orbiting spacecraft about Europa or Ganymede at height 100 km. The ejecta produced by sputtering of the surfaces of Europa and Ganymede has been shown to be representative of the surface composition. Level 2 science on surface geology and composition can then be further enhanced by addition of the following: 3D Ion Neutral Mass Spectrometer (INNS), 3D plasma electron spectrometer (ELS), and hot plasma energetic particle instrument. The measurement approach is to alternate between times measuring pickup ions and times measuring plasma and magnetic field parameters along the spacecraft trajectory. By measuring the pickup ion energy, arrival direction and mass-per-charge, the ion can be traced back along the ejection trajectory to the approximate area of origin if the 3-D electric field and magnetic field are known. In situ observations of plasma flow velocities and vector magnetic fields can be used to determine the local convective electric field (E = -VXB) along the spacecraft trajectory. By combining this information with models of the magnetospheric interaction with Europa, one can generate 3D maps of the electric and magnetic field and compute the trajectories of the pickup ions back to the surface or exospheric points of origin. In the case of Ganymede there is the additional complexity of its own internal dipole magnetic field, while Io's volcanic activity introduces the complexity of a highly structured denser atmosphere. Callisto with its less globally extended exosphere will have a simpler interaction than for Europa (i.e., more like our moon). We will discuss these differences in light of the above proposed technique. Finally, the INNS observations and neutral exosphere models are needed to estimate production rates of pickup ions. The hot plasma measurements are needed to correct for sputtering rates which can be time dependent and electron plasma observations for electron impact ionization rates. Instrument characteristics, field-of-view requirements, modes of operation and effects of radiation on instrument functionality will be discussed.

Adsorption of Zn(II) and Cd(II) ions in batch system by using the Eichhornia crassipes.

PubMed

Módenes, A N; Espinoza-Quiñones, F R; Borba, C E; Trigueros, D E G; Lavarda, F L; Abugderah, M M; Kroumov, A D

2011-01-01

In this work, the displacement effects on the sorption capacities of zinc and cadmium ions of the Eichornia crassipes-type biosorbent in batch binary system has been studied. Preliminary single metal sorption experiments were carried out. An improvement on the Zn(II) and Cd(II) ions removal was achieved by working at 30 °C temperature and with non-uniform biosorbent grain sizes. A 60 min equilibrium time was achieved for both Zn(II) and Cd(II) ions. Furthermore, it was found that the overall kinetic data were best described by the pseudo second-order kinetic model. Classical multi-component adsorption isotherms have been tested as well as a modified extended Langmuir isotherm model, showing good agreement with the equilibrium binary data. Around 0.65 mequiv./g maximum metal uptake associated with the E. crassipes biosorbent was attained and the E. crassipes biosorbent has shown higher adsorption affinity for the zinc ions than for the cadmium ones in the binary system.

Estimates of Ionospheric Transport and Ion Loss at Mars

NASA Astrophysics Data System (ADS)

Cravens, T. E.; Hamil, O.; Houston, S.; Bougher, S.; Ma, Y.; Brain, D.; Ledvina, S.

2017-10-01

Ion loss from the topside ionosphere of Mars associated with the solar wind interaction makes an important contribution to the loss of volatiles from this planet. Data from NASA's Mars Atmosphere and Volatile Evolution mission combined with theoretical modeling are now helping us to understand the processes involved in the ion loss process. Given the complexity of the solar wind interaction, motivation exists for considering a simple approach to this problem and for understanding how the loss rates might scale with solar wind conditions and solar extreme ultraviolet irradiance. This paper reviews the processes involved in the ionospheric dynamics. Simple analytical and semiempirical expressions for ion flow speeds and ion loss are derived. In agreement with more sophisticated models and with purely empirical studies, it is found that the oxygen loss rate from ion transport is about 5% (i.e., global O ion loss rate of Qion ≈ 4 × 1024 s-1) of the total oxygen loss rate. The ion loss is found to approximately scale as the square root of the solar ionizing photon flux and also as the square root of the solar wind dynamic pressure. Typical ion flow speeds are found to be about 1 km/s in the topside ionosphere near an altitude of 300 km on the dayside. Not surprisingly, the plasma flow speed is found to increase with altitude due to the decreasing ion-neutral collision frequency.

Electrostatic shock structures in dissipative multi-ion dusty plasmas

NASA Astrophysics Data System (ADS)

Elkamash, I. S.; Kourakis, I.

2018-06-01

A comprehensive analytical model is introduced for shock excitations in dusty bi-ion plasma mixtures, taking into account collisionality and kinematic (fluid) viscosity. A multicomponent plasma configuration is considered, consisting of positive ions, negative ions, electrons, and a massive charged component in the background (dust). The ionic dynamical scale is focused upon; thus, electrons are assumed to be thermalized, while the dust is stationary. A dissipative hybrid Korteweg-de Vries/Burgers equation is derived. An analytical solution is obtained, in the form of a shock structure (a step-shaped function for the electrostatic potential, or an electric field pulse) whose maximum amplitude in the far downstream region decays in time. The effect of relevant plasma configuration parameters, in addition to dissipation, is investigated. Our work extends earlier studies of ion-acoustic type shock waves in pure (two-component) bi-ion plasma mixtures.

Biomolecular electrostatics and solvation: a computational perspective

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

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G.

2012-11-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. Thismore » review discusses the solvation of biomolecules with a computational biophysics view towards describing the phenomenon. While our main focus lies on the computational aspect of the models, we summarize the common characteristics of biomolecular solvation (e.g., solvent structure, polarization, ion binding, and nonpolar behavior) in order to provide reasonable backgrounds to understand the solvation models.« less

Biomolecular electrostatics and solvation: a computational perspective

PubMed Central

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G.; Schnieders, Michael J.; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A.

2012-01-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view towards describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g., solvent structure, polarization, ion binding, and nonpolar behavior) in order to provide a background to understand the different types of solvation models. PMID:23217364

Biomolecular electrostatics and solvation: a computational perspective.

PubMed

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G; Schnieders, Michael J; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A

2012-11-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

A novel algorithm for the calculation of physical and biological irradiation quantities in scanned ion beam therapy: the beamlet superposition approach

NASA Astrophysics Data System (ADS)

Russo, G.; Attili, A.; Battistoni, G.; Bertrand, D.; Bourhaleb, F.; Cappucci, F.; Ciocca, M.; Mairani, A.; Milian, F. M.; Molinelli, S.; Morone, M. C.; Muraro, S.; Orts, T.; Patera, V.; Sala, P.; Schmitt, E.; Vivaldo, G.; Marchetto, F.

2016-01-01

The calculation algorithm of a modern treatment planning system for ion-beam radiotherapy should ideally be able to deal with different ion species (e.g. protons and carbon ions), to provide relative biological effectiveness (RBE) evaluations and to describe different beam lines. In this work we propose a new approach for ion irradiation outcomes computations, the beamlet superposition (BS) model, which satisfies these requirements. This model applies and extends the concepts of previous fluence-weighted pencil-beam algorithms to quantities of radiobiological interest other than dose, i.e. RBE- and LET-related quantities. It describes an ion beam through a beam-line specific, weighted superposition of universal beamlets. The universal physical and radiobiological irradiation effect of the beamlets on a representative set of water-like tissues is evaluated once, coupling the per-track information derived from FLUKA Monte Carlo simulations with the radiobiological effectiveness provided by the microdosimetric kinetic model and the local effect model. Thanks to an extension of the superposition concept, the beamlet irradiation action superposition is applicable for the evaluation of dose, RBE and LET distributions. The weight function for the beamlets superposition is derived from the beam phase space density at the patient entrance. A general beam model commissioning procedure is proposed, which has successfully been tested on the CNAO beam line. The BS model provides the evaluation of different irradiation quantities for different ions, the adaptability permitted by weight functions and the evaluation speed of analitical approaches. Benchmarking plans in simple geometries and clinical plans are shown to demonstrate the model capabilities.

Interaction of Simple Ions with Water: Theoretical Models for the Study of Ion Hydration

ERIC Educational Resources Information Center

Gancheff, Jorge S.; Kremer, Carlos; Ventura, Oscar N.

2009-01-01

A computational experiment aimed to create and systematically analyze models of simple cation hydrates is presented. The changes in the structure (bond distances and angles) and the electronic density distribution of the solvent and the thermodynamic parameters of the hydration process are calculated and compared with the experimental data. The…

Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel.

PubMed

Jalily Hasani, Horia; Ganesan, Aravindhan; Ahmed, Marawan; Barakat, Khaled H

2018-01-01

The voltage-gated KCNQ1 potassium ion channel interacts with the type I transmembrane protein minK (KCNE1) to generate the slow delayed rectifier (IKs) current in the heart. Mutations in these transmembrane proteins have been linked with several heart-related issues, including long QT syndromes (LQTS), congenital atrial fibrillation, and short QT syndrome. Off-target interactions of several drugs with that of KCNQ1/KCNE1 ion channel complex have been known to cause fatal cardiac irregularities. Thus, KCNQ1/KCNE1 remains an important avenue for drug-design and discovery research. In this work, we present the structural and mechanistic details of potassium ion permeation through an open KCNQ1 structural model using the combined molecular dynamics and steered molecular dynamics simulations. We discuss the processes and key residues involved in the permeation of a potassium ion through the KCNQ1 ion channel, and how the ion permeation is affected by (i) the KCNQ1-KCNE1 interactions and (ii) the binding of chromanol 293B ligand and its derivatives into the complex. The results reveal that interactions between KCNQ1 with KCNE1 causes a pore constriction in the former, which in-turn forms small energetic barriers in the ion-permeation pathway. These findings correlate with the previous experimental reports that interactions of KCNE1 dramatically slows the activation of KCNQ1. Upon ligand-binding onto the complex, the energy-barriers along ion permeation path are more pronounced, as expected, therefore, requiring higher force in our steered-MD simulations. Nevertheless, pulling the ion when a weak blocker is bound to the channel does not necessitate high force in SMD. This indicates that our SMD simulations have been able to discern between strong and week blockers and reveal their influence on potassium ion permeation. The findings presented here will have some implications in understanding the potential off-target interactions of the drugs with the KCNQ1/KCNE1 channel that lead to cardiotoxic effects.

Analog quantum simulation of generalized Dicke models in trapped ions

NASA Astrophysics Data System (ADS)

Aedo, Ibai; Lamata, Lucas

2018-04-01

We propose the analog quantum simulation of generalized Dicke models in trapped ions. By combining bicromatic laser interactions on multiple ions we can generate all regimes of light-matter coupling in these models, where here the light mode is mimicked by a motional mode. We present numerical simulations of the three-qubit Dicke model both in the weak field (WF) regime, where the Jaynes-Cummings behavior arises, and the ultrastrong coupling (USC) regime, where a rotating-wave approximation cannot be considered. We also simulate the two-qubit biased Dicke model in the WF and USC regimes and the two-qubit anisotropic Dicke model in the USC regime and the deep-strong coupling regime. The agreement between the mathematical models and the ion system convinces us that these quantum simulations can be implemented in the laboratory with current or near-future technology. This formalism establishes an avenue for the quantum simulation of many-spin Dicke models in trapped ions.

Phosphate effects on copper(II) and lead(II) sorption to ferrihydrite

NASA Astrophysics Data System (ADS)

Tiberg, Charlotta; Sjöstedt, Carin; Persson, Ingmar; Gustafsson, Jon Petter

2013-11-01

Transport of lead(II) and copper(II) ions in soil is affected by the soil phosphorus status. Part of the explanation may be that phosphate increases the adsorption of copper(II) and lead(II) to iron (hydr)oxides in soil, but the details of these interactions are poorly known. Knowledge about such mechanisms is important, for example, in risk assessments of contaminated sites and development of remediation methods. We used a combination of batch experiments, extended X-ray absorption fine structure (EXAFS) spectroscopy and surface complexation modeling with the three-plane CD-MUSIC model to study the effect of phosphate on sorption of copper(II) and lead(II) to ferrihydrite. The aim was to identify the surface complexes formed and to derive constants for the surface complexation reactions. In the batch experiments phosphate greatly enhanced the adsorption of copper(II) and lead(II) to ferrihydrite at pH < 6. The largest effects were seen for lead(II).

Spin-state transitions and magnetic polaron in lightly doped La1-xSrxCoO3.

NASA Astrophysics Data System (ADS)

Podlesnyak, A.; Haverkort, M. W.; Conder, K.; Pomyakushina, E.; Khomskii, Daniel

2007-03-01

Using the inelastic neutron scattering (INS) technique, we identified the energy levels of the thermally excited states of Co^3+ ions in both LaCoO3 and La0.998Sr0.002CoO3. In LaCoO3 an excitation at ˜0.6 meV appears at T>30K, whose intensity follows the bulk magnetization. Within a model including crystal field interaction and spin-orbit coupling we interpret this excitation as originating from a transition between thermally excited states located about 120 K above the ground state. Since the g-factor obtained from the field dependence of the INS is g˜ 3, we interpret this state as a high-spin state of Co^3+ . The lightly doped material x˜0:002 exhibits paramagnetic properties at low temperatures. An INS peak at energy transfer ˜0.75 meV was observed in it already at T = 1:5 K. We propose that the holes introduced in the LS state of LaCoO3 by doping are extended over the neighboring Co sites, forming thus magnetic polaron and transforming all the involved Co ions (e.g. 6 of them) to the high-spin state. Similarly to LaCoO3, we interpret the INS transition at 0.75 meV as that on these high-spin Co^3+ ions.

On-board adaptive model for state of charge estimation of lithium-ion batteries based on Kalman filter with proportional integral-based error adjustment

NASA Astrophysics Data System (ADS)

Wei, Jingwen; Dong, Guangzhong; Chen, Zonghai

2017-10-01

With the rapid development of battery-powered electric vehicles, the lithium-ion battery plays a critical role in the reliability of vehicle system. In order to provide timely management and protection for battery systems, it is necessary to develop a reliable battery model and accurate battery parameters estimation to describe battery dynamic behaviors. Therefore, this paper focuses on an on-board adaptive model for state-of-charge (SOC) estimation of lithium-ion batteries. Firstly, a first-order equivalent circuit battery model is employed to describe battery dynamic characteristics. Then, the recursive least square algorithm and the off-line identification method are used to provide good initial values of model parameters to ensure filter stability and reduce the convergence time. Thirdly, an extended-Kalman-filter (EKF) is applied to on-line estimate battery SOC and model parameters. Considering that the EKF is essentially a first-order Taylor approximation of battery model, which contains inevitable model errors, thus, a proportional integral-based error adjustment technique is employed to improve the performance of EKF method and correct model parameters. Finally, the experimental results on lithium-ion batteries indicate that the proposed EKF with proportional integral-based error adjustment method can provide robust and accurate battery model and on-line parameter estimation.

Removal of ammonium ion from water by Na-rich birnessite: Performance and mechanisms.

PubMed

Cheng, Ya; Huang, Tinglin; Shi, Xinxin; Wen, Gang; Sun, Yuankui

2017-07-01

Na-rich birnessite (NRB) was synthesized by a simple synthesis method and used as a high-efficiency adsorbent for the removal of ammonium ion (NH 4 + ) from aqueous solution. In order to demonstrate the adsorption performance of the synthesized material, the effects of contact time, pH, initial ammonium ion concentration, and temperature were investigated. Adsorption kinetics showed that the adsorption behavior followed the pseudo second-order kinetic model. The equilibrium adsorption data were fitted to Langmuir and Freundlich adsorption models and the model parameters were evaluated. The monolayer adsorption capacity of the adsorbent, as obtained from the Langmuir isotherm, was 22.61mg NH 4 + -N/g at 283K. Thermodynamic analyses showed that the adsorption was spontaneous and that it was also a physisorption process. Our data revealed that the higher NH 4 + adsorption capacity could be primarily attributed to the water absorption process and electrostatic interaction. Particularly, the high surface hydroxyl-content of NRB enables strong interactions with ammonium ion. The results obtained in this study illustrate that the NRB is expected to be an effective and economically viable adsorbent for ammonium ion removal from aqueous system. Copyright © 2016. Published by Elsevier B.V.

Acetonitrile Ion Suppression in Atmospheric Pressure Ionization Mass Spectrometry

NASA Astrophysics Data System (ADS)

Colizza, Kevin; Mahoney, Keira E.; Yevdokimov, Alexander V.; Smith, James L.; Oxley, Jimmie C.

2016-11-01

Efforts to analyze trace levels of cyclic peroxides by liquid chromatography/mass spectrometry gave evidence that acetonitrile suppressed ion formation. Further investigations extended this discovery to ketones, linear peroxides, esters, and possibly many other types of compounds, including triazole and menadione. Direct ionization suppression caused by acetonitrile was observed for multiple adduct types in both electrospray ionization and atmospheric pressure chemical ionization. The addition of only 2% acetonitrile significantly decreased the sensitivity of analyte response. Efforts to identify the mechanism were made using various nitriles. The ion suppression was reduced by substitution of an acetonitrile hydrogen with an electron-withdrawing group, but was exacerbated by electron-donating or steric groups adjacent to the nitrile. Although current theory does not explain this phenomenon, we propose that polar interactions between the various functionalities and the nitrile may be forming neutral aggregates that manifest as ionization suppression.

Benchmarking of Neutron Production of Heavy-Ion Transport Codes

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

Remec, Igor; Ronningen, Reginald M.; Heilbronn, Lawrence

Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondary neutron production. Results are encouraging; however, further improvements in models andmore » codes and additional benchmarking are required.« less

Benchmarking of Heavy Ion Transport Codes

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

Remec, Igor; Ronningen, Reginald M.; Heilbronn, Lawrence

Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in designing and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondary neutron production. Results are encouraging; however, further improvements in models andmore » codes and additional benchmarking are required.« less

Water-mediated ion–ion interactions are enhanced at the water vapor–liquid interface

PubMed Central

Venkateshwaran, Vasudevan; Vembanur, Srivathsan; Garde, Shekhar

2014-01-01

There is overwhelming evidence that ions are present near the vapor–liquid interface of aqueous salt solutions. Charged groups can also be driven to interfaces by attaching them to hydrophobic moieties. Despite their importance in many self-assembly phenomena, how ion–ion interactions are affected by interfaces is not understood. We use molecular simulations to show that the effective forces between small ions change character dramatically near the water vapor–liquid interface. Specifically, the water-mediated attraction between oppositely charged ions is enhanced relative to that in bulk water. Further, the repulsion between like-charged ions is weaker than that expected from a continuum dielectric description and can even become attractive as the ions are drawn to the vapor side. We show that thermodynamics of ion association are governed by a delicate balance of ion hydration, interfacial tension, and restriction of capillary fluctuations at the interface, leading to nonintuitive phenomena, such as water-mediated like charge attraction. “Sticky” electrostatic interactions may have important consequences on biomolecular structure, assembly, and aggregation at soft liquid interfaces. We demonstrate this by studying an interfacially active model peptide that changes its structure from α-helical to a hairpin-turn–like one in response to charging of its ends. PMID:24889634

A water stable europium coordination polymer as fluorescent sensor for detecting Fe3+, CrO42-, and Cr2O72- ions

NASA Astrophysics Data System (ADS)

Chen, Chen; Zhang, Xiaolei; Gao, Peng; Hu, Ming

2018-02-01

A europium coordination polymer constructed by the 4‧-(4-carboxyphenyl)- 2,2‧:6‧,2″-terpyridine ligand (HL), namely, [EuL(CH3COO)Cl]n (1), has been prepared by the solvothermal method. Compound 1 was structurally characterized by the elemental analysis, FT-IR, powder X-ray diffractions (PXRD), thermogravimetric (TG) analysis, and single-crystal X-ray diffraction. Complex 1 displays a novel linear chain structure, which further extends to the 3D supramolecular structure via π···π and hydrogen bonds interactions. The luminescent properties of 1 were investigated in detail, which exhibit the fluorescent sensing for detecting Fe3+, CrO42-, and Cr2O72- ions in aqueous solution, respectively. In addition, 1 shows high sensitive and selective sensing for CrO42- and Cr2O72- anions with the great quenching efficiency. Furthermore, the luminescent sensing mechanisms of differentiating analytes are explored in detail. It is worth noting that there exists the weak interaction between Fe3+ ions and carboxylate oxygen atoms of CH3COO- groups through XPS characterization, resulting in the high quenching effect of 1.

Ionic blockade of the rat connexin40 gap junction channel by large tetraalkylammonium ions.

PubMed

Musa, H; Gough, J D; Lees, W J; Veenstra, R D

2001-12-01

The rat connexin40 gap junction channel is permeable to monovalent cations including tetramethylammonium and tetraethylammonium ions. Larger tetraalkyammonium (TAA(+)) ions beginning with tetrabutylammonium (TBA(+)) reduced KCl junctional currents disproportionately. Ionic blockade by tetrapentylammonium (TPeA(+)) and tetrahexylammonium (THxA(+)) ions were concentration- and voltage-dependent and occurred only when TAA(+) ions were on the same side as net K(+) efflux across the junction, indicative of block of the ionic permeation pathway. The voltage-dependent dissociation constants (K(m)(V(j))) were lower for THxA(+) than TPeA(+), consistent with steric effects within the pore. The K(m)-V(j) relationships for TPeA(+) and THxA(+) were fit with different reaction rate models for a symmetrical (homotypic) connexin gap junction channel and were described by either a one- or two-site model that assumed each ion traversed the entire V(j) field. Bilateral addition of TPeA(+) ions confirmed a common site of interaction within the pore that possessed identical K(m)(V(j)) values for cis-trans concentrations of TPeA(+) ions as indicated by the modeled I-V relations and rapid channel block that precluded unitary current measurements. The TAA(+) block of K(+) currents and bilateral TPeA(+) interactions did not alter V(j)-gating of Cx40 gap junctions. N-octyl-tributylammonium and -triethylammonium also blocked rCx40 channels with higher affinity and faster kinetics than TBA(+) or TPeA(+), indicative of a hydrophobic site within the pore near the site of block.

Collision cross sections and transport coefficients of O-, O2 -, O3 - and O4 - negative ions in O2, N2 and dry air for non-thermal plasmas modelling

NASA Astrophysics Data System (ADS)

Hennad, Ali; Yousfi, Mohammed

2018-02-01

The ions interaction data such as interaction potential parameters, elastic and inelastic collision cross sections and the transport coefficients (reduced mobility and diffusion coefficients) have been determined and analyzed in the case of the main negative oxygen ions (O-, O2 -, O3 - and O4 -) present in low temperature plasma at atmospheric pressure when colliding O2, N2 and dry air. The ion transport has been determined from an optimized Monte Carlo simulation using calculated elastic and experimentally fitted inelastic collision cross sections. The elastic momentum transfer collision cross sections have been calculated from a semi-classical JWKB approximation based on a ( n-4) rigid core interaction potential model. The cross sections sets involving elastic and inelastic processes were then validated using measured reduced mobility data and also diffusion coefficient whenever available in the literature. From the sets of elastic and inelastic collision cross sections thus obtained for the first time for O3-/O2, O2 -/N2, O3 -/N2, and O4 -/N2 systems, the ion transport coefficients were calculated in pure gases and dry air over a wide range of the density reduced electric field E/N.

Nonlinear excitations in electron-positron-ion plasmas in accretion disks of active galactic nuclei

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

Moslem, W. M.; Kourakis, I.; Shukla, P. K.

2007-10-15

The propagation of acoustic nonlinear excitations in an electron-positron-ion (e-p-i) plasma composed of warm electrons and positrons, as well as hot ions, has been investigated by adopting a two-dimensional cylindrical geometry. The electrons and positrons are modeled by hydrodynamic fluid equations, while the ions are assumed to follow a temperature-parametrized Boltzmann distribution (the fixed ion model is recovered in the appropriate limit). This situation applies in the accretion disk near a black hole in active galactic nuclei, where the ion temperature may be as high as 3 to 300 times that of the electrons. Using a reductive perturbation technique, amore » cylindrical Kadomtsev-Petviashvili equation is derived and its exact soliton solutions are presented. Furthermore, real situations in which the strength of the nonlinearity may be weak are considered, so that higher-order nonlinearity plays an important role. Accordingly, an extended cylindrical Kadomtsev-Petviashvili equation is derived, which admits both soliton and double-layer solutions. The characteristics of the nonlinear excitations obtained are investigated in detail.« less

Heavy-ion dominance near Cluster perigees

NASA Astrophysics Data System (ADS)

Ferradas, C. P.; Zhang, J.-C.; Kistler, L. M.; Spence, H. E.

2015-12-01

Time periods in which heavy ions dominate over H+ in the energy range of 1-40 keV were observed by the Cluster Ion Spectrometry (CIS)/COmposition DIstribution Function (CODIF) instrument onboard Cluster Spacecraft 4 at L values less than 4. The characteristic feature is a narrow flux peak at around 10 keV that extends into low L values, with He+ and/or O+ dominating. In the present work we perform a statistical study of these events and examine their temporal occurrence and spatial distribution. The observed features, both the narrow energy range and the heavy-ion dominance, can be interpreted using a model of ion drift from the plasma sheet, subject to charge exchange losses. The narrow energy range corresponds to the only energy range that has direct drift access from the plasma sheet during quiet times. The drift time to these locations from the plasma sheet is > 30 h, so that charge exchange has a significant impact on the population. We show that a simple drift/loss model can explain the dependence on L shell and MLT of these heavy-ion-dominant time periods.

Non-thermalization in trapped atomic ion spin chains

NASA Astrophysics Data System (ADS)

Hess, P. W.; Becker, P.; Kaplan, H. B.; Kyprianidis, A.; Lee, A. C.; Neyenhuis, B.; Pagano, G.; Richerme, P.; Senko, C.; Smith, J.; Tan, W. L.; Zhang, J.; Monroe, C.

2017-10-01

Linear arrays of trapped and laser-cooled atomic ions are a versatile platform for studying strongly interacting many-body quantum systems. Effective spins are encoded in long-lived electronic levels of each ion and made to interact through laser-mediated optical dipole forces. The advantages of experiments with cold trapped ions, including high spatio-temporal resolution, decoupling from the external environment and control over the system Hamiltonian, are used to measure quantum effects not always accessible in natural condensed matter samples. In this review, we highlight recent work using trapped ions to explore a variety of non-ergodic phenomena in long-range interacting spin models, effects that are heralded by the memory of out-of-equilibrium initial conditions. We observe long-lived memory in static magnetizations for quenched many-body localization and prethermalization, while memory is preserved in the periodic oscillations of a driven discrete time crystal state. This article is part of the themed issue 'Breakdown of ergodicity in quantum systems: from solids to synthetic matter'.

Non-thermalization in trapped atomic ion spin chains.

PubMed

Hess, P W; Becker, P; Kaplan, H B; Kyprianidis, A; Lee, A C; Neyenhuis, B; Pagano, G; Richerme, P; Senko, C; Smith, J; Tan, W L; Zhang, J; Monroe, C

2017-12-13

Linear arrays of trapped and laser-cooled atomic ions are a versatile platform for studying strongly interacting many-body quantum systems. Effective spins are encoded in long-lived electronic levels of each ion and made to interact through laser-mediated optical dipole forces. The advantages of experiments with cold trapped ions, including high spatio-temporal resolution, decoupling from the external environment and control over the system Hamiltonian, are used to measure quantum effects not always accessible in natural condensed matter samples. In this review, we highlight recent work using trapped ions to explore a variety of non-ergodic phenomena in long-range interacting spin models, effects that are heralded by the memory of out-of-equilibrium initial conditions. We observe long-lived memory in static magnetizations for quenched many-body localization and prethermalization, while memory is preserved in the periodic oscillations of a driven discrete time crystal state.This article is part of the themed issue 'Breakdown of ergodicity in quantum systems: from solids to synthetic matter'. © 2017 The Author(s).

Reconstructing Ion Spectra from Low-Altitude ENAs: Moderate to Large Storms.

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Solution of the Dirac Coulomb equation for helium-like ions in the Poet-Temkin model

NASA Astrophysics Data System (ADS)

Tang, Li-Yan; Tang, Yong-Bo; Shi, Ting-Yun; Mitroy, J.

2013-10-01

The Dirac-Coulomb equation for the helium atom is studied under the restrictions of the Poet-Temkin model which replaces the 1/r12 interaction by the simplified 1/r> form. The effective reduction in the dimensionality made it possible to obtain binding energies for the singlet and triplet states in this model problem with a relative precision from 10-8 to 10-10. The energies for the singlet state were consistent with a previous configuration interaction calculation [H. Tatewaki and Y. Watanabe, Chem. Phys. 389, 58 (2011)]. Manifestations of Brown-Ravenhall disease were noted at higher values of nuclear charge and ultimately limited the accuracy of the Poet-Temkin model energy. The energies from a no-pair configuration interaction (CI) calculation (the negative-energy states for the appropriate hydrogen-like ion were excluded from the CI expansion) were found to be different from the unrestricted B-spline calculation.

Solution of the Dirac Coulomb equation for helium-like ions in the Poet-Temkin model.

PubMed

Tang, Li-Yan; Tang, Yong-Bo; Shi, Ting-Yun; Mitroy, J

2013-10-07

The Dirac-Coulomb equation for the helium atom is studied under the restrictions of the Poet-Temkin model which replaces the 1/r12 interaction by the simplified 1/r> form. The effective reduction in the dimensionality made it possible to obtain binding energies for the singlet and triplet states in this model problem with a relative precision from 10(-8) to 10(-10). The energies for the singlet state were consistent with a previous configuration interaction calculation [H. Tatewaki and Y. Watanabe, Chem. Phys. 389, 58 (2011)]. Manifestations of Brown-Ravenhall disease were noted at higher values of nuclear charge and ultimately limited the accuracy of the Poet-Temkin model energy. The energies from a no-pair configuration interaction (CI) calculation (the negative-energy states for the appropriate hydrogen-like ion were excluded from the CI expansion) were found to be different from the unrestricted B-spline calculation.

Four-fluid MHD Simulations of the Plasma and Neutral Gas Environment of Comet Churyumov-Gerasimenko Near Perihelio

NASA Astrophysics Data System (ADS)

Huang, Z.; Toth, G.; Gombosi, T. I.; Jia, X.; Rubin, M.; Hansen, K. C.; Fougere, N.; Bieler, A. M.; Shou, Y.; Altwegg, K.; Combi, M. R.; Tenishev, V.

2015-12-01

The neutral and plasma environment is critical in understanding the interaction of comet Churyumov-Gerasimenko (CG), the target of the Rosetta mission, and the solar wind. To serve this need and support the Rosetta mission, we develop a 3-D four fluid model, which is based on BATS-R-US within the SWMF (Space Weather Modeling Framework) that solves the governing multi-fluid MHD equations and the Euler equations for the neutral gas fluid. These equations describe the behavior and interactions of the cometary heavy ions, the solar wind protons, the electrons, and the neutrals. This model incorporates different mass loading processes, including photo and electron impact ionization, charge exchange, dissociative ion-electron recombination, and collisional interactions between different fluids. We simulate the near nucleus plasma and neutral gas environment near perihelion with a realistic shape model of CG and compare our simulation results with Rosetta observations.

Fidelity study of superconductivity in extended Hubbard models

NASA Astrophysics Data System (ADS)

Plonka, N.; Jia, C. J.; Wang, Y.; Moritz, B.; Devereaux, T. P.

2015-07-01

The Hubbard model with local on-site repulsion is generally thought to possess a superconducting ground state for appropriate parameters, but the effects of more realistic long-range Coulomb interactions have not been studied extensively. We study the influence of these interactions on superconductivity by including nearest- and next-nearest-neighbor extended Hubbard interactions in addition to the usual on-site terms. Utilizing numerical exact diagonalization, we analyze the signatures of superconductivity in the ground states through the fidelity metric of quantum information theory. We find that nearest and next-nearest neighbor interactions have thresholds above which they destabilize superconductivity regardless of whether they are attractive or repulsive, seemingly due to competing charge fluctuations.

Modeling multicomponent ion exchange equilibrium utilizing hydrous crystalline silicotitanates by a multiple interactive ion exchange site model

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

Zheng, Z.; Anthony, R.G.; Miller, J.E.

1997-06-01

An equilibrium multicomponent ion exchange model is presented for the ion exchange of group I metals by TAM-5, a hydrous crystalline silicotitanate. On the basis of the data from ion exchange and structure studies, the solid phase is represented as Na{sub 3}X instead of the usual form of NaX. By using this solid phase representation, the solid can be considered as an ideal phase. A set of model ion exchange reactions is proposed for ion exchange between H{sup +}, Na{sup +}, K{sup +}, Rb{sup +}, and Cs{sup +}. The equilibrium constants for these reactions were estimated from experiments with simplemore » ion exchange systems. Bromley`s model for activity coefficients of electrolytic solutions was used to account for liquid phase nonideality. Bromley`s model parameters for CsOH at high ionic strength and for NO{sub 2}{sup {minus}} and Al(OH){sub 4}{sup {minus}} were estimated in order to apply the model for complex waste simulants. The equilibrium compositions and distribution coefficients of counterions were calculated for complex simulants typical of DOE wastes by solving the equilibrium equations for the model reactions and material balance equations. The predictions match the experimental results within 10% for all of these solutions.« less

Multi-fluid MHD simulations of Europa's interaction with Jupiter's magnetosphere

NASA Astrophysics Data System (ADS)

Harris, C. D. K.; Jia, X.; Slavin, J. A.; Rubin, M.; Toth, G.

2017-12-01

Several distinct physical processes generate the interaction between Europa, the smallest of Jupiter's Galilean moons, and Jupiter's magnetosphere. The 10˚ tilt of Jupiter's dipole causes time varying magnetic fields at Europa's orbit which interact with Europa's subsurface conducting ocean to induce magnetic perturbations around the moon. Jovian plasma interacts with Europa's icy surface to sputter off neutral particles, forming a tenuous exosphere which is then ionized by impact and photo-ionization to form an ionosphere. As jovian plasma flows towards the moon, mass-loading and interaction with the ionosphere slow the flow, producing magnetic perturbations that propagate along the field lines to form an Alfvén wing current system, which connects Europa to its bright footprint in Jupiter's ionosphere. The Galileo mission has shown that the plasma interaction generates significant magnetic perturbations that obscure signatures of the induced field from the subsurface ocean. Modeling the plasma-related perturbations is critical to interpreting the magnetic signatures of Europa's induction field, and therefore to magnetic sounding of its interior, a central goal of the upcoming Europa Clipper mission. Here we model the Europa-Jupiter interaction with multi-fluid magnetohydrodynamic simulations to understand quantitatively how these physical processes affect the plasma and magnetic environment around the moon. Our model separately tracks the bulk motion of three different ion fluids (exospheric O2+, O+, and magnetospheric O+), and includes sources and losses of mass, momentum and energy to each of the ion fluids due to ionization, charge-exchange and recombination. We include calculations of the electron temperature allowing for field-aligned electron heat conduction, and Hall effects due to differential ion-electron motion. Compared to previous simulations, this multi-fluid model allows us to more accurately determine the precipitation flux of jovian plasma to Europa's surface, which has significant implications for space weathering at the moon. Including the Hall effect in our simulations enables us to determine the effects of separate ion-electron bulk motion throughout the interaction, and our simulations reveal noticeable asymmetries and small-scale features in the Alfvén wings.

Extended GTST-MLD for aerospace system safety analysis.

PubMed

Guo, Chiming; Gong, Shiyu; Tan, Lin; Guo, Bo

2012-06-01

The hazards caused by complex interactions in the aerospace system have become a problem that urgently needs to be settled. This article introduces a method for aerospace system hazard interaction identification based on extended GTST-MLD (goal tree-success tree-master logic diagram) during the design stage. GTST-MLD is a functional modeling framework with a simple architecture. Ontology is used to extend the ability of system interaction description in GTST-MLD by adding the system design knowledge and the past accident experience. From the level of functionality and equipment, respectively, this approach can help the technician detect potential hazard interactions. Finally, a case is used to show the method. © 2011 Society for Risk Analysis.

Oblique Interaction of Dust-ion Acoustic Solitons with Superthermal Electrons in a Magnetized Plasma

NASA Astrophysics Data System (ADS)

Parveen, Shahida; Mahmood, Shahzad; Adnan, Muhammad; Qamar, Anisa

2018-01-01

The oblique interaction between two dust-ion acoustic (DIA) solitons travelling in the opposite direction, in a collisionless magnetized plasma composed of dynamic ions, static dust (positive/negative) charged particles and interialess kappa distributed electrons is investigated. By employing extended Poincaré-Lighthill-Kuo (PLK) method, Korteweg-de Vries (KdV) equations are derived for the right and left moving low amplitude DIA solitons. Their trajectories and corresponding phase shifts before and after their interaction are also obtained. It is found that in negatively charged dusty plasma above the critical dust charged to ion density ratio the positive polarity pulse is formed, while below the critical dust charged density ratio the negative polarity pulse of DIA soliton exist. However it is found that only positive polarity pulse of DIA solitons exist for the positively charged dust particles case in a magnetized nonthermal plasma. The nonlinearity coefficient in the KdV equation vanishes for the negatively charged dusty plasma case for a particular set of parameters. Therefore, at critical plasma density composition for negatively charged dust particles case, the modified Korteweg-de Vries (mKdV) equations having cubic nonlinearity coefficient of the DIA solitons, and their corresponding phase shifts are derived for the left and right moving solitons. The effects of the system parameters including the obliqueness of solitons propagation with respect to magnetic field direction, superthermality of electrons and concentration of positively/negatively static dust charged particles on the phase shifts of the colliding solitons are also discussed and presented numerically. The results are applicable to space magnetized dusty plasma regimes.

Real-time dynamics of lattice gauge theories with a few-qubit quantum computer

NASA Astrophysics Data System (ADS)

Martinez, Esteban A.; Muschik, Christine A.; Schindler, Philipp; Nigg, Daniel; Erhard, Alexander; Heyl, Markus; Hauke, Philipp; Dalmonte, Marcello; Monz, Thomas; Zoller, Peter; Blatt, Rainer

2016-06-01

Gauge theories are fundamental to our understanding of interactions between the elementary constituents of matter as mediated by gauge bosons. However, computing the real-time dynamics in gauge theories is a notorious challenge for classical computational methods. This has recently stimulated theoretical effort, using Feynman’s idea of a quantum simulator, to devise schemes for simulating such theories on engineered quantum-mechanical devices, with the difficulty that gauge invariance and the associated local conservation laws (Gauss laws) need to be implemented. Here we report the experimental demonstration of a digital quantum simulation of a lattice gauge theory, by realizing (1 + 1)-dimensional quantum electrodynamics (the Schwinger model) on a few-qubit trapped-ion quantum computer. We are interested in the real-time evolution of the Schwinger mechanism, describing the instability of the bare vacuum due to quantum fluctuations, which manifests itself in the spontaneous creation of electron-positron pairs. To make efficient use of our quantum resources, we map the original problem to a spin model by eliminating the gauge fields in favour of exotic long-range interactions, which can be directly and efficiently implemented on an ion trap architecture. We explore the Schwinger mechanism of particle-antiparticle generation by monitoring the mass production and the vacuum persistence amplitude. Moreover, we track the real-time evolution of entanglement in the system, which illustrates how particle creation and entanglement generation are directly related. Our work represents a first step towards quantum simulation of high-energy theories using atomic physics experiments—the long-term intention is to extend this approach to real-time quantum simulations of non-Abelian lattice gauge theories.

Average-atom model for two-temperature states and ionic transport properties of aluminum in the warm dense matter regime

NASA Astrophysics Data System (ADS)

Hou, Yong; Fu, Yongsheng; Bredow, Richard; Kang, Dongdong; Redmer, Ronald; Yuan, Jianmin

2017-03-01

The average-atom model combined with the hyper-netted chain approximation is an efficient tool for electronic and ionic structure calculations for warm dense matter. Here we generalize this method in order to describe non-equilibrium states with different electron and ion temperature as produced in laser-matter interactions on ultra-short time scales. In particular, the electron-ion and ion-ion correlation effects are considered when calculating the electron structure. We derive an effective ion-ion pair-potential using the electron densities in the framework of temperature-depended density functional theory. Using this ion-ion potential we perform molecular dynamics simulations in order to determine the ionic transport properties such as the ionic diffusion coefficient and the shear viscosity through the ionic velocity autocorrelation functions.

Real-Time linux dynamic clamp: a fast and flexible way to construct virtual ion channels in living cells.

PubMed

Dorval, A D; Christini, D J; White, J A

2001-10-01

We describe a system for real-time control of biological and other experiments. This device, based around the Real-Time Linux operating system, was tested specifically in the context of dynamic clamping, a demanding real-time task in which a computational system mimics the effects of nonlinear membrane conductances in living cells. The system is fast enough to represent dozens of nonlinear conductances in real time at clock rates well above 10 kHz. Conductances can be represented in deterministic form, or more accurately as discrete collections of stochastically gating ion channels. Tests were performed using a variety of complex models of nonlinear membrane mechanisms in excitable cells, including simulations of spatially extended excitable structures, and multiple interacting cells. Only in extreme cases does the computational load interfere with high-speed "hard" real-time processing (i.e., real-time processing that never falters). Freely available on the worldwide web, this experimental control system combines good performance. immense flexibility, low cost, and reasonable ease of use. It is easily adapted to any task involving real-time control, and excels in particular for applications requiring complex control algorithms that must operate at speeds over 1 kHz.

Energy Deposition Processes in Titan's Upper Atmosphere

NASA Technical Reports Server (NTRS)

Sittler, Edward C., Jr.; Bertucci, Cesar; Coates, Andrew; Cravens, Tom; Dandouras, Iannis; Shemansky, Don

2008-01-01

Most of Titan's atmospheric organic and nitrogen chemistry, aerosol formation, and atmospheric loss are driven from external energy sources such as Solar UV, Saturn's magnetosphere, solar wind and galactic cosmic rays. The Solar UV tends to dominate the energy input at lower altitudes of approximately 1100 km but which can extend down to approximately 400 km, while the plasma interaction from Saturn's magnetosphere, Saturn's magnetosheath or solar wind are more important at higher altitudes of approximately 1400 km, but the heavy ion plasma [O(+)] of approximately 2 keV and energetic ions [H(+)] of approximately 30 keV or higher from Saturn's magnetosphere can penetrate below 950km. Cosmic rays with energies of greater than 1 GeV can penetrate much deeper into Titan's atmosphere with most of its energy deposited at approximately 100 km altitude. The haze layer tends to dominate between 100 km and 300 km. The induced magnetic field from Titan's interaction with the external plasma can be very complex and will tend to channel the flow of energy into Titan's upper atmosphere. Cassini observations combined with advanced hybrid simulations of the plasma interaction with Titan's upper atmosphere show significant changes in the character of the interaction with Saturn local time at Titan's orbit where the magnetosphere displays large and systematic changes with local time. The external solar wind can also drive sub-storms within the magnetosphere which can then modify the magnetospheric interaction with Titan. Another important parameter is solar zenith angle (SZA) with respect to the co-rotation direction of the magnetospheric flow. Titan's interaction can contribute to atmospheric loss via pickup ion loss, scavenging of Titan's ionospheric plasma, loss of ionospheric plasma down its induced magnetotail via an ionospheric wind, and non-thermal loss of the atmosphere via heating and sputtering induced by the bombardment of magnetospheric keV ions and electrons. This energy input evidently drives the large positive and negative ions observed below approximately 1100 km altitude with ion masses exceeding 10,000 daltons. We refer to these ions as seed particles for the aerosols observed below 300 km altitude. These seed particles can be formed, for example, from the polymerization of acetylene (C2H2) and benzene (C6H6) molecules in Titan's upper atmosphere to form polycyclic aromatic hydrocarbons (PAH) and/or fullerenes (C60). In the case of fullerenes, which are hollow spherical carbon shells, magnetospheric keV [O(+)] ions can become trapped inside the fullerenes and eventually find themselves inside the aerosols as free oxygen. The aerosols are then expected to fall to Titan's surface as polymerized hydrocarbons with trapped free oxygen where unknown surface chemistry can take place.

Track structure of protons and other light ions in liquid water: applications of the LIonTrack code at the nanometer scale.

PubMed

Bäckström, G; Galassi, M E; Tilly, N; Ahnesjö, A; Fernández-Varea, J M

2013-06-01

The LIonTrack (Light Ion Track) Monte Carlo (MC) code for the simulation of H(+), He(2+), and other light ions in liquid water is presented together with the results of a novel investigation of energy-deposition site properties from single ion tracks. The continuum distorted-wave formalism with the eikonal initial state approximation (CDW-EIS) is employed to generate the initial energy and angle of the electrons emitted in ionizing collisions of the ions with H2O molecules. The model of Dingfelder et al. ["Electron inelastic-scattering cross sections in liquid water," Radiat. Phys. Chem. 53, 1-18 (1998); "Comparisons of calculations with PARTRAC and NOREC: Transport of electrons in liquid water," Radiat. Res. 169, 584-594 (2008)] is linked to the general-purpose MC code PENELOPE/penEasy to simulate the inelastic interactions of the secondary electrons in liquid water. In this way, the extended PENELOPE/penEasy code may provide an improved description of the 3D distribution of energy deposits (EDs), making it suitable for applications at the micrometer and nanometer scales. Single-ionization cross sections calculated with the ab initio CDW-EIS formalism are compared to available experimental values, some of them reported very recently, and the theoretical electronic stopping powers are benchmarked against those recommended by the ICRU. The authors also analyze distinct aspects of the spatial patterns of EDs, such as the frequency of nearest-neighbor distances for various radiation qualities, and the variation of the mean specific energy imparted in nanoscopic targets located around the track. For 1 MeV/u particles, the C(6+) ions generate about 15 times more clusters of six EDs within an ED distance of 3 nm than H(+). On average clusters of two to three EDs for 1 MeV/u H(+) and clusters of four to five EDs for 1 MeV/u C(6+) could be expected for a modeling double strand break distance of 3.4 nm.

Ion beams in radiotherapy - from tracks to treatment planning

NASA Astrophysics Data System (ADS)

Krämer, M.; Scifoni, E.; Wälzlein, C.; Durante, M.

2012-07-01

Several dozen clinical sites around the world apply beams of fast light ions for radiotherapeutical purposes. Thus there is a vested interest in the various physical and radiobiological processes governing the interaction of ion beams with matter, specifically living systems. We discuss the various modelling steps which lead from basic interactions to the application in actual patient treatment planning. The nano- and microscopic scale is covered by sample calculations with our TRAX code. On the macroscopic scale we feature the TRiP98 treatment planning system, which was clinically used in GSI's radiotherapy pilot project.

Ion pairing and phase behaviour of an asymmetric restricted primitive model of ionic liquids

NASA Astrophysics Data System (ADS)

Lu, Hongduo; Li, Bin; Nordholm, Sture; Woodward, Clifford E.; Forsman, Jan

2016-12-01

An asymmetric restricted primitive model (ARPM) of electrolytes is proposed as a simple three parameter (charge q, diameter d, and charge displacement b) model of ionic liquids and solutions. Charge displacement allows electrostatic and steric interactions to operate between different centres, so that orientational correlations arise in ion-ion interactions. In this way the ionic system may have partly the character of a simple ionic fluid/solid and of a polar fluid formed from ion pairs. The present exploration of the system focuses on the ion pair formation mechanism, the relative concentration of paired and free ions and the consequences for the cohesive energy, and the tendency to form fluid or solid phase. In contrast to studies of similar (though not identical) models in the past, we focus on behaviours at room temperature. By MC and MD simulations of such systems composed of monovalent ions of hard-sphere (or essentially hard-sphere) diameter equal to 5 Å and a charge displacement ranging from 0 to 2 Å from the hard-sphere origin, we find that ion pairing dominates for b larger than 1 Å. When b exceeds about 1.5 Å, the system is essentially a liquid of dipolar ion pairs with a small presence of free ions. We also investigate dielectric behaviours of corresponding liquids, composed of purely dipolar species. Many basic features of ionic liquids appear to be remarkably consistent with those of our ARPM at ambient conditions, when b is around 1 Å. However, the rate of self-diffusion and, to a lesser extent, conductivity is overestimated, presumably due to the simple spherical shape of our ions in the ARPM. The relative simplicity of our ARPM in relation to the rich variety of new mechanisms and properties it introduces, and to the numerical simplicity of its exploration by theory or simulation, makes it an essential step on the way towards representation of the full complexity of ionic liquids.

Ion pairing and phase behaviour of an asymmetric restricted primitive model of ionic liquids.

PubMed

Lu, Hongduo; Li, Bin; Nordholm, Sture; Woodward, Clifford E; Forsman, Jan

2016-12-21

An asymmetric restricted primitive model (ARPM) of electrolytes is proposed as a simple three parameter (charge q, diameter d, and charge displacement b) model of ionic liquids and solutions. Charge displacement allows electrostatic and steric interactions to operate between different centres, so that orientational correlations arise in ion-ion interactions. In this way the ionic system may have partly the character of a simple ionic fluid/solid and of a polar fluid formed from ion pairs. The present exploration of the system focuses on the ion pair formation mechanism, the relative concentration of paired and free ions and the consequences for the cohesive energy, and the tendency to form fluid or solid phase. In contrast to studies of similar (though not identical) models in the past, we focus on behaviours at room temperature. By MC and MD simulations of such systems composed of monovalent ions of hard-sphere (or essentially hard-sphere) diameter equal to 5 Å and a charge displacement ranging from 0 to 2 Å from the hard-sphere origin, we find that ion pairing dominates for b larger than 1 Å. When b exceeds about 1.5 Å, the system is essentially a liquid of dipolar ion pairs with a small presence of free ions. We also investigate dielectric behaviours of corresponding liquids, composed of purely dipolar species. Many basic features of ionic liquids appear to be remarkably consistent with those of our ARPM at ambient conditions, when b is around 1 Å. However, the rate of self-diffusion and, to a lesser extent, conductivity is overestimated, presumably due to the simple spherical shape of our ions in the ARPM. The relative simplicity of our ARPM in relation to the rich variety of new mechanisms and properties it introduces, and to the numerical simplicity of its exploration by theory or simulation, makes it an essential step on the way towards representation of the full complexity of ionic liquids.

Determining fundamental properties of matter created in ultrarelativistic heavy-ion collisions

NASA Astrophysics Data System (ADS)

Novak, J.; Novak, K.; Pratt, S.; Vredevoogd, J.; Coleman-Smith, C. E.; Wolpert, R. L.

2014-03-01

Posterior distributions for physical parameters describing relativistic heavy-ion collisions, such as the viscosity of the quark-gluon plasma, are extracted through a comparison of hydrodynamic-based transport models to experimental results from 100AGeV+100AGeV Au +Au collisions at the Relativistic Heavy Ion Collider. By simultaneously varying six parameters and by evaluating several classes of observables, we are able to explore the complex intertwined dependencies of observables on model parameters. The methods provide a full multidimensional posterior distribution for the model output, including a range of acceptable values for each parameter, and reveal correlations between them. The breadth of observables and the number of parameters considered here go beyond previous studies in this field. The statistical tools, which are based upon Gaussian process emulators, are tested in detail and should be extendable to larger data sets and a higher number of parameters.

Nonlinear response and bistability of driven ion acoustic waves

NASA Astrophysics Data System (ADS)

Akbari-Moghanjoughi, M.

2017-08-01

The hydrodynamic model is used to obtain a generalized pseudoforce equation through which the nonlinear response of periodically driven ion acoustic waves is studied in an electron-ion plasma with isothermal and adiabatic ion fluids. The pseudotime series, corresponding to different driving frequencies, indicates that nonlinearity effects appear more strongly for smaller frequency values. The existence of extra harmonic resonances in the nonlinear amplitude spectrum is a clear indication of the interaction of an external force with harmonic components of the nonlinear ion acoustic waves. It is shown that many plasma parameters significantly and differently affect the nonlinear resonance spectrum of ion acoustic excitations. A heuristic but accurate model for the foldover effect is used which quite satisfactorily predicts the bistability of driven plasma oscillations. It is remarked that the characteristic resonance peak of isothermal ion plasma oscillations appears at lower frequencies but is stronger compared to that of adiabatic ions. Comparison of the exact numerical results for fully nonlinear and approximate (weakly nonlinear) models indicates that a weakly nonlinear model exaggerates the hysteresis and jump phenomenon for higher values of the external force amplitude.

Quantifying short-lived events in multistate ionic current measurements.

PubMed

Balijepalli, Arvind; Ettedgui, Jessica; Cornio, Andrew T; Robertson, Joseph W F; Cheung, Kin P; Kasianowicz, John J; Vaz, Canute

2014-02-25

We developed a generalized technique to characterize polymer-nanopore interactions via single channel ionic current measurements. Physical interactions between analytes, such as DNA, proteins, or synthetic polymers, and a nanopore cause multiple discrete states in the current. We modeled the transitions of the current to individual states with an equivalent electrical circuit, which allowed us to describe the system response. This enabled the estimation of short-lived states that are presently not characterized by existing analysis techniques. Our approach considerably improves the range and resolution of single-molecule characterization with nanopores. For example, we characterized the residence times of synthetic polymers that are three times shorter than those estimated with existing algorithms. Because the molecule's residence time follows an exponential distribution, we recover nearly 20-fold more events per unit time that can be used for analysis. Furthermore, the measurement range was extended from 11 monomers to as few as 8. Finally, we applied this technique to recover a known sequence of single-stranded DNA from previously published ion channel recordings, identifying discrete current states with subpicoampere resolution.

Pairwise Interaction Extended Point-Particle (PIEP) model for multiphase jets and sedimenting particles

NASA Astrophysics Data System (ADS)

Liu, Kai; Balachandar, S.

2017-11-01

We perform a series of Euler-Lagrange direct numerical simulations (DNS) for multiphase jets and sedimenting particles. The forces the flow exerts on the particles in these two-way coupled simulations are computed using the Basset-Bousinesq-Oseen (BBO) equations. These forces do not explicitly account for particle-particle interactions, even though such pairwise interactions induced by the perturbations from neighboring particles may be important especially when the particle volume fraction is high. Such effects have been largely unaddressed in the literature. Here, we implement the Pairwise Interaction Extended Point-Particle (PIEP) model to simulate the effect of neighboring particle pairs. A simple collision model is also applied to avoid unphysical overlapping of solid spherical particles. The simulation results indicate that the PIEP model provides a more elaborative and complicated movement of the dispersed phase (droplets and particles). Office of Naval Research (ONR) Multidisciplinary University Research Initiative (MURI) project N00014-16-1-2617.

Ion acceleration from thin foil and extended plasma targets by slow electromagnetic wave and related ion-ion beam instability

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

Bulanov, S. V.; A. M. Prokhorov Institute of General Physics RAS, Moscow, 119991; Esirkepov, T. Zh.

When ions are accelerated by the radiation pressure of a laser pulse, their velocity cannot exceed the pulse group velocity which can be considerably smaller than the speed of light in vacuum. This is demonstrated in two cases corresponding to a thin foil target irradiated by high intensity laser light and to the hole boring produced in an extended plasma by the laser pulse. It is found that the beams of accelerated ions are unstable against Buneman-like and Weibel-like instabilities which results in the broadening of the ion energy spectrum.

Extending the Community Multiscale Air Quality (CMAQ) Modeling System to Hemispheric Scales: Overview of Process Considerations and Initial Applications

PubMed Central

Mathur, Rohit; Xing, Jia; Gilliam, Robert; Sarwar, Golam; Hogrefe, Christian; Pleim, Jonathan; Pouliot, George; Roselle, Shawn; Spero, Tanya L.; Wong, David C.; Young, Jeffrey

2018-01-01

The Community Multiscale Air Quality (CMAQ) modeling system is extended to simulate ozone, particulate matter, and related precursor distributions throughout the Northern Hemisphere. Modelled processes were examined and enhanced to suitably represent the extended space and time scales for such applications. Hemispheric scale simulations with CMAQ and the Weather Research and Forecasting (WRF) model are performed for multiple years. Model capabilities for a range of applications including episodic long-range pollutant transport, long-term trends in air pollution across the Northern Hemisphere, and air pollution-climate interactions are evaluated through detailed comparison with available surface, aloft, and remotely sensed observations. The expansion of CMAQ to simulate the hemispheric scales provides a framework to examine interactions between atmospheric processes occurring at various spatial and temporal scales with physical, chemical, and dynamical consistency. PMID:29681922

Dynamical quantum phase transitions in extended transverse Ising models

NASA Astrophysics Data System (ADS)

Bhattacharjee, Sourav; Dutta, Amit

2018-04-01

We study the dynamical quantum phase transitions (DQPTs) manifested in the subsequent unitary dynamics of an extended Ising model with an additional three spin interactions following a sudden quench. Revisiting the equilibrium phase diagram of the model, where different quantum phases are characterized by different winding numbers, we show that in some situations the winding number may not change across a gap closing point in the energy spectrum. Although, usually there exists a one-to-one correspondence between the change in winding number and the number of critical time scales associated with DQPTs, we show that the extended nature of interactions may lead to unusual situations. Importantly, we show that in the limit of the cluster Ising model, three critical modes associated with DQPTs become degenerate, thereby leading to a single critical time scale for a given sector of Fisher zeros.

Modeling the structure and thermodynamics of ferrocenium-based ionic liquids.

PubMed

Bernardes, Carlos E S; Mochida, Tomoyuki; Canongia Lopes, José N

2015-04-21

A new force-field for the description of ferrocenium-based ionic liquids is reported. The proposed model was validated by confronting Molecular Dynamics simulations results with available experimental data-enthalpy of fusion, crystalline structure and liquid density-for a series of 1-alkyl-2,3,4,5,6,7,8,9-octamethylferrocenium bis(trifluoromethylsulfonyl)imide ionic liquids, [CnFc][NTf2] (3 ≤ n ≤ 10). The model is able to reproduce the densities and enthalpies of fusion with deviations smaller than 2.6% and 4.8 kJ mol(-1), respectively. The MD simulation trajectories were also used to compute relevant structural information for the different [CnFc][NTf2] ionic liquids. The results show that, unlike other ILs, the alkyl side chains present in the cations are able to interact directly with the ferrocenium core of other ions. Even the ferrocenium charged cores (with relatively mild charge densities) are able to form small contact aggregates. This causes the partial rupture of the polar network and precludes the formation of extended nano-segregated polar-nonpolar domains normally observed in other ionic liquids.

Analysis of the Cometary Plasma Environment of 67P/Churyumov-Gerasimenko Near Perihelion

NASA Astrophysics Data System (ADS)

Ostaszewski, K.; Goetz, C.; Motschmann, U.; Glassmeier, K. H.

2017-09-01

Over the course of its two year escort phase the Rosetta spacecraft has provided various observations that furthered our understanding of the cometary plasma environment. The use of numerical simulations is essential for this understanding because they allow to place the in situ measurements in a global context, in turn, through observations the numerical models can be ex- tended and improved. We use the simulation code A.I.K.E.F (Müller [7]) to simulate the cometary plasma environment of 67P/Churyumov-Gerasimenko (67P/CG). Based on observations made by the Rosetta spacecraft we extend the numerical model by electron impact ionization and the anisotropic outgassing model by Hansen et al. (2016). Both extensions result in an increase in the cometary ion production rate on the dayside. Therefore, the size of the interaction region and the contained structures increases. This causes the position of the different boundaries, e.g. bow shock, to shift further away from the comet. Considering this we can explain why no bow shock crossings could be observed during the dayside excursion of Rosetta in September 2015.

Synthesis, purification, and structural characterization of the dimethyldiselenoarsinate anion.

PubMed

Gailer, Jürgen; George, Graham N; Harris, Hugh H; Pickering, Ingrid J; Prince, Roger C; Somogyi, Arpad; Buttigieg, Gavin A; Glass, Richard S; Denton, M Bonner

2002-10-21

A novel arsenic-selenium solution species was synthesized by reacting equimolar sodium selenite and sodium dimethylarsinate with 10 mol equiv of glutathione (pH 7.5) in aqueous solution. The solution species showed a single (77)Se NMR resonance at 112.8 ppm. Size-exclusion chromatography (SEC) using an inductively coupled plasma atomic emission spectrometer (ICP-AES) as the simultaneous arsenic-, selenium-, sulfur-, and carbon-specific detector revealed an arsenic-selenium moiety with an As:Se molar ratio of 1:2. Electrospray ionization mass spectrometry (ESI-MS) of the chromatographically purified compound showed a molecular mass peak at m/z 263 in the negative ion mode. Fragmentation of the parent ion (ESI-MS-MS) produced (CH(3))(2)As(-) and Se(2)(-) fragments. Arsenic and selenium extended X-ray absorption fine structure spectroscopy (EXAFS) of the purified species revealed two As-C interactions at 1.943 A and two As-Se interactions at 2.279 A. On the basis of these results this novel solution species is identified as the dimethyldiselenoarsinate anion.

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

Farmer, R.W.; Dussert, B.W.; Kovacic, S.L.

Laboratory studies have identified the cause of the pH rise, which occurs during water treatment with activated carbon, as an interaction between the naturally occurring anions and protons in the water and the carbon surface. The interaction can be described as an ion exchange type of phenomenon, in which the carbon surface sorbs the anions and corresponding hydronium ions from the water. These studies have shown that the anion sorption and resulting pH increase is independent of the raw material used for the activated carbon production, e.g. bituminous or subbituminous coal, peat, wood or coconut. Also, the pH excursions occurmore » with virgin, reactivated, and acid washed granular carbons. Current pH control technologies focus on adjustment of the wastewater pH prior to discharge or recycle of the initial effluent water until the pH increase abates. However, improved water pH control options have been realized by altering the carbon surface through controlled oxidation rather than the water chemistry or extended preprocessing at the treatment site.« less

Complex multireference configuration interaction calculations for the K-vacancy Auger states of N{sup q+} (q = 2-5) ions

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

Peng, Yi-Geng; Data Center for High Energy Density Physics, Institute of Applied Physics and Computational Mathematics, P.O. Box 8009, Beijing 100088; Wu, Yong, E-mail: wu-yong@iapcm.ac.cn

2016-02-07

K-vacancy Auger states of N{sup q+} (q = 2-5) ions are studied by using the complex multireference single- and double-excitation configuration interaction (CMRD-CI) method. The calculated resonance parameters are in good agreement with the available experimental and theoretical data. It shows that the resonance positions and widths converge quickly with the increase of the atomic basis sets in the CMRD-CI calculations; the standard atomic basis set can be employed to describe the atomic K-vacancy Auger states well. The strong correlations between the valence and core electrons play important roles in accurately determining those resonance parameters, Rydberg electrons contribute negligibly inmore » the calculations. Note that it is the first time that the complex scaling method has been successfully applied for the B-like nitrogen. CMRD-CI is readily extended to treat the resonance states of molecules in the near future.« less

Coalescence of Magnetic Islands in the low resistivity Hall MHD Regime.

NASA Astrophysics Data System (ADS)

Knoll, D. A.; Chacon, L.; Simakov, A. N.

2006-10-01

We revisit the well-known problem of the coalescence of magnetic islands in the context of Hall MHD. Unlike previous work, we focus on regimes of small resistivity (S ˜10^6) and where the ion skin depth diL (system size). These conditions are of relevance, for instance, in the solar corona and the earth's magnetotail. We aim to address under which conditions such systems can exhibit fast reconnection. First, we revisit the resistive MHD problem to further understand the well-known sloshing result. Next, the interaction between the ion inertial length, di, and the dynamically evolving current sheet scale length, (δJ), is established. Initially, diδJ. If η is such that (δJ) dynamically thins down to di prior to the well-known sloshing phenomena, then sloshing is avoided. This results in peak reconnection rates which are η-independent and scale as √di. However, if di is small enough that resistivity prevents (δJ) from thinning down to this scale prior to sloshing, then reconnection (and sloshing) proceeds as in the resistive MHD model. Finally, we discuss our development of a semi-analytical model to describe the well-known sloshing result in the resistive MHD model, and our plans to extend it to Hall MHD. D. A. Knoll, L. Chac'on, Phys. Plasmas, 13 (3), p.032307 (2006). D. A. Knoll, L. Chac'on, Phys. Rev. Lett., 96, 135001 (2006). A. Simakov, L. Chac'on, D. A. Knoll, Phys. Plasmas, accepted (2006).

Modeling Ultraviolet Emissions Near Io

NASA Technical Reports Server (NTRS)

Linker, Jon A.

2000-01-01

In this report, we describe work awarded to Science Applications International Corporation, for the period 6/l/99 to 5/31/00. During this time period, we have investigated the interaction of Io, Jupiter's innermost Galilean satellite, with the Io plasma torus, and the role this interaction plays in producing ultraviolet (UV) emissions from neutral oxygen and sulfur. Io, the innermost of Jupiter's Galilean satellites, plays a unique role in the jovian magnetosphere. Neutral material that escapes from Io is ionized to form the lo torus, a dense, heavy-ion plasma that corotates with Jupiter and interacts with Io. Io supplies not only the torus, but is a major source of plasma for the entire magnetosphere. Ionization and charge-exchange of neutrals near lo strongly influences the plasma interaction, and Io's neutral atmosphere plays an important role in the generation of currents that couple Io to Jupiter. There have been no in situ measurements of the neutral density near Io, but remote observations of neutrals near lo have been performed for many years. Recent observations from the Hubble Space Telescope (HST) have shown detailed structure in UV emissions from neutral species near Io. Electron-impact of the neutrals by the Io torus plasma is the primary mechanism responsible for exciting these emissions. Previously, we have modeled the Io plasma environment using three-dimensional magnetohydrodynamic (MHD) simulations, and we have shown that the interaction between Io and the plasma torus plays an important role in producing the morphology of the observed emissions. In the past year, we have extended these studies to use both UV observations and Galileo particle and field measurements to investigate the Io interaction.

Modeling of surface-dominated plasmas: from electric thruster to negative ion source.

PubMed

Taccogna, F; Schneider, R; Longo, S; Capitelli, M

2008-02-01

This contribution shows two important applications of the particle-in-cell/monte Carlo technique on ion sources: modeling of the Hall thruster SPT-100 for space propulsion and of the rf negative ion source for ITER neutral beam injection. In the first case translational degrees of freedom are involved, while in the second case inner degrees of freedom (vibrational levels) are excited. Computational results show how in both cases, plasma-wall and gas-wall interactions play a dominant role. These are secondary electron emission from the lateral ceramic wall of SPT-100 and electron capture from caesiated surfaces by positive ions and atoms in the rf negative ion source.

Geant4 hadronic physics for space radiation environment.

PubMed

Ivantchenko, Anton V; Ivanchenko, Vladimir N; Molina, Jose-Manuel Quesada; Incerti, Sebastien L

2012-01-01

To test and to develop Geant4 (Geometry And Tracking version 4) Monte Carlo hadronic models with focus on applications in a space radiation environment. The Monte Carlo simulations have been performed using the Geant4 toolkit. Binary (BIC), its extension for incident light ions (BIC-ion) and Bertini (BERT) cascades were used as main Monte Carlo generators. For comparisons purposes, some other models were tested too. The hadronic testing suite has been used as a primary tool for model development and validation against experimental data. The Geant4 pre-compound (PRECO) and de-excitation (DEE) models were revised and improved. Proton, neutron, pion, and ion nuclear interactions were simulated with the recent version of Geant4 9.4 and were compared with experimental data from thin and thick target experiments. The Geant4 toolkit offers a large set of models allowing effective simulation of interactions of particles with matter. We have tested different Monte Carlo generators with our hadronic testing suite and accordingly we can propose an optimal configuration of Geant4 models for the simulation of the space radiation environment.

Electrostatic correlations at the Stern layer: Physics or chemistry?

NASA Astrophysics Data System (ADS)

Travesset, A.; Vangaveti, S.

2009-11-01

We introduce a minimal free energy describing the interaction of charged groups and counterions including both classical electrostatic and specific interactions. The predictions of the model are compared against the standard model for describing ions next to charged interfaces, consisting of Poisson-Boltzmann theory with additional constants describing ion binding, which are specific to the counterion and the interfacial charge ("chemical binding"). It is shown that the "chemical" model can be appropriately described by an underlying "physical" model over several decades in concentration, but the extracted binding constants are not uniquely defined, as they differ depending on the particular observable quantity being studied. It is also shown that electrostatic correlations for divalent (or higher valence) ions enhance the surface charge by increasing deprotonation, an effect not properly accounted within chemical models. The charged phospholipid phosphatidylserine is analyzed as a concrete example with good agreement with experimental results. We conclude with a detailed discussion on the limitations of chemical or physical models for describing the rich phenomenology of charged interfaces in aqueous media and its relevance to different systems with a particular emphasis on phospholipids.

Electromagnetic Dissociation Cross Sections for High LET Fragments

NASA Technical Reports Server (NTRS)

Norbury, John

2016-01-01

Nuclear interaction cross sections are used in space radiation transport codes to calculate the probability of fragment emission in high energy nucleus-nucleus collisions. Strong interactions usually dominate in these collisions, but electromagnetic (EM) interactions can also sometimes be important. Strong interactions typically occur when the projectile nucleus hits a target nucleus, with a small impact parameter. For impact parameters larger than the sum of the nuclear radii, EM reactions dominate and the process is called electromagnetic dissociation (EMD) if one of the nuclei undergo fragmentation. Previous models of EMD have been used to calculate single proton (p) production, single neutron (n) production or light ion production, where a light ion is defined as an isotope of hydrogen (H) or helium (He), such as a deuteron (2H), a triton (3H), a helion (3He) or an alpha particle (4He). A new model is described which can also account for multiple nucleon production, such as 2p, 2n, 1p1n, 2p1n, 2p2n, etc. in addition to light ion production. Such processes are important to include for the following reasons. Consider, for example, the EMD reaction 56Fe + Al --> 52Cr + X + Al, for a 56Fe projectile impacting Al, which produces the high linear energy transfer (LET) fragment 52Cr. In this reaction, the most probable particles representing X are either 2p2n or 4He. Therefore, production of the high LET fragment 52Cr, must include the multiple nucleon production of 2p2n in addition to the light ion production of 4He. Previous models, such as the NUCFRG3 model, could only account for the 4He production process in this reaction and could not account for 2p2n. The new EMD model presented in this work accounts for both the light ion and multiple nucleon processes, and is therefore able to correctly account for the production of high LET products such as 52Cr. The model will be described and calculations will be presented that show the importance of light ion and multiple nucleon production. The work will also show that EMD reactions contribute most to those fragments with the highest LET.

Oxygen Pickup Ions Measured by MAVEN Outside the Martian Bow Shock

NASA Astrophysics Data System (ADS)

Rahmati, A.; Cravens, T.; Larson, D. E.; Lillis, R. J.; Dunn, P.; Halekas, J. S.; Connerney, J. E. P.; Eparvier, F. G.; Thiemann, E.; Mitchell, D. L.; Jakosky, B. M.

2015-12-01

The MAVEN (Mars Atmosphere and Volatile EvolutioN) spacecraft entered orbit around Mars on September 21, 2014 and has since been detecting energetic oxygen pickup ions by its SEP (Solar Energetic Particles) and SWIA (Solar Wind Ion Analyzer) instruments. The oxygen pickup ions detected outside the Martian bowshock and in the upstream solar wind are associated with the extended hot oxygen exosphere of Mars, which is created mainly by the dissociative recombination of molecular oxygen ions with electrons in the ionosphere. We use analytic solutions to the equations of motion of pickup ions moving in the undisturbed upstream solar wind magnetic and motional electric fields and calculate the flux of oxygen pickup ions at the location of MAVEN. Our model calculates the ionization rate of oxygen atoms in the exosphere based on the hot oxygen densities predicted by Rahmati et al. (2014), and the sources of ionization include photo-ionization, charge exchange, and electron impact ionization. The photo-ionization frequency is calculated using the FISM (Flare Irradiance Spectral Model) solar flux model, based on MAVEN EUVM (Extreme Ultra-Violet Monitor) measurements. The frequency of charge exchange between a solar wind proton and an oxygen atom is calculated using MAVEN SWIA solar wind proton flux measurements, and the electron impact ionization frequency is calculated based on MAVEN SWEA (Solar Wind Electron Analyzer) solar wind electron flux measurements. The solar wind magnetic field used in the model is from the measurements taken by MAVEN MAG (magnetometer) in the upstream solar wind. The good agreement between our predicted pickup oxygen fluxes and the MAVEN SEP and SWIA measured ones confirms detection of oxygen pickup ions and these model-data comparisons can be used to constrain models of hot oxygen densities and photochemical escape flux.

Progress Report for the Joint Services Electronic Program for the Period April 1, 1989 through March 31, 1990 (Coordinated Science Laboratory, University of Illinois at Urbana-Champaign)

DTIC Science & Technology

1990-06-30

since the projected ion range is of the order of lattice constants. Thus, we have extended our thermal-dopant incorporation model and have developed...bombardment results in residual lattice damage, which degrades electrical and optical properties. Obviously, at sufficiently high acceleration energies...understand the details of collisional lattice dynamics and ion-induced defect for- mation and annihilation. In addition, the simulations are providing, for

Absolute emission cross sections for electron capture reactions of C2+, N3+, N4+ and O3+ ions in collisions with Li(2s) atoms

NASA Astrophysics Data System (ADS)

Rieger, G.; Pinnington, E. H.; Ciubotariu, C.

2000-12-01

Absolute photon emission cross sections following electron capture reactions have been measured for C2+, N3+, N4+ and O3+ ions colliding with Li(2s) atoms at keV energies. The results are compared with calculations using the extended classical over-the-barrier model by Niehaus. We explore the limits of our experimental method and present a detailed discussion of experimental errors.

Influence of asymmetries in the magnetic draping pattern at Titan on the emission of energetic neutral atoms

NASA Astrophysics Data System (ADS)

Kabanovic, Slawa; Feyerabend, Moritz; Simon, Sven; Meeks, Zachary; Wulms, Veit

2018-03-01

We model the emission of energetic neutral atoms (ENAs) that are generated by the interaction between energetic ions from Saturn's magnetosphere and neutrals from the upper atmosphere of the giant planet's largest moon Titan. The trajectories of the parent ions and the resulting ENA emission morphology are highly sensitive to the electromagnetic field configuration near the moon. We therefore compare the ENA emission pattern for spatially homogeneous fields to the emission obtained from a magnetohydrodynamic (MHD) and a hybrid (kinetic ions, fluid electrons) model of Titan's magnetospheric interaction, by computing the trajectories of several billion energetic test particles. While the MHD model takes into account the draping of the magnetic field lines around Titan, the hybrid approach also considers the significant asymmetries in the electromagnetic fields due to the large gyroradii of pick-up ions from Titan's ionosphere. In all three models, the upstream parameters correspond to the conditions during Cassini's TA flyby of Titan. The shape, magnitude, and location of the ENA emission maxima vary considerably between these three field configurations. The magnetic pile-up region at Titan's ramside deflects a large number of the energetic parent ions, thereby reducing the ENA flux. However, the draped magnetic field lines in Titan's lobes rotate the gyration planes of the incident energetic ions, thereby facilitating the observable ENA production. Overall, the ENA flux calculated for the MHD model is weaker than the emission obtained for the electromagnetic fields from the hybrid code. In addition, we systematically investigate the dependency of the ENA emission morphology on the energy of the parent ions and on the upstream magnetic field strength.

The FLUKA code for space applications: recent developments

NASA Technical Reports Server (NTRS)

Andersen, V.; Ballarini, F.; Battistoni, G.; Campanella, M.; Carboni, M.; Cerutti, F.; Empl, A.; Fasso, A.; Ferrari, A.; Gadioli, E.;

Discriminant analysis of fused positive and negative ion mobility spectra using multivariate self-modeling mixture analysis and neural networks.

PubMed

Chen, Ping; Harrington, Peter B

2008-02-01

A new method coupling multivariate self-modeling mixture analysis and pattern recognition has been developed to identify toxic industrial chemicals using fused positive and negative ion mobility spectra (dual scan spectra). A Smiths lightweight chemical detector (LCD), which can measure positive and negative ion mobility spectra simultaneously, was used to acquire the data. Simple-to-use interactive self-modeling mixture analysis (SIMPLISMA) was used to separate the analytical peaks in the ion mobility spectra from the background reactant ion peaks (RIP). The SIMPLSIMA analytical components of the positive and negative ion peaks were combined together in a butterfly representation (i.e., negative spectra are reported with negative drift times and reflected with respect to the ordinate and juxtaposed with the positive ion mobility spectra). Temperature constrained cascade-correlation neural network (TCCCN) models were built to classify the toxic industrial chemicals. Seven common toxic industrial chemicals were used in this project to evaluate the performance of the algorithm. Ten bootstrapped Latin partitions demonstrated that the classification of neural networks using the SIMPLISMA components was statistically better than neural network models trained with fused ion mobility spectra (IMS).

Local Aqueous Solvation Structure Around Ca2+ During Ca2+---Cl– Pair Formation

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

Baer, Marcel D.; Mundy, Christopher J.

2016-03-03

The molecular details of single ion solvation around Ca2+ and ion-pairing of Ca2--Cl- are investigated using ab initio molecular dynamics. The use of empirical dispersion corrections to the BLYP functional are investigated by comparison to experimentally available extended X-ray absorption fine structure (EXAFS) measurements, which probes the first solvation shell in great detail. Besides finding differences in the free-energy for both ion-pairing and the coordination number of ion solvation between the quantum and classical descriptions of interaction, there were important differences found between dispersion corrected and uncorrected density functional theory (DFT). Specifically, we show significantly different free-energy landscapes for bothmore » coordination number of Ca2+ and its ion-pairing with Cl- depending on the DFT simulation protocol. Our findings produce a self-consistent treatment of short-range solvent response to the ion and the intermediate to long-range collective response of the electrostatics of the ion-ion interaction to produce a detailed picture of ion-pairing that is consistent with experiment. MDB is supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative at Pacific Northwest National Laboratory. It was conducted under the Laboratory Directed Research and Development Program at PNNL, a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy. CJM acknowledges support from US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. This research used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Additional computing resources were generously allocated by PNNL's Institutional Computing program. The authors thank Prof. Tom Beck for discussions regarding QCT, and Drs. Greg Schenter and Shawn Kathmann for insightful comments.« less

Coarse Grained Model for Exploring Voltage Dependent Ion Channels

PubMed Central

Dryga, Anatoly; Chakrabarty, Suman; Vicatos, Spyridon; Warshel, Arieh

2011-01-01

The relationship between the membrane voltage and the gating of voltage activated ion channels and other systems have been a problem of great current interest. Unfortunately, reliable molecular simulations of external voltage effects present a major challenge, since meaningful converging microscopic simulations are not yet available and macroscopic treatments involve major uncertainties in terms of the dielectric used and other key features. This work extends our coarse grained (CG) model to simulations of membrane/protein systems under external potential. Special attention has been devoted to a consistent modeling of the effect of external potential due to the electrodes, emphasizing semimacroscopic description of the electrolytes in the solution regions between the membranes and the electrodes, as well as the coupling between the combined potential from the electrodes and electrolytes, and the protein ionization states. We also provide a clear connection to microscopic treatment of the electrolytes and thus can explore possible conceptual problems that are hard to resolve by other current approaches. For example, we obtain a clear description of the charge distribution in the entire electrolyte system, including near the electrodes in membrane/electrodes systems (where continuum models do not seem to provide the relevant results). Furthermore, the present treatment provides an insight on the distribution of the electrolyte charges before and after equilibration across the membrane, and thus on the nature of the gating charge. The different aspects of the model have been carefully validated by considering problems ranging for the simple Debye-Huckel, Gouy-Chapman models to the evaluation of the electrolyte distribution between two electrodes, as well as the effect of extending the simulation system by periodic replicas. Overall the clear connection to microscopic descriptions combined with the power of the CG modeling seems to offer a powerful tool for exploring the balance between the protein conformational energy and the interaction with the external potential in voltage activated channels. With this in mind we present a preliminary study of the gating charge in the voltage activated Kv1.2 channel, using the actual change in the electrolyte charge distribution rather than the conventional macroscopic estimate. We also discuss other special features of the model, which include the ability to capture the effect of changes in the protonation states of the protein residues during the open to close voltage induced transition. PMID:21843502

Lithium-ion battery cell-level control using constrained model predictive control and equivalent circuit models

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

Xavier, MA; Trimboli, MS

This paper introduces a novel application of model predictive control (MPC) to cell-level charging of a lithium-ion battery utilizing an equivalent circuit model of battery dynamics. The approach employs a modified form of the MPC algorithm that caters for direct feed-though signals in order to model near-instantaneous battery ohmic resistance. The implementation utilizes a 2nd-order equivalent circuit discrete-time state-space model based on actual cell parameters; the control methodology is used to compute a fast charging profile that respects input, output, and state constraints. Results show that MPC is well-suited to the dynamics of the battery control problem and further suggestmore » significant performance improvements might be achieved by extending the result to electrochemical models. (C) 2015 Elsevier B.V. All rights reserved.« less

Filling the Gap in Extended Metal Atom Chains: Ferromagnetic Interactions in a Tetrairon(II) String Supported by Oligo-α-pyridylamido Ligands.

PubMed

Nicolini, Alessio; Galavotti, Rita; Barra, Anne-Laure; Borsari, Marco; Caleffi, Matteo; Luo, Guangpu; Novitchi, Ghenadie; Park, Kyungwha; Ranieri, Antonio; Rigamonti, Luca; Roncaglia, Fabrizio; Train, Cyrille; Cornia, Andrea

2018-05-07

The stringlike complex [Fe 4 (tpda) 3 Cl 2 ] (2; H 2 tpda = N 2 , N 6 -bis(pyridin-2-yl)pyridine-2,6-diamine) was obtained as the first homometallic extended metal atom chain based on iron(II) and oligo-α-pyridylamido ligands. The synthesis was performed under strictly anaerobic and anhydrous conditions using dimesityliron, [Fe 2 (Mes) 4 ] (1; HMes = mesitylene), as both an iron source and a deprotonating agent for H 2 tpda. The four lined-up iron(II) ions in the structure of 2 (Fe···Fe = 2.94-2.99 Å, Fe···Fe···Fe = 171.7-168.8°) are wrapped by three doubly deprotonated twisted ligands, and the chain is capped at its termini by two chloride ions. The spectroscopic and electronic properties of 2 were investigated in dichloromethane by UV-vis-NIR absorption spectroscopy, 1 H NMR spectroscopy, and cyclic voltammetry. The electrochemical measurements showed four fully resolved, quasi-reversible one-electron-redox processes, implying that 2 can adopt five oxidation states in a potential window of only 0.8 V. Direct current (dc) magnetic measurements indicate dominant ferromagnetic coupling at room temperature, although the ground state is only weakly magnetic. On the basis of density functional theory and angular overlap model calculations, this magnetic behavior was explained as being due to two pairs of ferromagnetically coupled iron(II) ions ( J = -21 cm -1 using JŜ i ·Ŝ j convention) weakly antiferromagnetically coupled with each other. Alternating-current susceptibility data in the presence of a 2 kOe dc field and at frequencies up to 1.5 kHz revealed the onset of slow magnetic relaxation below 2.8 K, with the estimated energy barrier U eff / k B = 10.1(1.3) K.

Monte-Carlo Orbit/Full Wave Simulation of Fast Alfvén Wave (FW) Damping on Resonant Ions in Tokamaks

NASA Astrophysics Data System (ADS)

Choi, M.; Chan, V. S.; Tang, V.; Bonoli, P.; Pinsker, R. I.; Wright, J.

2005-09-01

To simulate the resonant interaction of fast Alfvén wave (FW) heating and Coulomb collisions on energetic ions, including finite orbit effects, a Monte-Carlo code ORBIT-RF has been coupled with a 2D full wave code TORIC4. ORBIT-RF solves Hamiltonian guiding center drift equations to follow trajectories of test ions in 2D axisymmetric numerical magnetic equilibrium under Coulomb collisions and ion cyclotron radio frequency quasi-linear heating. Monte-Carlo operators for pitch-angle scattering and drag calculate the changes of test ions in velocity and pitch angle due to Coulomb collisions. A rf-induced random walk model describing fast ion stochastic interaction with FW reproduces quasi-linear diffusion in velocity space. FW fields and its wave numbers from TORIC are passed on to ORBIT-RF to calculate perpendicular rf kicks of resonant ions valid for arbitrary cyclotron harmonics. ORBIT-RF coupled with TORIC using a single dominant toroidal and poloidal wave number has demonstrated consistency of simulations with recent DIII-D FW experimental results for interaction between injected neutral-beam ions and FW, including measured neutron enhancement and enhanced high energy tail. Comparison with C-Mod fundamental heating discharges also yielded reasonable agreement.

Design, Fabrication, and Testing of Emissive Probes to Determine the Plasma Potential of the Plumes of Various Electric Thrusters

NASA Technical Reports Server (NTRS)

Chen, Erinna M.

2005-01-01

A significant problem in the use of electric thrusters in spacecraft is the formation of low-energy ions in the thruster plume. Low-energy ions are formed in the plume via random collisions between high-velocity ions ejected from the thruster and slow-moving neutral atoms of propellant effusing from the engine. The sputtering of spacecraft materials due to interactions with low-energy ions may result in erosion or contamination of the spacecraft. The trajectory of these ions is determined primarily by the plasma potential of the plume. Thus, accurate characterization of the plasma potential is essential to predicting low-energy ion contamination. Emissive probes were utilized to determine the plasma potential. When the ion and electron currents to the probe are balanced, the potential of such probes float to the plasma potential. Two emissive probes were fabricated; one utilizing a DC power supply, another utilizing a rectified AC power source. Labview programs were written to coordinate and automate probe motion in the thruster plume. Employing handshaking interaction, these motion programs were synchronized to various data acquisition programs to ensure precision and accuracy of the measurements. Comparing these experimental values to values from theoretical models will allow for a more accurate prediction of low-energy ion interaction.

Parameterization of Highly Charged Metal Ions Using the 12-6-4 LJ-Type Nonbonded Model in Explicit Water

PubMed Central

2015-01-01

Highly charged metal ions act as catalytic centers and structural elements in a broad range of chemical complexes. The nonbonded model for metal ions is extensively used in molecular simulations due to its simple form, computational speed, and transferability. We have proposed and parametrized a 12-6-4 LJ (Lennard-Jones)-type nonbonded model for divalent metal ions in previous work, which showed a marked improvement over the 12-6 LJ nonbonded model. In the present study, by treating the experimental hydration free energies and ion–oxygen distances of the first solvation shell as targets for our parametrization, we evaluated 12-6 LJ parameters for 18 M(III) and 6 M(IV) metal ions for three widely used water models (TIP3P, SPC/E, and TIP4PEW). As expected, the interaction energy underestimation of the 12-6 LJ nonbonded model increases dramatically for the highly charged metal ions. We then parametrized the 12-6-4 LJ-type nonbonded model for these metal ions with the three water models. The final parameters reproduced the target values with good accuracy, which is consistent with our previous experience using this potential. Finally, tests were performed on a protein system, and the obtained results validate the transferability of these nonbonded model parameters. PMID:25145273

From The Cover: The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties.

PubMed

Xu, Xin; Goddard, William A

2004-03-02

We derive the form for an exact exchange energy density for a density decaying with Gaussian-like behavior at long range. Based on this, we develop the X3LYP (extended hybrid functional combined with Lee-Yang-Parr correlation functional) extended functional for density functional theory to significantly improve the accuracy for hydrogen-bonded and van der Waals complexes while also improving the accuracy in heats of formation, ionization potentials, electron affinities, and total atomic energies [over the most popular and accurate method, B3LYP (Becke three-parameter hybrid functional combined with Lee-Yang-Parr correlation functional)]. X3LYP also leads to a good description of dipole moments, polarizabilities, and accurate excitation energies from s to d orbitals for transition metal atoms and ions. We suggest that X3LYP will be useful for predicting ligand binding in proteins and DNA.

From The Cover: The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties

NASA Astrophysics Data System (ADS)

Xu, Xin; Goddard, William A., III

2004-03-01

We derive the form for an exact exchange energy density for a density decaying with Gaussian-like behavior at long range. Based on this, we develop the X3LYP (extended hybrid functional combined with Lee-Yang-Parr correlation functional) extended functional for density functional theory to significantly improve the accuracy for hydrogen-bonded and van der Waals complexes while also improving the accuracy in heats of formation, ionization potentials, electron affinities, and total atomic energies [over the most popular and accurate method, B3LYP (Becke three-parameter hybrid functional combined with Lee-Yang-Parr correlation functional)]. X3LYP also leads to a good description of dipole moments, polarizabilities, and accurate excitation energies from s to d orbitals for transition metal atoms and ions. We suggest that X3LYP will be useful for predicting ligand binding in proteins and DNA.

The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties

PubMed Central

Xu, Xin; Goddard, William A.

2004-01-01

We derive the form for an exact exchange energy density for a density decaying with Gaussian-like behavior at long range. Based on this, we develop the X3LYP (extended hybrid functional combined with Lee–Yang–Parr correlation functional) extended functional for density functional theory to significantly improve the accuracy for hydrogen-bonded and van der Waals complexes while also improving the accuracy in heats of formation, ionization potentials, electron affinities, and total atomic energies [over the most popular and accurate method, B3LYP (Becke three-parameter hybrid functional combined with Lee–Yang–Parr correlation functional)]. X3LYP also leads to a good description of dipole moments, polarizabilities, and accurate excitation energies from s to d orbitals for transition metal atoms and ions. We suggest that X3LYP will be useful for predicting ligand binding in proteins and DNA. PMID:14981235

Determination of the diffusion coefficient of hydrogen ion in hydrogels.

PubMed

Schuszter, Gábor; Gehér-Herczegh, Tünde; Szűcs, Árpád; Tóth, Ágota; Horváth, Dezső

2017-05-17

The role of diffusion in chemical pattern formation has been widely studied due to the great diversity of patterns emerging in reaction-diffusion systems, particularly in H + -autocatalytic reactions where hydrogels are applied to avoid convection. A custom-made conductometric cell is designed to measure the effective diffusion coefficient of a pair of strong electrolytes containing sodium ions or hydrogen ions with a common anion. This together with the individual diffusion coefficient for sodium ions, obtained from PFGSE-NMR spectroscopy, allows the determination of the diffusion coefficient of hydrogen ions in hydrogels. Numerical calculations are also performed to study the behavior of a diffusion-migration model describing ionic diffusion in our system. The method we present for one particular case may be extended for various hydrogels and diffusing ions (such as hydroxide) which are relevant e.g. for the development of pH-regulated self-healing mechanisms and hydrogels used for drug delivery.

Nonlinear quantum Rabi model in trapped ions

NASA Astrophysics Data System (ADS)

Cheng, Xiao-Hang; Arrazola, Iñigo; Pedernales, Julen S.; Lamata, Lucas; Chen, Xi; Solano, Enrique

2018-02-01

We study the nonlinear dynamics of trapped-ion models far away from the Lamb-Dicke regime. This nonlinearity induces a blockade on the propagation of quantum information along the Hilbert space of the Jaynes-Cummings and quantum Rabi models. We propose to use this blockade as a resource for the dissipative generation of high-number Fock states. Also, we compare the linear and nonlinear cases of the quantum Rabi model in the ultrastrong and deep strong-coupling regimes. Moreover, we propose a scheme to simulate the nonlinear quantum Rabi model in all coupling regimes. This can be done via off-resonant nonlinear red- and blue-sideband interactions in a single trapped ion, yielding applications as a dynamical quantum filter.

Simulation of the Boltzmann Process: An Energy Space Model.

ERIC Educational Resources Information Center

Eger, Martin; Kress, Michael

1982-01-01

A model is introduced for the simulation of Boltzmann-like binary interactions which may be extended to exhibit the effect of angular dependence in the scattering cross section and other dynamical aspects of two-body interactions. (Author/SK)

Electroviscous Effects in Ceramic Nanofiltration Membranes.

PubMed

Farsi, Ali; Boffa, Vittorio; Christensen, Morten Lykkegaard

2015-11-16

Membrane permeability and salt rejection of a γ-alumina nanofiltration membrane were studied and modeled for different salt solutions. Salt rejection was predicted by using the Donnan-steric pore model, in which the extended Nernst-Planck equation was applied to predict ion transport through the pores. The solvent flux was modeled by using the Hagen-Poiseuille equation by introducing electroviscosity instead of bulk viscosity. γ-Alumina particles were used for ζ-potential measurements. The ζ-potential measurements show that monovalent ions did not adsorb on the γ-alumina surface, whereas divalent ions were highly adsorbed. Thus, for divalent ions, the model was modified, owing to pore shrinkage caused by ion adsorption. The ζ-potential lowered the membrane permeability, especially for membranes with a pore radius lower than 3 nm, a ζ-potential higher than 20 mV, and an ionic strength lower than 0.01 m. The rejection model showed that, for a pore radius lower than 3 nm and for solutions with ionic strengths lower than 0.01 m, there is an optimum ζ-potential for rejection, because of the concurrent effects of electromigration and convection. Hence, the model can be used as a prediction tool to optimize membrane perm-selectivity by designing a specific pore size and surface charge for application at specific ionic strengths and pH levels. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interactions of calcium and fulvic acid at the goethite-water interface

NASA Astrophysics Data System (ADS)

Weng, Li Ping; Koopal, Luuk K.; Hiemstra, Tjisse; Meeussen, Johannes C. L.; Van Riemsdijk, Willem H.

2005-01-01

Interactions of calcium and fulvic acid (Strichen ) with the surface of goethite were studied with batch and titration experiments. The mutual influence of the interactions on the adsorption of fulvic acid, calcium ions and protons were examined. Adsorption of the fulvic acid to goethite decreased with increase in pH (pH range 3-11). Addition of Ca (1.0 mM) at intermediate and high pH significantly enhanced the adsorption of fulvic acid. Compared to the adsorption to pure goethite, the presence of fulvic acid enhanced the adsorption of Ca significantly. In comparison to the simple linear sum of Ca bound to fulvic acid and goethite, the interactions between goethite and fulvic acid led to a reduced adsorption of Ca at low pH and an enhanced adsorption at high pH. With the adsorption of fulvic acid, protons were released at low pH and coadsorbed at high pH. When Ca was added, fewer protons were released at low pH and fewer coadsorbed at high pH. The experimental results can be adequately described using a surface complexation model, the Ligand and Charge Distribution (LCD) model, in which the CD-MUSIC model for ion adsorption to mineral oxides and the NICA model for ion binding to humics are integrated. In the model calculations, adequate descriptions of the ternary system data (Ca-fulvic acid-goethite) were obtained with parameters derived from three binary systems (fulvic acid-goethite, Ca-goethite and Ca-fulvic acid) without further adjustment. The model calculations suggest that the interactions between Ca and fulvic acid at the surface of goethite are mainly due to the electrostatic effects.

Hybrid simulations of magnetic reconnection with kinetic ions and fluid electron pressure anisotropy

DOE PAGES

Le, A.; Daughton, W.; Karimabadi, H.; ...

2016-03-16

We present the first hybrid simulations with kinetic ions and recently developed equations of state for the electron fluid appropriate for reconnection with a guide field. The equations of state account for the main anisotropy of the electron pressure tensor.Magnetic reconnection is studied in two systems, an initially force-free current sheet and a Harris sheet. The hybrid model with the equations of state is compared to two other models, hybrid simulations with isothermal electrons and fully kinetic simulations. Including the anisotropicequations of state in the hybrid model provides a better match to the fully kinetic model. In agreement with fullymore » kinetic results, the main feature captured is the formation of an electron current sheet that extends several ion inertial lengths. This electron current sheet modifies the Hall magnetic field structure near the X-line, and it is not observed in the standard hybrid model with isotropic electrons. The saturated reconnection rate in this regime nevertheless remains similar in all three models. Here, implications for global modeling are discussed.« less

Double layers in expanding plasmas and their relevance to the auroral plasma processes

NASA Astrophysics Data System (ADS)

Singh, Nagendra; Khazanov, George

2003-04-01

When a dense plasma consisting of a cold and a sufficiently warm electron population expands, a rarefaction shock forms [, 1978]. In the expansion of the polar wind in the magnetosphere, it has been previously shown that when a sufficiently warm electron population also exists, in addition to the usual cold ionospheric one, a discontinuity forms in the electrostatic potential distribution along the magnetic field lines [, 1984]. Despite the lack of spatial resolution and the assumption of quasi-neutrality in the polar wind models, such discontinuities have been called double layers (DLs). Recently similar discontinuities have been invoked to partly explain the auroral acceleration of electrons and ions in the upward current region [, 2000]. By means of one-dimensional Vlasov simulations of expanding plasmas, for the first time we make here the connection between (1) the rarefaction shocks, (2) the discontinuities in the potential distributions, and (3) DLs. We show that when plasmas expand from opposite directions into a deep density cavity with a potential drop across it and when the plasma on the high-potential side contains hot and cold electron populations, the temporal evolution of the potential and the plasma distribution generates evolving multiple double layers with an extended density cavity between them. One of the DLs is the rarefaction-shock (RFS) and it forms by the reflections of the cold electrons coming from the high-potential side; it supports a part of the potential drop approximately determined by the hot electron temperature. The other DLs evolve from charge separations arising either from reflection of ions coming from the low-potential side or stemming from plasma instabilities; they support the rest of the potential drop. The instabilities forming these additional double layers involve electron-ion (e-i) Buneman or ion-ion (i-i) two-stream interactions. The electron-electron two-stream interactions on the high-potential side of the RFS generate electron-acoustic waves, which evolve into electron phase-space holes. The ion population originating from the low-potential side and trapped by the RFS is energized by the e-i and i-i instabilities and it eventually precipitates into the high-potential plasma along with an electron beam. Applications of these findings to the auroral plasma physics are discussed.

Double Layers in Expanding Plasmas and Their Relevance to the Auroral Plasma Processes

NASA Technical Reports Server (NTRS)

Singh, Nagendra; Khazanov, George

2003-01-01

When a dense plasma consisting of a cold and a sufficiently warm electron population expands, a rarefaction shock forms [Bezzerides et al., 1978]. In the expansion of the polar wind in the magnetosphere, it has been previously shown that when a sufficiently warm electron population also exists, in addition to the usual cold ionospheric one, a discontinuity forms in the electrostatic potential distribution along the magnetic field lines [Barakat and Schunk, 1984]. Despite the lack of spatial resolution and the assumption of quasi-neutrality in the polar wind models, such discontinuities have been called double layers (DLs). Recently similar discontinuities have been invoked to partly explain the auroral acceleration of electrons and ions in the upward current region [Ergun et al., 2000]. By means of one-dimensional Vlasov simulations of expanding plasmas, for the first time we make here the connection between (1) the rarefaction shocks, (2) the discontinuities in the potential distributions, and (3) DLs. We show that when plasmas expand from opposite directions into a deep density cavity with a potential drop across it and when the plasma on the high-potential side contains hot and cold electron populations, the temporal evolution of the potential and the plasma distribution generates evolving multiple double layers with an ,extended density cavity between them. One of the DLs is the rarefaction-shock (RFS) and it forms by the reflections of the cold electrons coming from the high-potential side; it supports a part of the potential drop approximately determined by the hot electron temperature. The other DLs evolve from charge separations arising either from reflection of ions coming from the low-potential side or stemming from plasma instabilities; they support the rest of the potential drop. The instabilities forming these additional double layers involve electron-ion (e-i) Buneman or ion-ion (i-i) two-stream interactions. The electron-electron two-stream interactions on the high-potential side of the RFS generate electron-acoustic waves, which evolve into electron phase-space holes. The ion population originating from the low-potential side and trapped by the RFS is energized by the e-i and i-i instabilities and it eventually precipitates into the high-potential plasma along with an electron beam. Applications of these findings to the auroral plasma physics are discussed.

The Equivalent Electrokinetic Circuit Model of Ion Concentration Polarization Layer: Electrical Double Layer, Extended Space Charge and Electro-convection

NASA Astrophysics Data System (ADS)

Cho, Inhee; Huh, Keon; Kwak, Rhokyun; Lee, Hyomin; Kim, Sung Jae

2016-11-01

The first direct chronopotentiometric measurement was provided to distinguish the potential difference through the extended space charge (ESC) layer which is formed with the electrical double layer (EDL) near a perm-selective membrane. From this experimental result, the linear relationship was obtained between the resistance of ESC and the applied current density. Furthermore, we observed the step-wise distributions of relaxation time at the limiting current regime, confirming the existence of ESC capacitance other than EDL's. In addition, we proposed the equivalent electrokinetic circuit model inside ion concentration polarization (ICP) layer under rigorous consideration of EDL, ESC and electro-convection (EC). In order to elucidate the voltage configuration in chronopotentiometric measurement, the EC component was considered as the "dependent voltage source" which is serially connected to the ESC layer. This model successfully described the charging behavior of the ESC layer with or without EC, where both cases determined each relaxation time, respectively. Finally, we quantitatively verified their values utilizing the Poisson-Nernst-Planck equations. Therefore, this unified circuit model would provide a key insight of ICP system and potential energy-efficient applications.

Development of Continuum-Atomistic Approach for Modeling Metal Irradiation by Heavy Ions

NASA Astrophysics Data System (ADS)

Batgerel, Balt; Dimova, Stefka; Puzynin, Igor; Puzynina, Taisia; Hristov, Ivan; Hristova, Radoslava; Tukhliev, Zafar; Sharipov, Zarif

2018-02-01

Over the last several decades active research in the field of materials irradiation by high-energy heavy ions has been worked out. The experiments in this area are labor-consuming and expensive. Therefore the improvement of the existing mathematical models and the development of new ones based on the experimental data of interaction of high-energy heavy ions with materials are of interest. Presently, two approaches are used for studying these processes: a thermal spike model and molecular dynamics methods. The combination of these two approaches - the continuous-atomistic model - will give the opportunity to investigate more thoroughly the processes of irradiation of materials by high-energy heavy ions. To solve the equations of the continuous-atomistic model, a software package was developed and the block of molecular dynamics software was tested on the heterogeneous cluster HybriLIT.

Developing Battery Computer Aided Engineering Tools for Military Vehicles

DTIC Science & Technology

2013-12-01

Task 1.b Modeling Bullet penetration. The purpose of Task 1.a was to extend the chemical kinetics models of CoO2 cathodes developed under CAEBAT to...lithium- ion batteries. The new finite element model captures swelling/shrinking in cathodes /anodes due to thermal expansion and lithium intercalation...Solid Electrolyte Interphase (SEI) layer decomposition 80 2 Anode — electrolyte 100 3 Cathode — electrolyte 130 4 Electrolyte decomposition 180

An Efficient Variable Screening Method for Effective Surrogate Models for Reliability-Based Design Optimization

DTIC Science & Technology

2014-04-01

surrogate model generation is difficult for high -dimensional problems, due to the curse of dimensionality. Variable screening methods have been...a variable screening model was developed for the quasi-molecular treatment of ion-atom collision [16]. In engineering, a confidence interval of...for high -level radioactive waste [18]. Moreover, the design sensitivity method can be extended to the variable screening method because vital

Experiments on the interaction of heavy ions with dense plasma at GSI-Darmstadt

NASA Astrophysics Data System (ADS)

Stöckl, C.; Boine-Frankenheim, O.; Geißel, M.; Roth, M.; Wetzler, H.; Seelig, W.; Iwase, O.; Spiller, P.; Bock, R.; Süß, W.; Hoffmann, D. H. H.

One of the main objectives of the experimental plasma physics activities at the Gesellschaft für Schwerionenforschung (GSI) are the interaction processes of heavy ions with dense ionized matter. Gas-discharge plasma targets were used for energy loss and charge state measurements in a regime of electron density and temperature up to 10 19 cm -3 and 20 eV, respectively. An improved model of the charge exchange processes in fully ionized hydrogen plasma, taking into account multiple excited electronic configurations which subsequently ionize, has removed the discrepancies of previous theoretical descriptions. The energy loss of the ion beam in partially ionized plasmas such as argon was found to agree very well with our simple theoretical model based on the modified Bethe-Bloch theory. A new setup with a 100 J/5 GW Nd-glass laser now provides access to density ranges up to 10 21 cm -3 and temperatures of up to 100 eV. First results of interaction experiments with laser-produced plasma are presented. To fully exploit the experimental possibilities of the new laser-plasma setup both improved charge state detection systems and better plasma diagnostics are indispensable. Present developments and future possibilities in these fields are presented. This paper summarizes the following contributions: Interaction of heavy-ion beams with laser plasma by C. Stöckl et al. Energy Loss of Heavy Ions in a laser-produced plasma by M. Roth et al. Charge state measurements of heavy ions passing a laser produced plasma with high time resolution by W. Süß et al. Plasma diagnostics for laser-produced plasma by O. Iwase et al. Future possibilities of plasma diagnostics at GSI by M. Geißel et al.

Effective electrostatic interactions among charged thermo-responsive microgels immersed in a simple electrolyte

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

González-Mozuelos, P.

This work explores the nature and thermodynamic behavior of the effective electrostatic interactions among charged microgels immersed in a simple electrolyte, taking special interest in the effects due to the thermally induced variation of the microgel size while the remaining parameters (microgel charge and concentration, plus the amount of added salt) are kept constant. To this end, the rigorous approach obtained from applying the precise methodology of the dressed ion theory to the proper definition of the effective direct correlation functions, which emerge from tracing-out the degrees of freedom of the microscopic ions, is employed to provide an exact descriptionmore » of the parameters characterizing such interactions: screening length, effective permittivity, and renormalized charges. A model solution with three components is assumed: large permeable anionic spheres for the microgels, plus small charged hard spheres of equal size for the monovalent cations and anions. The two-body correlations among the components of this model suspension, used as the input for the determination of the effective interaction parameters, are here calculated by using the hyper-netted chain approximation. It is then found that at finite microgel concentrations the values of these parameters change as the microgel size increases, even though the ionic strength of the supporting electrolyte and the bare charge of the microgels remain fixed during this process. The variation of the screening length, as well as that of the effective permittivity, is rather small, but still interesting in view of the fact that the corresponding Debye length stays constant. The renormalized charges, in contrast, increase markedly as the microgels swell. The ratio of the renormalized charge to the corresponding analytic result obtained in the context of an extended linear response theory allows us to introduce an effective charge that accounts for the non-linear effects induced by the short-ranged association of microions to the microgels. The behavior of these effective charges as a function of the amount of added salt and the macroion charge, size, and concentration reveals the interplay among all these system parameters.« less

Benchmarking of neutron production of heavy-ion transport codes

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

Remec, I.; Ronningen, R. M.; Heilbronn, L.

Document available in abstract form only, full text of document follows: Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondarymore » neutron production. Results are encouraging; however, further improvements in models and codes and additional benchmarking are required. (authors)« less

Laser-Matter Interaction in Dielectrics: Insight from Picosecond-Pulsed Second-Harmonic Generation in Periodically Poled LiTaO3

NASA Astrophysics Data System (ADS)

Louchev, Oleg A.; Wada, Satoshi; Panchenko, Vladislav Ya.

2017-08-01

We develop a modified two-temperature (2T) model of laser-matter interaction in dielectrics based on experimental insight from picosecond-pulsed high-frequency temperature-controlled second-harmonic (515 nm) generation in periodically poled stoichiometric LiTaO3 crystal and required for computational treatment of short-pulsed nonlinear optics and materials processing applications. We show that the incorporation of an extended set of recombination-kinetics-related energy-release and heat-exchange processes following short-pulsed photoionization by two-photon absorption of the second harmonic allows accurate simulation of the electron-lattice relaxation dynamics and electron-lattice temperature evolution in LiTaO3 crystal in nonlinear laser-frequency conversion. Our experimentally confirmed model and detailed simulation study show that two-photon ionization with the recombination mechanism via ion-electron-lattice interaction followed by a direct transfer of the recombination energy to the lattice is the main laser-matter energy-transfer pathway responsible for the majority of the crystal lattice heating (approximately 90%) continuing for approximately 50 ps after laser-pulse termination and competing with effect of electron-phonon energy transfer from the free electrons. This time delay is due to a recombination bottleneck which hinders faster relaxation to thermal equilibrium in photoionized dielectric crystal. Generally, our study suggests that in dielectrics photoionized by short-pulsed radiation with intensity range used in nonlinear laser-frequency conversion, the electron-lattice relaxation period is defined by the recombination-stage bottleneck of a few tens of picoseconds and not by the time of the electron-phonon energy transfer. This modification of the 2T model can be applied to a broad range of processes involving laser-matter interactions in dielectrics and semiconductors for charge density reaching the range of 1021- 1022 cm-3 .